From cd8d1eb1f631f59106d2bbdf27354a367d8ae4a4 Mon Sep 17 00:00:00 2001
From: "piotr.gawron" <piotr.gawron@uni-new>
Date: Mon, 3 Oct 2016 17:38:01 +0200
Subject: [PATCH] base refactoring finsihed
classes renamed to species (there are no aliases anymore)
database data about annotators cleared
---
.../annotation/services/ModelAnnotator.java | 16 +-
.../annotators/BiocompendiumAnnotator.java | 4 +-
.../services/annotators/ChebiAnnotator.java | 6 +-
.../services/annotators/ElementAnnotator.java | 26 +-
.../services/annotators/EnsemblAnnotator.java | 18 +-
.../services/annotators/EntrezAnnotator.java | 18 +-
.../services/annotators/GoAnnotator.java | 14 +-
.../services/annotators/HgncAnnotator.java | 18 +-
.../services/annotators/ReconAnnotator.java | 28 +-
.../services/annotators/UniprotAnnotator.java | 8 +-
.../services/ImproperAnnotationsTest.java | 6 +-
.../services/MissingAnnotationTest.java | 4 +-
.../MissingRequiredAnnotationsTest.java | 6 +-
.../services/ModelAnnotatorTest.java | 30 +-
.../annotators/ChebiAnnotatorTest.java | 12 +-
.../annotators/ElementAnnotatorTest.java | 16 +-
.../annotators/EnsemblAnnotatorTest.java | 14 +-
.../annotators/EntrezAnnotatorTest.java | 12 +-
.../services/annotators/GoAnnotatorTest.java | 4 +-
.../annotators/HgncAnnotatorTest.java | 16 +-
.../annotators/ReconAnnotatorTest.java | 8 +-
.../annotators/UniprotAnnotatorTest.java | 12 +-
.../java/lcsb/mapviewer/run/BellExport.java | 6 +-
.../lcsb/mapviewer/run/ConsoleConverter.java | 32 +-
.../mapviewer/run/ReactomeComparison.java | 4 +-
.../lcsb/mapviewer/run/ReactomeExport.java | 56 +-
.../java/lcsb/mapviewer/run/RunOptions.java | 14 +-
.../java/lcsb/mapviewer/run/Statistics.java | 20 +-
.../run/UnknownReactionInReactome.java | 4 +-
.../lcsb/mapviewer/run/VibineSnippet.java | 4 +-
.../CellDesignerElementCollection.java | 28 +-
.../celldesigner/CellDesignerXmlParser.java | 102 +-
.../model/celldesigner/CommonXmlParser.java | 212 ++--
.../model/celldesigner/LayerXmlParser.java | 12 +-
.../alias/AbstractAliasXmlParser.java | 4 +-
.../alias/AliasCollectionXmlParser.java | 42 +-
.../alias/CompartmentAliasXmlParser.java | 58 +-
.../alias/ComplexAliasXmlParser.java | 52 +-
.../alias/SpeciesAliasXmlParser.java | 50 +-
.../celldesigner/annotation/NoteField.java | 14 +-
.../annotation/RestAnnotationParser.java | 24 +-
.../CompartmentCollectionXmlParser.java | 21 +-
.../compartment/CompartmentXmlParser.java | 18 +-
.../AbstractCellDesignerAliasConverter.java | 4 +-
...ntisenseRnaCellDesignerAliasConverter.java | 218 ++--
.../geometry/CellDesignerAliasConverter.java | 74 +-
.../ComplexCellDesignerAliasConverter.java | 120 +-
.../DegradedCellDesignerAliasConverter.java | 18 +-
.../DrugCellDesignerAliasConverter.java | 162 +--
.../GeneCellDesignerAliasConverter.java | 142 +--
.../geometry/ICellDesignerAliasConverter.java | 122 +-
.../IonCellDesignerAliasConverter.java | 18 +-
.../PhenotypeCellDesignerAliasConverter.java | 166 +--
.../ProteinCellDesignerAliasConverter.java | 44 +-
.../RnaCellDesignerAliasConverter.java | 216 ++--
...pleMoleculeCellDesignerAliasConverter.java | 10 +-
.../UnknownCellDesignerAliasConverter.java | 12 +-
.../geometry/helper/PolylineDataFactory.java | 122 +-
.../reaction/ReactionCollectionXmlParser.java | 2 -
.../reaction/ReactionFromXml.java | 30 +-
.../celldesigner/reaction/ReactionToXml.java | 44 +-
.../reaction/ReactionXmlParser.java | 3 -
.../species/AbstractElementXmlParser.java | 6 +-
.../species/AntisenseRnaXmlParser.java | 28 +-
.../celldesigner/species/GeneXmlParser.java | 32 +-
.../species/InternalModelSpeciesData.java | 108 +-
.../celldesigner/species/ProteinMapping.java | 59 +-
.../species/ProteinXmlParser.java | 34 +-
.../celldesigner/species/RnaXmlParser.java | 24 +-
.../species/SpeciesCollection.java | 8 +-
.../species/SpeciesCollectionXmlParser.java | 128 +-
.../celldesigner/species/SpeciesMapping.java | 98 +-
.../species/SpeciesSbmlParser.java | 154 +--
.../celldesigner/species/package-info.java | 12 +-
...Rna.java => CellDesignerAntisenseRna.java} | 56 +-
...> CellDesignerAntisenseRnaComparator.java} | 18 +-
...va => CellDesignerAntisenseRnaRegion.java} | 34 +-
...hemical.java => CellDesignerChemical.java} | 12 +-
...ment.java => CellDesignerCompartment.java} | 36 +-
...=> CellDesignerCompartmentComparator.java} | 16 +-
...s.java => CellDesignerComplexSpecies.java} | 58 +-
...CellDesignerComplexSpeciesComparator.java} | 50 +-
...egraded.java => CellDesignerDegraded.java} | 18 +-
.../CellDesignerDegradedComparator.java | 82 ++
.../{Drug.java => CellDesignerDrug.java} | 18 +-
...r.java => CellDesignerDrugComparator.java} | 16 +-
...{Element.java => CellDesignerElement.java} | 24 +-
...ava => CellDesignerElementComparator.java} | 24 +-
.../{Gene.java => CellDesignerGene.java} | 47 +-
...r.java => CellDesignerGeneComparator.java} | 23 +-
...n.java => CellDesignerGenericProtein.java} | 20 +-
.../{Ion.java => CellDesignerIon.java} | 18 +-
...ava => CellDesignerIonChannelProtein.java} | 18 +-
...or.java => CellDesignerIonComparator.java} | 31 +-
...notype.java => CellDesignerPhenotype.java} | 18 +-
.../CellDesignerPhenotypeComparator.java | 91 ++
...{Protein.java => CellDesignerProtein.java} | 45 +-
...ava => CellDesignerProteinComparator.java} | 27 +-
....java => CellDesignerReceptorProtein.java} | 18 +-
.../{Rna.java => CellDesignerRna.java} | 58 +-
...or.java => CellDesignerRnaComparator.java} | 26 +-
.../structure/CellDesignerRnaRegion.java | 86 +-
...e.java => CellDesignerSimpleMolecule.java} | 20 +-
...CellDesignerSimpleMoleculeComparator.java} | 22 +-
...{Species.java => CellDesignerSpecies.java} | 20 +-
.../CellDesignerSpeciesComparator.java | 231 ++++
...java => CellDesignerTruncatedProtein.java} | 18 +-
...{Unknown.java => CellDesignerUnknown.java} | 18 +-
...ava => CellDesignerUnknownComparator.java} | 22 +-
.../structure/SpeciesComparator.java | 231 ----
.../CellDesignerModificationResidue.java | 102 +-
.../structure/{ => fields}/ConnectScheme.java | 2 +-
.../structure/{ => fields}/EditPoints.java | 2 +-
.../{ => fields}/LineProperties.java | 2 +-
.../structure/{ => fields}/SingleLine.java | 66 +-
.../structure/{ => fields}/SpeciesState.java | 56 +-
.../structure/{ => fields}/View.java | 2 +-
.../celldesigner/types/ModifierTypeUtils.java | 6 +-
.../CellDesignerXmlParserTest.java | 32 +-
.../celldesigner/ComplexParserTests.java | 76 +-
.../celldesigner/LayerXmlParserTest.java | 18 +-
.../NestedComplexParsingTests.java | 52 +-
.../ReconDataInCellDesignerXmlParserTest.java | 4 +-
.../alias/AliasCollectionXmlParserTest.java | 128 +-
.../alias/CompartmentAliasXmlParserTest.java | 44 +-
.../alias/ComplexAliasXmlParserTest.java | 16 +-
.../alias/SpeciesAliasXmlParserTest.java | 46 +-
.../annotation/RestAnnotationParserTest.java | 26 +-
.../CompartmentCollectionXmlParserTest.java | 18 +-
.../compartment/CompartmentXmlParserTest.java | 22 +-
...bstractCellDesignerAliasConverterTest.java | 14 +-
...enseRnaCellDesignerAliasConverterTest.java | 8 +-
.../CellDesignerAliasConverterTest.java | 4 +-
...egradedCellDesignerAliasConverterTest.java | 8 +-
.../GeneCellDesignerAliasConverterTest.java | 10 +-
.../IonCellDesignerAliasConverterTest.java | 8 +-
...ProteinCellDesignerAliasConverterTest.java | 4 +-
.../geometry/ProteinConverterTest.java | 4 +-
.../RnaCellDesignerAliasConverterTest.java | 8 +-
...oleculeCellDesignerAliasConverterTest.java | 10 +-
...UnknownCellDesignerAliasConverterTest.java | 6 +-
.../ReactionCollectionXmlParserTest.java | 28 +-
.../reaction/ReactionFromXmlTest.java | 22 +-
.../reaction/ReactionParserTests.java | 68 +-
.../reaction/ReactionToXmlTest.java | 14 +-
.../species/AntisenseRnaXmlParserTest.java | 24 +-
.../species/ComplexParserTest.java | 46 +-
.../species/GeneXmlParserTest.java | 26 +-
.../species/InternalModelSpeciesDataTest.java | 5 +-
.../species/ProteinMappingTest.java | 7 +-
.../species/ProteinXmlParserTest.java | 22 +-
.../species/RnaXmlParserTest.java | 18 +-
.../species/SpeciesCollectionTest.java | 35 +-
.../SpeciesCollectionXmlParserTest.java | 114 +-
.../species/SpeciesMappingTest.java | 9 +-
.../species/SpeciesSbmlParserTest.java | 220 ++--
.../structure/AntisenseRnaComparatorTest.java | 34 +-
.../structure/AntisenseRnaRegionTest.java | 28 +-
.../structure/AntisenseRnaTest.java | 41 +-
.../structure/CompartmentComparatorTest.java | 24 +-
.../structure/CompartmentTest.java | 26 +-
.../ComplexSpeciesComparatorTest.java | 94 +-
.../structure/ComplexSpeciesTest.java | 41 +-
.../structure/ConnectSchemeTest.java | 2 +
.../structure/DegradedComparatorTest.java | 28 +-
.../celldesigner/structure/DegradedTest.java | 15 +-
.../structure/DrugComparatorTest.java | 26 +-
.../celldesigner/structure/DrugTest.java | 15 +-
.../structure/ElementComparatorTest.java | 30 +-
.../celldesigner/structure/ElementTest.java | 14 +-
.../structure/GeneComparatorTest.java | 29 +-
.../celldesigner/structure/GeneTest.java | 35 +-
.../structure/GenericProteinTest.java | 13 +-
.../structure/IonChannelProteinTest.java | 13 +-
.../structure/IonComparatorTest.java | 26 +-
.../model/celldesigner/structure/IonTest.java | 15 +-
.../structure/LinePropertiesTest.java | 2 +
.../structure/ModificationResidueTest.java | 22 +-
.../structure/PhenotypeComparatorTest.java | 22 +-
.../celldesigner/structure/PhenotypeTest.java | 10 +-
.../structure/ProteinComparatorTest.java | 25 +-
.../celldesigner/structure/ProteinTest.java | 62 +-
.../structure/ReceptorProteinTest.java | 13 +-
.../structure/RnaComparatorTest.java | 28 +-
.../celldesigner/structure/RnaRegionTest.java | 22 +-
.../model/celldesigner/structure/RnaTest.java | 41 +-
.../SimpleMoleculeComparatorTest.java | 30 +-
.../structure/SimpleMoleculeTest.java | 13 +-
.../structure/SpeciesComparatorTest.java | 54 +-
.../structure/SpeciesStateTest.java | 24 +-
.../celldesigner/structure/SpeciesTest.java | 45 +-
.../structure/TruncatedProteinTest.java | 13 +-
.../structure/UnknownComparatorTest.java | 26 +-
.../celldesigner/structure/UnknownTest.java | 15 +-
.../celldesigner/structure/ViewTest.java | 2 +
.../types/ModifierTypeUtilsTest.java | 10 +-
.../model/sbgnml/SbgnmlXmlExporter.java | 112 +-
.../model/sbgnml/SbgnmlXmlParser.java | 116 +-
.../graphics/AbstractImageGenerator.java | 60 +-
.../converter/graphics/AliasConverter.java | 106 +-
.../converter/graphics/IAliasConverter.java | 6 +-
.../ArtifitialCompartmentConverter.java | 134 +-
.../BottomSquareCompartmentConverter.java | 160 +--
.../compartment/CompartmentConverter.java | 4 +-
.../LeftSquareCompartmentConverter.java | 160 +--
.../compartment/OvalCompartmentConverter.java | 182 +--
.../RightSquareCompartmentConverter.java | 172 +--
.../SquareCompartmentConverter.java | 196 +--
.../TopSquareCompartmentConverter.java | 152 +--
.../graphics/compartment/package-info.java | 12 +-
.../graphics/placefinder/PlaceFinder.java | 932 +++++++-------
.../species/AntisenseRnaConverter.java | 20 +-
.../graphics/species/ComplexConverter.java | 16 +-
.../graphics/species/DegradedConverter.java | 242 ++--
.../graphics/species/DrugConverter.java | 212 ++--
.../graphics/species/GeneConverter.java | 20 +-
.../graphics/species/IonConverter.java | 18 +-
.../graphics/species/PhenotypeConverter.java | 12 +-
.../graphics/species/ProteinConverter.java | 77 +-
.../graphics/species/RnaConverter.java | 25 +-
.../SBGNNucleicAcidFeatureConverter.java | 12 +-
.../species/SimpleMoleculeConverter.java | 15 +-
.../graphics/species/SpeciesConverter.java | 28 +-
.../graphics/species/UnknownConverter.java | 10 +-
.../converter/graphics/ConverterTest.java | 73 +-
.../graphics/NormalImageGeneratorTest.java | 24 +-
.../graphics/PdfImageGeneratorTest.java | 4 +-
.../placefinder/AllPlaceFinderTest.java | 22 +-
.../species/SpeciesConverterTest.java | 24 +-
.../converter/ComplexZipConverter.java | 36 +-
.../converter/ComplexZipConverterTest.java | 48 +-
.../lcsb/mapviewer/editor/SelectedPoint.java | 118 +-
.../editor/gui/ElementModifiedEvent.java | 130 +-
.../mapviewer/editor/gui/WindowContent.java | 272 ++--
.../gui/canvas/CanvasSelectMouseListener.java | 250 ++--
.../CreateChangeAbbreviationCommand.java | 66 +-
.../detailstab/CreateChangeColorCommand.java | 64 +-
.../CreateChangeFontSizeCommand.java | 82 +-
.../CreateChangeFormerSymbolCommand.java | 12 +-
.../CreateChangeFormulaCommand.java | 66 +-
.../CreateChangeFullNameCommand.java | 66 +-
.../CreateChangeMiriamDataCommand.java | 98 +-
.../detailstab/CreateChangeNameCommand.java | 6 +-
.../detailstab/CreateChangeNotesCommand.java | 64 +-
.../detailstab/CreateChangeSymbolCommand.java | 66 +-
.../CreateChangeSynonymCommand.java | 12 +-
.../CreateListPropertyChangeCommand.java | 188 +--
.../CreatePropertyChangeCommand.java | 120 +-
.../gui/detailstab/ElementDetailsPanel.java | 108 +-
.../mapviewer/commands/ColorModelCommand.java | 28 +-
.../lcsb/mapviewer/commands/CopyCommand.java | 60 +-
.../commands/CreateHierarchyCommand.java | 172 +--
.../lcsb/mapviewer/commands/ModelCommand.java | 4 +-
.../lcsb/mapviewer/commands/MoveCommand.java | 152 +--
.../commands/MoveElementsCommand.java | 362 +++---
.../mapviewer/commands/SubModelCommand.java | 34 +-
.../AddElementFormerSymbolsCommand.java | 8 +-
.../AddElementMiriamDataCommand.java | 6 +-
.../AddElementPropertyListEntryCommand.java | 14 +-
.../properties/AddElementSynonymsCommand.java | 8 +-
.../ChangeElementAbbreviationCommand.java | 6 +-
.../properties/ChangeElementColorCommand.java | 98 +-
.../ChangeElementFontSizeCommand.java | 102 +-
.../ChangeElementFormerSymbolCommand.java | 10 +-
.../ChangeElementFormulaCommand.java | 8 +-
.../ChangeElementFullNameCommand.java | 8 +-
.../ChangeElementMiriamDataCommand.java | 6 +-
.../properties/ChangeElementNameCommand.java | 6 +-
.../properties/ChangeElementNotesCommand.java | 8 +-
.../ChangeElementPropertyCommand.java | 240 ++--
...ChangeElementPropertyListEntryCommand.java | 14 +-
.../ChangeElementSymbolCommand.java | 8 +-
.../ChangeElementSynonymCommand.java | 10 +-
.../RemoveElementFormerSymbolsCommand.java | 8 +-
.../RemoveElementMiriamDataCommand.java | 8 +-
...RemoveElementPropertyListEntryCommand.java | 14 +-
.../RemoveElementSynonymsCommand.java | 8 +-
.../commands/properties/package-info.java | 16 +-
.../commands/ColorModelCommandTest.java | 8 +-
.../commands/CommandTestFunctions.java | 8 +-
.../mapviewer/commands/CopyCommandTest.java | 18 +-
.../commands/CreateHierarchyCommandTest.java | 38 +-
.../commands/MoveElementsCommandTest.java | 16 +-
.../ChangeElementAbbreviationCommandTest.java | 6 +-
.../ChangeElementColorCommandTest.java | 156 +--
.../ChangeElementFontSizeCommandTest.java | 150 +--
.../ChangeElementFormerSymbolCommandTest.java | 4 +-
.../ChangeElementFormulaCommandTest.java | 6 +-
.../ChangeElementFullNameCommandTest.java | 6 +-
.../ChangeElementMiriamDataCommandTest.java | 8 +-
.../ChangeElementNameCommandTest.java | 6 +-
.../ChangeElementNotesCommandTest.java | 6 +-
.../ChangeElementSymbolCommandTest.java | 6 +-
.../ChangeElementSynonymCommandTest.java | 8 +-
.../lcsb/mapviewer/model/map/MiriamType.java | 72 +-
.../map/{layout/alias => }/SearchIndex.java | 11 +-
.../BottomSquareCompartment.java} | 16 +-
.../Compartment.java} | 55 +-
.../CompartmentComparator.java} | 32 +-
.../LeftSquareCompartment.java} | 16 +-
.../OvalCompartment.java} | 14 +-
.../PathwayCompartment.java} | 16 +-
.../RightSquareCompartment.java} | 18 +-
.../SquareCompartment.java} | 16 +-
.../TopSquareCompartment.java} | 16 +-
.../mapviewer/model/map/graph/DataMining.java | 8 +-
.../map/layout/{alias => }/BlockDiagram.java | 38 +-
.../model/map/layout/ColorSchema.java | 16 +-
.../AliasGroup.java => ElementGroup.java} | 152 +--
.../layout/alias/DegradedAliasComparator.java | 83 --
.../map/layout/alias/IonAliasComparator.java | 83 --
.../map/model/AliasSubmodelConnection.java | 14 +-
.../AliasSubmodelConnectionComparator.java | 224 ++--
.../lcsb/mapviewer/model/map/model/Model.java | 56 +-
.../model/map/model/ModelComparator.java | 20 +-
.../mapviewer/model/map/model/ModelData.java | 28 +-
.../model/map/model/ModelFullIndexed.java | 151 +--
.../model/map/modifier/Catalysis.java | 4 +-
.../model/map/modifier/Inhibition.java | 4 +-
.../model/map/modifier/Modulation.java | 4 +-
.../map/modifier/PhysicalStimulation.java | 4 +-
.../mapviewer/model/map/modifier/Trigger.java | 4 +-
.../model/map/modifier/UnknownCatalysis.java | 4 +-
.../model/map/modifier/UnknownInhibition.java | 4 +-
.../model/map/reaction/Modifier.java | 6 +-
.../mapviewer/model/map/reaction/Product.java | 6 +-
.../model/map/reaction/Reactant.java | 6 +-
.../model/map/reaction/Reaction.java | 4 +-
.../model/map/reaction/ReactionNode.java | 12 +-
.../map/reaction/ReactionNodeComparator.java | 4 +-
.../AntisenseRna.java} | 29 +-
.../AntisenseRnaComparator.java} | 18 +-
.../Chemical.java} | 8 +-
.../ChemicalComparator.java} | 34 +-
.../Complex.java} | 50 +-
.../ComplexComparator.java} | 34 +-
.../Degraded.java} | 16 +-
.../map/species}/DegradedComparator.java | 29 +-
.../DrugAlias.java => species/Drug.java} | 16 +-
.../DrugComparator.java} | 18 +-
.../alias/Alias.java => species/Element.java} | 34 +-
.../ElementComparator.java} | 34 +-
.../GeneAlias.java => species/Gene.java} | 29 +-
.../GeneComparator.java} | 18 +-
.../GenericProtein.java} | 16 +-
.../GenericProteinComparator.java} | 22 +-
.../alias/IonAlias.java => species/Ion.java} | 16 +-
.../IonChannelProtein.java} | 16 +-
.../IonChannelProteinComparator.java} | 18 +-
.../model/map/species}/IonComparator.java | 30 +-
.../Phenotype.java} | 16 +-
.../PhenotypeComparator.java} | 18 +-
.../Protein.java} | 24 +-
.../ProteinComparator.java} | 50 +-
.../ReceptorProtein.java} | 16 +-
.../ReceptorProteinComparator.java} | 18 +-
.../alias/RnaAlias.java => species/Rna.java} | 29 +-
.../RnaComparator.java} | 18 +-
.../SimpleMolecule.java} | 16 +-
.../SimpleMoleculeComparator.java} | 18 +-
.../Species.java} | 25 +-
.../SpeciesComparator.java} | 104 +-
.../TruncatedProtein.java} | 16 +-
.../TruncatedProteinComparator.java} | 18 +-
.../Unknown.java} | 16 +-
.../UnknownComparator.java} | 18 +-
.../field/AntisenseRnaRegion.java} | 32 +-
.../species/field}/ModificationResidue.java | 68 +-
.../field}/ModificationState.java | 2 +-
.../field}/PositionToCompartment.java | 4 +-
.../model/map/species/field}/RnaRegion.java | 70 +-
.../alias => species}/package-info.java | 12 +-
.../modelutils/map/ElementUtils.java | 32 +-
.../modelutils/map/RequireAnnotationMap.java | 32 +-
.../lcsb/mapviewer/model/map/AllMapTests.java | 4 +-
.../map/compartment/AllCompartmentTests.java | 17 +
.../BottomSquareCompartmentAliasTest.java | 14 +-
.../CompartmentAliasComparatorTest.java | 55 +-
.../CompartmentAliasTest.java | 94 +-
.../LeftSquareCompartmentAliasTest.java | 14 +-
.../RightSquareCompartmentAliasTest.java | 16 +-
.../TopSquareCompartmentAliasTest.java | 14 +-
.../model/map/graph/DataMiningTest.java | 6 +-
.../model/map/layout/AllLayoutTests.java | 4 +-
.../model/map/layout/ColorSchemaTest.java | 16 +-
.../model/map/layout/alias/AllAliasTests.java | 28 -
...AliasSubmodelConnectionComparatorTest.java | 16 +-
.../model/map/model/ModelComparatorTest.java | 28 +-
.../model/map/model/ModelDataTest.java | 16 +-
.../model/map/model/ModelFullIndexedTest.java | 92 +-
...ModelSubmodelConnectionComparatorTest.java | 10 +-
.../mapviewer/model/map/model/ModelTest.java | 61 +-
.../SubmodelConnectionComparatorTest.java | 10 +-
.../model/map/modifier/CatalysisTest.java | 8 +-
.../model/map/modifier/InhibitionTest.java | 8 +-
.../model/map/modifier/ModulationTest.java | 8 +-
.../map/modifier/PhysicalStimulationTest.java | 8 +-
.../model/map/modifier/TriggerTest.java | 8 +-
.../map/modifier/UnknownCatalysisTest.java | 8 +-
.../map/modifier/UnknownInhibitionTest.java | 8 +-
.../reaction/NodeOperatorComparatorTest.java | 14 +-
.../map/reaction/ReactionComparatorTest.java | 16 +-
.../reaction/ReactionNodeComparatorTest.java | 10 +-
.../model/map/reaction/ReactionTest.java | 12 +-
.../AliasComparatorTest.java | 63 +-
.../alias => species}/AliasGroupTest.java | 16 +-
.../{layout/alias => species}/AliasTest.java | 45 +-
.../model/map/species/AllSpeciesTests.java | 27 +
.../ArtifitialCompartmentAliasTest.java | 19 +-
.../ComplexAliasComparatorTest.java | 54 +-
.../alias => species}/ComplexAliasTest.java | 43 +-
.../ModificationStateTest.java | 4 +-
.../OvalCompartmentAliasTest.java | 15 +-
.../PositionToCompartmentTest.java | 4 +-
.../alias => species}/SearchIndexTest.java | 7 +-
.../SpeciesAliasComparatorTest.java | 26 +-
.../alias => species}/SpeciesAliasTest.java | 6 +-
.../SquareCompartmentAliasTest.java | 15 +-
.../modelutils/map/ElementUtilsTest.java | 18 +-
.../wikipathway/XML/ModelContructor.java | 182 +--
.../wikipathway/XML/ModelToGPML.java | 82 +-
.../model/GpmlModificationType.java | 2 +-
.../mapviewer/wikipathway/model/State.java | 6 +-
.../ComplexReactionToModelTest.java | 6 +-
.../wikipathway/GPMLToModelTest.java | 22 +-
.../mapviewer/wikipathway/XML/BugTest.java | 8 +-
.../wikipathway/XML/ModelToGPMLTest.java | 8 +-
.../wikipathway/XML/StateParserTest.java | 2 +-
persist/src/db/10.0.3/fix_db_20161003.sql | 12 +-
.../persist/dao/map/graph/DataMiningDao.java | 4 +-
.../dao/map/layout/alias/AliasDao.java | 42 +-
.../resources/applicationContext-persist.xml | 65 +-
.../mapviewer/persist/dao/ProjectDaoTest.java | 26 +-
.../persist/dao/map/CommentDaoTest.java | 32 +-
.../persist/dao/map/LayoutDaoTest.java | 36 +-
.../persist/dao/map/ModelDaoTest.java | 50 +-
.../dao/map/graph/DataMiningDaoTest.java | 10 +-
.../dao/map/layout/alias/AliasDaoTest.java | 36 +-
.../dao/map/layout/alias/AliasDaoTest2.java | 80 +-
.../map/layout/alias/AntisenseRnaTest.java | 18 +-
.../persist/dao/map/layout/alias/RnaTest.java | 18 +-
.../persist/dao/user/UserDaoTest.java | 6 +-
.../reactome/utils/DataFormatter.java | 12 +-
.../mapviewer/reactome/utils/ElementUtil.java | 6 +-
.../reactome/utils/ReactionComparator.java | 24 +-
.../reactome/utils/ReactomeQueryUtil.java | 50 +-
.../utils/comparators/ANodeComparator.java | 10 +-
.../ComplexAndCandidateSetComparator.java | 9 +-
.../ComplexAndCatalystComparator.java | 10 +-
.../ComplexAndComplexComparator.java | 11 +-
.../ComplexAndDefinedSetComparator.java | 9 +-
...tityWithAccessionedSequenceComparator.java | 10 +-
.../ComplexAndOtherEntityComparator.java | 9 +-
.../ComplexAndSimpleEntityComparator.java | 10 +-
...tityWithAccessionedSequenceComparator.java | 8 +-
.../DrugAndCatalystComparator.java | 10 +-
.../GeneAndDefinedSetComparator.java | 10 +-
.../GeneAndOtherEntityComparator.java | 10 +-
.../comparators/IonAndCatalystComparator.java | 10 +-
.../comparators/IonAndComplexComparator.java | 10 +-
.../IonAndDefinedSetComparator.java | 10 +-
...tityWithAccessionedSequenceComparator.java | 10 +-
.../IonAndSimpleEntityComparator.java | 10 +-
.../utils/comparators/MatchResult.java | 26 +-
.../MoleculeAndCatalystComparator.java | 10 +-
.../MoleculeAndComplexComparator.java | 10 +-
.../MoleculeAndDefinedSetComparator.java | 10 +-
...tityWithAccessionedSequenceComparator.java | 10 +-
.../MoleculeAndSimpleEntityComparator.java | 10 +-
.../utils/comparators/NodeComparator.java | 16 +-
.../ProteinAndCandidateSetComparator.java | 10 +-
.../ProteinAndCatalystComparator.java | 10 +-
.../ProteinAndComplexComparator.java | 10 +-
.../ProteinAndDefinedSetComparator.java | 10 +-
...tityWithAccessionedSequenceComparator.java | 10 +-
.../ProteinAndGenomeEncodedEntity.java | 10 +-
.../ProteinAndOtherEntityComparator.java | 10 +-
.../ProteinAndPolymerComparator.java | 10 +-
.../ProteinAndSimpleEntityComparator.java | 10 +-
.../UnknownAndCatalystComparator.java | 10 +-
...knownAndGenomeEncodedEntityComparator.java | 10 +-
.../reactome/utils/ReactomeQueryUtilTest.java | 10 +-
.../utils/comparators/NodeComparatorTest.java | 58 +-
.../services/impl/CommentService.java | 14 +-
.../services/impl/DataMiningService.java | 34 +-
.../services/impl/ExporterService.java | 232 ++--
.../services/impl/LayoutService.java | 16 +-
.../mapviewer/services/impl/ModelService.java | 18 +-
.../services/impl/ProjectService.java | 4 +-
.../services/impl/SearchService.java | 114 +-
.../interfaces/IDataMiningService.java | 10 +-
.../services/interfaces/IExporterService.java | 24 +-
.../services/interfaces/ILayoutService.java | 4 +-
.../services/interfaces/IModelService.java | 290 ++---
.../services/search/SearchResultFactory.java | 30 +-
.../comment/FullCommentViewFactory.java | 6 +-
.../search/data/ElementIdentifier.java | 8 +-
.../services/search/data/FullAliasView.java | 44 +-
.../search/data/FullAliasViewFactory.java | 30 +-
.../services/search/data/LightAliasView.java | 208 ++--
.../search/data/LightAliasViewFactory.java | 118 +-
.../services/search/db/IDbSearchService.java | 4 +-
.../search/db/chemical/ChemicalService.java | 14 +-
.../db/chemical/ChemicalViewFactory.java | 4 +-
.../services/search/db/drug/DrugService.java | 12 +-
.../search/db/drug/DrugViewFactory.java | 8 +-
.../search/db/mirna/MiRNAService.java | 14 +-
.../search/db/mirna/MiRNAViewFactory.java | 4 +-
.../search/layout/FullLayoutAliasView.java | 4 +-
.../layout/FullLayoutAliasViewFactory.java | 6 +-
.../search/layout/LightLayoutAliasView.java | 186 +--
.../layout/LightLayoutAliasViewFactory.java | 6 +-
.../services/utils/SearchIndexer.java | 15 +-
.../services/utils/data/ExportColumn.java | 16 +-
.../services/view/CommentViewFactory.java | 4 +-
.../view/PubmedAnnotatedElementsView.java | 6 +-
.../services/impl/CommentServiceTest.java | 12 +-
.../services/impl/DataMiningServiceTest.java | 20 +-
.../services/impl/DataMiningServiceTest2.java | 32 +-
.../services/impl/ExporterServiceTest.java | 60 +-
.../services/impl/LayoutServiceTest2.java | 6 +-
.../services/impl/LogServiceTest.java | 6 +-
.../services/impl/ModelServiceTest.java | 6 +-
.../services/impl/ProjectServiceTest.java | 18 +-
.../services/impl/SearchServiceTest.java | 64 +-
.../search/SearchResultFactoryTest.java | 6 +-
.../search/data/FullAliasViewFactoryTest.java | 32 +-
.../data/LightAliasViewFactoryTest.java | 6 +-
.../db/chemical/ChemicalServiceTest.java | 8 +-
.../search/db/drug/DrugServiceTest.java | 18 +-
.../search/db/drug/DrugViewFactoryTest.java | 4 +-
.../FullLayoutAliasViewFactoryTest.java | 8 +-
.../LightLayoutAliasViewFactoryTest.java | 8 +-
.../utils/graph/MissingConnectionDaoTest.java | 6 +-
.../mapviewer/bean/AbstractManagedBean.java | 1094 ++++++++---------
.../lcsb/mapviewer/bean/ChemicalBean.java | 6 +-
.../java/lcsb/mapviewer/bean/DrugBean.java | 6 +-
.../java/lcsb/mapviewer/bean/ExportBean.java | 62 +-
.../lcsb/mapviewer/bean/FeedbackBean.java | 6 +-
.../java/lcsb/mapviewer/bean/MapBean.java | 4 +-
.../java/lcsb/mapviewer/bean/MiRNABean.java | 6 +-
541 files changed, 11065 insertions(+), 11047 deletions(-)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{AntisenseRna.java => CellDesignerAntisenseRna.java} (54%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{AntisenseRnaComparator.java => CellDesignerAntisenseRnaComparator.java} (71%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{AntisenseRnaRegion.java => CellDesignerAntisenseRnaRegion.java} (80%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Chemical.java => CellDesignerChemical.java} (80%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Compartment.java => CellDesignerCompartment.java} (64%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{CompartmentComparator.java => CellDesignerCompartmentComparator.java} (71%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ComplexSpecies.java => CellDesignerComplexSpecies.java} (59%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ComplexSpeciesComparator.java => CellDesignerComplexSpeciesComparator.java} (69%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Degraded.java => CellDesignerDegraded.java} (60%)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegradedComparator.java
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Drug.java => CellDesignerDrug.java} (62%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{DrugComparator.java => CellDesignerDrugComparator.java} (72%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Element.java => CellDesignerElement.java} (91%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ElementComparator.java => CellDesignerElementComparator.java} (82%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Gene.java => CellDesignerGene.java} (51%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{GeneComparator.java => CellDesignerGeneComparator.java} (67%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{GenericProtein.java => CellDesignerGenericProtein.java} (51%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Ion.java => CellDesignerIon.java} (63%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{IonChannelProtein.java => CellDesignerIonChannelProtein.java} (51%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{PhenotypeComparator.java => CellDesignerIonComparator.java} (62%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Phenotype.java => CellDesignerPhenotype.java} (60%)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotypeComparator.java
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Protein.java => CellDesignerProtein.java} (61%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ProteinComparator.java => CellDesignerProteinComparator.java} (70%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ReceptorProtein.java => CellDesignerReceptorProtein.java} (52%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Rna.java => CellDesignerRna.java} (53%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{RnaComparator.java => CellDesignerRnaComparator.java} (68%)
rename model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRnaRegion.java (69%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{SimpleMolecule.java => CellDesignerSimpleMolecule.java} (56%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{SimpleMoleculeComparator.java => CellDesignerSimpleMoleculeComparator.java} (72%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Species.java => CellDesignerSpecies.java} (91%)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpeciesComparator.java
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{TruncatedProtein.java => CellDesignerTruncatedProtein.java} (52%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{Unknown.java => CellDesignerUnknown.java} (61%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{UnknownComparator.java => CellDesignerUnknownComparator.java} (64%)
delete mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparator.java
rename model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java (67%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ => fields}/ConnectScheme.java (91%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ => fields}/EditPoints.java (93%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ => fields}/LineProperties.java (88%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ => fields}/SingleLine.java (80%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ => fields}/SpeciesState.java (60%)
rename converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/{ => fields}/View.java (89%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias => }/SearchIndex.java (88%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/BottomSquareCompartmentAlias.java => compartment/BottomSquareCompartment.java} (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/CompartmentAlias.java => compartment/Compartment.java} (83%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/CompartmentAliasComparator.java => compartment/CompartmentComparator.java} (78%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/LeftSquareCompartmentAlias.java => compartment/LeftSquareCompartment.java} (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/OvalCompartmentAlias.java => compartment/OvalCompartment.java} (67%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ArtifitialCompartmentAlias.java => compartment/PathwayCompartment.java} (61%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/RightSquareCompartmentAlias.java => compartment/RightSquareCompartment.java} (75%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/SquareCompartmentAlias.java => compartment/SquareCompartment.java} (64%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/TopSquareCompartmentAlias.java => compartment/TopSquareCompartment.java} (71%)
rename model/src/main/java/lcsb/mapviewer/model/map/layout/{alias => }/BlockDiagram.java (82%)
rename model/src/main/java/lcsb/mapviewer/model/map/layout/{alias/AliasGroup.java => ElementGroup.java} (70%)
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAliasComparator.java
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAliasComparator.java
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/AntisenseRnaAlias.java => species/AntisenseRna.java} (59%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/AntisenseRnaAliasComparator.java => species/AntisenseRnaComparator.java} (68%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ChemicalAlias.java => species/Chemical.java} (86%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ChemicalAliasComparator.java => species/ChemicalComparator.java} (59%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ComplexAlias.java => species/Complex.java} (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ComplexAliasComparator.java => species/ComplexComparator.java} (71%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/DegradedAlias.java => species/Degraded.java} (59%)
rename {converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure => model/src/main/java/lcsb/mapviewer/model/map/species}/DegradedComparator.java (71%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/DrugAlias.java => species/Drug.java} (60%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/DrugAliasComparator.java => species/DrugComparator.java} (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/Alias.java => species/Element.java} (96%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/AliasComparator.java => species/ElementComparator.java} (86%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/GeneAlias.java => species/Gene.java} (62%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/GeneAliasComparator.java => species/GeneComparator.java} (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/GenericProteinAlias.java => species/GenericProtein.java} (52%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/GenericProteinAliasComparator.java => species/GenericProteinComparator.java} (64%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/IonAlias.java => species/Ion.java} (61%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/IonChannelProteinAlias.java => species/IonChannelProtein.java} (51%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/IonChannelProteinAliasComparator.java => species/IonChannelProteinComparator.java} (69%)
rename {converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure => model/src/main/java/lcsb/mapviewer/model/map/species}/IonComparator.java (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/PhenotypeAlias.java => species/Phenotype.java} (58%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/PhenotypeAliasComparator.java => species/PhenotypeComparator.java} (69%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ProteinAlias.java => species/Protein.java} (69%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ProteinAliasComparator.java => species/ProteinComparator.java} (51%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ReceptorProteinAlias.java => species/ReceptorProtein.java} (52%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/ReceptorProteinAliasComparator.java => species/ReceptorProteinComparator.java} (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/RnaAlias.java => species/Rna.java} (64%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/RnaAliasComparator.java => species/RnaComparator.java} (71%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/SimpleMoleculeAlias.java => species/SimpleMolecule.java} (56%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/SimpleMoleculeAliasComparator.java => species/SimpleMoleculeComparator.java} (67%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/SpeciesAlias.java => species/Species.java} (89%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/SpeciesAliasComparator.java => species/SpeciesComparator.java} (59%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/TruncatedProteinAlias.java => species/TruncatedProtein.java} (51%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/TruncatedProteinAliasComparator.java => species/TruncatedProteinComparator.java} (70%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/UnknownAlias.java => species/Unknown.java} (59%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/UnknownAliasComparator.java => species/UnknownComparator.java} (69%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias/AntisenseRnaRegionAlias.java => species/field/AntisenseRnaRegion.java} (86%)
rename {converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure => model/src/main/java/lcsb/mapviewer/model/map/species/field}/ModificationResidue.java (79%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias => species/field}/ModificationState.java (93%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias => species/field}/PositionToCompartment.java (86%)
rename {converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure => model/src/main/java/lcsb/mapviewer/model/map/species/field}/RnaRegion.java (75%)
rename model/src/main/java/lcsb/mapviewer/model/map/{layout/alias => species}/package-info.java (70%)
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => compartment}/BottomSquareCompartmentAliasTest.java (70%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => compartment}/CompartmentAliasComparatorTest.java (68%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => compartment}/CompartmentAliasTest.java (68%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => compartment}/LeftSquareCompartmentAliasTest.java (70%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => compartment}/RightSquareCompartmentAliasTest.java (70%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => compartment}/TopSquareCompartmentAliasTest.java (71%)
delete mode 100644 model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AllAliasTests.java
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/AliasComparatorTest.java (59%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/AliasGroupTest.java (65%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/AliasTest.java (85%)
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/ArtifitialCompartmentAliasTest.java (67%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/ComplexAliasComparatorTest.java (68%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/ComplexAliasTest.java (65%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/ModificationStateTest.java (83%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/OvalCompartmentAliasTest.java (70%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/PositionToCompartmentTest.java (83%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/SearchIndexTest.java (87%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/SpeciesAliasComparatorTest.java (75%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/SpeciesAliasTest.java (74%)
rename model/src/test/java/lcsb/mapviewer/model/map/{layout/alias => species}/SquareCompartmentAliasTest.java (69%)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 580bfcdccb..bb3bede1cb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -31,10 +31,10 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ClassTreeNode;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -241,10 +241,10 @@ public class ModelAnnotator {
protected void copyAnnotationFromOtherSpecies(Model model, IProgressUpdater progressUpdater) {
double counter = 0;
double amount = model.getAliases().size();
- for (SpeciesAlias element : model.getSpeciesAliases()) {
+ for (Species element : model.getSpeciesAliases()) {
if (element.getMiriamData().size() == 0) {
- List<Alias> speciesList = model.getAliasByName(element.getName());
- for (Alias species2 : speciesList) {
+ List<Element> speciesList = model.getAliasByName(element.getName());
+ for (Element species2 : speciesList) {
if (species2.getClass().equals(element.getClass()) && species2.getMiriamData().size() > 0 && element.getMiriamData().size() == 0) {
for (MiriamData md : species2.getMiriamData()) {
element.addMiriamData(new MiriamData(md));
@@ -278,7 +278,7 @@ public class ModelAnnotator {
double amount = model.getAliases().size() + model.getReactions().size();
// annotate all elements
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
List<ElementAnnotator> list = null;
if (annotators != null) {
list = annotators.get(element.getClass());
@@ -363,7 +363,7 @@ public class ModelAnnotator {
double ratio = modelCounter / modelSize;
double size = model.getAliases().size() + model.getReactions().size();
double counter = 0;
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
result.addAll(findImproperAnnotations(element, validAnnotations.get(element.getClass())));
counter++;
updater.setProgress(ratio * IProgressUpdater.MAX_PROGRESS + (counter / size * IProgressUpdater.MAX_PROGRESS) / modelSize);
@@ -427,7 +427,7 @@ public class ModelAnnotator {
models.add(m);
models.addAll(m.getSubmodels());
for (Model model : models) {
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
result.addAll(findMissing(alias, requestedAnnotations.get(alias.getClass())));
}
for (Reaction reaction : model.getReactions()) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
index 833d1dd0d0..be9a83cdc8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
@@ -35,7 +35,7 @@ import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationPars
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
/**
* This class is responsible for connection to Vencata annotation service. The
@@ -75,7 +75,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
* Default constructor.
*/
public BiocompendiumAnnotator() {
- super(BiocompendiumAnnotator.class, new Class[] { ProteinAlias.class, ProteinAlias.class, ProteinAlias.class }, true);
+ super(BiocompendiumAnnotator.class, new Class[] { Protein.class, Protein.class, Protein.class }, true);
}
@Override
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
index b2790e358d..bc37df5ec1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
@@ -24,7 +24,7 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
+import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
import uk.ac.ebi.chebi.webapps.chebiWS.model.ChebiWebServiceFault_Exception;
@@ -132,7 +132,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
* {@link Chebi} from/to xml.
*/
public ChebiAnnotator() {
- super(ChebiAnnotator.class, new Class[] { ChemicalAlias.class }, true);
+ super(ChebiAnnotator.class, new Class[] { Chemical.class }, true);
chebiSerializer = new XmlSerializer<>(Chebi.class);
}
@@ -457,7 +457,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
chebi = getChebiElementForChebiId(md);
}
}
- ChemicalAlias species = (ChemicalAlias) element;
+ Chemical species = (Chemical) element;
if (chebi != null) {
super.setFullName(species, chebi.getName(), warnPrefix);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index ff1e497ac7..c0f499bbb9 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -7,14 +7,14 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Interface that allows to annotate {@link AnnotatedObject elements} in the
@@ -186,7 +186,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setFullName(Alias element, String name, String prefix) {
+ protected void setFullName(Element element, String name, String prefix) {
if (element.getFullName() == null || element.getFullName().equals("") || element.getFullName().equals(name)) {
element.setFullName(name);
} else {
@@ -223,7 +223,7 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
- * Sets {@link Chemical#inChI}.
+ * Sets {@link CellDesignerChemical#inChI}.
*
* @param element
* element where annotation should be added
@@ -232,7 +232,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* value to set
*/
- protected void setInchi(ChemicalAlias element, String value, String prefix) {
+ protected void setInchi(Chemical element, String value, String prefix) {
if (element.getInChI() == null || element.getInChI().isEmpty() || element.getInChI().equals(value)) {
element.setInChI(value);
} else {
@@ -242,7 +242,7 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
- * Sets {@link Chemical#inChIKey}.
+ * Sets {@link CellDesignerChemical#inChIKey}.
*
* @param element
* element where annotation should be added
@@ -251,7 +251,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* value to set
*/
- protected void setInchiKey(ChemicalAlias element, String value, String prefix) {
+ protected void setInchiKey(Chemical element, String value, String prefix) {
if (element.getInChIKey() == null || element.getInChIKey().equals("")) {
element.setInChIKey(value);
} else if (!element.getInChIKey().equalsIgnoreCase(value)) {
@@ -261,7 +261,7 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
- * Sets {@link Chemical#smiles}.
+ * Sets {@link CellDesignerChemical#smiles}.
*
* @param element
* element where annotation should be added
@@ -270,7 +270,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* value to set
*/
- protected void setSmile(ChemicalAlias element, String value, String prefix) {
+ protected void setSmile(Chemical element, String value, String prefix) {
if (element.getSmiles() == null || element.getSmiles().isEmpty() || element.getSmiles().equals(value)) {
element.setSmiles(value);
} else {
@@ -295,7 +295,7 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
- * Sets {@link SpeciesAlias#charge}.
+ * Sets {@link Species#charge}.
*
* @param element
* element where annotation should be added
@@ -304,7 +304,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setCharge(SpeciesAlias element, String value, String prefix) {
+ protected void setCharge(Species element, String value, String prefix) {
Integer charge = Integer.parseInt(value);
if (element.getCharge() == null || element.getCharge() == 0 || element.getCharge().equals(charge)) {
element.setCharge(Integer.valueOf(charge));
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index defee8a8f7..378054263a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -23,11 +23,11 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -66,7 +66,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
* Default constructor.
*/
public EnsemblAnnotator() {
- super(EnsemblAnnotator.class, new Class[] { ProteinAlias.class, RnaAlias.class, GeneAlias.class }, false);
+ super(EnsemblAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
}
@Override
@@ -112,7 +112,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
try {
- GenericProteinAlias proteinAlias = new GenericProteinAlias("mock_id");
+ GenericProtein proteinAlias = new GenericProtein("mock_id");
proteinAlias.addMiriamData(new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764"));
annotateElement(proteinAlias);
@@ -219,7 +219,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
}
String fullName = super.getNodeAttr("description", node);
if (symbol != null) {
- setFullName((Alias) annotatedObject, fullName, prefix);
+ setFullName((Element) annotatedObject, fullName, prefix);
}
NodeList synonymNodeList = node.getChildNodes();
@@ -280,7 +280,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
if (!MiriamType.ENSEMBL.equals(miriamData.getDataType())) {
throw new InvalidArgumentException("Only " + MiriamType.ENSEMBL + " identifier is accepted as an input");
}
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
annotateElement(proteinAlias, miriamData, "");
for (MiriamData md : proteinAlias.getMiriamData()) {
if (MiriamType.ENTREZ.equals(md.getDataType())) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
index 00985d9a87..72ab25bc9d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
@@ -27,11 +27,11 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -72,7 +72,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
* Default constructor.
*/
public EntrezAnnotator() {
- super(EntrezAnnotator.class, new Class[] { ProteinAlias.class, RnaAlias.class, GeneAlias.class }, false);
+ super(EntrezAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
entrezSerializer = new XmlSerializer<>(EntrezData.class);
}
@@ -130,7 +130,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
this.setCache(null);
try {
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.ENTREZ, "9999"));
annotateElement(proteinAlias);
@@ -186,7 +186,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
if (data != null) {
setSymbol(element, data.getSymbol(), prefix);
- setFullName((Alias) element, data.getFullName(), prefix);
+ setFullName((Element) element, data.getFullName(), prefix);
element.addMiriamData(data.getMiriamData());
element.setSynonyms(data.getSynonyms());
@@ -343,7 +343,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
String key = CACHE_HGNC_ID_PREFIX + miriamData.getResource();
String value = getCacheValue(key);
if (value == null) {
- GenericProteinAlias proteinAlias = new GenericProteinAlias("some_id");
+ GenericProtein proteinAlias = new GenericProtein("some_id");
annotateElement(proteinAlias, miriamData, "");
for (MiriamData md : proteinAlias.getMiriamData()) {
if (MiriamType.HGNC.equals(md.getDataType())) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index c85d695aa6..a6ac2d4c67 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -25,10 +25,10 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -90,7 +90,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
* {@link Go} from/to xml.
*/
public GoAnnotator() {
- super(GoAnnotator.class, new Class[] { PhenotypeAlias.class, CompartmentAlias.class, ComplexAlias.class }, true);
+ super(GoAnnotator.class, new Class[] { Phenotype.class, Compartment.class, Complex.class }, true);
goSerializer = new XmlSerializer<>(Go.class);
}
@@ -112,7 +112,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
String commonName = go.getCommonName();
- setFullName((Alias) object, commonName, new ElementUtils().getElementTag(object, this));
+ setFullName((Element) object, commonName, new ElementUtils().getElementTag(object, this));
String description = go.getDescription();
setDescription(object, description);
} catch (GoSearchException e) {
@@ -173,7 +173,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
this.setCache(null);
try {
- CompartmentAlias compartmentAlias = new CompartmentAlias("some_id");
+ Compartment compartmentAlias = new Compartment("some_id");
compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
annotateElement(compartmentAlias);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index e5a17cfc26..0388009aee 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -19,11 +19,11 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -45,7 +45,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
* Default constructor.
*/
public HgncAnnotator() {
- super(HgncAnnotator.class, new Class[] { ProteinAlias.class, RnaAlias.class, GeneAlias.class }, true);
+ super(HgncAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, true);
}
@Override
@@ -90,7 +90,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
this.setCache(null);
try {
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.HGNC_SYMBOL, "SNCA"));
annotateElement(proteinAlias);
@@ -184,7 +184,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
setSymbol(element, getNodeValue(node), prefix);
} else if (type.equals("name")) {
- setFullName((Alias) element, getNodeValue(node), prefix);
+ setFullName((Element) element, getNodeValue(node), prefix);
}
} else if (node.getNodeName().equals("arr")) {
String type = getNodeAttr("name", node);
@@ -205,7 +205,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
strings.add(getNodeValue(subnode));
}
}
- ((Alias) element).setFormerSymbols(strings);
+ ((Element) element).setFormerSymbols(strings);
} else if (type.equals("alias_symbol")) {
List<String> strings = new ArrayList<String>();
NodeList sublist = node.getChildNodes();
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index 09a0fb2c3c..b5a4a5b8a7 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -17,13 +17,13 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -79,7 +79,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
* Default constructor.
*/
public ReconAnnotator() {
- super(ReconAnnotator.class, new Class[] { ChemicalAlias.class, Reaction.class }, false);
+ super(ReconAnnotator.class, new Class[] { Chemical.class, Reaction.class }, false);
}
@Override
@@ -91,7 +91,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
Logger.getRootLogger().addAppender(appender);
try {
- SimpleMoleculeAlias smallMoleculeAlias = new SimpleMoleculeAlias("some_id");
+ SimpleMolecule smallMoleculeAlias = new SimpleMolecule("some_id");
smallMoleculeAlias.setName("h2o");
annotateElement(smallMoleculeAlias);
status.setStatus(ExternalServiceStatusType.OK);
@@ -124,7 +124,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
id = tmp[tmp.length - 1];
}
String url = null;
- if (annotatedObject instanceof Alias) {
+ if (annotatedObject instanceof Element) {
url = ELEMENT_ANNOTATION_URL_PREFIX + id;
} else if (annotatedObject instanceof Reaction) {
url = REACTION_ANNOTATION_URL_PREFIX + id;
@@ -194,20 +194,20 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
} else if (key.equals("chargedFormula")) {
setFormula(annotatedObject, value, prefix);
} else if (key.equals("charge")) {
- if (annotatedObject instanceof SpeciesAlias) {
- setCharge((SpeciesAlias) annotatedObject, value, prefix);
+ if (annotatedObject instanceof Species) {
+ setCharge((Species) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("inchiString")) {
- if (annotatedObject instanceof ChemicalAlias) {
- setInchi((ChemicalAlias) annotatedObject, value, prefix);
+ if (annotatedObject instanceof Chemical) {
+ setInchi((Chemical) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("smile")) {
- if (annotatedObject instanceof Chemical) {
- setSmile((ChemicalAlias) annotatedObject, value, prefix);
+ if (annotatedObject instanceof CellDesignerChemical) {
+ setSmile((Chemical) annotatedObject, value, prefix);
} else {
unknown = true;
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index 17f559a9f7..705d8e1586 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -20,9 +20,9 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -57,7 +57,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
* Default constructor.
*/
public UniprotAnnotator() {
- super(UniprotAnnotator.class, new Class[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, false);
+ super(UniprotAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
}
@Override
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
index 611cb1163b..2af983bf77 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
@@ -15,7 +15,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class ImproperAnnotationsTest {
@@ -36,7 +36,7 @@ public class ImproperAnnotationsTest {
try {
List<MiriamData> list = new ArrayList<>();
list.add(new MiriamData(MiriamType.CAS, "a"));
- ImproperAnnotations ie = new ImproperAnnotations(new GenericProteinAlias("id"), list);
+ ImproperAnnotations ie = new ImproperAnnotations(new GenericProtein("id"), list);
assertNotNull(ie.toString());
} catch (InvalidArgumentException e) {
assertTrue(e.getMessage().contains("Only miriam data from elements are accepted"));
@@ -46,7 +46,7 @@ public class ImproperAnnotationsTest {
@Test
public void testConstructor4() {
try {
- new ImproperAnnotations(new GenericProteinAlias("id"), new ArrayList<>());
+ new ImproperAnnotations(new GenericProtein("id"), new ArrayList<>());
fail("Exception expected");
} catch (InvalidArgumentException e) {
assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
index 2cb12ed5e6..84490b1219 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
@@ -7,7 +7,7 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingAnnotationTest {
@@ -25,7 +25,7 @@ public class MissingAnnotationTest {
@Test
public void test() {
- MissingAnnotation annotation = new MissingAnnotation(new GenericProteinAlias("id"));
+ MissingAnnotation annotation = new MissingAnnotation(new GenericProtein("id"));
assertTrue(annotation.toString().contains("misses annotations"));
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
index e68b7cdd69..9b901b6e7b 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
@@ -12,7 +12,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingRequiredAnnotationsTest {
@@ -31,7 +31,7 @@ public class MissingRequiredAnnotationsTest {
@Test
public void testConstructorWithInvalidParams() {
try {
- new MissingRequiredAnnotations(new GenericProteinAlias("id"), new ArrayList<>());
+ new MissingRequiredAnnotations(new GenericProtein("id"), new ArrayList<>());
} catch (InvalidArgumentException e) {
assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
}
@@ -42,7 +42,7 @@ public class MissingRequiredAnnotationsTest {
try {
List<MiriamType> list = new ArrayList<>();
list.add(MiriamType.CAS);
- MissingRequiredAnnotations mre = new MissingRequiredAnnotations(new GenericProteinAlias("id"), list);
+ MissingRequiredAnnotations mre = new MissingRequiredAnnotations(new GenericProtein("id"), list);
assertTrue(mre.toString().contains("misses one of the following annotations"));
} catch (InvalidArgumentException e) {
assertTrue(e.getMessage().contains("List of improper annotations cannot be null"));
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index bba1c52d6f..e2ad6b257a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -33,15 +33,15 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.dao.map.ModelDao;
public class ModelAnnotatorTest extends AnnotationTestFunctions {
@@ -73,10 +73,10 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
model.addReaction(new Reaction());
- SpeciesAlias proteinAlias1 = new GenericProteinAlias("a1");
+ Species proteinAlias1 = new GenericProtein("a1");
proteinAlias1.setName("SNCA");
- SpeciesAlias proteinAlias2 = new GenericProteinAlias("a2");
+ Species proteinAlias2 = new GenericProtein("a2");
proteinAlias2.setName("PDK1");
proteinAlias2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
@@ -98,11 +98,11 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
public void testAnnotateModelWithGivenAnnotators() {
try {
Model model = new ModelFullIndexed(null);
- GenericProteinAlias species = new GenericProteinAlias("id1");
+ GenericProtein species = new GenericProtein("id1");
species.setName("SNCA");
model.addAlias(species);
- GenericProteinAlias species2 = new GenericProteinAlias("id2");
+ GenericProtein species2 = new GenericProtein("id2");
species2.setName("PDK1");
species2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
model.addAlias(species2);
@@ -112,7 +112,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
List<ElementAnnotator> annotatorList = new ArrayList<>();
annotatorList.addAll(modelAnnotator.getDefaultAnnotators());
annotators.put(Reaction.class, annotatorList);
- annotators.put(GenericProteinAlias.class, new ArrayList<>());
+ annotators.put(GenericProtein.class, new ArrayList<>());
ReconAnnotator reconMock = Mockito.mock(ReconAnnotator.class);
Mockito.doThrow(new AnnotatorException("")).when(reconMock).annotateElement(any());
@@ -135,7 +135,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
modelAnnotator.copyAnnotationFromOtherSpecies(model, updater);
- for (SpeciesAlias element : model.getSpeciesAliases()) {
+ for (Species element : model.getSpeciesAliases()) {
if (element.getName().equals("s4"))
assertEquals(0, element.getMiriamData().size());
else if (element.getName().equals("hello"))
@@ -192,8 +192,8 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
public void testGetAnnotationsForSYN() throws Exception {
try {
Model model = getModelForFile("testFiles/annotation/emptyAnnotationsSyn1.xml", true);
- Alias sa1 = model.getAliasByAliasId("sa1");
- Alias sa2 = model.getAliasByAliasId("sa2");
+ Element sa1 = model.getAliasByAliasId("sa1");
+ Element sa2 = model.getAliasByAliasId("sa2");
assertFalse(sa1.getNotes().contains("Symbol"));
assertFalse(sa2.getNotes().contains("Symbol"));
@@ -208,7 +208,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
assertFalse(sa2.getNotes().contains("Symbol"));
assertNull(sa2.getSymbol());
- for (SpeciesAlias el : model.getSpeciesAliases()) {
+ for (Species el : model.getSpeciesAliases()) {
if (el.getNotes() != null) {
assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("Symbol"));
assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("HGNC"));
@@ -300,7 +300,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
Model submodel = new ModelFullIndexed(null);
Model submodel2 = new ModelFullIndexed(null);
- GenericProteinAlias protein = new GenericProteinAlias("el");
+ GenericProtein protein = new GenericProtein("el");
model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
model.addSubmodelConnection(new ModelSubmodelConnection(submodel2, SubmodelType.UNKNOWN));
@@ -328,7 +328,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetAvailableAnnotators() {
try {
- List<ElementAnnotator> list = modelAnnotator.getAvailableAnnotators(ProteinAlias.class);
+ List<ElementAnnotator> list = modelAnnotator.getAvailableAnnotators(Protein.class);
assertTrue(list.size() > 0);
} catch (Exception e) {
e.printStackTrace();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
index dfed5a1f58..8ca9b43561 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
@@ -28,7 +28,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
import uk.ac.ebi.chebi.webapps.chebiWS.model.ChebiWebServiceFault_Exception;
import uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem;
@@ -316,7 +316,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateChemical() throws Exception {
try {
- SimpleMoleculeAlias simpleMolecule = new SimpleMoleculeAlias("id");
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
simpleMolecule.setName("water");
backend.annotateElement(simpleMolecule);
@@ -336,7 +336,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateWhenConnectionFails() throws Exception {
try {
- SimpleMoleculeAlias simpleMolecule = new SimpleMoleculeAlias("id");
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
simpleMolecule.setName("water");
ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
@@ -372,7 +372,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateChemicalWithInvalidName() throws Exception {
try {
- SimpleMoleculeAlias simpleMolecule = new SimpleMoleculeAlias("id");
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
simpleMolecule.setName("blasdh");
backend.annotateElement(simpleMolecule);
@@ -388,7 +388,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testUpdateChemicalFromDb() throws Exception {
try {
- SimpleMoleculeAlias simpleMolecule = new SimpleMoleculeAlias("id");
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
simpleMolecule.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:15377"));
backend.annotateElement(simpleMolecule);
@@ -408,7 +408,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testUpdateChemicalFromDbWithDifferentData() throws Exception {
try {
- SimpleMoleculeAlias simpleMolecule = new SimpleMoleculeAlias("id");
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
simpleMolecule.setName("water");
simpleMolecule.setFullName("xxx");
simpleMolecule.setInChI("x");
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
index 4324fef802..bb65b83da6 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
@@ -12,9 +12,9 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
public class ElementAnnotatorTest extends AnnotationTestFunctions {
@@ -60,7 +60,7 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testSetNotMatchingSymbol() {
- GenericProteinAlias species = new GenericProteinAlias("id");
+ GenericProtein species = new GenericProtein("id");
species.setSymbol("X");
annotator.setSymbol(species, "Y", null);
@@ -69,7 +69,7 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testSetNotMatchingFullname() {
- GenericProteinAlias species = new GenericProteinAlias("id");
+ GenericProtein species = new GenericProtein("id");
species.setFullName("X");
annotator.setFullName(species, "Y", null);
@@ -78,7 +78,7 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testSetNotMatchingNotes() {
- GenericProteinAlias species = new GenericProteinAlias("id");
+ GenericProtein species = new GenericProtein("id");
species.setNotes("X");
annotator.setDescription(species, "Y");
@@ -87,7 +87,7 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testSetNotMatchingIchi() {
- IonAlias species = new IonAlias("id");
+ Ion species = new Ion("id");
species.setInChI("X");
annotator.setInchi(species, "Y", null);
@@ -96,7 +96,7 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testSetNotMatchingSmile() {
- IonAlias species = new IonAlias("id");
+ Ion species = new Ion("id");
annotator.setSmile(species, "X", null);
annotator.setSmile(species, "Y", null);
@@ -105,7 +105,7 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testSetNotMatchingCharge() {
- IonAlias species = new IonAlias("id");
+ Ion species = new Ion("id");
species.setCharge(2);
annotator.setCharge(species, "3", null);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
index d72467f1d5..89e2b2707a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
@@ -26,8 +26,8 @@ import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
@@ -46,7 +46,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
public void testGetAnnotationsForEnsemblId() throws Exception {
try {
MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(nsmf);
ensemblAnnotator.annotateElement(proteinAlias);
assertNotNull(proteinAlias.getSymbol());
@@ -88,7 +88,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
try {
MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157764");
MiriamData nsmf1 = new MiriamData(MiriamType.ENSEMBL, "ENSG00000157765");
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(nsmf);
proteinAlias.addMiriamData(nsmf1);
ensemblAnnotator.annotateElement(proteinAlias);
@@ -104,7 +104,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetAnnotationsWhenNoIdFound() throws Exception {
try {
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
ensemblAnnotator.annotateElement(proteinAlias);
assertEquals(1, getWarnings().size());
@@ -119,7 +119,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
public void testGetAnnotationsForInvalid() throws Exception {
try {
MiriamData nsmf = new MiriamData(MiriamType.ENSEMBL, "blabla");
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(nsmf);
ensemblAnnotator.annotateElement(proteinAlias);
@@ -281,7 +281,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
when(mockDownloader.getFromNetwork(anyString())).thenThrow(new WrongResponseCodeIOException(null, 0));
ensemblAnnotator.setWebPageDownloader(mockDownloader);
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(new MiriamData(MiriamType.ENSEMBL, "1234"));
ensemblAnnotator.annotateElement(proteinAlias);
fail("Exception expected");
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
index 4498de25fb..40b24bc0e2 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
@@ -30,8 +30,8 @@ import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class EntrezAnnotatorTest extends AnnotationTestFunctions {
@@ -50,7 +50,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
public void testGetAnnotationsForEntrezId() throws Exception {
try {
MiriamData nsmf = new MiriamData(MiriamType.ENTREZ, "84532");
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(nsmf);
entrezAnnotator.annotateElement(proteinAlias);
assertNotNull(proteinAlias.getSymbol());
@@ -87,7 +87,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
public void testGetAnnotationsForInvalid() throws Exception {
try {
MiriamData nsmf = new MiriamData(MiriamType.ENTREZ, "blabla");
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(nsmf);
entrezAnnotator.annotateElement(proteinAlias);
@@ -310,7 +310,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateElementWithoutId() throws Exception {
try {
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
entrezAnnotator.annotateElement(proteinAlias);
assertEquals(1, getWarnings().size());
@@ -324,7 +324,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateElementWithTwoEntrez() throws Exception {
try {
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "6647"));
proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "6648"));
entrezAnnotator.annotateElement(proteinAlias);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
index 709270c056..ce4045811d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotatorTest.java
@@ -28,7 +28,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
public class GoAnnotatorTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(GoAnnotatorTest.class);
@@ -50,7 +50,7 @@ public class GoAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testContent() throws Exception {
try {
- CompartmentAlias compartmentAlias = new CompartmentAlias("id");
+ Compartment compartmentAlias = new Compartment("id");
compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.GO, "GO:0046902"));
goAnnotator.annotateElement(compartmentAlias);
assertFalse(compartmentAlias.getFullName().equals(""));
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index 0ff8111c11..56a549a5e9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -18,8 +18,8 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class HgncAnnotatorTest extends AnnotationTestFunctions {
@@ -40,7 +40,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
public void testGetAnnotationsForSNCA() throws Exception {
try {
MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(snca);
hgncAnnotator.annotateElement(proteinAlias);
assertNotNull(proteinAlias.getSymbol());
@@ -89,7 +89,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
public void testGetAnnotationsForHGNC_ID() throws Exception {
try {
MiriamData nsmf = new MiriamData(MiriamType.HGNC, "11138");
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(nsmf);
hgncAnnotator.annotateElement(proteinAlias);
assertNotNull(proteinAlias.getSymbol());
@@ -132,7 +132,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetAnnotationsForSNCA2() throws Exception {
try {
- GenericProteinAlias proteinAlias = new GenericProteinAlias("id");
+ GenericProtein proteinAlias = new GenericProtein("id");
proteinAlias.setName("SNCA");
hgncAnnotator.annotateElement(proteinAlias);
assertNotNull(proteinAlias.getSymbol());
@@ -176,7 +176,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetAnnotationsForInvalid() throws Exception {
try {
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
proteinAlias.setName("UNKNNOWNASD asd");
hgncAnnotator.annotateElement(proteinAlias);
@@ -191,7 +191,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetAnnotationsForInvalid2() throws Exception {
try {
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
proteinAlias.setName("cAMP/cGMP-dependent protein kinase");
hgncAnnotator.annotateElement(proteinAlias);
@@ -245,7 +245,7 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
try {
MiriamData md1 = new MiriamData(MiriamType.HGNC, "11138");
MiriamData md2 = new MiriamData(MiriamType.HGNC, "111382");
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
proteinAlias.addMiriamData(md1);
proteinAlias.addMiriamData(md2);
hgncAnnotator.annotateElement(proteinAlias);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
index 0382edadfe..bb8137e1ac 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
@@ -21,9 +21,9 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
public class ReconAnnotatorTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(ReconAnnotatorTest.class);
@@ -55,7 +55,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateElement() throws Exception {
try {
- SimpleMoleculeAlias smallMolecule = new SimpleMoleculeAlias("id");
+ SimpleMolecule smallMolecule = new SimpleMolecule("id");
smallMolecule.setAbbreviation("h2o");
reconAnnotator.annotateElement(smallMolecule);
assertTrue("No new annotations from recon db imported", smallMolecule.getMiriamData().size() > 0);
@@ -69,7 +69,7 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateElement2() throws Exception {
try {
- SpeciesAlias smallMolecule = new SimpleMoleculeAlias("id");
+ Species smallMolecule = new SimpleMolecule("id");
smallMolecule.setAbbreviation("P5CRm");
reconAnnotator.annotateElement(smallMolecule);
assertEquals(0, smallMolecule.getMiriamData().size());
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
index 1dd9020950..89f1c18669 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
@@ -21,8 +21,8 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class UniprotAnnotatorTest extends AnnotationTestFunctions {
@@ -41,7 +41,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
public void testAnnotate1() throws Exception {
try {
- SpeciesAlias protein = new GenericProteinAlias("id");
+ Species protein = new GenericProtein("id");
protein.setName("P01308");
uniprotAnnotator.annotateElement(protein);
@@ -74,7 +74,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotate2() throws Exception {
try {
- SpeciesAlias protein = new GenericProteinAlias("id");
+ Species protein = new GenericProtein("id");
protein.setName("bla");
protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P01308"));
uniprotAnnotator.annotateElement(protein);
@@ -108,7 +108,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateInvalidUniprot() throws Exception {
try {
- SpeciesAlias protein = new GenericProteinAlias("id");
+ Species protein = new GenericProtein("id");
protein.setName("bla");
protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "bla"));
uniprotAnnotator.annotateElement(protein);
@@ -127,7 +127,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateInvalid() throws Exception {
try {
- SpeciesAlias protein = new GenericProteinAlias("id");
+ Species protein = new GenericProtein("id");
protein.setName("bla");
uniprotAnnotator.annotateElement(protein);
diff --git a/console/src/main/java/lcsb/mapviewer/run/BellExport.java b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
index 04c2a09111..fb59ddcb95 100644
--- a/console/src/main/java/lcsb/mapviewer/run/BellExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
@@ -7,8 +7,8 @@ import lcsb.mapviewer.annotation.services.ModelAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.services.interfaces.IExporterService;
@@ -94,7 +94,7 @@ public class BellExport {
ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
fileName("out/bell/" + version + "-reactions.txt").//
fileType(ExportFileType.TAB_SEPARATED).//
- type(SpeciesAlias.class).//
+ type(Species.class).//
moleculeEdges(false);
exporter.exportReactions(params);
@@ -102,7 +102,7 @@ public class BellExport {
params = new IExporterService.ExporterParameters().model(model).//
fileName("out/bell/" + version + "-species.txt").//
fileType(ExportFileType.TAB_SEPARATED).//
- type(SpeciesAlias.class).//
+ type(Species.class).//
// column(ExportColumn.FULL).//
moleculeEdges(false);
exporter.exportSpecies(params);
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index 5aa503bf51..13f7337c2e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -24,8 +24,6 @@ import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Catalysis;
@@ -33,6 +31,8 @@ import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -60,7 +60,7 @@ public class ConsoleConverter {
private MiriamConnector mc = new MiriamConnector();
/**
- * Util class used to access some information about {@link Alias}.
+ * Util class used to access some information about {@link Element}.
*/
private ElementUtils elementUtils = new ElementUtils();
@@ -111,7 +111,7 @@ public class ConsoleConverter {
model.setWidth(inputOptions.getModelSize());
model.setHeight(inputOptions.getModelSize());
- Set<Alias> elements = null;
+ Set<Element> elements = null;
try {
elements = getNodes(nodesFilename);
} catch (IOException e) {
@@ -124,7 +124,7 @@ public class ConsoleConverter {
double size = elements.size();
double x = 0;
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
alias.setWidth(inputOptions.getAliasWidth());
alias.setHeight(inputOptions.getAliasHeight());
double angle = x / size * 2 * Math.PI;
@@ -240,7 +240,7 @@ public class ConsoleConverter {
String productString = cols[productsColumn];
for (String string : productString.split(",")) {
if (!string.isEmpty()) {
- SpeciesAlias alias = model.getAliasByAliasId(string.trim());
+ Species alias = model.getAliasByAliasId(string.trim());
Product product = new Product(alias);
products.add(product);
}
@@ -253,7 +253,7 @@ public class ConsoleConverter {
String reactantString = cols[reactantsColumn];
for (String string : reactantString.split(",")) {
if (!string.isEmpty()) {
- SpeciesAlias element = model.getAliasByAliasId(string.trim());
+ Species element = model.getAliasByAliasId(string.trim());
Reactant product = new Reactant(element);
reactants.add(product);
}
@@ -266,13 +266,13 @@ public class ConsoleConverter {
String modifierString = cols[modifiersColumn];
for (String string : modifierString.split(",")) {
if (!string.isEmpty()) {
- SpeciesAlias element = model.getAliasByAliasId(string.trim());
+ Species element = model.getAliasByAliasId(string.trim());
Modifier modifier = new Catalysis(element);
modifiers.add(modifier);
}
}
- Alias alias1 = products.get(0).getAlias();
- Alias alias2 = reactants.get(0).getAlias();
+ Element alias1 = products.get(0).getAlias();
+ Element alias2 = reactants.get(0).getAlias();
Point2D middle = new Point2D.Double((alias1.getCenterX() + alias2.getCenterX()) / 2, (alias1.getCenterY() + alias2.getCenterY()) / 2);
@@ -324,21 +324,21 @@ public class ConsoleConverter {
}
/**
- * This method parses the data from input file into set of {@link Alias
+ * This method parses the data from input file into set of {@link Element
* elements}.
*
* @param filename
* nam of input file
- * @return set of {@link Alias elements}
+ * @return set of {@link Element elements}
* @throws InvalidInputDataExecption
* thrown when the input data is invalid
* @throws IOException
* thrown when there is a problem with input file
*/
- private Set<Alias> getNodes(String filename) throws InvalidInputDataExecption, IOException {
+ private Set<Element> getNodes(String filename) throws InvalidInputDataExecption, IOException {
ElementUtils elementUtils = new ElementUtils();
- Set<Alias> result = new HashSet<>();
+ Set<Element> result = new HashSet<>();
Set<String> ids = new HashSet<>();
Integer identifierColumn = null;
@@ -412,10 +412,10 @@ public class ConsoleConverter {
}
try {
- if (!Alias.class.isAssignableFrom(clazz)) {
+ if (!Element.class.isAssignableFrom(clazz)) {
throw new InvalidInputDataExecption("Invliad element type: " + className, filename);
}
- Alias element = (Alias) clazz.getConstructor(String.class).newInstance(id);
+ Element element = (Element) clazz.getConstructor(String.class).newInstance(id);
element.setName(name);
element.addMiriamData(annotations);
result.add(element);
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
index 8f27f97d6c..7b5f0f24a6 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
@@ -21,9 +21,9 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
@@ -112,7 +112,7 @@ public class ReactomeComparison {
Set<String> list = new HashSet<String>();
- for (SpeciesAlias element : model.getSpeciesAliases()) {
+ for (Species element : model.getSpeciesAliases()) {
list.add(element.getName());
}
logger.debug("Species: " + list.size());
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
index f6fde1ee7c..2af675a904 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
@@ -18,13 +18,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -33,6 +27,12 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
@@ -109,7 +109,7 @@ public class ReactomeExport {
* Map between aliases in our model and identifiers that will be used in the
* reactome vizualization model.
*/
- private Map<Alias, Integer> tempIds = new HashMap<Alias, Integer>();
+ private Map<Element, Integer> tempIds = new HashMap<Element, Integer>();
/**
* Creates reactome identifier for alias.
@@ -118,7 +118,7 @@ public class ReactomeExport {
* object for which identifier is created
* @return identifier of the alias
*/
- public int addElement(Alias alias) {
+ public int addElement(Element alias) {
int result = -1;
if (tempIds.containsKey(alias)) {
result = tempIds.get(alias);
@@ -126,12 +126,12 @@ public class ReactomeExport {
tempIds.put(alias, ++id);
result = id;
- if (alias instanceof ComplexAlias) {
- for (Alias a : ((ComplexAlias) alias).getAliases()) {
+ if (alias instanceof Complex) {
+ for (Element a : ((Complex) alias).getAliases()) {
addElement(a);
}
- } else if (alias instanceof CompartmentAlias) {
- for (Alias a : ((CompartmentAlias) alias).getAliases()) {
+ } else if (alias instanceof Compartment) {
+ for (Element a : ((Compartment) alias).getAliases()) {
addElement(a);
}
}
@@ -177,10 +177,10 @@ public class ReactomeExport {
*/
private void printAliases(Model model) throws IOException {
print("<Nodes>\n");
- List<Alias> aliases = new ArrayList<Alias>();
+ List<Element> aliases = new ArrayList<Element>();
aliases.addAll(model.getAliases());
- Collections.sort(aliases, Alias.SIZE_COMPARATOR);
- for (Alias alias : aliases) {
+ Collections.sort(aliases, Element.SIZE_COMPARATOR);
+ for (Element alias : aliases) {
if (!aliasFeasible(alias)) {
continue;
}
@@ -197,7 +197,7 @@ public class ReactomeExport {
Set<Integer> components = new HashSet<Integer>();
String type = "";
- if (alias instanceof SpeciesAlias) {
+ if (alias instanceof Species) {
String stableIdentifier = rcu.getReactomeIdentifierForSpecies(alias);
if (stableIdentifier != null) {
ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
@@ -206,32 +206,32 @@ public class ReactomeExport {
}
}
parameters.put("displayName", alias.getName());
- if (alias instanceof ComplexAlias) {
- for (Alias a : ((ComplexAlias) alias).getAliases()) {
+ if (alias instanceof Complex) {
+ for (Element a : ((Complex) alias).getAliases()) {
components.add(addElement(a));
}
}
}
- if (alias instanceof CompartmentAlias) {
+ if (alias instanceof Compartment) {
parameters.put("displayName", alias.getName());
- for (Alias a : ((CompartmentAlias) alias).getAliases()) {
+ for (Element a : ((Compartment) alias).getAliases()) {
components.add(addElement(a));
}
}
- if (alias instanceof ComplexAlias) {
+ if (alias instanceof Complex) {
type = "org.gk.render.RenderableComplex";
attributes.put("hideComponents", "true");
attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) (alias.getY() + alias.getHeight()));
- } else if (alias instanceof SimpleMoleculeAlias) {
+ } else if (alias instanceof SimpleMolecule) {
type = "org.gk.render.RenderableChemical";
- } else if (alias instanceof IonAlias) {
+ } else if (alias instanceof Ion) {
type = "org.gk.render.RenderableChemical";
- } else if (alias instanceof ProteinAlias) {
+ } else if (alias instanceof Protein) {
type = "org.gk.render.RenderableProtein";
- } else if (alias instanceof SpeciesAlias) {
+ } else if (alias instanceof Species) {
type = "org.gk.render.RenderableEntity";
- } else if (alias instanceof CompartmentAlias) {
+ } else if (alias instanceof Compartment) {
type = "org.gk.render.RenderableCompartment";
} else {
logger.debug("Ignoring: " + parameters.get("displayName") + "(" + alias.getClass() + ")");
@@ -563,7 +563,7 @@ public class ReactomeExport {
* @return <code>true</code> if alias can be put into reactome vizualization,
* <code>false</code> otherwise
*/
- public boolean aliasFeasible(Alias alias) {
+ public boolean aliasFeasible(Element alias) {
Point2D point = new Point2D.Double(alias.getX(), alias.getY());
Point2D point2 = new Point2D.Double(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
if (bound.contains(point) && bound.contains(point2)) {
diff --git a/console/src/main/java/lcsb/mapviewer/run/RunOptions.java b/console/src/main/java/lcsb/mapviewer/run/RunOptions.java
index d6e0c47361..c8a80569ab 100644
--- a/console/src/main/java/lcsb/mapviewer/run/RunOptions.java
+++ b/console/src/main/java/lcsb/mapviewer/run/RunOptions.java
@@ -12,8 +12,8 @@ import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -304,9 +304,9 @@ public class RunOptions {
public void printFormat() {
String desc = NODES_DESCRIPTION;
ElementUtils eu = new ElementUtils();
- List<Class<? extends Alias>> classes = eu.getAvailableElementSubclasses();
+ List<Class<? extends Element>> classes = eu.getAvailableElementSubclasses();
String classString = "";
- for (Class<? extends Alias> class1 : classes) {
+ for (Class<? extends Element> class1 : classes) {
classString += class1.getSimpleName() + ", ";
}
desc = desc.replaceAll("\\$TYPES", classString);
@@ -380,10 +380,10 @@ public class RunOptions {
/**
* Returns width of created
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias}.
+ * {@link lcsb.mapviewer.model.map.species.Element}.
*
* @return width of created
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias}
+ * {@link lcsb.mapviewer.model.map.species.Element}
*/
public int getAliasWidth() {
return RunOptions.ALIAS_WIDTH;
@@ -391,10 +391,10 @@ public class RunOptions {
/**
* Returns height of created
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias}.
+ * {@link lcsb.mapviewer.model.map.species.Element}.
*
* @return height of created
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias}
+ * {@link lcsb.mapviewer.model.map.species.Element}
*/
public int getAliasHeight() {
return RunOptions.ALIAS_HEIGHT;
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index 8754380e03..90e6e1f4af 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -22,12 +22,12 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import lcsb.mapviewer.persist.DbUtils;
@@ -188,8 +188,8 @@ public class Statistics {
Map<String, Set<String>> typeNames = new HashMap<>();
for (Model model : models) {
- for (Alias element : model.getAliases()) {
- if (element instanceof SpeciesAlias) {
+ for (Element element : model.getAliases()) {
+ if (element instanceof Species) {
names.add(element.getName());
Set<String> tmp = typeNames.get(element.getClass().getName());
if (tmp == null) {
@@ -223,7 +223,7 @@ public class Statistics {
Set<String> set = new HashSet<String>();
for (Model model : models) {
- for (CompartmentAlias comp : model.getCompartmentsAliases()) {
+ for (Compartment comp : model.getCompartmentsAliases()) {
set.add(comp.getName());
}
}
@@ -255,8 +255,8 @@ public class Statistics {
}
print("-----------------------------");
print("Complex annotations:");
- for (Alias element : model.getAliases()) {
- if (element instanceof ComplexAlias && element.getMiriamData().size() > 0) {
+ for (Element element : model.getAliases()) {
+ if (element instanceof Complex && element.getMiriamData().size() > 0) {
print(element.getClass().getSimpleName() + ";\t\tname=" + element.getName() + ";\t\tid=" + element.getAliasId());
}
}
@@ -316,7 +316,7 @@ public class Statistics {
*/
protected String createPubmedExportString(Model model) throws Exception {
Map<String, List<String>> links = new HashMap<String, List<String>>();
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.PUBMED.equals(md.getDataType())) {
List<String> list = links.get(md.getResource());
diff --git a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
index 3c104e7aa7..f9153e1376 100644
--- a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
+++ b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
@@ -21,7 +21,7 @@ import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
@@ -208,7 +208,7 @@ public class UnknownReactionInReactome {
Set<String> ontologies = new HashSet<String>();
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
for (ReactionNode node : result.getLocalReaction().getReactionNodes()) {
if (alias.contains(node.getAlias())) {
ontologies.add(alias.getName());
diff --git a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
index f40554f26b..a5c577a07e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
+++ b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
@@ -7,10 +7,10 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class is a snippet for Vibine collaboration project. It shows how to
@@ -84,7 +84,7 @@ public class VibineSnippet {
String speciesId = "sa7208";
String reactionId = "re332";
- SpeciesAlias species = model.getAliasByAliasId(speciesId);
+ Species species = model.getAliasByAliasId(speciesId);
logger.debug("Element with id: " + speciesId);
logger.debug("Element type: " + species.getClass());
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
index 757a4ae6b1..008e12601d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
@@ -5,41 +5,41 @@ import java.util.List;
import java.util.Map;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
public class CellDesignerElementCollection {
- private Map<String, Element<?>> elementById = new HashMap<>();
+ private Map<String, CellDesignerElement<?>> elementById = new HashMap<>();
@SuppressWarnings("unchecked")
- public <T extends Element<?>> T getSpeciesBySpeciesId(String speciesId) {
+ public <T extends CellDesignerElement<?>> T getSpeciesBySpeciesId(String speciesId) {
return (T) elementById.get(speciesId);
}
- public Compartment getCompartmentByCompartmentId(String compartmentId) {
- return (Compartment) elementById.get(compartmentId);
+ public CellDesignerCompartment getCompartmentByCompartmentId(String compartmentId) {
+ return (CellDesignerCompartment) elementById.get(compartmentId);
}
- public String getElementId(Alias alias) {
+ public String getElementId(Element alias) {
// TODO
// silly implementation for now (if CD won't crash than we can keep it)
return "s_id_" + alias.getAliasId();
}
- public void addElements(List<? extends Element<?>> elements) {
- for (Element<?> element : elements) {
+ public void addElements(List<? extends CellDesignerElement<?>> elements) {
+ for (CellDesignerElement<?> element : elements) {
addElement(element);
}
}
- public void addElement(Element<?> element) {
+ public void addElement(CellDesignerElement<?> element) {
addElement(element, element.getElementId());
}
- private void addElement(Element<?> element, String id) {
+ private void addElement(CellDesignerElement<?> element, String id) {
if (elementById.get(id) != null) {
throw new InvalidArgumentException(
"[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t" + "Element with given id alread exists. ID: " + id);
@@ -47,7 +47,7 @@ public class CellDesignerElementCollection {
elementById.put(id, element);
}
- public void addAlias(SpeciesAlias alias, Element<?> element) {
+ public void addAlias(Species alias, CellDesignerElement<?> element) {
addElement(element, getElementId(alias));
if (getSpeciesBySpeciesId(element.getElementId()) == null) {
addElement(element);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 42b24a9e7f..2c990f4f37 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -33,18 +33,11 @@ import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionCollectionXm
import lcsb.mapviewer.converter.model.celldesigner.reaction.UnknownReactionClassException;
import lcsb.mapviewer.converter.model.celldesigner.species.InternalModelSpeciesData;
import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
@@ -52,6 +45,13 @@ import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class is a parser for CellDesigner files. There are two typical use
@@ -99,7 +99,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
*/
private AliasCollectionXmlParser aliasCollectionParser;
- private RestAnnotationParser rap = new RestAnnotationParser();
+ private RestAnnotationParser rap = new RestAnnotationParser();
@Override
public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
@@ -115,7 +115,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
if (params.getFilename() != null) {
model.setName(FilenameUtils.getBaseName(params.getFilename()));
}
- speciesSbmlParser = new SpeciesCollectionXmlParser(model, elements);
+ speciesSbmlParser = new SpeciesCollectionXmlParser(elements);
aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
@@ -147,7 +147,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
if (compartmentNode != null) {
- List<Compartment> compartments = compartmentCollectionXmlParser.parseXmlCompartmentCollection(compartmentNode);
+ List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser.parseXmlCompartmentCollection(compartmentNode);
elements.addElements(compartments);
}
@@ -155,7 +155,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
if (speciesNode != null) {
- List<Pair<String, ? extends Species<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
modelData.updateSpecies(species);
}
Node reactionsNode = null;
@@ -195,7 +195,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
parseAnnotation(model, annotationNode, modelData, elements);
if (speciesNode != null) {
- List<Pair<String, ? extends Species<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser.parseSbmlSpeciesCollection(speciesNode);
modelData.updateSpecies(species);
}
@@ -264,7 +264,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
double maxY = 0;
double minX = model.getWidth();
double minY = model.getHeight();
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
maxX = Math.max(maxX, alias.getWidth() + alias.getX());
maxY = Math.max(maxY, alias.getHeight() + alias.getY());
@@ -355,7 +355,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
*/
private void parseAnnotation(Model model, Node annotationNode, InternalModelSpeciesData modelData, CellDesignerElementCollection elements)
throws InvalidXmlSchemaException {
- SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(model, elements);
+ SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
Node extensionNode = getNode("celldesigner:extension", annotationNode.getChildNodes());
if (extensionNode == null) {
@@ -411,36 +411,36 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
if (listOfComparmentAlias != null) {
- List<CompartmentAlias> aliases = aliasCollectionParser.parseXmlCompartmentAliasCollection(listOfComparmentAlias);
- for (Alias alias : aliases) {
+ List<Compartment> aliases = aliasCollectionParser.parseXmlCompartmentAliasCollection(listOfComparmentAlias);
+ for (Element alias : aliases) {
rap.processNotes(alias);
model.addAlias(alias);
}
}
if (includedSpecies != null) {
- List<Pair<String, ? extends Species<?>>> species = parser.parseIncludedSpeciesCollection(includedSpecies);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseIncludedSpeciesCollection(includedSpecies);
modelData.updateSpecies(species);
}
if (listOfProteins != null) {
- List<Pair<String, ? extends Species<?>>> species = parser.parseXmlProteinCollection(listOfProteins);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlProteinCollection(listOfProteins);
modelData.updateSpecies(species);
}
if (listOfGenes != null) {
- List<Pair<String, ? extends Species<?>>> species = parser.parseXmlGeneCollection(listOfGenes);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlGeneCollection(listOfGenes);
modelData.updateSpecies(species);
}
if (listOfRnas != null) {
- List<Pair<String, ? extends Species<?>>> species = parser.parseXmlRnaCollection(listOfRnas);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlRnaCollection(listOfRnas);
modelData.updateSpecies(species);
}
if (listOfAntisenseRnas != null) {
- List<Pair<String, ? extends Species<?>>> species = parser.parseXmlAntisenseRnaCollection(listOfAntisenseRnas);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlAntisenseRnaCollection(listOfAntisenseRnas);
modelData.updateSpecies(species);
}
- for (Species species : modelData.getAll()) {
+ for (CellDesignerSpecies<?> species : modelData.getAll()) {
if (!species.getElementId().equals("")) {
elements.addElement(species);
} else {
@@ -451,16 +451,16 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
if (listOfComplexSpeciesAlias != null) {
- List<ComplexAlias> aliases = aliasCollectionParser.parseXmlComplexAliasCollection(listOfComplexSpeciesAlias);
- for (Alias alias : aliases) {
+ List<Complex> aliases = aliasCollectionParser.parseXmlComplexAliasCollection(listOfComplexSpeciesAlias);
+ for (Element alias : aliases) {
rap.processNotes(alias);
model.addAlias(alias);
}
}
if (listofSpeciesAlias != null) {
- List<SpeciesAlias> aliases = aliasCollectionParser.parseXmlSpeciesAliasCollection(listofSpeciesAlias);
- for (Alias alias : aliases) {
+ List<Species> aliases = aliasCollectionParser.parseXmlSpeciesAliasCollection(listofSpeciesAlias);
+ for (Element alias : aliases) {
rap.processNotes(alias);
model.addAlias(alias);
}
@@ -497,11 +497,11 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
String aliasId = getNodeAttr("id", node);
String complexId = getNodeAttr("complexSpeciesAlias", node);
- ComplexAlias alias = (ComplexAlias) model.getAliasByAliasId(aliasId);
+ Complex alias = (Complex) model.getAliasByAliasId(aliasId);
if (alias == null) {
throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
}
- ComplexAlias complex = (ComplexAlias) model.getAliasByAliasId(complexId);
+ Complex complex = (Complex) model.getAliasByAliasId(complexId);
if (complex != null) {
complex.addAlias(alias);
alias.setParent(complex);
@@ -534,14 +534,14 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
String aliasId = getNodeAttr("id", node);
String complexId = getNodeAttr("complexSpeciesAlias", node);
- Alias alias = model.getAliasByAliasId(aliasId);
+ Element alias = model.getAliasByAliasId(aliasId);
if (alias == null) {
throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
- } else if (alias instanceof SpeciesAlias) {
- ComplexAlias complex = (ComplexAlias) model.getAliasByAliasId(complexId);
+ } else if (alias instanceof Species) {
+ Complex complex = (Complex) model.getAliasByAliasId(complexId);
if (complex != null) {
alias.setParent(complex);
- complex.addAlias((SpeciesAlias) alias);
+ complex.addAlias((Species) alias);
}
}
} else {
@@ -563,7 +563,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
public String toXml(Model model) throws InconsistentModelException {
CellDesignerElementCollection elements = new CellDesignerElementCollection();
- SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(model, elements);
+ SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements);
aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
@@ -585,7 +585,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
result.append(annotationToXml(model, elements));
compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
-
+
result.append(compartmentCollectionXmlParser.toXml(model.getCompartmentsAliases()));
result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesAliases()));
@@ -605,7 +605,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
* @return annotation xml string for the model
*/
private String annotationToXml(Model model, CellDesignerElementCollection elements) {
- SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(model, elements);
+ SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
StringBuilder result = new StringBuilder();
result.append("<annotation>\n");
@@ -619,19 +619,19 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
result.append(aliasCollectionParser.complexAliasCollectionToXmlString(model.getComplexAliases()));
result.append(aliasCollectionParser.speciesAliasCollectionToXmlString(model.getNotComplexSpeciesAliases()));
- List<ProteinAlias> proteins = new ArrayList<>();
- List<GeneAlias> genes = new ArrayList<>();
- List<RnaAlias> rnas = new ArrayList<>();
- List<AntisenseRnaAlias> antisenseRnas = new ArrayList<>();
- for (Alias element : model.getAliases()) {
- if (element instanceof ProteinAlias) {
- proteins.add((ProteinAlias) element);
- } else if (element instanceof GeneAlias) {
- genes.add((GeneAlias) element);
- } else if (element instanceof AntisenseRnaAlias) {
- antisenseRnas.add((AntisenseRnaAlias) element);
- } else if (element instanceof RnaAlias) {
- rnas.add((RnaAlias) element);
+ List<Protein> proteins = new ArrayList<>();
+ List<Gene> genes = new ArrayList<>();
+ List<Rna> rnas = new ArrayList<>();
+ List<AntisenseRna> antisenseRnas = new ArrayList<>();
+ for (Element element : model.getAliases()) {
+ if (element instanceof Protein) {
+ proteins.add((Protein) element);
+ } else if (element instanceof Gene) {
+ genes.add((Gene) element);
+ } else if (element instanceof AntisenseRna) {
+ antisenseRnas.add((AntisenseRna) element);
+ } else if (element instanceof Rna) {
+ rnas.add((Rna) element);
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
index 98aff110e0..a334aac73e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
@@ -1,106 +1,106 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SingleLine;
-import lcsb.mapviewer.converter.model.celldesigner.structure.View;
-
-import org.w3c.dom.Node;
-
-/**
- * Class with parsers for common CellDesigner objects.
- *
- * @author Piotr Gawron
- *
- */
-public class CommonXmlParser extends XmlParser {
- /**
- * Parse xml representation of position into Poin2D object.
- *
- * @param node
- * xml node to parse
- * @return Point2D object
- */
- public Point2D getPosition(Node node) {
- double x = Double.parseDouble(getNodeAttr("x", node));
- double y = Double.parseDouble(getNodeAttr("y", node));
- return new Point2D.Double(x, y);
-
- }
-
- /**
- * Parse xml representation of dimension.
- *
- * @param node
- * xml node to parse
- * @return dimension (with width and height fields)
- */
- public Dimension getDimension(Node node) {
- double width = Double.parseDouble(getNodeAttr("width", node));
- double height = Double.parseDouble(getNodeAttr("height", node));
- Dimension result = new Dimension();
- result.setSize(width, height);
- return result;
- }
-
- /**
- * Parse xml representation of CellDesigner SingleLine.
- *
- * @param node
- * xml node to parse
- * @return sinle line object (with width field)
- */
- public SingleLine getSingleLine(Node node) {
- SingleLine result = new SingleLine();
- result.setWidth(Double.parseDouble(getNodeAttr("width", node)));
- return result;
- }
-
- /**
- * Parse xml representation of CellDesigner color.
- *
- * @param node
- * xml node to parse
- * @return Color value stored in xml
- */
- public Color getColor(Node node) {
- String color = getNodeAttr("color", node);
- return stringToColor(color);
- }
-
- /**
- * Parse xml representation of CellDesigner view.
- *
- * @param node
- * xml node to parse
- * @return view parsed from xml
- * @see View
- */
- public View getView(Node node) {
- View result = new View();
- Node tmpNode = getNode("celldesigner:innerPosition", node.getChildNodes());
- if (tmpNode != null) {
- result.setInnerPosition(getPosition(tmpNode));
- }
-
- tmpNode = getNode("celldesigner:boxSize", node.getChildNodes());
- if (tmpNode != null) {
- result.setBoxSize(getDimension(tmpNode));
- }
-
- tmpNode = getNode("celldesigner:singleLine", node.getChildNodes());
- if (tmpNode != null) {
- result.setSingleLine(getSingleLine(tmpNode));
- }
-
- tmpNode = getNode("celldesigner:paint", node.getChildNodes());
- if (tmpNode != null) {
- result.setColor(getColor(tmpNode));
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+
+import org.w3c.dom.Node;
+
+/**
+ * Class with parsers for common CellDesigner objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CommonXmlParser extends XmlParser {
+ /**
+ * Parse xml representation of position into Poin2D object.
+ *
+ * @param node
+ * xml node to parse
+ * @return Point2D object
+ */
+ public Point2D getPosition(Node node) {
+ double x = Double.parseDouble(getNodeAttr("x", node));
+ double y = Double.parseDouble(getNodeAttr("y", node));
+ return new Point2D.Double(x, y);
+
+ }
+
+ /**
+ * Parse xml representation of dimension.
+ *
+ * @param node
+ * xml node to parse
+ * @return dimension (with width and height fields)
+ */
+ public Dimension getDimension(Node node) {
+ double width = Double.parseDouble(getNodeAttr("width", node));
+ double height = Double.parseDouble(getNodeAttr("height", node));
+ Dimension result = new Dimension();
+ result.setSize(width, height);
+ return result;
+ }
+
+ /**
+ * Parse xml representation of CellDesigner SingleLine.
+ *
+ * @param node
+ * xml node to parse
+ * @return sinle line object (with width field)
+ */
+ public SingleLine getSingleLine(Node node) {
+ SingleLine result = new SingleLine();
+ result.setWidth(Double.parseDouble(getNodeAttr("width", node)));
+ return result;
+ }
+
+ /**
+ * Parse xml representation of CellDesigner color.
+ *
+ * @param node
+ * xml node to parse
+ * @return Color value stored in xml
+ */
+ public Color getColor(Node node) {
+ String color = getNodeAttr("color", node);
+ return stringToColor(color);
+ }
+
+ /**
+ * Parse xml representation of CellDesigner view.
+ *
+ * @param node
+ * xml node to parse
+ * @return view parsed from xml
+ * @see View
+ */
+ public View getView(Node node) {
+ View result = new View();
+ Node tmpNode = getNode("celldesigner:innerPosition", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setInnerPosition(getPosition(tmpNode));
+ }
+
+ tmpNode = getNode("celldesigner:boxSize", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setBoxSize(getDimension(tmpNode));
+ }
+
+ tmpNode = getNode("celldesigner:singleLine", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setSingleLine(getSingleLine(tmpNode));
+ }
+
+ tmpNode = getNode("celldesigner:paint", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setColor(getColor(tmpNode));
+ }
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
index f232c0aad7..c7566f716d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
@@ -14,14 +14,14 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Parser used for parsing CellDesigner xml to get {@link Layer} object.
@@ -164,15 +164,15 @@ public class LayerXmlParser extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- AliasGroup getAliasGroup(Node groupNode, Model model) throws InvalidXmlSchemaException {
- AliasGroup result = new AliasGroup();
+ ElementGroup getAliasGroup(Node groupNode, Model model) throws InvalidXmlSchemaException {
+ ElementGroup result = new ElementGroup();
String id = getNodeAttr("id", groupNode);
result.setIdGroup(id);
String members = getNodeAttr("members", groupNode);
String[] list = members.split(",");
for (String string : list) {
- Alias alias = model.getAliasByAliasId(string);
+ Element alias = model.getAliasByAliasId(string);
if (alias == null) {
throw new InvalidGroupException("Group \"" + id + "\" contains alias with id: \"" + string + "\", but such alias doesn't exist in the model.");
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
index fa7a8f4414..a4a9319242 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
@@ -8,7 +8,7 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Generic abstract interface for parsing CellDesigner xml nodes with species
@@ -19,7 +19,7 @@ import lcsb.mapviewer.model.map.layout.alias.Alias;
* @param <T>
* type of the object to parse
*/
-public abstract class AbstractAliasXmlParser<T extends Alias> extends XmlParser {
+public abstract class AbstractAliasXmlParser<T extends Element> extends XmlParser {
/**
* Default class logger.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
index f2bb7f53f8..f1ffccc93d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
@@ -12,11 +12,11 @@ import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class contains function to parse CellDesigner xml nodes containing
@@ -76,14 +76,14 @@ public class AliasCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public List<SpeciesAlias> parseXmlSpeciesAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
- List<SpeciesAlias> result = new ArrayList<SpeciesAlias>();
+ public List<Species> parseXmlSpeciesAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
+ List<Species> result = new ArrayList<Species>();
NodeList nodes = aliasListNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
- SpeciesAlias alias = speciesAliasParser.parseXmlAlias(node);
+ Species alias = speciesAliasParser.parseXmlAlias(node);
rap.processNotes(alias);
result.add(alias);
} else {
@@ -101,9 +101,9 @@ public class AliasCollectionXmlParser extends XmlParser {
* collection of SpeciesAlias
* @return xml string representing collection of SpeciesAlias
*/
- public String speciesAliasCollectionToXmlString(Collection<SpeciesAlias> collection) {
+ public String speciesAliasCollectionToXmlString(Collection<Species> collection) {
StringBuilder sb = new StringBuilder("<celldesigner:listOfSpeciesAliases>\n");
- for (SpeciesAlias alias : collection) {
+ for (Species alias : collection) {
sb.append(speciesAliasParser.toXml(alias));
}
sb.append("</celldesigner:listOfSpeciesAliases>\n");
@@ -120,21 +120,21 @@ public class AliasCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when xmlString is invalid
*/
- public List<ComplexAlias> parseXmlComplexAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
- List<ComplexAlias> result = new ArrayList<ComplexAlias>();
+ public List<Complex> parseXmlComplexAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
+ List<Complex> result = new ArrayList<Complex>();
NodeList nodes = aliasListNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
- ComplexAlias alias = complexAliasParser.parseXmlAlias(node);
+ Complex alias = complexAliasParser.parseXmlAlias(node);
result.add(alias);
} else {
throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfComplexSpeciesAliases: " + node.getNodeName());
}
}
}
- for (ComplexAlias complexAlias : result) {
+ for (Complex complexAlias : result) {
complexAliasParser.addReference(complexAlias);
}
return result;
@@ -147,9 +147,9 @@ public class AliasCollectionXmlParser extends XmlParser {
* collection of ComplexAlias
* @return xml string representing collection of ComplexAlias
*/
- public String complexAliasCollectionToXmlString(Collection<ComplexAlias> collection) {
+ public String complexAliasCollectionToXmlString(Collection<Complex> collection) {
StringBuilder sb = new StringBuilder("<celldesigner:listOfComplexSpeciesAliases>\n");
- for (ComplexAlias alias : collection) {
+ for (Complex alias : collection) {
sb.append(complexAliasParser.toXml(alias));
}
sb.append("</celldesigner:listOfComplexSpeciesAliases>\n");
@@ -166,14 +166,14 @@ public class AliasCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when xmlString is invalid
*/
- public List<CompartmentAlias> parseXmlCompartmentAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
- List<CompartmentAlias> result = new ArrayList<CompartmentAlias>();
+ public List<Compartment> parseXmlCompartmentAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
+ List<Compartment> result = new ArrayList<Compartment>();
NodeList nodes = aliasListNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:compartmentAlias")) {
- CompartmentAlias alias = compartmentAliasParser.parseXmlAlias(node);
+ Compartment alias = compartmentAliasParser.parseXmlAlias(node);
result.add(alias);
} else {
@@ -191,11 +191,11 @@ public class AliasCollectionXmlParser extends XmlParser {
* collection of CompartmentAlias
* @return xml string representing collection of CompartmentAlias
*/
- public String compartmentAliasCollectionToXmlString(Collection<CompartmentAlias> collection) {
+ public String compartmentAliasCollectionToXmlString(Collection<Compartment> collection) {
StringBuilder sb = new StringBuilder("<celldesigner:listOfCompartmentAliases>\n");
- for (CompartmentAlias alias : collection) {
+ for (Compartment alias : collection) {
// artifitial compartment aliases cannot be exported
- if (!(alias instanceof ArtifitialCompartmentAlias)) {
+ if (!(alias instanceof PathwayCompartment)) {
sb.append(compartmentAliasParser.toXml(alias));
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
index b3a9c6865b..47d06cb3a5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
@@ -7,14 +7,14 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.BottomSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.LeftSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.OvalCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.RightSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.TopSquareCompartmentAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
/**
@@ -23,7 +23,7 @@ import lcsb.mapviewer.model.map.model.Model;
* @author Piotr Gawron
*
*/
-public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<CompartmentAlias> {
+public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartment> {
/**
* Default class logger.
@@ -50,15 +50,15 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
}
@Override
- CompartmentAlias parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+ Compartment parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
String compartmentId = getNodeAttr("compartment", aliasNode);
- Compartment compartment = elements.getCompartmentByCompartmentId(compartmentId);
+ CellDesignerCompartment compartment = elements.getCompartmentByCompartmentId(compartmentId);
if (compartment == null) {
throw new InvalidXmlSchemaException("Compartment does not exist in a model: " + compartmentId);
}
String aliasId = getNodeAttr("id", aliasNode);
- CompartmentAlias result = compartment.createAlias(aliasId);
+ Compartment result = compartment.createAlias(aliasId);
NodeList nodes = aliasNode.getChildNodes();
for (int i = 0; i < nodes.getLength(); i++) {
@@ -67,17 +67,17 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
String type = getNodeValue(node);
if (type.equalsIgnoreCase("SQUARE")) {
- result = new SquareCompartmentAlias(result);
+ result = new SquareCompartment(result);
} else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_NORTH")) {
- result = new BottomSquareCompartmentAlias(result, model);
+ result = new BottomSquareCompartment(result, model);
} else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_SOUTH")) {
- result = new TopSquareCompartmentAlias(result, model);
+ result = new TopSquareCompartment(result, model);
} else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_WEST")) {
- result = new RightSquareCompartmentAlias(result, model);
+ result = new RightSquareCompartment(result, model);
} else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_EAST")) {
- result = new LeftSquareCompartmentAlias(result, model);
+ result = new LeftSquareCompartment(result, model);
} else if (type.equalsIgnoreCase("OVAL")) {
- result = new OvalCompartmentAlias(result);
+ result = new OvalCompartment(result);
} else {
throw new InvalidXmlSchemaException("Unknown compartment type: " + type);
}
@@ -96,14 +96,14 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
// not handled
continue;
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:point")) {
- if (result instanceof BottomSquareCompartmentAlias) {
+ if (result instanceof BottomSquareCompartment) {
result.setY(getNodeAttr("y", node));
- } else if (result instanceof LeftSquareCompartmentAlias) {
+ } else if (result instanceof LeftSquareCompartment) {
result.setX(getNodeAttr("x", node));
- } else if (result instanceof RightSquareCompartmentAlias) {
+ } else if (result instanceof RightSquareCompartment) {
result.setX(getNodeAttr("x", node));
result.setWidth(result.getWidth() - result.getX());
- } else if (result instanceof TopSquareCompartmentAlias) {
+ } else if (result instanceof TopSquareCompartment) {
result.setY(getNodeAttr("y", node));
} else {
throw new InvalidXmlSchemaException("Don't know what to do with celldesigner:point for class: " + result.getClass());
@@ -119,7 +119,7 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
}
@Override
- public String toXml(CompartmentAlias alias) {
+ public String toXml(Compartment alias) {
StringBuilder sb = new StringBuilder("");
sb.append("<celldesigner:compartmentAlias ");
@@ -128,23 +128,23 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
boolean bounds = true;
- if (alias.getClass().getName().equals(SquareCompartmentAlias.class.getName())) {
+ if (alias.getClass().getName().equals(SquareCompartment.class.getName())) {
sb.append("<celldesigner:class>SQUARE</celldesigner:class>\n");
- } else if (alias.getClass().getName().equals(OvalCompartmentAlias.class.getName())) {
+ } else if (alias.getClass().getName().equals(OvalCompartment.class.getName())) {
sb.append("<celldesigner:class>OVAL</celldesigner:class>\n");
- } else if (alias.getClass().getName().equals(BottomSquareCompartmentAlias.class.getName())) {
+ } else if (alias.getClass().getName().equals(BottomSquareCompartment.class.getName())) {
sb.append("<celldesigner:class>SQUARE_CLOSEUP_NORTH</celldesigner:class>\n");
bounds = false;
sb.append("<celldesigner:point x=\"10\" y=\"" + alias.getY() + "\"/>");
- } else if (alias.getClass().getName().equals(TopSquareCompartmentAlias.class.getName())) {
+ } else if (alias.getClass().getName().equals(TopSquareCompartment.class.getName())) {
sb.append("<celldesigner:class>SQUARE_CLOSEUP_SOUTH</celldesigner:class>\n");
bounds = false;
sb.append("<celldesigner:point x=\"10\" y=\"" + alias.getY() + "\"/>");
- } else if (alias.getClass().getName().equals(LeftSquareCompartmentAlias.class.getName())) {
+ } else if (alias.getClass().getName().equals(LeftSquareCompartment.class.getName())) {
sb.append("<celldesigner:class>SQUARE_CLOSEUP_EAST</celldesigner:class>\n");
bounds = false;
sb.append("<celldesigner:point x=\"" + alias.getWidth() + "\" y=\"10\"/>");
- } else if (alias.getClass().getName().equals(RightSquareCompartmentAlias.class.getName())) {
+ } else if (alias.getClass().getName().equals(RightSquareCompartment.class.getName())) {
sb.append("<celldesigner:class>SQUARE_CLOSEUP_WEST</celldesigner:class>\n");
bounds = false;
sb.append("<celldesigner:point x=\"" + alias.getX() + "\" y=\"10\"/>");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
index 20d178c1f9..ae29b5a2fa 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
@@ -11,14 +11,14 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.View;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Parser of CellDesigner xml used for parsing complex aliases. Important: Only
@@ -26,9 +26,9 @@ import lcsb.mapviewer.model.map.model.ModelData;
*
* @author Piotr Gawron
*
- * @see ComplexAlias
+ * @see Complex
*/
-public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias> {
+public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
/**
* Default class logger.
@@ -41,7 +41,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias>
* all processed Complexes. This infomrmation later on is used for connecting
* complexes in hierarchical view.
*/
- private Map<String, ComplexAlias> complexAliasesMapById = new HashMap<String, ComplexAlias>();
+ private Map<String, Complex> complexAliasesMapById = new HashMap<String, Complex>();
/**
* Because of the CellDesigner xml model we have to store information about
@@ -70,16 +70,16 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias>
}
@Override
- ComplexAlias parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+ Complex parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
String aliasId = getNodeAttr("id", aliasNode);
String speciesId = getNodeAttr("species", aliasNode);
- ComplexSpecies species = (ComplexSpecies) elements.getSpeciesBySpeciesId(speciesId);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) elements.getSpeciesBySpeciesId(speciesId);
if (species == null) {
throw new InvalidXmlSchemaException("No species with id=\"" + speciesId + "\" for complex alias \"" + aliasId + "\"");
}
- ComplexAlias result = species.createAlias(aliasId);
+ Complex result = species.createAlias(aliasId);
String state = "usual";
NodeList nodes = aliasNode.getChildNodes();
@@ -140,7 +140,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias>
result.setState(state);
String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
if (!compartmentAliasId.isEmpty()) {
- CompartmentAlias ca = model.getCompartmentAliasByCompartmentAliasId(compartmentAliasId);
+ Compartment ca = model.getCompartmentAliasByCompartmentAliasId(compartmentAliasId);
if (ca == null) {
throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
} else {
@@ -164,7 +164,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias>
* @param alias
* alias object to be modified if necessary
*/
- private void processAliasState(Node node, SpeciesAlias alias) {
+ private void processAliasState(Node node, Species alias) {
String state = getNodeAttr("state", node);
if ("open".equalsIgnoreCase(state)) {
String prefix = getNodeAttr("prefix", node);
@@ -187,10 +187,10 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias>
* @param alias
* alias for which we want to add parent information
*/
- public void addReference(ComplexAlias alias) {
+ public void addReference(Complex alias) {
String parentId = parents.get(alias.getAliasId());
if (parentId != null) {
- ComplexAlias ca = complexAliasesMapById.get(parentId);
+ Complex ca = complexAliasesMapById.get(parentId);
if (ca == null) {
throw new InvalidArgumentException("Parent complex alias does not exist: " + parentId + " for alias: " + alias.getAliasId());
} else {
@@ -201,19 +201,19 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias>
}
@Override
- public String toXml(ComplexAlias alias) {
- CompartmentAlias ca = null;
+ public String toXml(Complex alias) {
+ Compartment ca = null;
// we have to exclude artifitial compartment aliases, becuase they aren't
// exported to CellDesigner file
- if (alias.getParent() instanceof CompartmentAlias && !(alias.getParent() instanceof ArtifitialCompartmentAlias)) {
- ca = (CompartmentAlias) alias.getParent();
- } else if (alias.getCompartmentAlias() != null && !(alias.getCompartmentAlias() instanceof ArtifitialCompartmentAlias)) {
+ if (alias.getParent() instanceof Compartment && !(alias.getParent() instanceof PathwayCompartment)) {
+ ca = (Compartment) alias.getParent();
+ } else if (alias.getCompartmentAlias() != null && !(alias.getCompartmentAlias() instanceof PathwayCompartment)) {
ca = alias.getCompartmentAlias();
} else if (alias.getComplexAlias() == null) {
ModelData modelData = alias.getModelData();
if (modelData != null) {
- for (CompartmentAlias cAlias : modelData.getModel().getCompartmentsAliases()) {
- if (!(cAlias instanceof ArtifitialCompartmentAlias) && cAlias.cross(alias)) {
+ for (Compartment cAlias : modelData.getModel().getCompartmentsAliases()) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(alias)) {
if (ca == null) {
ca = cAlias;
} else if (ca.getSize() > cAlias.getSize()) {
@@ -224,9 +224,9 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<ComplexAlias>
}
}
- ComplexAlias complexAlias = null;
- if (alias.getParent() instanceof ComplexAlias) {
- complexAlias = (ComplexAlias) alias.getParent();
+ Complex complexAlias = null;
+ if (alias.getParent() instanceof Complex) {
+ complexAlias = (Complex) alias.getParent();
}
String compartmentAliasId = null;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index 4fb76150be..f72a2f4d4d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -7,24 +7,24 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.converter.model.celldesigner.structure.View;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Parser of CellDesigner xml used for parsing SpeciesAlias.
*
* @author Piotr Gawron
*
- * @see ComplexAlias
+ * @see Complex
*/
-public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<SpeciesAlias> {
+public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
/**
* Default class logger.
*/
@@ -46,19 +46,19 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<SpeciesAlias>
}
@Override
- SpeciesAlias parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+ Species parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
String speciesId = getNodeAttr("species", aliasNode);
String aliasId = getNodeAttr("id", aliasNode);
- Species species = elements.getSpeciesBySpeciesId(speciesId);
+ CellDesignerSpecies<?> species = elements.getSpeciesBySpeciesId(speciesId);
if (species == null) {
throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
}
- if (species instanceof ComplexSpecies) {
+ if (species instanceof CellDesignerComplexSpecies) {
logger.warn("[" + speciesId + "," + aliasId + "]\tSpecies is defined as a complex, but alias is not a complex. Changing alias to complex.");
}
- SpeciesAlias result = species.createAlias(aliasId);
+ Species result = species.createAlias(aliasId);
String state = "usual";
NodeList nodes = aliasNode.getChildNodes();
@@ -111,7 +111,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<SpeciesAlias>
result.setState(state);
String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
if (!compartmentAliasId.isEmpty()) {
- CompartmentAlias ca = model.getCompartmentAliasByCompartmentAliasId(compartmentAliasId);
+ Compartment ca = model.getCompartmentAliasByCompartmentAliasId(compartmentAliasId);
if (ca == null) {
throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
} else {
@@ -121,7 +121,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<SpeciesAlias>
}
String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
if (!complexAliasId.isEmpty()) {
- ComplexAlias alias = (ComplexAlias) model.getAliasByAliasId(complexAliasId);
+ Complex alias = (Complex) model.getAliasByAliasId(complexAliasId);
if (alias == null) {
throw new InvalidXmlSchemaException("ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getAliasId());
} else {
@@ -140,7 +140,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<SpeciesAlias>
* @param alias
* alias object to be modified if necessary
*/
- private void processAliasState(Node node, SpeciesAlias alias) {
+ private void processAliasState(Node node, Species alias) {
String state = getNodeAttr("state", node);
if ("open".equalsIgnoreCase(state)) {
String prefix = getNodeAttr("prefix", node);
@@ -158,16 +158,16 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<SpeciesAlias>
}
@Override
- public String toXml(SpeciesAlias alias) {
- CompartmentAlias ca = null;
+ public String toXml(Species alias) {
+ Compartment ca = null;
// artifitial compartment aliases should be excluded
- if (alias.getParent() instanceof CompartmentAlias && !(alias.getParent() instanceof ArtifitialCompartmentAlias)) {
- ca = (CompartmentAlias) alias.getParent();
+ if (alias.getParent() instanceof Compartment && !(alias.getParent() instanceof PathwayCompartment)) {
+ ca = (Compartment) alias.getParent();
} else if (alias.getComplexAlias() == null) {
ModelData model = alias.getModelData();
if (model != null) {
- for (CompartmentAlias cAlias : model.getModel().getCompartmentsAliases()) {
- if (!(cAlias instanceof ArtifitialCompartmentAlias) && cAlias.cross(alias)) {
+ for (Compartment cAlias : model.getModel().getCompartmentsAliases()) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(alias)) {
if (ca == null) {
ca = cAlias;
} else if (ca.getSize() > cAlias.getSize()) {
@@ -178,9 +178,9 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<SpeciesAlias>
}
}
- ComplexAlias complexAlias = null;
- if (alias.getParent() instanceof ComplexAlias) {
- complexAlias = (ComplexAlias) alias.getParent();
+ Complex complexAlias = null;
+ if (alias.getParent() instanceof Complex) {
+ complexAlias = (Complex) alias.getParent();
}
String compartmentAliasId = null;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
index f64ef822ac..db00f59da0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.annotation;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -51,12 +51,12 @@ public enum NoteField {
/**
* {@link Element#symbol}.
*/
- SYMBOL("Symbol", Element.class, null), //
+ SYMBOL("Symbol", CellDesignerElement.class, null), //
/**
* {@link Element#fullName}.
*/
- NAME("Name", Element.class, null), //
+ NAME("Name", CellDesignerElement.class, null), //
/**
* {@link Element#notes} or {@link Reaction#notes} .
@@ -66,7 +66,7 @@ public enum NoteField {
/**
* {@link Element#formerSymbols}.
*/
- PREVIOUS_SYMBOLS("Previous Symbols", Element.class, null), //
+ PREVIOUS_SYMBOLS("Previous Symbols", CellDesignerElement.class, null), //
/**
* {@link Element#synonyms} or {@link Reaction#synonyms}.
@@ -111,12 +111,12 @@ public enum NoteField {
/**
* {@link Element#formula}.
*/
- CHARGED_FORMULA("ChargedFormula", Element.class, null), //
+ CHARGED_FORMULA("ChargedFormula", CellDesignerElement.class, null), //
/**
* {@link Species#charge}.
*/
- CHARGE("Charge", Species.class, null); //
+ CHARGE("Charge", CellDesignerSpecies.class, null); //
/**
* Name used in the notes to distinguish fields.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index 40d0164073..b938e0ed8d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -25,9 +25,9 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -99,7 +99,7 @@ public class RestAnnotationParser extends XmlParser {
* element for which notes are created
* @return note string with structural information about element
*/
- public String createAnnotationString(Alias element) {
+ public String createAnnotationString(Element element) {
String symbol = element.getSymbol();
if (symbol == null) {
symbol = "";
@@ -319,7 +319,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setFormerSymbolsToSpecies(Alias element, String annotationString) {
+ private void setFormerSymbolsToSpecies(Element element, String annotationString) {
List<String> formerSymbols = getFormerSymbols(annotationString);
if (formerSymbols.size() == 0) {
return;
@@ -344,7 +344,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setFullNameToSpecies(Alias element, String annotationString) {
+ private void setFullNameToSpecies(Element element, String annotationString) {
StringComparator stringComparator = new StringComparator();
String fullName = getParamByPrefix(annotationString, NoteField.NAME.getCommonName() + ":");
if (fullName == null) {
@@ -480,7 +480,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setCharge(SpeciesAlias element, String annotationString) {
+ private void setCharge(Species element, String annotationString) {
IntegerComparator integerComparator = new IntegerComparator();
String value = getParamByPrefix(annotationString, NoteField.CHARGE.getCommonName() + ":");
if (value == null || value.trim().equals("") || value.trim().equals("-")) {
@@ -634,11 +634,11 @@ public class RestAnnotationParser extends XmlParser {
setUpperBoundToReaction(reaction, ann);
setSubsystemToReaction(reaction, ann);
setGeneProteinReactionToReaction(reaction, ann);
- } else if (object instanceof Alias) {
- setFullNameToSpecies((Alias) object, ann);
- setFormerSymbolsToSpecies((Alias) object, ann);
- if (object instanceof SpeciesAlias) {
- setCharge((SpeciesAlias) object, ann);
+ } else if (object instanceof Element) {
+ setFullNameToSpecies((Element) object, ann);
+ setFormerSymbolsToSpecies((Element) object, ann);
+ if (object instanceof Species) {
+ setCharge((Species) object, ann);
}
} else {
throw new NotImplementedException("Don't know how to process class: " + object.getClass());
@@ -674,7 +674,7 @@ public class RestAnnotationParser extends XmlParser {
}
}
- public void processNotes(Alias alias) {
+ public void processNotes(Element alias) {
processNotes(alias.getNotes(), alias);
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
index 8cf2978af5..fd8b7d2abf 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
@@ -12,8 +12,8 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
/**
* CellDEsigner xml parser for collection of compartments.
@@ -27,20 +27,17 @@ public class CompartmentCollectionXmlParser extends XmlParser {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CompartmentCollectionXmlParser.class.getName());
+ private Logger logger = Logger.getLogger(CompartmentCollectionXmlParser.class.getName());
/**
* CellDesigner xml parser for single compartment.
*/
- private CompartmentXmlParser compartmentParser;
-
- private CellDesignerElementCollection elements;
+ private CompartmentXmlParser compartmentParser;
/**
* Default constructor.
*/
public CompartmentCollectionXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
compartmentParser = new CompartmentXmlParser(elements);
}
@@ -53,14 +50,14 @@ public class CompartmentCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public List<Compartment> parseXmlCompartmentCollection(Node compartmentsNode) throws InvalidXmlSchemaException {
- List<Compartment> result = new ArrayList<Compartment>();
+ public List<CellDesignerCompartment> parseXmlCompartmentCollection(Node compartmentsNode) throws InvalidXmlSchemaException {
+ List<CellDesignerCompartment> result = new ArrayList<CellDesignerCompartment>();
NodeList nodes = compartmentsNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("compartment")) {
- Pair<String, Compartment> compartmentPair = compartmentParser.parseXmlElement(node);
+ Pair<String, CellDesignerCompartment> compartmentPair = compartmentParser.parseXmlElement(node);
result.add(compartmentPair.getRight());
} else {
throw new InvalidXmlSchemaException("Unknown element of model/listOfCompartments: " + node.getNodeName());
@@ -77,10 +74,10 @@ public class CompartmentCollectionXmlParser extends XmlParser {
* collection of compartments to be transformed into xml
* @return xml representation of the compartments
*/
- public String toXml(Collection<CompartmentAlias> collection) {
+ public String toXml(Collection<Compartment> collection) {
String result = "";
result += "<listOfCompartments>\n";
- for (CompartmentAlias compartment : collection) {
+ for (Compartment compartment : collection) {
result += compartmentParser.toXml(compartment);
}
result += "</listOfCompartments>\n";
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
index ca0cbbbe61..c1ba9e05a9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
@@ -9,8 +9,8 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
/**
* Parser of CellDesginer xml nodes for compartment elements.
@@ -18,7 +18,7 @@ import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
* @author Piotr Gawron
*
*/
-public class CompartmentXmlParser extends AbstractElementXmlParser<Compartment, CompartmentAlias> {
+public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerCompartment, Compartment> {
/**
* Default class logger.
@@ -38,8 +38,8 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<Compartment,
}
@Override
- public Pair<String, Compartment> parseXmlElement(Node compartmentNode) throws InvalidXmlSchemaException {
- Compartment compartment = new Compartment();
+ public Pair<String, CellDesignerCompartment> parseXmlElement(Node compartmentNode) throws InvalidXmlSchemaException {
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
// we ignore metaid - it's useless and obstruct data model
// compartment.setMetaId(getNodeAttr("metaid", compartmentNode));
compartment.setElementId(getNodeAttr("id", compartmentNode));
@@ -55,7 +55,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<Compartment,
}
}
}
- return new Pair<String, Compartment>(compartment.getElementId(), compartment);
+ return new Pair<String, CellDesignerCompartment>(compartment.getElementId(), compartment);
}
/**
@@ -68,7 +68,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<Compartment,
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- private void parseAnnotationNode(Compartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
+ private void parseAnnotationNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
NodeList annotationNodes = xmlNode.getChildNodes();
for (int y = 0; y < annotationNodes.getLength(); y++) {
Node annotationNode = annotationNodes.item(y);
@@ -94,7 +94,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<Compartment,
* @throws InvalidXmlSchemaException
* thrown when xmlNode is invalid
*/
- private void parseExtensionNode(Compartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
+ private void parseExtensionNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
NodeList annotationNodes = xmlNode.getChildNodes();
for (int y = 0; y < annotationNodes.getLength(); y++) {
Node annotationNode = annotationNodes.item(y);
@@ -110,7 +110,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<Compartment,
}
@Override
- public String toXml(CompartmentAlias compartment) {
+ public String toXml(Compartment compartment) {
StringBuilder sb = new StringBuilder("");
sb.append("<compartment ");
sb.append("metaid=\"" + elements.getElementId(compartment) + "\" ");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
index 6ef03b86f2..0c70c484da 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerE
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPolygonTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerRectangleTransformation;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This abstract class is an interface for setting up graphical data for alias
@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.map.layout.alias.Alias;
*
* @param <T>
*/
-public abstract class AbstractCellDesignerAliasConverter<T extends Alias> implements ICellDesignerAliasConverter<T> {
+public abstract class AbstractCellDesignerAliasConverter<T extends Element> implements ICellDesignerAliasConverter<T> {
/**
* Default class logger.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
index bd881768e3..946fc4ab37 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverter.java
@@ -1,109 +1,109 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * AntisenseRna. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (alias.getModel().isSbgnFormat()) {
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
- alias.getWidth(), alias.getHeight(), anchor);
- }
- ArrayList<Point2D> points = getPoints(alias);
- return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- }
-
- @Override
- protected PathIterator getBoundPathIterator(SpeciesAlias alias) {
- return getAntisebseRnaPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the AntisenseRna as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPoints(Alias alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
-
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x + width / 8, y + height / 2));
- points.add(new Point2D.Double(x, y));
- points.add(new Point2D.Double(x + width * 3 / 8, y));
- points.add(new Point2D.Double(x + width * 3 / 4, y));
- points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
- points.add(new Point2D.Double(x + width, y + height));
- points.add(new Point2D.Double(x + width * 5 / 8, y + height));
- points.add(new Point2D.Double(x + width / 4, y + height));
- // CHECKSTYLE:ON
- return points;
- }
-
- /**
- * Returns shape of the AntisenseRna as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getAntisebseRnaPath(Alias alias) {
- // CHECKSTYLE:OFF
- GeneralPath path;
- if (!alias.getModel().isSbgnFormat()) {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + alias.getWidth() / 4, alias.getY() + alias.getHeight());
- path.closePath();
- } else {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- }
- // CHECKSTYLE:ON
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for
+ * AntisenseRna. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AntisenseRnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (alias.getModel().isSbgnFormat()) {
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
+ alias.getWidth(), alias.getHeight(), anchor);
+ }
+ ArrayList<Point2D> points = getPoints(alias);
+ return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Species alias) {
+ return getAntisebseRnaPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the AntisenseRna as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x + width / 8, y + height / 2));
+ points.add(new Point2D.Double(x, y));
+ points.add(new Point2D.Double(x + width * 3 / 8, y));
+ points.add(new Point2D.Double(x + width * 3 / 4, y));
+ points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width, y + height));
+ points.add(new Point2D.Double(x + width * 5 / 8, y + height));
+ points.add(new Point2D.Double(x + width / 4, y + height));
+ // CHECKSTYLE:ON
+ return points;
+ }
+
+ /**
+ * Returns shape of the AntisenseRna as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getAntisebseRnaPath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path;
+ if (!alias.getModel().isSbgnFormat()) {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
+ path.moveTo(alias.getX(), alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + alias.getWidth() / 4, alias.getY() + alias.getHeight());
+ path.closePath();
+ } else {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height,
+ x + RECTANGLE_CORNER_ARC_SIZE, y + height,
+ x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height,
+ x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
+ x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ }
+ // CHECKSTYLE:ON
+ return path;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
index 4328d77ca5..fe8993bbdd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverter.java
@@ -7,21 +7,21 @@ import java.util.Map;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -33,7 +33,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*
*/
-public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<Alias> {
+public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<Element> {
// *****************************************************************
//
@@ -47,7 +47,7 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<A
* a converter that can process the alias with the specific element type
* reference.
*/
- private static Map<Class<? extends Alias>, ICellDesignerAliasConverter<?>> elementConverters;
+ private static Map<Class<? extends Element>, ICellDesignerAliasConverter<?>> elementConverters;
private static ElementUtils eu = new ElementUtils();
@@ -57,20 +57,20 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<A
// at the beginning lets add all implemented aliases
// for alias reference
- addElementConverter(GenericProteinAlias.class, new ProteinCellDesignerAliasConverter());
- addElementConverter(TruncatedProteinAlias.class, new ProteinCellDesignerAliasConverter());
- addElementConverter(ReceptorProteinAlias.class, new ProteinCellDesignerAliasConverter());
- addElementConverter(IonChannelProteinAlias.class, new ProteinCellDesignerAliasConverter());
- addElementConverter(DegradedAlias.class, new DegradedCellDesignerAliasConverter());
- addElementConverter(ComplexAlias.class, new ComplexCellDesignerAliasConverter());
- addElementConverter(SimpleMoleculeAlias.class, new SimpleMoleculeCellDesignerAliasConverter());
- addElementConverter(DrugAlias.class, new DrugCellDesignerAliasConverter());
- addElementConverter(IonAlias.class, new IonCellDesignerAliasConverter());
- addElementConverter(PhenotypeAlias.class, new PhenotypeCellDesignerAliasConverter());
- addElementConverter(RnaAlias.class, new RnaCellDesignerAliasConverter());
- addElementConverter(AntisenseRnaAlias.class, new AntisenseRnaCellDesignerAliasConverter());
- addElementConverter(GeneAlias.class, new GeneCellDesignerAliasConverter());
- addElementConverter(UnknownAlias.class, new UnknownCellDesignerAliasConverter());
+ addElementConverter(GenericProtein.class, new ProteinCellDesignerAliasConverter());
+ addElementConverter(TruncatedProtein.class, new ProteinCellDesignerAliasConverter());
+ addElementConverter(ReceptorProtein.class, new ProteinCellDesignerAliasConverter());
+ addElementConverter(IonChannelProtein.class, new ProteinCellDesignerAliasConverter());
+ addElementConverter(Degraded.class, new DegradedCellDesignerAliasConverter());
+ addElementConverter(Complex.class, new ComplexCellDesignerAliasConverter());
+ addElementConverter(SimpleMolecule.class, new SimpleMoleculeCellDesignerAliasConverter());
+ addElementConverter(Drug.class, new DrugCellDesignerAliasConverter());
+ addElementConverter(Ion.class, new IonCellDesignerAliasConverter());
+ addElementConverter(Phenotype.class, new PhenotypeCellDesignerAliasConverter());
+ addElementConverter(Rna.class, new RnaCellDesignerAliasConverter());
+ addElementConverter(AntisenseRna.class, new AntisenseRnaCellDesignerAliasConverter());
+ addElementConverter(Gene.class, new GeneCellDesignerAliasConverter());
+ addElementConverter(Unknown.class, new UnknownCellDesignerAliasConverter());
}
@@ -82,7 +82,7 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<A
* @param converter
* converter that should be used for conversion of this alias
*/
- protected static void addElementConverter(Class<? extends Alias> clazz, ICellDesignerAliasConverter<?> converter) {
+ protected static void addElementConverter(Class<? extends Element> clazz, ICellDesignerAliasConverter<?> converter) {
elementConverters.put(clazz, converter);
}
@@ -95,7 +95,7 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<A
* @return converter that can be applied for the given alias; null if such
* converter doesn't exist
*/
- private static ICellDesignerAliasConverter<? extends Alias> getConverterForAlias(Alias alias) {
+ private static ICellDesignerAliasConverter<? extends Element> getConverterForAlias(Element alias) {
if (alias == null) {
throw new InvalidArgumentException("alias cannot be null");
}
@@ -122,7 +122,7 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<A
* @param alias
* alias for which this converter will be used
*/
- public CellDesignerAliasConverter(Alias alias) {
+ public CellDesignerAliasConverter(Element alias) {
converter = getConverterForAlias(alias);
// if we don't know which converter to use then throw an exception
if (converter == null) {
@@ -132,19 +132,19 @@ public class CellDesignerAliasConverter implements ICellDesignerAliasConverter<A
@SuppressWarnings("unchecked")
@Override
- public CellDesignerAnchor getAnchorForCoordinates(Alias alias, Point2D point) {
+ public CellDesignerAnchor getAnchorForCoordinates(Element alias, Point2D point) {
return converter.getAnchorForCoordinates(alias, point);
}
@SuppressWarnings("unchecked")
@Override
- public Point2D getPointCoordinates(Alias alias, CellDesignerAnchor anchor) {
+ public Point2D getPointCoordinates(Element alias, CellDesignerAnchor anchor) {
return converter.getPointCoordinates(alias, anchor);
}
@SuppressWarnings("unchecked")
@Override
- public Point2D getAnchorPointCoordinates(Alias alias, CellDesignerAnchor anchor, PolylineData line) {
+ public Point2D getAnchorPointCoordinates(Element alias, CellDesignerAnchor anchor, PolylineData line) {
return converter.getAnchorPointCoordinates(alias, anchor, line);
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java
index 4fd078e5a0..6e7e3b279c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java
@@ -1,60 +1,60 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * ComplexAlias. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class ComplexCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<ComplexAlias> {
-
- /**
- * How big is the triangle trimmed part of the complex.
- */
- private static final int TRIMMED_CORNER_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(ComplexAlias alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
-
- @Override
- public PathIterator getBoundPathIterator(ComplexAlias alias) {
- return getAliasPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns the border of complex alias.
- *
- * @param alias
- * exact object for which we want to get a border
- * @return border of the alias
- */
- private GeneralPath getAliasPath(Alias alias) {
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- path.moveTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX(), alias.getY() + TRIMMED_CORNER_SIZE);
- path.closePath();
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+
+/**
+ * Class that provides CellDesigner specific graphical information for
+ * ComplexAlias. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ComplexCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Complex> {
+
+ /**
+ * How big is the triangle trimmed part of the complex.
+ */
+ private static final int TRIMMED_CORNER_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Complex alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Complex alias) {
+ return getAliasPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns the border of complex alias.
+ *
+ * @param alias
+ * exact object for which we want to get a border
+ * @return border of the alias
+ */
+ private GeneralPath getAliasPath(Element alias) {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+ path.moveTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + TRIMMED_CORNER_SIZE);
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(alias.getX(), alias.getY() + TRIMMED_CORNER_SIZE);
+ path.closePath();
+ return path;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java
index 34c657eed6..cdd6afa00f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java
@@ -5,8 +5,8 @@ import java.awt.geom.Point2D;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class that provides CellDesigner specific graphical information for Degraded
@@ -15,7 +15,7 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
* @author Piotr Gawron
*
*/
-public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
+public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
/**
* Part of height of the line used to cross degraded circle that goes behind
@@ -24,7 +24,7 @@ public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAlia
private static final int DEGRADED_MARGIN = 7;
@Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
double diameter = getDiameter(alias);
double x = getXCoord(alias, diameter);
double y = getYCoord(alias);
@@ -42,7 +42,7 @@ public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAlia
* object alias to to which we are looking for y coordinate
* @return y coordinate of the alias
*/
- private double getYCoord(Alias alias) {
+ private double getYCoord(Element alias) {
double y = alias.getY() + DEGRADED_MARGIN;
return y;
}
@@ -56,7 +56,7 @@ public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAlia
* diameter of cross line used in this alias
* @return x coordinate of the alias
*/
- private double getXCoord(Alias alias, double diameter) {
+ private double getXCoord(Element alias, double diameter) {
double x = alias.getX() + (alias.getWidth() - diameter) / 2;
return x;
}
@@ -68,7 +68,7 @@ public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAlia
* object alias to to which we are looking for diameter.
* @return diameter of the cross line
*/
- private double getDiameter(Alias alias) {
+ private double getDiameter(Element alias) {
double diameter = Math.min(alias.getWidth(), alias.getHeight()) - 2 * DEGRADED_MARGIN;
if (diameter < 0) {
diameter = 0;
@@ -77,7 +77,7 @@ public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAlia
}
@Override
- public Point2D getAnchorPointCoordinates(SpeciesAlias alias, double angle) {
+ public Point2D getAnchorPointCoordinates(Species alias, double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
return alias.getCenter();
}
@@ -90,7 +90,7 @@ public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAlia
}
@Override
- public PathIterator getBoundPathIterator(SpeciesAlias alias) {
+ public PathIterator getBoundPathIterator(Species alias) {
throw new NotImplementedException("This class doesn't have bound");
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java
index c5c1ddfcbd..f7eb9b728a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java
@@ -1,81 +1,81 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-
-/**
- * Class that provides CellDesigner specific graphical information for Drug.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class DrugCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
- /**
- * How big should be the arc in rectangle for drug representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
-
- @Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- ArrayList<Point2D> list = getDrugPoints(alias);
-
- return getPolygonTransformation().getPointOnPolygonByAnchor(list, anchor);
- }
-
- @Override
- protected PathIterator getBoundPathIterator(SpeciesAlias alias) {
- return getDrugShape(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the Drug as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- protected ArrayList<Point2D> getDrugPoints(SpeciesAlias alias) {
- ArrayList<Point2D> list = new ArrayList<Point2D>();
-
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
-
- // CHECKSTYLE:OFF
- list.add(new Point2D.Double(x, y + height / 2));
- list.add(new Point2D.Double(x + width / 12, y));
- list.add(new Point2D.Double(x + width / 2, y));
- list.add(new Point2D.Double(x + width * 11 / 12, y));
- list.add(new Point2D.Double(x + width, y + height / 2));
- list.add(new Point2D.Double(x + width * 11 / 12, y + height));
- list.add(new Point2D.Double(x + width / 2, y + height));
- list.add(new Point2D.Double(x + width / 12, y + height));
- // CHECKSTYLE:ON
- return list;
- }
-
- /**
- * Returns shape of the Drug.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- private Shape getDrugShape(Alias alias) {
- return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Drug.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+ /**
+ * How big should be the arc in rectangle for drug representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ ArrayList<Point2D> list = getDrugPoints(alias);
+
+ return getPolygonTransformation().getPointOnPolygonByAnchor(list, anchor);
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Species alias) {
+ return getDrugShape(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the Drug as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ protected ArrayList<Point2D> getDrugPoints(Species alias) {
+ ArrayList<Point2D> list = new ArrayList<Point2D>();
+
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+
+ // CHECKSTYLE:OFF
+ list.add(new Point2D.Double(x, y + height / 2));
+ list.add(new Point2D.Double(x + width / 12, y));
+ list.add(new Point2D.Double(x + width / 2, y));
+ list.add(new Point2D.Double(x + width * 11 / 12, y));
+ list.add(new Point2D.Double(x + width, y + height / 2));
+ list.add(new Point2D.Double(x + width * 11 / 12, y + height));
+ list.add(new Point2D.Double(x + width / 2, y + height));
+ list.add(new Point2D.Double(x + width / 12, y + height));
+ // CHECKSTYLE:ON
+ return list;
+ }
+
+ /**
+ * Returns shape of the Drug.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ private Shape getDrugShape(Element alias) {
+ return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
index 476f1e4242..f7e9a9c9e2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverter.java
@@ -1,71 +1,71 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.Rectangle;
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-
-/**
- * Class that provides CellDesigner specific graphical information for Gene.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
-
- /**
- * Shape representation of the gene alias.
- *
- * @param alias
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
- */
- private Shape getGeneShape(Alias alias) {
- if (!alias.getModel().isSbgnFormat()) {
- Shape shape;
- shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
- return shape;
- } else {
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- return path;
- }
- }
-
- @Override
- public PathIterator getBoundPathIterator(SpeciesAlias alias) {
- return getGeneShape(alias).getPathIterator(new AffineTransform());
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.Rectangle;
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Gene.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GeneCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
+ }
+
+ /**
+ * Shape representation of the gene alias.
+ *
+ * @param alias
+ * alias for which we are looking for a Shape
+ * @return Shape object that represents alias
+ */
+ private Shape getGeneShape(Element alias) {
+ if (!alias.getModel().isSbgnFormat()) {
+ Shape shape;
+ shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
+ return shape;
+ } else {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height,
+ x + RECTANGLE_CORNER_ARC_SIZE, y + height,
+ x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height,
+ x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
+ x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ return path;
+ }
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ return getGeneShape(alias).getPathIterator(new AffineTransform());
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java
index eb32400a8a..a42fa6d4b6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-
-/**
- * Interface that defines functions usefull in transforming graphical
- * information from objects retrieved from CellDesigner xml into abslote values.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- */
-public interface ICellDesignerAliasConverter<T extends Alias> {
- /**
- * This method computes which anchor is the most probable for describing the
- * point on the border of alias. There are 16 possible anchors on the border
- * of every alias and one undefined point that will be used if no point can be
- * found (see {@link CellDesignerAnchor} to find information about anchors).
- *
- * @param alias
- * object for which we try to find anchor
- * @param point
- * point on the border of alias for which we try to find anchor
- * @return CellDesigner anchor point that describe the best point on the
- * border
- */
- CellDesignerAnchor getAnchorForCoordinates(T alias, Point2D point);
-
- /**
- * This method transform CellDesigner anchor point on the alias into x,y
- * coordinates.
- *
- * @param alias
- * we want to find coordinates on this alias border
- * @param anchor
- * CelDesigner anchor that defines point on the border
- * @return point on the border that is defined by the anchor point
- */
- Point2D getPointCoordinates(T alias, CellDesignerAnchor anchor);
-
- /**
- * This method transform CellDesigner anchor point on the alias into x,y
- * coordinates. If the anchor point doesn't define point then the line
- * parameter is used to find the right angle on the alias border and point on
- * the border with this angle is used as a result.
- *
- * @param alias
- * we want to find coordinates on this alias border
- * @param anchor
- * CelDesigner anchor that defines point on the border
- * @param line
- * line that starts in the alias
- * @return point on the border that is defined by the anchor point
- */
- Point2D getAnchorPointCoordinates(T alias, CellDesignerAnchor anchor, PolylineData line);
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Interface that defines functions usefull in transforming graphical
+ * information from objects retrieved from CellDesigner xml into abslote values.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ */
+public interface ICellDesignerAliasConverter<T extends Element> {
+ /**
+ * This method computes which anchor is the most probable for describing the
+ * point on the border of alias. There are 16 possible anchors on the border
+ * of every alias and one undefined point that will be used if no point can be
+ * found (see {@link CellDesignerAnchor} to find information about anchors).
+ *
+ * @param alias
+ * object for which we try to find anchor
+ * @param point
+ * point on the border of alias for which we try to find anchor
+ * @return CellDesigner anchor point that describe the best point on the
+ * border
+ */
+ CellDesignerAnchor getAnchorForCoordinates(T alias, Point2D point);
+
+ /**
+ * This method transform CellDesigner anchor point on the alias into x,y
+ * coordinates.
+ *
+ * @param alias
+ * we want to find coordinates on this alias border
+ * @param anchor
+ * CelDesigner anchor that defines point on the border
+ * @return point on the border that is defined by the anchor point
+ */
+ Point2D getPointCoordinates(T alias, CellDesignerAnchor anchor);
+
+ /**
+ * This method transform CellDesigner anchor point on the alias into x,y
+ * coordinates. If the anchor point doesn't define point then the line
+ * parameter is used to find the right angle on the alias border and point on
+ * the border with this angle is used as a result.
+ *
+ * @param alias
+ * we want to find coordinates on this alias border
+ * @param anchor
+ * CelDesigner anchor that defines point on the border
+ * @param line
+ * line that starts in the alias
+ * @return point on the border that is defined by the anchor point
+ */
+ Point2D getAnchorPointCoordinates(T alias, CellDesignerAnchor anchor, PolylineData line);
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
index b7d0c6c83b..80b206935d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
@@ -5,8 +5,8 @@ import java.awt.geom.Point2D;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class that provides CellDesigner specific graphical information for Ion. It's
@@ -15,10 +15,10 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
* @author Piotr Gawron
*
*/
-public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
+public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
@Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
double diameter = getDiameter(alias);
double x = getXCoord(alias, diameter);
double y = getYCoord(alias);
@@ -36,7 +36,7 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
* object alias to to which we are looking for y coordinate
* @return y coordinate of the alias
*/
- private double getYCoord(Alias alias) {
+ private double getYCoord(Element alias) {
double y = alias.getY();
return y;
}
@@ -50,7 +50,7 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
* diameter of the circle representing alias
* @return x coordinate of the alias
*/
- private double getXCoord(Alias alias, double diameter) {
+ private double getXCoord(Element alias, double diameter) {
double x = alias.getX() + (alias.getWidth() - diameter) / 2;
return x;
}
@@ -62,7 +62,7 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
* object alias to to which we are looking for diameter.
* @return diameter of the alias
*/
- private double getDiameter(Alias alias) {
+ private double getDiameter(Element alias) {
double diameter = Math.min(alias.getWidth(), alias.getHeight());
if (diameter < 0) {
diameter = 0;
@@ -71,7 +71,7 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
}
@Override
- public Point2D getAnchorPointCoordinates(SpeciesAlias alias, double angle) {
+ public Point2D getAnchorPointCoordinates(Species alias, double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
return alias.getCenter();
}
@@ -84,7 +84,7 @@ public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConv
}
@Override
- protected PathIterator getBoundPathIterator(SpeciesAlias alias) {
+ protected PathIterator getBoundPathIterator(Species alias) {
throw new NotImplementedException("This class doesn't have bound");
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java
index 7d46c15936..25e9b8e934 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java
@@ -1,83 +1,83 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-
-/**
- * Class that provides CellDesigner specific graphical information for Phenotype.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class PhenotypeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
- @Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getPolygonTransformation().getPointOnPolygonByAnchor(getPointsForAlias(alias), anchor);
- }
-
- /**
- * Returns shape of the Phenotype as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPointsForAlias(Alias alias) {
- ArrayList<Point2D> list = new ArrayList<Point2D>();
-
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
-
- // CHECKSTYLE:OFF
- list.add(new Point2D.Double(x, y + height / 2));
- list.add(new Point2D.Double(x + width / 6, y));
- list.add(new Point2D.Double(x + width / 2, y));
- list.add(new Point2D.Double(x + width * 5 / 6, y));
- list.add(new Point2D.Double(x + width, y + height / 2));
- list.add(new Point2D.Double(x + width * 5 / 6, y + height));
- list.add(new Point2D.Double(x + width / 2, y + height));
- list.add(new Point2D.Double(x + width / 6, y + height));
- // CHECKSTYLE:ON
- return list;
- }
-
- @Override
- public PathIterator getBoundPathIterator(SpeciesAlias alias) {
- return getPhenotypePath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the Phenotype as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getPhenotypePath(Alias alias) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- path.moveTo(alias.getX() + alias.getWidth() / 6, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() / 2);
- path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + alias.getWidth() / 6, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight() / 2);
- // CHECKSTYLE:ON
- path.closePath();
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Phenotype.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PhenotypeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getPolygonTransformation().getPointOnPolygonByAnchor(getPointsForAlias(alias), anchor);
+ }
+
+ /**
+ * Returns shape of the Phenotype as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPointsForAlias(Element alias) {
+ ArrayList<Point2D> list = new ArrayList<Point2D>();
+
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+
+ // CHECKSTYLE:OFF
+ list.add(new Point2D.Double(x, y + height / 2));
+ list.add(new Point2D.Double(x + width / 6, y));
+ list.add(new Point2D.Double(x + width / 2, y));
+ list.add(new Point2D.Double(x + width * 5 / 6, y));
+ list.add(new Point2D.Double(x + width, y + height / 2));
+ list.add(new Point2D.Double(x + width * 5 / 6, y + height));
+ list.add(new Point2D.Double(x + width / 2, y + height));
+ list.add(new Point2D.Double(x + width / 6, y + height));
+ // CHECKSTYLE:ON
+ return list;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ return getPhenotypePath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the Phenotype as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getPhenotypePath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ path.moveTo(alias.getX() + alias.getWidth() / 6, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() / 2);
+ path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + alias.getWidth() / 6, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX(), alias.getY() + alias.getHeight() / 2);
+ // CHECKSTYLE:ON
+ path.closePath();
+ return path;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
index 12da63203e..9a9b3794a0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
@@ -13,12 +13,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -28,7 +28,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
* @author Piotr Gawron
*
*/
-public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<ProteinAlias> {
+public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Protein> {
/**
* Default class logger.
*/
@@ -43,7 +43,7 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
private ElementUtils eu = new ElementUtils();
@Override
- public Point2D getPointCoordinates(ProteinAlias alias, CellDesignerAnchor anchor) {
+ public Point2D getPointCoordinates(Protein alias, CellDesignerAnchor anchor) {
Point2D result = null;
if (invalidAnchorPosition(alias, anchor)) {
result = alias.getCenter();
@@ -53,14 +53,14 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
alias.setWidth(alias.getWidth() - AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
alias.setHeight(alias.getHeight() - AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
- if (alias instanceof GenericProteinAlias) {
+ if (alias instanceof GenericProtein) {
result = getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- } else if (alias instanceof ReceptorProteinAlias) {
+ } else if (alias instanceof ReceptorProtein) {
ArrayList<Point2D> points = getReceptorPoints(alias);
result = getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- } else if (alias instanceof IonChannelProteinAlias) {
+ } else if (alias instanceof IonChannelProtein) {
result = getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- } else if (alias instanceof TruncatedProteinAlias) {
+ } else if (alias instanceof TruncatedProtein) {
ArrayList<Point2D> points = getTruncatedPoints(alias);
result = getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
} else {
@@ -74,14 +74,14 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
}
@Override
- public PathIterator getBoundPathIterator(ProteinAlias alias) {
- if (alias instanceof GenericProteinAlias) {
+ public PathIterator getBoundPathIterator(Protein alias) {
+ if (alias instanceof GenericProtein) {
return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof ReceptorProteinAlias) {
+ } else if (alias instanceof ReceptorProtein) {
return getReceptorShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof IonChannelProteinAlias) {
+ } else if (alias instanceof IonChannelProtein) {
return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof TruncatedProteinAlias) {
+ } else if (alias instanceof TruncatedProtein) {
return getTruncatedShape(alias).getPathIterator(new AffineTransform());
} else {
throw new NotImplementedException(eu.getElementTag(alias) + "Not implemented protein converter for type: " + alias.getClass());
@@ -95,7 +95,7 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- private Shape getGenericShape(Alias alias) {
+ private Shape getGenericShape(Element alias) {
return new RoundRectangle2D.Double(
alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE, GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE);
}
@@ -107,7 +107,7 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
* alias for which we are looking for a border
* @return list of points defining border of the given alias
*/
- private ArrayList<Point2D> getTruncatedPoints(Alias alias) {
+ private ArrayList<Point2D> getTruncatedPoints(Element alias) {
double x = alias.getX();
double y = alias.getY();
double width = alias.getWidth();
@@ -143,7 +143,7 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- protected Shape getReceptorShape(Alias alias) {
+ protected Shape getReceptorShape(Element alias) {
Shape shape;
GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
ArrayList<Point2D> points = getReceptorPoints(alias);
@@ -163,7 +163,7 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- protected Shape getTruncatedShape(Alias alias) {
+ protected Shape getTruncatedShape(Element alias) {
Shape shape;
GeneralPath path = new GeneralPath();
@@ -194,7 +194,7 @@ public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAlias
* alias for which we are looking for a border
* @return list of points defining border of the given alias
*/
- private ArrayList<Point2D> getReceptorPoints(Alias alias) {
+ private ArrayList<Point2D> getReceptorPoints(Element alias) {
double x = alias.getX();
double y = alias.getY();
double width = alias.getWidth();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
index 413837fcf3..71567f6ca9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverter.java
@@ -1,108 +1,108 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-
-/**
- * Class that provides CellDesigner specific graphical information for Rna.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (alias.getModel().isSbgnFormat()) {
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
- alias.getWidth(), alias.getHeight(), anchor);
- }
- ArrayList<Point2D> points = getPoints(alias);
- return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- }
-
- @Override
- public PathIterator getBoundPathIterator(SpeciesAlias alias) {
- return getRnaPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the Rna as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPoints(Alias alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x + width / 8, y + height / 2));
- points.add(new Point2D.Double(x + width / 4, y));
- points.add(new Point2D.Double(x + width * 5 / 8, y));
- points.add(new Point2D.Double(x + width, y));
- points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
- points.add(new Point2D.Double(x + width * 3 / 4, y + height));
- points.add(new Point2D.Double(x + width * 3 / 8, y + height));
- // CHECKSTYLE:ON
- points.add(new Point2D.Double(x, y + height));
- return points;
- }
-
- /**
- * Returns shape of the Rna as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getRnaPath(Alias alias) {
- // CHECKSTYLE:OFF
- GeneralPath path;
- if (!alias.getModel().isSbgnFormat()) {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
- path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight());
- path.closePath();
- } else {
- path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
- path.moveTo(x, y);
- path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.curveTo(x, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- path.curveTo(x + width, y + height,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- path.lineTo(x + width, y);
- path.closePath();
- }
- // CHECKSTYLE:ON
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Rna.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RnaCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (alias.getModel().isSbgnFormat()) {
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(),
+ alias.getWidth(), alias.getHeight(), anchor);
+ }
+ ArrayList<Point2D> points = getPoints(alias);
+ return getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ return getRnaPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the Rna as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x + width / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width / 4, y));
+ points.add(new Point2D.Double(x + width * 5 / 8, y));
+ points.add(new Point2D.Double(x + width, y));
+ points.add(new Point2D.Double(x + width * 7 / 8, y + height / 2));
+ points.add(new Point2D.Double(x + width * 3 / 4, y + height));
+ points.add(new Point2D.Double(x + width * 3 / 8, y + height));
+ // CHECKSTYLE:ON
+ points.add(new Point2D.Double(x, y + height));
+ return points;
+ }
+
+ /**
+ * Returns shape of the Rna as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getRnaPath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path;
+ if (!alias.getModel().isSbgnFormat()) {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 4);
+ path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 3 / 4, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX(), alias.getY() + alias.getHeight());
+ path.closePath();
+ } else {
+ path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
+
+ path.moveTo(x, y);
+ path.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.curveTo(x, y + height,
+ x + RECTANGLE_CORNER_ARC_SIZE, y + height,
+ x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ path.curveTo(x + width, y + height,
+ x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
+ x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ path.lineTo(x + width, y);
+ path.closePath();
+ }
+ // CHECKSTYLE:ON
+ return path;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
index 1c558af529..1023676545 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
@@ -5,7 +5,7 @@ import java.awt.geom.Point2D;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class that provides CellDesigner specific graphical information for
@@ -14,10 +14,10 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
* @author Piotr Gawron
*
*/
-public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
+public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
@Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
double x = alias.getX();
double y = alias.getY();
double width = Math.max(alias.getWidth(), 1);
@@ -32,7 +32,7 @@ public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesign
}
@Override
- public Point2D getAnchorPointCoordinates(SpeciesAlias alias, double angle) {
+ public Point2D getAnchorPointCoordinates(Species alias, double angle) {
if (alias.getWidth().equals(0.0) && alias.getHeight().equals(0.0)) {
return alias.getCenter();
}
@@ -48,7 +48,7 @@ public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesign
}
@Override
- public PathIterator getBoundPathIterator(SpeciesAlias alias) {
+ public PathIterator getBoundPathIterator(Species alias) {
throw new NotImplementedException("This class doesn't provide boundPath");
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
index 719c38f3b8..3be9ff8abc 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverter.java
@@ -5,19 +5,19 @@ import java.awt.geom.Point2D;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class that provides CellDesigner specific graphical information for
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Unknown Unknown}. It's used for
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown.model.map.species.Unknown Unknown}. It's used for
* conversion from xml to normal x,y coordinates.
*
* @author Piotr Gawron
*
*/
-public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
+public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
@Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
if (invalidAnchorPosition(alias, anchor)) {
return alias.getCenter();
}
@@ -25,12 +25,12 @@ public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAlias
}
@Override
- public PathIterator getBoundPathIterator(SpeciesAlias alias) {
+ public PathIterator getBoundPathIterator(Species alias) {
throw new NotImplementedException("This class doesn't provide boundPath");
}
@Override
- public Point2D getAnchorPointCoordinates(SpeciesAlias alias, double angle) {
+ public Point2D getAnchorPointCoordinates(Species alias, double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
return alias.getCenter();
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java
index df3e1dabb9..64483cb31c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-/**
- * Facory util that creates {@link PolylineData} objects from CellDesigner
- * structure.
- *
- * @author Piotr Gawron
- *
- */
-public final class PolylineDataFactory {
-
- /**
- * Default constructore that prevent instantiation.
- */
- private PolylineDataFactory() {
- }
-
- /**
- * Creates {@link PolylineData} object from two CellDesigner base points and
- * list of points (in CellDesigner formet).
- *
- * @param baseA
- * first base point
- * @param baseB
- * second base point
- * @param points
- * intermediate points in CellDesigner format
- * @return {@link PolylineData} object representing input data
- */
- public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, List<Point2D> points) {
- List<Point2D> pointsList = new CellDesignerLineTransformation().getLinePointsFromPoints(baseA, baseB, points);
- return new PolylineData(pointsList);
- }
-
- /**
- * Creates {@link PolylineData} object from two CellDesigner base points and
- * list of points (in CellDesigner formet).
- *
- * @param baseA
- * first base point
- * @param baseB
- * second base point
- * @param points
- * structure with intermediate points in CellDesigner format
- * @return {@link PolylineData} object representing input data
- */
- public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, EditPoints points) {
- if (points != null) {
- return createPolylineDataFromEditPoints(baseA, baseB, points.getPoints());
- } else {
- return createPolylineDataFromEditPoints(baseA, baseB, new ArrayList<Point2D>());
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+/**
+ * Facory util that creates {@link PolylineData} objects from CellDesigner
+ * structure.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class PolylineDataFactory {
+
+ /**
+ * Default constructore that prevent instantiation.
+ */
+ private PolylineDataFactory() {
+ }
+
+ /**
+ * Creates {@link PolylineData} object from two CellDesigner base points and
+ * list of points (in CellDesigner formet).
+ *
+ * @param baseA
+ * first base point
+ * @param baseB
+ * second base point
+ * @param points
+ * intermediate points in CellDesigner format
+ * @return {@link PolylineData} object representing input data
+ */
+ public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, List<Point2D> points) {
+ List<Point2D> pointsList = new CellDesignerLineTransformation().getLinePointsFromPoints(baseA, baseB, points);
+ return new PolylineData(pointsList);
+ }
+
+ /**
+ * Creates {@link PolylineData} object from two CellDesigner base points and
+ * list of points (in CellDesigner formet).
+ *
+ * @param baseA
+ * first base point
+ * @param baseB
+ * second base point
+ * @param points
+ * structure with intermediate points in CellDesigner format
+ * @return {@link PolylineData} object representing input data
+ */
+ public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, EditPoints points) {
+ if (points != null) {
+ return createPolylineDataFromEditPoints(baseA, baseB, points.getPoints());
+ } else {
+ return createPolylineDataFromEditPoints(baseA, baseB, new ArrayList<Point2D>());
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
index 94c27b11d3..0bcaec942f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
@@ -38,7 +38,6 @@ public class ReactionCollectionXmlParser extends XmlParser {
* Object used for parsing single reaction.
*/
private ReactionXmlParser xmlStructureFactory;
- private CellDesignerElementCollection elements;
/**
* Default constructor. Model is required because some nodes require access to
@@ -49,7 +48,6 @@ public class ReactionCollectionXmlParser extends XmlParser {
*/
public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements) {
this.model = model;
- this.elements = elements;
xmlStructureFactory = new ReactionXmlParser(elements);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index dcaec51edc..3bf8dc5200 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -25,9 +25,9 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesigner
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ConnectScheme;
-import lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints;
-import lcsb.mapviewer.converter.model.celldesigner.structure.LineProperties;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
@@ -36,8 +36,6 @@ import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
@@ -61,6 +59,8 @@ import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This is a part of {@link ReactionXmlParser} class functionality that allows
@@ -481,7 +481,7 @@ public class ReactionFromXml extends XmlParser {
* modifier to update
*/
private void createLineForModifier(Reaction reaction, Modifier modifier) {
- Alias alias = modifier.getAlias();
+ Element alias = modifier.getAlias();
CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias);
Point2D startPoint = converter.getPointCoordinates(alias, anchorsByNodes.get(modifier));
ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
@@ -891,9 +891,9 @@ public class ReactionFromXml extends XmlParser {
Point2D p2 = reactantConverter2.getPointCoordinates(reactant2.getAlias(), anchorsByNodes.get(reactant2));
Point2D p3 = productConverter.getPointCoordinates(product.getAlias(), anchorsByNodes.get(product));
- Alias alias1 = reactant1.getAlias();
- Alias alias2 = reactant2.getAlias();
- Alias alias3 = product.getAlias();
+ Element alias1 = reactant1.getAlias();
+ Element alias2 = reactant2.getAlias();
+ Element alias3 = product.getAlias();
Point2D pointA = alias2.getCenter();
Point2D pointC = alias1.getCenter();
@@ -1133,7 +1133,7 @@ public class ReactionFromXml extends XmlParser {
*/
private Reactant getReactantLink(Node rootNode, Model model, Reaction reaction, CellDesignerElementCollection elements) throws ReactionParserException {
String aliasId = getNodeAttr("alias", rootNode);
- SpeciesAlias al = (SpeciesAlias) model.getAliasByAliasId(aliasId);
+ Species al = (Species) model.getAliasByAliasId(aliasId);
if (al == null) {
throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
}
@@ -1232,7 +1232,7 @@ public class ReactionFromXml extends XmlParser {
*/
private Product getProductLink(Node rootNode, Model model, Reaction reaction, CellDesignerElementCollection elements) throws ReactionParserException {
String aliasId = getNodeAttr("alias", rootNode);
- SpeciesAlias al = (SpeciesAlias) model.getAliasByAliasId(aliasId);
+ Species al = (Species) model.getAliasByAliasId(aliasId);
if (al == null) {
throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
}
@@ -1367,11 +1367,11 @@ public class ReactionFromXml extends XmlParser {
String lineConnectionType = getNodeAttr("targetLineIndex", rootNode);
String points = getNodeAttr("editPoints", rootNode);
- List<SpeciesAlias> aliasList = new ArrayList<SpeciesAlias>();
+ List<Species> aliasList = new ArrayList<Species>();
String[] list = aliasId.split(",");
for (String string : list) {
- SpeciesAlias al = (SpeciesAlias) model.getAliasByAliasId(string);
+ Species al = (Species) model.getAliasByAliasId(string);
if (al != null) {
aliasList.add(al);
} else {
@@ -1571,7 +1571,7 @@ public class ReactionFromXml extends XmlParser {
*/
private void parseBaseReactant(Reaction result, Node reactantNode, Model model, CellDesignerElementCollection elements) throws ReactionParserException {
String aliasId = getNodeAttr("alias", reactantNode);
- SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId(aliasId);
+ Species alias = (Species) model.getAliasByAliasId(aliasId);
if (alias == null) {
throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
}
@@ -1607,7 +1607,7 @@ public class ReactionFromXml extends XmlParser {
*/
private void parseBaseProduct(Model model, Reaction result, Node reactantNode, CellDesignerElementCollection elements) throws ReactionParserException {
String aliasId = getNodeAttr("alias", reactantNode);
- SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId(aliasId);
+ Species alias = (Species) model.getAliasByAliasId(aliasId);
if (alias == null) {
throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index 65d6cd0a9d..75e72f5e0b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -26,9 +26,6 @@ import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
@@ -38,6 +35,9 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -179,7 +179,7 @@ public class ReactionToXml extends XmlParser {
* @return modifierSpeciesReference sbml node for given modifer
*/
private String getModifierReferenceXmlString(Modifier modifier) {
- Alias alias = modifier.getAlias();
+ Element alias = modifier.getAlias();
StringBuilder sb = new StringBuilder();
sb.append("<modifierSpeciesReference ");
sb.append("metaid=\"" + elements.getElementId(alias) + "\" ");
@@ -348,7 +348,7 @@ public class ReactionToXml extends XmlParser {
for (Product product : reaction.getProducts()) {
// metaid is missing, maybe it will work ;)
- Alias alias = product.getAlias();
+ Element alias = product.getAlias();
sb.append("<speciesReference species=\"" + elements.getElementId(alias) + "\">\n");
@@ -375,9 +375,9 @@ public class ReactionToXml extends XmlParser {
sb.append("<listOfReactants>\n");
for (Reactant reactant : reaction.getReactants()) {
// metaid is missing, maybe it will work ;)
- SpeciesAlias species = (SpeciesAlias) reactant.getAlias();
+ Species species = (Species) reactant.getAlias();
- Set<Alias> parents = new HashSet<>();
+ Set<Element> parents = new HashSet<>();
// we need top parent species
while (species.getComplexAlias() != null) {
@@ -388,8 +388,8 @@ public class ReactionToXml extends XmlParser {
parents.add(species);
}
// and top parent alias (for sbml compliant view of celldesigner file)
- Alias alias = reactant.getAlias();
- while (alias.getParent() instanceof ComplexAlias) {
+ Element alias = reactant.getAlias();
+ while (alias.getParent() instanceof Complex) {
alias = alias.getParent();
}
sb.append("<speciesReference species=\"" + elements.getElementId(species) + "\">\n");
@@ -466,8 +466,8 @@ public class ReactionToXml extends XmlParser {
result.append("<celldesigner:listOfGateMember>\n");
ReactionLineData lineData = ReactionLineData
.getByLineType(reaction.getProducts().get(0).getLine().getType(), reaction.getProducts().get(0).getLine().getEndAtd().getArrowType());
- Alias alias1 = reactant1.getAlias();
- Alias alias2 = reactant2.getAlias();
+ Element alias1 = reactant1.getAlias();
+ Element alias2 = reactant2.getAlias();
// product line
result.append("<celldesigner:GateMember type=\"" + type.getStringName() + "\"");
@@ -596,7 +596,7 @@ public class ReactionToXml extends XmlParser {
* @return xml node describing reactantLink
*/
private String getReactantLinkXmlString(Reactant reactant) {
- Alias alias = reactant.getAlias();
+ Element alias = reactant.getAlias();
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:reactantLink ");
sb.append("reactant=\"" + elements.getElementId(alias) + "\" ");
@@ -633,7 +633,7 @@ public class ReactionToXml extends XmlParser {
* @return xml node describing productLink
*/
private String getProductLinkXmlString(Product product) {
- Alias alias = product.getAlias();
+ Element alias = product.getAlias();
PolylineData[] lines = new PolylineData[] { product.getLine() };
StringBuilder sb = new StringBuilder();
@@ -695,12 +695,12 @@ public class ReactionToXml extends XmlParser {
/**
* Creates
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints}
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure representing lines in CellDesigner.
*
* @param lines
* lines to be transformed into single
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints}
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure
* @param centerIndex
* where the central line is positioned
@@ -712,12 +712,12 @@ public class ReactionToXml extends XmlParser {
/**
* Creates
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints}
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure representing lines in CellDesigner.
*
* @param lines
* lines to be transformed into single
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints}
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure
* @param centerPoint
* central point whene list of lines is greater than 1
@@ -767,13 +767,13 @@ public class ReactionToXml extends XmlParser {
/**
* Returns xml node representing
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints}
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure.
*
* @param reaction
* reaction for which xml node is generated
* @return xml node representing
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.EditPoints}
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure
*/
String getEditPointsXmlStringForReaction(Reaction reaction) {
@@ -972,7 +972,7 @@ public class ReactionToXml extends XmlParser {
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:baseProducts>\n");
for (Product product : products) {
- Alias alias = product.getAlias();
+ Element alias = product.getAlias();
sb.append("<celldesigner:baseProduct ");
sb.append("species=\"" + elements.getElementId(product.getAlias()) + "\" ");
sb.append("alias=\"" + product.getAlias().getAliasId() + "\" ");
@@ -1002,7 +1002,7 @@ public class ReactionToXml extends XmlParser {
StringBuilder sb = new StringBuilder();
sb.append("<celldesigner:baseReactants>\n");
for (Reactant reactant : reactants) {
- Alias alias = reactant.getAlias();
+ Element alias = reactant.getAlias();
sb.append("<celldesigner:baseReactant ");
sb.append("species=\"" + elements.getElementId(reactant.getAlias()) + "\" ");
sb.append("alias=\"" + reactant.getAlias().getAliasId() + "\" ");
@@ -1025,7 +1025,7 @@ public class ReactionToXml extends XmlParser {
* point
* @return xml node with anchor point
*/
- private String getAnchorXml(Alias alias, Point2D point) {
+ private String getAnchorXml(Element alias, Point2D point) {
CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias);
CellDesignerAnchor anchor = converter.getAnchorForCoordinates(alias, point);
if (anchor != null) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
index a51a7f7392..92ca7c65bc 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
@@ -27,10 +27,7 @@ public class ReactionXmlParser extends XmlParser {
*/
private ReactionFromXml reactionFromXml;
- private CellDesignerElementCollection elements;
-
public ReactionXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
reactionToXml = new ReactionToXml(elements);
reactionFromXml = new ReactionFromXml(elements);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
index 5dc3dea215..5d6268512a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
@@ -7,9 +7,9 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
import org.apache.log4j.Logger;
import org.w3c.dom.Document;
@@ -24,7 +24,7 @@ import org.w3c.dom.NodeList;
* @param <T>
* type of the object to parse
*/
-public abstract class AbstractElementXmlParser<T extends Element<?>, S extends Alias> extends XmlParser {
+public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>, S extends Element> extends XmlParser {
/**
* Default class logger.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
index 02a2833012..0535c416c8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
@@ -8,11 +8,11 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion.AntisenseRnaRegionType;
/**
* Class that performs parsing of the CellDesigner xml for AntisenseRna object.
@@ -20,7 +20,7 @@ import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRn
* @author Piotr Gawron
*
*/
-public class AntisenseRnaXmlParser extends AbstractElementXmlParser<AntisenseRna, AntisenseRnaAlias> {
+public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesignerAntisenseRna, AntisenseRna> {
/**
* Default class logger.
@@ -35,8 +35,8 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<AntisenseRna
}
@Override
- public Pair<String, AntisenseRna> parseXmlElement(Node antisenseRnaNode) throws InvalidXmlSchemaException {
- AntisenseRna antisenseRna = new AntisenseRna();
+ public Pair<String, CellDesignerAntisenseRna> parseXmlElement(Node antisenseRnaNode) throws InvalidXmlSchemaException {
+ CellDesignerAntisenseRna antisenseRna = new CellDesignerAntisenseRna();
String identifier = getNodeAttr("id", antisenseRnaNode);
antisenseRna.setName(decodeName(getNodeAttr("name", antisenseRnaNode)));
NodeList list = antisenseRnaNode.getChildNodes();
@@ -62,12 +62,12 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<AntisenseRna
}
}
}
- Pair<String, AntisenseRna> result = new Pair<String, AntisenseRna>(identifier, antisenseRna);
+ Pair<String, CellDesignerAntisenseRna> result = new Pair<String, CellDesignerAntisenseRna>(identifier, antisenseRna);
return result;
}
@Override
- public String toXml(AntisenseRnaAlias antisenseRna) {
+ public String toXml(AntisenseRna antisenseRna) {
String attributes = "";
String result = "";
attributes += " id=\"ar_" + elements.getElementId(antisenseRna) + "\"";
@@ -85,7 +85,7 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<AntisenseRna
result += "</celldesigner:notes>";
if (antisenseRna.getRegions().size() > 0) {
result += "<celldesigner:listOfRegions>";
- for (AntisenseRnaRegionAlias region : antisenseRna.getRegions()) {
+ for (AntisenseRnaRegion region : antisenseRna.getRegions()) {
result += toXml(region);
}
result += "</celldesigner:listOfRegions>";
@@ -101,7 +101,7 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<AntisenseRna
* object to be transformed
* @return xml representation of the given region
*/
- private String toXml(AntisenseRnaRegionAlias region) {
+ private String toXml(AntisenseRnaRegion region) {
String result = "";
String attributes = "";
if (!region.getIdAntisenseRnaRegion().equals("")) {
@@ -134,8 +134,8 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<AntisenseRna
* @throws InvalidXmlSchemaException
* thrown when input xml node doesn't follow defined schema
*/
- private AntisenseRnaRegion getAntisenseRnaRegion(Node regionNode) throws InvalidXmlSchemaException {
- AntisenseRnaRegion residue = new AntisenseRnaRegion();
+ private CellDesignerAntisenseRnaRegion getAntisenseRnaRegion(Node regionNode) throws InvalidXmlSchemaException {
+ CellDesignerAntisenseRnaRegion residue = new CellDesignerAntisenseRnaRegion();
residue.setIdAntisenseRnaRegion(getNodeAttr("id", regionNode));
residue.setName(getNodeAttr("name", regionNode));
residue.setSize(getNodeAttr("size", regionNode));
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
index a113aff089..273be9a258 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
@@ -8,18 +8,18 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
- * Class that performs parsing of the CellDesigner xml for {@link Gene} object.
+ * Class that performs parsing of the CellDesigner xml for {@link CellDesignerGene} object.
*
* @author Piotr Gawron
*
*/
-public class GeneXmlParser extends AbstractElementXmlParser<Gene, GeneAlias> {
+public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Gene> {
/**
* Default class logger.
@@ -34,8 +34,8 @@ public class GeneXmlParser extends AbstractElementXmlParser<Gene, GeneAlias> {
}
@Override
- public Pair<String, Gene> parseXmlElement(Node geneNode) throws InvalidXmlSchemaException {
- Gene gene = new Gene();
+ public Pair<String, CellDesignerGene> parseXmlElement(Node geneNode) throws InvalidXmlSchemaException {
+ CellDesignerGene gene = new CellDesignerGene();
String identifier = getNodeAttr("id", geneNode);
gene.setName(decodeName(getNodeAttr("name", geneNode)));
NodeList list = geneNode.getChildNodes();
@@ -61,7 +61,7 @@ public class GeneXmlParser extends AbstractElementXmlParser<Gene, GeneAlias> {
}
}
}
- return new Pair<String, Gene>(identifier, gene);
+ return new Pair<String, CellDesignerGene>(identifier, gene);
}
/**
@@ -73,8 +73,8 @@ public class GeneXmlParser extends AbstractElementXmlParser<Gene, GeneAlias> {
* @throws InvalidXmlSchemaException
* thrown when input xml node doesn't follow defined schema
*/
- ModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
- ModificationResidue residue = new ModificationResidue();
+ CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
residue.setIdModificationResidue(getNodeAttr("id", residueNode));
residue.setName(getNodeAttr("name", residueNode));
residue.setSide(getNodeAttr("side", residueNode));
@@ -90,7 +90,7 @@ public class GeneXmlParser extends AbstractElementXmlParser<Gene, GeneAlias> {
}
@Override
- public String toXml(GeneAlias gene) {
+ public String toXml(Gene gene) {
String attributes = "";
String result = "";
attributes += " id=\"g_" + elements.getElementId(gene) + "\"";
@@ -108,7 +108,7 @@ public class GeneXmlParser extends AbstractElementXmlParser<Gene, GeneAlias> {
if (gene.getModificationResidues().size() > 0) {
result += "<celldesigner:listOfRegions>\n";
- for (ModificationResidueAlias mr : gene.getModificationResidues()) {
+ for (ModificationResidue mr : gene.getModificationResidues()) {
result += toXml(mr);
}
result += "</celldesigner:listOfRegions>\n";
@@ -119,13 +119,13 @@ public class GeneXmlParser extends AbstractElementXmlParser<Gene, GeneAlias> {
}
/**
- * Generates CellDesigner xml for {@link ModificationResidue}.
+ * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
*
* @param mr
* object to transform into xml
- * @return CellDesigner xml for {@link ModificationResidue}
+ * @return CellDesigner xml for {@link CellDesignerModificationResidue}
*/
- String toXml(ModificationResidueAlias mr) {
+ String toXml(ModificationResidue mr) {
String result = "";
String attributes = "";
if (!mr.getIdModificationResidue().equals("")) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java
index 79b6301913..fe20ad5b43 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java
@@ -8,18 +8,18 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
/**
* This class contains information about all species in model that are relevant
@@ -39,57 +39,57 @@ public class InternalModelSpeciesData {
/**
* Collection of proteins. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Protein<?>> proteins;
+ private SpeciesCollection<CellDesignerProtein<?>> proteins;
/**
* Collection of genes. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Gene> genes;
+ private SpeciesCollection<CellDesignerGene> genes;
/**
* Collection of genes. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Rna> rnas;
+ private SpeciesCollection<CellDesignerRna> rnas;
/**
* Collection of antisense rnas. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<AntisenseRna> antisenseRnas;
+ private SpeciesCollection<CellDesignerAntisenseRna> antisenseRnas;
/**
* Collection of phenotypes. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Phenotype> phenotypes;
+ private SpeciesCollection<CellDesignerPhenotype> phenotypes;
/**
* Collection of ions. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Ion> ions;
+ private SpeciesCollection<CellDesignerIon> ions;
/**
* Collection of simple molecules. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<SimpleMolecule> simpleMolecules;
+ private SpeciesCollection<CellDesignerSimpleMolecule> simpleMolecules;
/**
* Collection of drugs. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Drug> drugs;
+ private SpeciesCollection<CellDesignerDrug> drugs;
/**
* Collection of unknowns. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Unknown> unknowns;
+ private SpeciesCollection<CellDesignerUnknown> unknowns;
/**
* Collection of degraded elements. Used only by the CellDesigner parser.
*/
- private SpeciesCollection<Degraded> degradeds;
+ private SpeciesCollection<CellDesignerDegraded> degradeds;
/**
* Collection of complexes.
*/
- private List<ComplexSpecies> complexes = new ArrayList<>();
+ private List<CellDesignerComplexSpecies> complexes = new ArrayList<>();
/**
* Default constructor.
@@ -111,7 +111,7 @@ public class InternalModelSpeciesData {
*
* @return {@link #proteins}
*/
- public Collection<Protein<?>> getProteins() {
+ public Collection<CellDesignerProtein<?>> getProteins() {
return proteins.getAll();
}
@@ -119,7 +119,7 @@ public class InternalModelSpeciesData {
*
* @return {@link #genes}
*/
- public Collection<Gene> getGenes() {
+ public Collection<CellDesignerGene> getGenes() {
return genes.getAll();
}
@@ -127,7 +127,7 @@ public class InternalModelSpeciesData {
*
* @return {@link #rnas}
*/
- public Collection<Rna> getRnas() {
+ public Collection<CellDesignerRna> getRnas() {
return rnas.getAll();
}
@@ -135,7 +135,7 @@ public class InternalModelSpeciesData {
*
* @return {@link #antisenseRnas}
*/
- public Collection<AntisenseRna> getAntisenseRnas() {
+ public Collection<CellDesignerAntisenseRna> getAntisenseRnas() {
return antisenseRnas.getAll();
}
@@ -146,8 +146,8 @@ public class InternalModelSpeciesData {
* set of species to be updated, first element in pair defines
* celldesigner identifier, second is the species
*/
- public void updateSpecies(Collection<Pair<String, ? extends Species<?>>> collection) {
- for (Pair<String, ? extends Species<?>> species : collection) {
+ public void updateSpecies(Collection<Pair<String, ? extends CellDesignerSpecies<?>>> collection) {
+ for (Pair<String, ? extends CellDesignerSpecies<?>> species : collection) {
updateSpecies(species.getRight(), species.getLeft());
}
}
@@ -161,29 +161,29 @@ public class InternalModelSpeciesData {
* @param identifier
* celldesigner identifier
*/
- public void updateSpecies(Species<?> sp, String identifier) {
- if (sp instanceof Gene) {
- genes.updateSpeciesByLocalId((Gene) sp, identifier);
- } else if (sp instanceof Protein) {
- proteins.updateSpeciesByLocalId((Protein<?>) sp, identifier);
- } else if (sp instanceof Rna) {
- rnas.updateSpeciesByLocalId((Rna) sp, identifier);
- } else if (sp instanceof AntisenseRna) {
- antisenseRnas.updateSpeciesByLocalId((AntisenseRna) sp, identifier);
- } else if (sp instanceof Degraded) {
- degradeds.updateSpeciesByLocalId((Degraded) sp, identifier);
- } else if (sp instanceof Unknown) {
- unknowns.updateSpeciesByLocalId((Unknown) sp, identifier);
- } else if (sp instanceof Drug) {
- drugs.updateSpeciesByLocalId((Drug) sp, identifier);
- } else if (sp instanceof SimpleMolecule) {
- simpleMolecules.updateSpeciesByLocalId((SimpleMolecule) sp, identifier);
- } else if (sp instanceof Ion) {
- ions.updateSpeciesByLocalId((Ion) sp, identifier);
- } else if (sp instanceof Phenotype) {
- phenotypes.updateSpeciesByLocalId((Phenotype) sp, identifier);
- } else if (sp instanceof ComplexSpecies) {
- complexes.add((ComplexSpecies) sp);
+ public void updateSpecies(CellDesignerSpecies<?> sp, String identifier) {
+ if (sp instanceof CellDesignerGene) {
+ genes.updateSpeciesByLocalId((CellDesignerGene) sp, identifier);
+ } else if (sp instanceof CellDesignerProtein) {
+ proteins.updateSpeciesByLocalId((CellDesignerProtein<?>) sp, identifier);
+ } else if (sp instanceof CellDesignerRna) {
+ rnas.updateSpeciesByLocalId((CellDesignerRna) sp, identifier);
+ } else if (sp instanceof CellDesignerAntisenseRna) {
+ antisenseRnas.updateSpeciesByLocalId((CellDesignerAntisenseRna) sp, identifier);
+ } else if (sp instanceof CellDesignerDegraded) {
+ degradeds.updateSpeciesByLocalId((CellDesignerDegraded) sp, identifier);
+ } else if (sp instanceof CellDesignerUnknown) {
+ unknowns.updateSpeciesByLocalId((CellDesignerUnknown) sp, identifier);
+ } else if (sp instanceof CellDesignerDrug) {
+ drugs.updateSpeciesByLocalId((CellDesignerDrug) sp, identifier);
+ } else if (sp instanceof CellDesignerSimpleMolecule) {
+ simpleMolecules.updateSpeciesByLocalId((CellDesignerSimpleMolecule) sp, identifier);
+ } else if (sp instanceof CellDesignerIon) {
+ ions.updateSpeciesByLocalId((CellDesignerIon) sp, identifier);
+ } else if (sp instanceof CellDesignerPhenotype) {
+ phenotypes.updateSpeciesByLocalId((CellDesignerPhenotype) sp, identifier);
+ } else if (sp instanceof CellDesignerComplexSpecies) {
+ complexes.add((CellDesignerComplexSpecies) sp);
} else {
throw new InvalidArgumentException("Unknown species type: " + sp.getClass().getName());
}
@@ -194,8 +194,8 @@ public class InternalModelSpeciesData {
*
* @return list of all species in dataset
*/
- public Collection<Species<?>> getAll() {
- List<Species<?>> result = new ArrayList<>();
+ public Collection<CellDesignerSpecies<?>> getAll() {
+ List<CellDesignerSpecies<?>> result = new ArrayList<>();
result.addAll(genes.getAll());
result.addAll(rnas.getAll());
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
index 1c2c682218..64ff8471cb 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
@@ -3,20 +3,20 @@ package lcsb.mapviewer.converter.model.celldesigner.species;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.IonChannelProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ReceptorProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.TruncatedProtein;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIonChannelProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerReceptorProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerTruncatedProtein;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
/**
* This enum contains information about mapping between CellDesigner xml nodes
- * and classes that extend {@link Protein}.
+ * and classes that extend {@link CellDesignerProtein}.
*
* @author Piotr Gawron
*
@@ -26,22 +26,22 @@ public enum ProteinMapping {
/**
* {@link GenericProtein}.
*/
- GENERIC_PROTEIN(GenericProteinAlias.class, GenericProtein.class, "GENERIC"),
+ GENERIC_PROTEIN(GenericProtein.class, CellDesignerGenericProtein.class, "GENERIC"),
/**
* {@link IonChannelProtein}.
*/
- ION_CHANNEL_PROTEIN(IonChannelProteinAlias.class, IonChannelProtein.class, "ION_CHANNEL"),
+ ION_CHANNEL_PROTEIN(IonChannelProtein.class, CellDesignerIonChannelProtein.class, "ION_CHANNEL"),
/**
* {@link ReceptorProtein}.
*/
- RECEPTOR_PROTEIN(ReceptorProteinAlias.class, ReceptorProtein.class, "RECEPTOR"),
+ RECEPTOR_PROTEIN(ReceptorProtein.class, CellDesignerReceptorProtein.class, "RECEPTOR"),
/**
* {@link TruncatedProtein}.
*/
- TRUNCATED_PROTEIN(TruncatedProteinAlias.class, TruncatedProtein.class, "TRUNCATED");
+ TRUNCATED_PROTEIN(TruncatedProtein.class, CellDesignerTruncatedProtein.class, "TRUNCATED");
/**
* CellDesigner xml node type.
@@ -51,11 +51,12 @@ public enum ProteinMapping {
/**
* Class that should be used to represent cell designer node.
*/
- private Class<? extends ProteinAlias> clazz;
+ private Class<? extends Protein> clazz;
- private static Logger logger = Logger.getLogger(ProteinMapping.class);
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ProteinMapping.class);
- private Class<? extends Protein> cellDesignerClazz;
+ private Class<? extends CellDesignerProtein<?>> cellDesignerClazz;
/**
* Default constructor.
@@ -65,7 +66,7 @@ public enum ProteinMapping {
* @param cellDesignerString
* {@link #cellDesignerString}
*/
- ProteinMapping(Class<? extends ProteinAlias> modelClazz, Class<? extends Protein> cellDesignerClazz, String cellDesignerString) {
+ ProteinMapping(Class<? extends Protein> modelClazz, Class<? extends CellDesignerProtein<?>> cellDesignerClazz, String cellDesignerString) {
this.cellDesignerString = cellDesignerString;
this.clazz = modelClazz;
this.cellDesignerClazz = cellDesignerClazz;
@@ -83,11 +84,11 @@ public enum ProteinMapping {
* @return the clazz
* @see #clazz
*/
- public Class<? extends ProteinAlias> getClazz() {
+ public Class<? extends Protein> getClazz() {
return clazz;
}
- public Class<? extends Protein> getCellDesignerClazz() {
+ public Class<? extends CellDesignerProtein<?>> getCellDesignerClazz() {
return cellDesignerClazz;
}
@@ -108,13 +109,13 @@ public enum ProteinMapping {
}
/**
- * Returns {@link ProteinMapping} for given {@link Protein} class.
+ * Returns {@link ProteinMapping} for given {@link CellDesignerProtein} class.
*
* @param searchClazz
- * {@link Protein} class
- * @return {@link ProteinMapping} for given {@link Protein} class
+ * {@link CellDesignerProtein} class
+ * @return {@link ProteinMapping} for given {@link CellDesignerProtein} class
*/
- public static ProteinMapping getMappingByClass(Class<? extends ProteinAlias> searchClazz) {
+ public static ProteinMapping getMappingByClass(Class<? extends Protein> searchClazz) {
for (ProteinMapping mapping : ProteinMapping.values()) {
if (mapping.getClazz().isAssignableFrom(searchClazz)) {
return mapping;
@@ -124,13 +125,13 @@ public enum ProteinMapping {
}
/**
- * Creates instance of {@link Protein} specific for this
+ * Creates instance of {@link CellDesignerProtein} specific for this
* {@link ProteinMapping}.
*
- * @return new instance of {@link Protein} specific for this
+ * @return new instance of {@link CellDesignerProtein} specific for this
* {@link ProteinMapping}.
*/
- public Protein createProtein() {
+ public CellDesignerProtein<?> createProtein() {
try {
return cellDesignerClazz.getConstructor().newInstance();
} catch (Exception e) {
@@ -138,7 +139,7 @@ public enum ProteinMapping {
}
}
- public ProteinAlias createProteinAlias() {
+ public Protein createProteinAlias() {
try {
return clazz.getConstructor().newInstance();
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
index 90a9750784..7d41df9d79 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
@@ -8,20 +8,20 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
- * Class that performs parsing of the CellDesigner xml for {@link Protein}
+ * Class that performs parsing of the CellDesigner xml for {@link CellDesignerProtein}
* object.
*
* @author Piotr Gawron
*
*/
-public class ProteinXmlParser extends AbstractElementXmlParser<Protein<?>, ProteinAlias> {
+public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProtein<?>, Protein> {
/**
* Default class logger.
@@ -36,8 +36,8 @@ public class ProteinXmlParser extends AbstractElementXmlParser<Protein<?>, Prote
}
@Override
- public Pair<String, Protein<?>> parseXmlElement(Node proteinNode) throws InvalidXmlSchemaException {
- Protein<?> protein = null;
+ public Pair<String, CellDesignerProtein<?>> parseXmlElement(Node proteinNode) throws InvalidXmlSchemaException {
+ CellDesignerProtein<?> protein = null;
String value = getNodeAttr("type", proteinNode);
ProteinMapping mapping = ProteinMapping.getMappingByString(value);
if (mapping != null) {
@@ -72,11 +72,11 @@ public class ProteinXmlParser extends AbstractElementXmlParser<Protein<?>, Prote
}
}
- return new Pair<String, Protein<?>>(identifier, protein);
+ return new Pair<String, CellDesignerProtein<?>>(identifier, protein);
}
@Override
- public String toXml(ProteinAlias protein) {
+ public String toXml(Protein protein) {
String attributes = "";
String result = "";
attributes += " id=\"p_" + elements.getElementId(protein) + "\"";
@@ -94,7 +94,7 @@ public class ProteinXmlParser extends AbstractElementXmlParser<Protein<?>, Prote
result += "<celldesigner:protein" + attributes + ">\n";
if (protein.getModificationResidues().size() > 0) {
result += "<celldesigner:listOfModificationResidues>";
- for (ModificationResidueAlias mr : protein.getModificationResidues()) {
+ for (ModificationResidue mr : protein.getModificationResidues()) {
result += toXml(mr);
}
result += "</celldesigner:listOfModificationResidues>\n";
@@ -107,13 +107,13 @@ public class ProteinXmlParser extends AbstractElementXmlParser<Protein<?>, Prote
}
/**
- * Generates CellDesigner xml for {@link ModificationResidue}.
+ * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
*
* @param mr
* object to transform into xml
- * @return CellDesigner xml for {@link ModificationResidue}
+ * @return CellDesigner xml for {@link CellDesignerModificationResidue}
*/
- private String toXml(ModificationResidueAlias mr) {
+ private String toXml(ModificationResidue mr) {
String result = "";
String attributes = "";
if (!mr.getIdModificationResidue().equals("")) {
@@ -139,12 +139,12 @@ public class ProteinXmlParser extends AbstractElementXmlParser<Protein<?>, Prote
*
* @param residueNode
* xml node to parse
- * @return {@link ModificationResidue} object created from the node
+ * @return {@link CellDesignerModificationResidue} object created from the node
* @throws InvalidXmlSchemaException
* thrown when input xml node doesn't follow defined schema
*/
- private ModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
- ModificationResidue residue = new ModificationResidue();
+ private CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
residue.setIdModificationResidue(getNodeAttr("id", residueNode));
residue.setName(getNodeAttr("name", residueNode));
residue.setSide(getNodeAttr("side", residueNode));
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
index 816c08eefe..025e5e3d12 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
@@ -8,18 +8,18 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.RnaRegion;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRnaRegion;
+import lcsb.mapviewer.model.map.species.Rna;
/**
- * Class that performs parsing of the CellDesigner xml for {@link Rna} object.
+ * Class that performs parsing of the CellDesigner xml for {@link CellDesignerRna} object.
*
* @author Piotr Gawron
*
*/
-public class RnaXmlParser extends AbstractElementXmlParser<Rna, RnaAlias> {
+public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna> {
/**
* Default class logger.
@@ -34,8 +34,8 @@ public class RnaXmlParser extends AbstractElementXmlParser<Rna, RnaAlias> {
}
@Override
- public Pair<String, Rna> parseXmlElement(Node rnaNode) throws InvalidXmlSchemaException {
- Rna rna = new Rna();
+ public Pair<String, CellDesignerRna> parseXmlElement(Node rnaNode) throws InvalidXmlSchemaException {
+ CellDesignerRna rna = new CellDesignerRna();
String identifier = getNodeAttr("id", rnaNode);
rna.setName(decodeName(getNodeAttr("name", rnaNode)));
NodeList list = rnaNode.getChildNodes();
@@ -61,7 +61,7 @@ public class RnaXmlParser extends AbstractElementXmlParser<Rna, RnaAlias> {
}
}
}
- return new Pair<String, Rna>(identifier, rna);
+ return new Pair<String, CellDesignerRna>(identifier, rna);
}
/**
@@ -69,12 +69,12 @@ public class RnaXmlParser extends AbstractElementXmlParser<Rna, RnaAlias> {
*
* @param residueNode
* xml node to parse
- * @return {@link RnaRegion} object created from the node
+ * @return {@link CellDesignerRnaRegion} object created from the node
* @throws InvalidXmlSchemaException
* thrown when input xml node doesn't follow defined schema
*/
- private RnaRegion getRnaRegion(Node residueNode) throws InvalidXmlSchemaException {
- RnaRegion residue = new RnaRegion();
+ private CellDesignerRnaRegion getRnaRegion(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerRnaRegion residue = new CellDesignerRnaRegion();
residue.setIdRnaRegion(getNodeAttr("id", residueNode));
residue.setSize(getNodeAttr("size", residueNode));
residue.setPos(getNodeAttr("pos", residueNode));
@@ -90,7 +90,7 @@ public class RnaXmlParser extends AbstractElementXmlParser<Rna, RnaAlias> {
}
@Override
- public String toXml(RnaAlias rna) {
+ public String toXml(Rna rna) {
String attributes = "";
String result = "";
attributes += " id=\"r_" + elements.getElementId(rna) + "\"";
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java
index 7594604db1..8741c3038d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java
@@ -8,7 +8,7 @@ import java.util.Map;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
/**
* This collection performs some magic, so please try no to understand it :). It
@@ -23,7 +23,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
* @param <C>
* class of the species
*/
-public class SpeciesCollection<C extends Species> {
+public class SpeciesCollection<C extends CellDesignerSpecies<?>> {
/**
* Default class logger.
@@ -38,7 +38,7 @@ public class SpeciesCollection<C extends Species> {
/**
* Map of species identified by specific identifier of the species (like
- * {@link lcsb.mapviewer.db.model.map.species.Protein#proteinId
+ * {@link lcsb.mapviewer.db.model.map.species.CellDesignerProtein#proteinId
* Protein#proteinId}.
*/
private Map<String, ArrayList<C>> speciesListByLocalId;
@@ -155,7 +155,7 @@ public class SpeciesCollection<C extends Species> {
@SuppressWarnings({ "rawtypes", "unchecked" })
protected C createNewInstance(Class clazz, C c) {
try {
- return (C) clazz.getConstructor(Species.class).newInstance(c);
+ return (C) clazz.getConstructor(CellDesignerSpecies.class).newInstance(c);
} catch (Exception e) {
throw new InvalidStateException("Problem with creating object", e);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
index 0abe096913..131b7beea9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
@@ -16,25 +16,24 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class used to parse CellDesigner xml nodes containing collections of
- * {@link Species}.
+ * {@link CellDesignerSpecies}.
*
* @author Piotr Gawron
*
@@ -48,27 +47,22 @@ public class SpeciesCollectionXmlParser extends XmlParser {
private Logger logger = Logger.getLogger(SpeciesCollectionXmlParser.class.getName());
/**
- * Model for which parsing (or transformation to xml) is being done.
- */
- private Model model;
-
- /**
- * Parser used for {@link Rna} objects.
+ * Parser used for {@link CellDesignerRna} objects.
*/
private RnaXmlParser rnaParser;
/**
- * Parser used for {@link Gene} objects.
+ * Parser used for {@link CellDesignerGene} objects.
*/
private GeneXmlParser geneParser;
/**
- * Parser used for {@link Protein} objects.
+ * Parser used for {@link CellDesignerProtein} objects.
*/
private ProteinXmlParser proteinParser;
/**
- * Parser used for {@link AntisenseRna} objects.
+ * Parser used for {@link CellDesignerAntisenseRna} objects.
*/
private AntisenseRnaXmlParser antisenseRnaParser;
@@ -90,19 +84,19 @@ public class SpeciesCollectionXmlParser extends XmlParser {
/**
* Helper class used to decode/encode CellDesigner strings.
*/
- private AbstractElementXmlParser<Element<?>, Alias> helpParser = new AbstractElementXmlParser<Element<?>, Alias>() {
+ private AbstractElementXmlParser<CellDesignerElement<?>, Element> helpParser = new AbstractElementXmlParser<CellDesignerElement<?>, Element>() {
@Override
public String encodeName(String name) {
return super.encodeName(name);
}
@Override
- public String toXml(Alias element) throws InconsistentModelException {
+ public String toXml(Element element) throws InconsistentModelException {
throw new NotImplementedException();
}
@Override
- public Pair<String, Element<?>> parseXmlElement(Node node)
+ public Pair<String, CellDesignerElement<?>> parseXmlElement(Node node)
throws InvalidXmlSchemaException {
throw new NotImplementedException();
}
@@ -113,12 +107,8 @@ public class SpeciesCollectionXmlParser extends XmlParser {
/**
* Default constructor. Model is required because some CellDesigner nodes
* require access to other parts of the model.
- *
- * @param model
- * model that is parsed/transformed into xml
*/
- public SpeciesCollectionXmlParser(Model model, CellDesignerElementCollection elements) {
- this.model = model;
+ public SpeciesCollectionXmlParser(CellDesignerElementCollection elements) {
sbmlSpeciesParser = new SpeciesSbmlParser(elements);
this.elements = elements;
rnaParser = new RnaXmlParser(elements);
@@ -137,14 +127,14 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when node contains problematic data
*/
- public List<Pair<String, ? extends Species<?>>> parseXmlRnaCollection(Node rnaNode) throws InvalidXmlSchemaException {
- List<Pair<String, ? extends Species<?>>> result = new ArrayList<>();
+ public List<Pair<String, ? extends CellDesignerSpecies<?>>> parseXmlRnaCollection(Node rnaNode) throws InvalidXmlSchemaException {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> result = new ArrayList<>();
NodeList nodes = rnaNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:RNA")) {
- Pair<String, Rna> rna = rnaParser.parseXmlElement(node);
+ Pair<String, CellDesignerRna> rna = rnaParser.parseXmlElement(node);
result.add(rna);
} else {
throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfRNAs: " + node.getNodeName());
@@ -161,10 +151,10 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* set of rnas
* @return CellDesigner xml node corrseponding to the input
*/
- public String rnaCollectionToXmlString(Collection<RnaAlias> collection) {
+ public String rnaCollectionToXmlString(Collection<Rna> collection) {
StringBuilder result = new StringBuilder();
result.append("<celldesigner:listOfRNAs>");
- for (RnaAlias species : collection) {
+ for (Rna species : collection) {
result.append(rnaParser.toXml(species));
}
result.append("</celldesigner:listOfRNAs>\n");
@@ -180,14 +170,14 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public List<Pair<String, ? extends Species<?>>> parseXmlGeneCollection(Node geneNode) throws InvalidXmlSchemaException {
- List<Pair<String, ? extends Species<?>>> result = new ArrayList<>();
+ public List<Pair<String, ? extends CellDesignerSpecies<?>>> parseXmlGeneCollection(Node geneNode) throws InvalidXmlSchemaException {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> result = new ArrayList<>();
NodeList nodes = geneNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:gene")) {
- Pair<String, Gene> gene = geneParser.parseXmlElement(node);
+ Pair<String, CellDesignerGene> gene = geneParser.parseXmlElement(node);
result.add(gene);
} else {
throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfGenes: " + node.getNodeName());
@@ -204,10 +194,10 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* set of genes
* @return CellDesigner xml node corrseponding to the input
*/
- public String geneCollectionToXmlString(Collection<GeneAlias> collection) {
+ public String geneCollectionToXmlString(Collection<Gene> collection) {
StringBuilder result = new StringBuilder();
result.append("<celldesigner:listOfGenes>");
- for (GeneAlias species : collection) {
+ for (Gene species : collection) {
result.append(geneParser.toXml(species));
}
result.append("</celldesigner:listOfGenes>\n");
@@ -223,14 +213,14 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public List<Pair<String, ? extends Species<?>>> parseXmlProteinCollection(Node proteinNode) throws InvalidXmlSchemaException {
- List<Pair<String, ? extends Species<?>>> result = new ArrayList<>();
+ public List<Pair<String, ? extends CellDesignerSpecies<?>>> parseXmlProteinCollection(Node proteinNode) throws InvalidXmlSchemaException {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> result = new ArrayList<>();
NodeList nodes = proteinNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:protein")) {
- Pair<String, Protein<?>> protein = proteinParser.parseXmlElement(node);
+ Pair<String, CellDesignerProtein<?>> protein = proteinParser.parseXmlElement(node);
result.add(protein);
} else {
throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfProteins: " + node.getNodeName());
@@ -247,10 +237,10 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* set of proteins
* @return CellDesigner xml node corrseponding to the input
*/
- public String proteinCollectionToXmlString(Collection<ProteinAlias> collection) {
+ public String proteinCollectionToXmlString(Collection<Protein> collection) {
StringBuilder result = new StringBuilder();
result.append("<celldesigner:listOfProteins>");
- for (ProteinAlias species : collection) {
+ for (Protein species : collection) {
result.append(proteinParser.toXml(species));
}
result.append("</celldesigner:listOfProteins>\n");
@@ -267,14 +257,14 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public List<Pair<String, ? extends Species<?>>> parseXmlAntisenseRnaCollection(Node rnaNode) throws InvalidXmlSchemaException {
- List<Pair<String, ? extends Species<?>>> result = new ArrayList<>();
+ public List<Pair<String, ? extends CellDesignerSpecies<?>>> parseXmlAntisenseRnaCollection(Node rnaNode) throws InvalidXmlSchemaException {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> result = new ArrayList<>();
NodeList nodes = rnaNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:AntisenseRNA")) {
- Pair<String, AntisenseRna> antisenseRna = antisenseRnaParser.parseXmlElement(node);
+ Pair<String, CellDesignerAntisenseRna> antisenseRna = antisenseRnaParser.parseXmlElement(node);
result.add(antisenseRna);
} else {
throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfAntisenseRNAs: " + node.getNodeName());
@@ -291,10 +281,10 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* set of antisense rnas
* @return CellDesigner xml node corrseponding to the input
*/
- public String antisenseRnaCollectionToXmlString(Collection<AntisenseRnaAlias> collection) {
+ public String antisenseRnaCollectionToXmlString(Collection<AntisenseRna> collection) {
StringBuilder result = new StringBuilder();
result.append("<celldesigner:listOfAntisenseRNAs>");
- for (AntisenseRnaAlias species : collection) {
+ for (AntisenseRna species : collection) {
result.append(antisenseRnaParser.toXml(species));
}
result.append("</celldesigner:listOfAntisenseRNAs>\n");
@@ -310,14 +300,14 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public List<Pair<String, ? extends Species<?>>> parseSbmlSpeciesCollection(Node spieciesNode) throws InvalidXmlSchemaException {
- List<Pair<String, ? extends Species<?>>> result = new ArrayList<>();
+ public List<Pair<String, ? extends CellDesignerSpecies<?>>> parseSbmlSpeciesCollection(Node spieciesNode) throws InvalidXmlSchemaException {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> result = new ArrayList<>();
NodeList nodes = spieciesNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("species") || node.getNodeName().equalsIgnoreCase("celldesigner:species")) {
- Pair<String, Species<?>> sp = sbmlSpeciesParser.parseXmlElement(node);
+ Pair<String, CellDesignerSpecies<?>> sp = sbmlSpeciesParser.parseXmlElement(node);
result.add(sp);
} else {
throw new InvalidXmlSchemaException("Unknown element of listOfSpecies: " + node.getNodeName());
@@ -328,7 +318,7 @@ public class SpeciesCollectionXmlParser extends XmlParser {
}
/**
- * Transforms set of {@link Species} into SBML node.
+ * Transforms set of {@link CellDesignerSpecies} into SBML node.
*
* @param collection
* set of species to transform
@@ -337,14 +327,14 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* thrown when xml cannot be generated because structure of objects
* is invalid
*/
- public String speciesCollectionToSbmlString(Collection<SpeciesAlias> collection) throws InconsistentModelException {
+ public String speciesCollectionToSbmlString(Collection<Species> collection) throws InconsistentModelException {
StringBuilder result = new StringBuilder();
result.append("<listOfSpecies>");
- for (SpeciesAlias species : collection) {
+ for (Species species : collection) {
// not all elements should be added to the result string: elements that
// are in complexes should be excluded
boolean add = false;
- if (!(species.getParent() instanceof ComplexAlias)) {
+ if (!(species.getParent() instanceof Complex)) {
add = true;
}
if (add) {
@@ -367,8 +357,8 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public List<Pair<String, ? extends Species<?>>> parseIncludedSpeciesCollection(Node spieciesNode) throws InvalidXmlSchemaException {
- List<Pair<String, ? extends Species<?>>> result = new ArrayList<>();
+ public List<Pair<String, ? extends CellDesignerSpecies<?>>> parseIncludedSpeciesCollection(Node spieciesNode) throws InvalidXmlSchemaException {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> result = new ArrayList<>();
// What should be done here?
// What are the inclusions?
// Probably this should be improved, this part of a CD model is really
@@ -404,8 +394,8 @@ public class SpeciesCollectionXmlParser extends XmlParser {
} else {
Node spNode = getNode("celldesigner:speciesIdentity", annNode.getChildNodes());
if (spNode != null) {
- Pair<String, Species<?>> row = parser.parseSpeciesIdentity(spNode);
- Species<?> sp = row.getRight();
+ Pair<String, CellDesignerSpecies<?>> row = parser.parseSpeciesIdentity(spNode);
+ CellDesignerSpecies<?> sp = row.getRight();
sp.setElementId(idIncluded);
sp.setName(helpParser.decodeName(nameIncluded));
sp.setNotes(rap.getNotes(notesNode));
@@ -433,14 +423,14 @@ public class SpeciesCollectionXmlParser extends XmlParser {
* list of Species
* @return CellDesigner included species xml node
*/
- public String speciesCollectionToXmlIncludedString(Collection<SpeciesAlias> collection) {
+ public String speciesCollectionToXmlIncludedString(Collection<Species> collection) {
StringBuilder sb = new StringBuilder("");
sb.append("<celldesigner:listOfIncludedSpecies>\n");
- for (Alias species : collection) {
- if (species instanceof ComplexAlias) {
- ComplexAlias cs = (ComplexAlias) species;
- for (Alias element : cs.getAliases()) {
- SpeciesAlias child = (SpeciesAlias) element;
+ for (Element species : collection) {
+ if (species instanceof Complex) {
+ Complex cs = (Complex) species;
+ for (Element element : cs.getAliases()) {
+ Species child = (Species) element;
sb.append(
"<celldesigner:species id=\"" + elements.getElementId(child) + "\" name=\"" + StringEscapeUtils.escapeXml(helpParser.encodeName(child.getName()))
+ "\">");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
index abe71c3ce1..857c7e4454 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMapping.java
@@ -1,34 +1,34 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Unknown;
/**
* This enum contains information about mapping between CellDesigner xml nodes
- * and classes that extend {@link Species}.
+ * and classes that extend {@link CellDesignerSpecies}.
*
* @author Piotr Gawron
*
@@ -37,57 +37,57 @@ public enum SpeciesMapping {
/**
* {@link Protein}.
*/
- PROTEIN(Protein.class, ProteinAlias.class, "PROTEIN"), //
+ PROTEIN(CellDesignerProtein.class, Protein.class, "PROTEIN"), //
/**
* {@link Gene}.
*/
- GENE(Gene.class, GeneAlias.class, "GENE"), //
+ GENE(CellDesignerGene.class, Gene.class, "GENE"), //
/**
* {@link ComplexSpecies}.
*/
- COMPLEX(ComplexSpecies.class, ComplexAlias.class, "COMPLEX"), //
+ COMPLEX(CellDesignerComplexSpecies.class, Complex.class, "COMPLEX"), //
/**
* {@link SimpleMolecule}.
*/
- SIMPLE_MOLECULE(SimpleMolecule.class, SimpleMoleculeAlias.class, "SIMPLE_MOLECULE"), //
+ SIMPLE_MOLECULE(CellDesignerSimpleMolecule.class, SimpleMolecule.class, "SIMPLE_MOLECULE"), //
/**
* {@link Ion}.
*/
- ION(Ion.class, IonAlias.class, "ION"), //
+ ION(CellDesignerIon.class, Ion.class, "ION"), //
/**
* {@link Phenotype}.
*/
- PHENOTYPE(Phenotype.class, PhenotypeAlias.class, "PHENOTYPE"), //
+ PHENOTYPE(CellDesignerPhenotype.class, Phenotype.class, "PHENOTYPE"), //
/**
* {@link Drug}.
*/
- DRUG(Drug.class, DrugAlias.class, "DRUG"), //
+ DRUG(CellDesignerDrug.class, Drug.class, "DRUG"), //
/**
* {@link Rna}.
*/
- RNA(Rna.class, RnaAlias.class, "RNA"), //
+ RNA(CellDesignerRna.class, Rna.class, "RNA"), //
/**
* {@link AntisenseRna}.
*/
- ANTISENSE_RNA(AntisenseRna.class, AntisenseRnaAlias.class, "ANTISENSE_RNA"), //
+ ANTISENSE_RNA(CellDesignerAntisenseRna.class, AntisenseRna.class, "ANTISENSE_RNA"), //
/**
* {@link Unknown}.
*/
- UNKNOWN(Unknown.class, UnknownAlias.class, "UNKNOWN"), //
+ UNKNOWN(CellDesignerUnknown.class, Unknown.class, "UNKNOWN"), //
/**
* {@link Degraded}.
*/
- DEGRADED(Degraded.class, DegradedAlias.class, "DEGRADED");
+ DEGRADED(CellDesignerDegraded.class, Degraded.class, "DEGRADED");
/**
* CellDesigner xml node type.
@@ -97,9 +97,9 @@ public enum SpeciesMapping {
/**
* Class that should be used to represent cell designer node.
*/
- private Class<? extends Species> cellDesignerClazz;
+ private Class<? extends CellDesignerSpecies> cellDesignerClazz;
- private Class<? extends Alias> modelClazz;
+ private Class<? extends Element> modelClazz;
/**
* Default constructor.
@@ -109,7 +109,7 @@ public enum SpeciesMapping {
* @param cellDesignerString
* {@link #cellDesignerString}
*/
- SpeciesMapping(Class<? extends Species> cellDesignerClazz, Class<? extends Alias> modelClazz, String cellDesignerString) {
+ SpeciesMapping(Class<? extends CellDesignerSpecies> cellDesignerClazz, Class<? extends Element> modelClazz, String cellDesignerString) {
this.cellDesignerString = cellDesignerString;
this.cellDesignerClazz = cellDesignerClazz;
this.modelClazz = modelClazz;
@@ -127,24 +127,24 @@ public enum SpeciesMapping {
* @return the clazz
* @see #clazz
*/
- public Class<? extends Species> getCellDesignerClazz() {
+ public Class<? extends CellDesignerSpecies> getCellDesignerClazz() {
return cellDesignerClazz;
}
- public Class<? extends Alias> getModelClazz() {
+ public Class<? extends Element> getModelClazz() {
return modelClazz;
}
/**
- * Creates instance of {@link Species} specific for this
+ * Creates instance of {@link CellDesignerSpecies} specific for this
* {@link SpeciesMapping}.
*
* @param result
* parameter that should be passed to the constructor
- * @return new instance of {@link Species} specific for this
+ * @return new instance of {@link CellDesignerSpecies} specific for this
* {@link SpeciesMapping}.
*/
- public Species createSpecies(Species result) {
+ public CellDesignerSpecies createSpecies(CellDesignerSpecies result) {
try {
return cellDesignerClazz.getConstructor(result.getClass()).newInstance(result);
} catch (Exception e) {
@@ -169,13 +169,13 @@ public enum SpeciesMapping {
}
/**
- * Returns {@link SpeciesMapping} for given {@link Species} class.
+ * Returns {@link SpeciesMapping} for given {@link CellDesignerSpecies} class.
*
* @param searchClazz
- * {@link Species} class
- * @return {@link SpeciesMapping} for given {@link Species} class
+ * {@link CellDesignerSpecies} class
+ * @return {@link SpeciesMapping} for given {@link CellDesignerSpecies} class
*/
- public static SpeciesMapping getMappingByCellDesignerClass(Class<? extends Species> searchClazz) {
+ public static SpeciesMapping getMappingByCellDesignerClass(Class<? extends CellDesignerSpecies> searchClazz) {
for (SpeciesMapping mapping : SpeciesMapping.values()) {
if (mapping.getCellDesignerClazz().isAssignableFrom(searchClazz)) {
return mapping;
@@ -184,7 +184,7 @@ public enum SpeciesMapping {
return null;
}
- public static SpeciesMapping getMappingByModelClass(Class<? extends Alias> searchClazz) {
+ public static SpeciesMapping getMappingByModelClass(Class<? extends Element> searchClazz) {
for (SpeciesMapping mapping : SpeciesMapping.values()) {
if (mapping.getModelClazz().isAssignableFrom(searchClazz)) {
return mapping;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index 439b5d9b5a..fd0bfcbd71 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -11,26 +11,26 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRnaRegion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.RnaRegion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SpeciesState;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.PositionToCompartment;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
/**
* Parser for sbml part of CellDesigner format. It's used for retrieving Species
@@ -39,7 +39,7 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
* @author Piotr Gawron
*
*/
-public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, SpeciesAlias> {
+public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpecies<?>, Species> {
/**
* Default class logger.
@@ -58,7 +58,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
@Override
- public Pair<String, Species<?>> parseXmlElement(Node spieciesNode) throws InvalidXmlSchemaException {
+ public Pair<String, CellDesignerSpecies<?>> parseXmlElement(Node spieciesNode) throws InvalidXmlSchemaException {
NodeList list = spieciesNode.getChildNodes();
@@ -126,9 +126,9 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
throw new InvalidXmlSchemaException("No celldesigner:speciesIdentity node in SBML/model/listOfSpecies/species/annotation/extension");
}
- Pair<String, Species<?>> result = parseSpeciesIdentity(speciesIdentity);
+ Pair<String, CellDesignerSpecies<?>> result = parseSpeciesIdentity(speciesIdentity);
- Species<?> species = result.getRight();
+ CellDesignerSpecies<?> species = result.getRight();
if (positionToCompartment != null) {
PositionToCompartment position = PositionToCompartment.getByString(getNodeValue(positionToCompartment));
if (position == null) {
@@ -146,7 +146,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
species.setCharge(getNodeAttr("charge", spieciesNode));
species.setOnlySubstanceUnits(getNodeAttr("hasOnlySubstanceUnits", spieciesNode));
- Compartment compartment = elements.getCompartmentByCompartmentId(getNodeAttr("compartment", spieciesNode));
+ CellDesignerCompartment compartment = elements.getCompartmentByCompartmentId(getNodeAttr("compartment", spieciesNode));
if (compartment != null) {
species.setParent(compartment);
}
@@ -164,7 +164,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
@Override
- public String toXml(SpeciesAlias species) {
+ public String toXml(Species species) {
StringBuilder builder = new StringBuilder();
StringBuilder attributesBuilder = new StringBuilder();
attributesBuilder.append(" name=\"" + escapeXml(encodeName(species.getName())) + "\"");
@@ -182,8 +182,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
if (species.hasOnlySubstanceUnits() != null) {
attributesBuilder.append(" hasOnlySubstanceUnits=\"" + species.hasOnlySubstanceUnits() + "\"");
}
- if (species.getParent() != null && species.getParent() instanceof CompartmentAlias) {
- CompartmentAlias comp = (CompartmentAlias) species.getParent();
+ if (species.getParent() != null && species.getParent() instanceof Compartment) {
+ Compartment comp = (Compartment) species.getParent();
attributesBuilder.append(" compartment=\"" + elements.getElementId(comp) + "\"");
} else {
attributesBuilder.append(" compartment=\"default\"");
@@ -221,13 +221,13 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
/**
- * Creates speciesIdentity xml node for the {@link Species}.
+ * Creates speciesIdentity xml node for the {@link CellDesignerSpecies}.
*
* @param species
* species to be transformed into xml
* @return speciesIdentity xml node
*/
- String speciesIdentityToXml(SpeciesAlias species) {
+ String speciesIdentityToXml(Species species) {
StringBuilder sb = new StringBuilder();
String classType = "";
SpeciesMapping mapping = SpeciesMapping.getMappingByModelClass(species.getClass());
@@ -238,13 +238,13 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
sb.append("<celldesigner:speciesIdentity>");
sb.append("<celldesigner:class>" + classType + "</celldesigner:class>\n");
- if (species instanceof RnaAlias) {
+ if (species instanceof Rna) {
sb.append("<celldesigner:rnaReference>r_" + elements.getElementId(species) + "</celldesigner:rnaReference>\n");
- } else if (species instanceof ProteinAlias) {
+ } else if (species instanceof Protein) {
sb.append("<celldesigner:proteinReference>p_" + elements.getElementId(species) + "</celldesigner:proteinReference>\n");
- } else if (species instanceof GeneAlias) {
+ } else if (species instanceof Gene) {
sb.append("<celldesigner:geneReference>g_" + elements.getElementId(species) + "</celldesigner:geneReference>\n");
- } else if (species instanceof AntisenseRnaAlias) {
+ } else if (species instanceof AntisenseRna) {
sb.append("<celldesigner:antisensernaReference>ar_" + elements.getElementId(species) + "</celldesigner:antisensernaReference>\n");
}
SpeciesState state = new SpeciesState(species);
@@ -281,7 +281,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
if (state.getModifications().size() > 0) {
sb.append("<celldesigner:listOfModifications>\n");
- for (ModificationResidue mr : state.getModifications()) {
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
sb.append(modificationResidueToXml(mr));
}
sb.append("</celldesigner:listOfModifications>\n");
@@ -294,7 +294,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
/**
- * Parses CellDesigner SpeciesIdentity node into {@link Species}.
+ * Parses CellDesigner SpeciesIdentity node into {@link CellDesignerSpecies}.
*
* @param rootNode
* xml node to parse
@@ -303,9 +303,9 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- public Pair<String, Species<?>> parseSpeciesIdentity(Node rootNode) throws InvalidXmlSchemaException {
+ public Pair<String, CellDesignerSpecies<?>> parseSpeciesIdentity(Node rootNode) throws InvalidXmlSchemaException {
NodeList nodes = rootNode.getChildNodes();
- Species<?> result = new Species();
+ CellDesignerSpecies<?> result = new CellDesignerSpecies();
Node classNode = getNode("celldesigner:class", nodes);
if (classNode == null) {
throw new InvalidXmlSchemaException("Species node in Sbml model doesn't contain node \"celldesigner:class\".");
@@ -325,25 +325,25 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
continue;
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:proteinReference")) {
- if (result instanceof Protein) {
+ if (result instanceof CellDesignerProtein) {
identifier = getNodeValue(node);
} else {
throw new InvalidXmlSchemaException("Wrong class type for protein reference: " + result.getClass().getName());
}
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:geneReference")) {
- if (result instanceof Gene) {
+ if (result instanceof CellDesignerGene) {
identifier = getNodeValue(node);
} else {
throw new InvalidXmlSchemaException("Wrong class type for gene reference: " + result.getClass().getName());
}
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:rnaReference")) {
- if (result instanceof Rna) {
+ if (result instanceof CellDesignerRna) {
identifier = getNodeValue(node);
} else {
throw new InvalidXmlSchemaException("Wrong class type for rna reference: " + result.getClass().getName());
}
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:antisensernaReference")) {
- if (result instanceof AntisenseRna) {
+ if (result instanceof CellDesignerAntisenseRna) {
identifier = getNodeValue(node);
} else {
throw new InvalidXmlSchemaException("Wrong class type for antisense rna reference: " + result.getClass().getName());
@@ -361,7 +361,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
}
- return new Pair<String, Species<?>>(identifier, result);
+ return new Pair<String, CellDesignerSpecies<?>>(identifier, result);
}
/**
@@ -374,39 +374,39 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
* @param species
* where the data should be saved
*/
- void processStateDataInSpecies(Species<?> species, SpeciesState state) {
+ void processStateDataInSpecies(CellDesignerSpecies<?> species, SpeciesState state) {
species.setHomodimer(state.getHomodimer());
- if (species instanceof ComplexSpecies) {
- ComplexSpecies complex = (ComplexSpecies) species;
+ if (species instanceof CellDesignerComplexSpecies) {
+ CellDesignerComplexSpecies complex = (CellDesignerComplexSpecies) species;
complex.setStructuralState(state.getStructuralState());
if (state.getModifications().size() != 0) {
throw new NotImplementedException("Modification not supported in Complex");
}
- } else if (species instanceof Gene) {
- Gene gene = (Gene) species;
+ } else if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
if (state.getStructuralState() != null) {
throw new NotImplementedException("StructuralState not supported in Gene");
}
- for (ModificationResidue mr : state.getModifications()) {
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
gene.addModificationResidue(mr);
}
- } else if (species instanceof Protein) {
- Protein<?> protein = (Protein<?>) species;
+ } else if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
protein.setStructuralState(state.getStructuralState());
- for (ModificationResidue mr : state.getModifications()) {
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
protein.addModificationResidue(mr);
}
- } else if (species instanceof Rna) {
- Rna rna = (Rna) species;
+ } else if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
throw new NotImplementedException("Structural state not supported in RNA");
}
- for (ModificationResidue mr : state.getModifications()) {
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
rna.addRegion(createRnaRegion(mr));
}
- } else if (species instanceof SimpleMolecule) {
+ } else if (species instanceof CellDesignerSimpleMolecule) {
if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
throw new NotImplementedException("Structural state not supported in SimpleMolecule");
}
@@ -414,14 +414,14 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
throw new NotImplementedException("Modification not supported in SimpleMolecule");
}
- } else if (species instanceof AntisenseRna) {
- AntisenseRna antisenseRna = (AntisenseRna) species;
+ } else if (species instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna antisenseRna = (CellDesignerAntisenseRna) species;
if (state.getStructuralState() != null && !state.getStructuralState().isEmpty()) {
throw new NotImplementedException("Structural state not supported in AntisenseRna");
}
- for (ModificationResidue mr : state.getModifications()) {
- AntisenseRnaRegion region = createAntisenseRnaRegion(mr);
+ for (CellDesignerModificationResidue mr : state.getModifications()) {
+ CellDesignerAntisenseRnaRegion region = createAntisenseRnaRegion(mr);
antisenseRna.addRegion(region);
}
} else {
@@ -475,7 +475,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
Node structureNode = modificationNodeList.item(y);
if (structureNode.getNodeType() == Node.ELEMENT_NODE) {
if (structureNode.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
- ModificationResidue modification = getSpeciesModification(structureNode);
+ CellDesignerModificationResidue modification = getSpeciesModification(structureNode);
result.addModificationResidue(modification);
} else {
@@ -492,17 +492,17 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
/**
- * Creates {@link ModificationResidue} from the apropriate xml node.
+ * Creates {@link CellDesignerModificationResidue} from the apropriate xml node.
*
* @param rootNode
* xml node
- * @return {@link ModificationResidue} retrieved from the node
+ * @return {@link CellDesignerModificationResidue} retrieved from the node
* @throws InvalidXmlSchemaException
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private ModificationResidue getSpeciesModification(Node rootNode) throws InvalidXmlSchemaException {
- ModificationResidue modification = new ModificationResidue();
+ private CellDesignerModificationResidue getSpeciesModification(Node rootNode) throws InvalidXmlSchemaException {
+ CellDesignerModificationResidue modification = new CellDesignerModificationResidue();
modification.setIdModificationResidue(getNodeAttr("residue", rootNode));
String state = getNodeAttr("state", rootNode);
if (state != null) {
@@ -529,13 +529,13 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
/**
- * Creates xml node representing {@link ModificationResidue}.
+ * Creates xml node representing {@link CellDesignerModificationResidue}.
*
* @param mr
* object to be transformed into xml
* @return xml node representing param object
*/
- private String modificationResidueToXml(ModificationResidue mr) {
+ private String modificationResidueToXml(CellDesignerModificationResidue mr) {
String state = "";
if (mr.getState() != null) {
state = mr.getState().getFullName();
@@ -547,15 +547,15 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
/**
- * Creates {@link AntisenseRnaRegion} from {@link ModificationResidue}
+ * Creates {@link CellDesignerAntisenseRnaRegion} from {@link CellDesignerModificationResidue}
* description.
*
* @param mr
- * object from which we create {@link AntisenseRnaRegion}
- * @return {@link AntisenseRnaRegion} object created from param
+ * object from which we create {@link CellDesignerAntisenseRnaRegion}
+ * @return {@link CellDesignerAntisenseRnaRegion} object created from param
*/
- AntisenseRnaRegion createAntisenseRnaRegion(ModificationResidue mr) {
- AntisenseRnaRegion region = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion createAntisenseRnaRegion(CellDesignerModificationResidue mr) {
+ CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion();
region.setIdAntisenseRnaRegion(mr.getIdModificationResidue());
if (mr.getSize() != null) {
region.setSize(mr.getSize());
@@ -569,14 +569,14 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<Species<?>, Spec
}
/**
- * Creates {@link RnaRegion} from {@link ModificationResidue} description.
+ * Creates {@link CellDesignerRnaRegion} from {@link CellDesignerModificationResidue} description.
*
* @param mr
- * object from which we create {@link RnaRegion}
- * @return {@link RnaRegion} object created from param
+ * object from which we create {@link CellDesignerRnaRegion}
+ * @return {@link CellDesignerRnaRegion} object created from param
*/
- public RnaRegion createRnaRegion(ModificationResidue mr) {
- RnaRegion result = new RnaRegion();
+ public CellDesignerRnaRegion createRnaRegion(CellDesignerModificationResidue mr) {
+ CellDesignerRnaRegion result = new CellDesignerRnaRegion();
result.setIdRnaRegion(mr.getIdModificationResidue());
if (mr.getSize() != null) {
result.setSize(mr.getSize());
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java
index a0c3c1535f..7b15345c0e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains parsers used for parsing CellDesiger xml for
- * {@link lcsb.mapviewer.db.model.map.species.Species Species}.
- */
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
+/**
+ * This package contains parsers used for parsing CellDesiger xml for
+ * {@link lcsb.mapviewer.db.model.map.species.CellDesignerSpecies Species}.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
similarity index 54%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
index d1aa4bfb89..190eeac25e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
@@ -6,7 +6,7 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
/**
* Class representing antisense rna in the model.
@@ -14,7 +14,7 @@ import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
* @author Piotr Gawron
*
*/
-public class AntisenseRna extends Species<AntisenseRnaAlias> {
+public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna> {
/**
*
@@ -25,12 +25,12 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRna.class);
+ private static Logger logger = Logger.getLogger(CellDesignerAntisenseRna.class);
/**
* List of antisense rna regions (some rna sequences) in this object.
*/
- private List<AntisenseRnaRegion> regions = new ArrayList<AntisenseRnaRegion>();
+ private List<CellDesignerAntisenseRnaRegion> regions = new ArrayList<CellDesignerAntisenseRnaRegion>();
/**
* Constructor that copies the data from species given in the argument.
@@ -38,12 +38,12 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
* @param species
* parent species from which we want to copy data
*/
- public AntisenseRna(Species<?> species) {
+ public CellDesignerAntisenseRna(CellDesignerSpecies<?> species) {
super(species);
- if (species instanceof AntisenseRna) {
- AntisenseRna asRna = (AntisenseRna) species;
- for (AntisenseRnaRegion region : asRna.getRegions()) {
- addRegion(new AntisenseRnaRegion(region));
+ if (species instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna asRna = (CellDesignerAntisenseRna) species;
+ for (CellDesignerAntisenseRnaRegion region : asRna.getRegions()) {
+ addRegion(new CellDesignerAntisenseRnaRegion(region));
}
}
}
@@ -51,14 +51,14 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
/**
* Default constructor.
*/
- public AntisenseRna() {
+ public CellDesignerAntisenseRna() {
super();
}
@Override
- public AntisenseRna copy() {
- if (this.getClass() == AntisenseRna.class) {
- return new AntisenseRna(this);
+ public CellDesignerAntisenseRna copy() {
+ if (this.getClass() == CellDesignerAntisenseRna.class) {
+ return new CellDesignerAntisenseRna(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -72,14 +72,14 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
/**
* Addd antisense rna region (part of rna sequence that has some meaning) to
* the object. If the region with given id exists then the data of this region
- * is copied to the one that is already in the {@link AntisenseRna}.
+ * is copied to the one that is already in the {@link CellDesignerAntisenseRna}.
*
*
* @param region
* region to add
*/
- public void addRegion(AntisenseRnaRegion region) {
- for (AntisenseRnaRegion region2 : regions) {
+ public void addRegion(CellDesignerAntisenseRnaRegion region) {
+ for (CellDesignerAntisenseRnaRegion region2 : regions) {
if (region2.getIdAntisenseRnaRegion().equals(region.getIdAntisenseRnaRegion())) {
region2.update(region);
return;
@@ -91,15 +91,15 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
}
@Override
- public void update(Species<?> sp) {
+ public void update(CellDesignerSpecies<?> sp) {
super.update(sp);
- if (sp instanceof AntisenseRna) {
- AntisenseRna rna = (AntisenseRna) sp;
- for (AntisenseRnaRegion mr : getRegions()) {
+ if (sp instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna rna = (CellDesignerAntisenseRna) sp;
+ for (CellDesignerAntisenseRnaRegion mr : getRegions()) {
mr.setState(null);
}
- for (AntisenseRnaRegion region : rna.getRegions()) {
+ for (CellDesignerAntisenseRnaRegion region : rna.getRegions()) {
updateRegion(region);
}
}
@@ -113,8 +113,8 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
* @param param
* - object with new data from where update should be performed
*/
- private void updateRegion(AntisenseRnaRegion param) {
- for (AntisenseRnaRegion region : regions) {
+ private void updateRegion(CellDesignerAntisenseRnaRegion param) {
+ for (CellDesignerAntisenseRnaRegion region : regions) {
if (region.getIdAntisenseRnaRegion().equals(param.getIdAntisenseRnaRegion())) {
region.update(param);
return;
@@ -127,7 +127,7 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
* @return the regions
* @see #regions
*/
- public List<AntisenseRnaRegion> getRegions() {
+ public List<CellDesignerAntisenseRnaRegion> getRegions() {
return regions;
}
@@ -136,15 +136,15 @@ public class AntisenseRna extends Species<AntisenseRnaAlias> {
* the regions to set
* @see #regions
*/
- public void setRegions(List<AntisenseRnaRegion> regions) {
+ public void setRegions(List<CellDesignerAntisenseRnaRegion> regions) {
this.regions = regions;
}
@Override
- public AntisenseRnaAlias createAlias(String aliasId) {
- AntisenseRnaAlias result = new AntisenseRnaAlias(aliasId);
+ public AntisenseRna createAlias(String aliasId) {
+ AntisenseRna result = new AntisenseRna(aliasId);
super.setAliasFields(result);
- for (AntisenseRnaRegion region : regions) {
+ for (CellDesignerAntisenseRnaRegion region : regions) {
result.addRegion(region.createAntisenseRegionAlias());
}
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRnaComparator.java
similarity index 71%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRnaComparator.java
index 2bb9ff7cb0..e63de6bd26 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRnaComparator.java
@@ -14,7 +14,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
+public class CellDesignerAntisenseRnaComparator implements Comparator<CellDesignerAntisenseRna> {
/**
* Epsilon value used for comparison of doubles.
@@ -27,19 +27,19 @@ public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
* @param epsilon
* {@link #epsilon}
*/
- public AntisenseRnaComparator(double epsilon) {
+ public CellDesignerAntisenseRnaComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public AntisenseRnaComparator() {
+ public CellDesignerAntisenseRnaComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(AntisenseRna arg0, AntisenseRna arg1) {
+ public int compare(CellDesignerAntisenseRna arg0, CellDesignerAntisenseRna arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -51,7 +51,7 @@ public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(AntisenseRna.class)) {
+ if (arg0.getClass().equals(CellDesignerAntisenseRna.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -73,8 +73,8 @@ public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerAntisenseRna arg0, CellDesignerAntisenseRna arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
@@ -84,11 +84,11 @@ public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
Set<String> set1 = new HashSet<String>();
Set<String> set2 = new HashSet<String>();
- for (AntisenseRnaRegion region : arg0.getRegions()) {
+ for (CellDesignerAntisenseRnaRegion region : arg0.getRegions()) {
set1.add(region.toString());
}
- for (AntisenseRnaRegion region : arg1.getRegions()) {
+ for (CellDesignerAntisenseRnaRegion region : arg1.getRegions()) {
set2.add(region.toString());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRnaRegion.java
similarity index 80%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRnaRegion.java
index 8ec3bb9181..e2c933ab7d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRnaRegion.java
@@ -6,20 +6,20 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion.AntisenseRnaRegionType;
/**
* This structure contains information about antisense rna region (rna fragment
* of interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna
* AntisenseRna}.
*
* @author Piotr Gawron
*
*/
-public class AntisenseRnaRegion implements Serializable {
+public class CellDesignerAntisenseRnaRegion implements Serializable {
/**
*
@@ -35,7 +35,7 @@ public class AntisenseRnaRegion implements Serializable {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaRegion.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesignerAntisenseRnaRegion.class.getName());
/**
* Unique identifier in the database.
@@ -82,12 +82,12 @@ public class AntisenseRnaRegion implements Serializable {
/**
* Defines a species where the region belongs to.
*/
- private AntisenseRna species;
+ private CellDesignerAntisenseRna species;
/**
* Default constructor.
*/
- public AntisenseRnaRegion() {
+ public CellDesignerAntisenseRnaRegion() {
}
@@ -97,7 +97,7 @@ public class AntisenseRnaRegion implements Serializable {
* @param original
* object from which we initialize data
*/
- public AntisenseRnaRegion(AntisenseRnaRegion original) {
+ public CellDesignerAntisenseRnaRegion(CellDesignerAntisenseRnaRegion original) {
this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
this.name = original.name;
this.size = original.size;
@@ -110,9 +110,9 @@ public class AntisenseRnaRegion implements Serializable {
*
* @return copy of the object
*/
- public AntisenseRnaRegion copy() {
- if (this.getClass() == AntisenseRnaRegion.class) {
- return new AntisenseRnaRegion(this);
+ public CellDesignerAntisenseRnaRegion copy() {
+ if (this.getClass() == CellDesignerAntisenseRnaRegion.class) {
+ return new CellDesignerAntisenseRnaRegion(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -156,7 +156,7 @@ public class AntisenseRnaRegion implements Serializable {
* @param mr
* object from which we are updating data
*/
- public void update(AntisenseRnaRegion mr) {
+ public void update(CellDesignerAntisenseRnaRegion mr) {
if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("") && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
throw new InvalidArgumentException("Cannot update from mr with different id");
}
@@ -285,7 +285,7 @@ public class AntisenseRnaRegion implements Serializable {
* @return the species
* @see #species
*/
- public AntisenseRna getSpecies() {
+ public CellDesignerAntisenseRna getSpecies() {
return species;
}
@@ -294,7 +294,7 @@ public class AntisenseRnaRegion implements Serializable {
* the species to set
* @see #species
*/
- public void setSpecies(AntisenseRna species) {
+ public void setSpecies(CellDesignerAntisenseRna species) {
this.species = species;
}
@@ -315,8 +315,8 @@ public class AntisenseRnaRegion implements Serializable {
this.id = id;
}
- public AntisenseRnaRegionAlias createAntisenseRegionAlias() {
- AntisenseRnaRegionAlias result = new AntisenseRnaRegionAlias();
+ public AntisenseRnaRegion createAntisenseRegionAlias() {
+ AntisenseRnaRegion result = new AntisenseRnaRegion();
result.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
result.setName(name);
result.setSize(size);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
similarity index 80%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
index 200e0d5882..bd53e231ea 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
+import lcsb.mapviewer.model.map.species.Chemical;
/**
* Class representing chemical in the model.
@@ -8,7 +8,7 @@ import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
* @author Piotr Gawron
*
*/
-public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
+public abstract class CellDesignerChemical<T extends Chemical> extends CellDesignerSpecies<T> {
/**
*
@@ -43,10 +43,10 @@ public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
* @param species
* original species from which this chemical will be created
*/
- public Chemical(Species<?> species) {
+ public CellDesignerChemical(CellDesignerSpecies<?> species) {
super(species);
- if (species instanceof Chemical) {
- Chemical<?> chemical = (Chemical<?>) species;
+ if (species instanceof CellDesignerChemical) {
+ CellDesignerChemical<?> chemical = (CellDesignerChemical<?>) species;
this.smiles = chemical.smiles;
this.inChI = chemical.inChI;
this.inChIKey = chemical.inChIKey;
@@ -56,7 +56,7 @@ public abstract class Chemical<T extends ChemicalAlias> extends Species<T> {
/**
* Default constructor.
*/
- public Chemical() {
+ public CellDesignerChemical() {
super();
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
similarity index 64%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
index bd710e3e22..93bfaf9a7e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartment.java
@@ -6,7 +6,7 @@ import java.util.Set;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
/**
* This class describes compartment element in the model.
@@ -14,7 +14,7 @@ import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
* @author Piotr Gawron
*
*/
-public class Compartment extends Element<CompartmentAlias> implements Comparable<Compartment> {
+public class CellDesignerCompartment extends CellDesignerElement<Compartment> implements Comparable<CellDesignerCompartment> {
/**
*
@@ -25,7 +25,7 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Compartment.class);
+ private static Logger logger = Logger.getLogger(CellDesignerCompartment.class);
/**
* Identifier of the compartment. Unique in the model
@@ -35,7 +35,7 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
/**
* List of agregated elements.
*/
- private Set<Element<?>> elements = new HashSet<>();
+ private Set<CellDesignerElement<?>> elements = new HashSet<>();
/**
* Default constructor with identifier given as a parameter.
@@ -43,14 +43,14 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
* @param id
* identifier of the compartment
*/
- public Compartment(String id) {
+ public CellDesignerCompartment(String id) {
compartmentId = id;
}
/**
* Default constructor.
*/
- public Compartment() {
+ public CellDesignerCompartment() {
super();
}
@@ -61,16 +61,16 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
* @param compartment
* object which is used for data intialization
*/
- public Compartment(Compartment compartment) {
+ public CellDesignerCompartment(CellDesignerCompartment compartment) {
super(compartment);
setElementId(compartment.getElementId());
- for (Element<?> element : compartment.getElements()) {
+ for (CellDesignerElement<?> element : compartment.getElements()) {
addElement(element.copy());
}
}
@Override
- public int compareTo(Compartment param) {
+ public int compareTo(CellDesignerCompartment param) {
if (param == null) {
return -1;
}
@@ -88,11 +88,11 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
if (this == param) {
return true;
}
- if (!(param instanceof Compartment)) {
+ if (!(param instanceof CellDesignerCompartment)) {
return false;
}
- return compareTo((Compartment) param) == 0;
+ return compareTo((CellDesignerCompartment) param) == 0;
}
@Override
@@ -102,11 +102,11 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
}
@Override
- public Compartment copy() {
- if (this.getClass() != Compartment.class) {
+ public CellDesignerCompartment copy() {
+ if (this.getClass() != CellDesignerCompartment.class) {
throw new NotImplementedException("this method should be overloaded");
}
- return new Compartment(this);
+ return new CellDesignerCompartment(this);
}
@Override
@@ -130,7 +130,7 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
* @param element
* element to add
*/
- public void addElement(Element<?> element) {
+ public void addElement(CellDesignerElement<?> element) {
elements.add(element);
element.setParent(this);
}
@@ -139,13 +139,13 @@ public class Compartment extends Element<CompartmentAlias> implements Comparable
*
* @return {@link #elements}
*/
- public Set<Element<?>> getElements() {
+ public Set<CellDesignerElement<?>> getElements() {
return elements;
}
@Override
- public CompartmentAlias createAlias(String aliasId) {
- CompartmentAlias result = new CompartmentAlias(aliasId);
+ public Compartment createAlias(String aliasId) {
+ Compartment result = new Compartment(aliasId);
super.setAliasFields(result);
if (elements.size() > 0) {
throw new NotImplementedException();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartmentComparator.java
similarity index 71%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartmentComparator.java
index 0034469773..5cc8147618 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerCompartmentComparator.java
@@ -10,10 +10,10 @@ import lcsb.mapviewer.common.exception.InvalidClassException;
*
* @author Piotr Gawron
*
- * @see Compartment
+ * @see CellDesignerCompartment
*
*/
-public class CompartmentComparator implements Comparator<Compartment> {
+public class CellDesignerCompartmentComparator implements Comparator<CellDesignerCompartment> {
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class CompartmentComparator implements Comparator<Compartment> {
* @param epsilon
* {@link #epsilon}
*/
- public CompartmentComparator(double epsilon) {
+ public CellDesignerCompartmentComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public CompartmentComparator() {
+ public CellDesignerCompartmentComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Compartment arg0, Compartment arg1) {
+ public int compare(CellDesignerCompartment arg0, CellDesignerCompartment arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class CompartmentComparator implements Comparator<Compartment> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Compartment.class)) {
+ if (arg0.getClass().equals(CellDesignerCompartment.class)) {
return internalCompare(arg0, arg1);
} else {
throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class CompartmentComparator implements Comparator<Compartment> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(Compartment arg0, Compartment arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
+ private int internalCompare(CellDesignerCompartment arg0, CellDesignerCompartment arg1) {
+ CellDesignerElementComparator elementComparator = new CellDesignerElementComparator(epsilon);
int result = elementComparator.internalCompare(arg0, arg1);
if (result != 0) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
similarity index 59%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
index 2da11f9215..a4458341b8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
@@ -7,7 +7,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
/**
* Class representing complex in the model.
@@ -15,7 +15,7 @@ import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
* @author Piotr Gawron
*
*/
-public class ComplexSpecies extends Species<ComplexAlias> {
+public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
/**
*
@@ -25,12 +25,12 @@ public class ComplexSpecies extends Species<ComplexAlias> {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ComplexSpecies.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesignerComplexSpecies.class.getName());
/**
* Elements that exists in this complex.
*/
- private Set<Element<?>> elements = new HashSet<>();
+ private Set<CellDesignerElement<?>> elements = new HashSet<>();
/**
* State of the complex species.
@@ -40,7 +40,7 @@ public class ComplexSpecies extends Species<ComplexAlias> {
/**
* Default constructor.
*/
- public ComplexSpecies() {
+ public CellDesignerComplexSpecies() {
super();
}
@@ -51,12 +51,12 @@ public class ComplexSpecies extends Species<ComplexAlias> {
* @param original
* object used for initializing data
*/
- public ComplexSpecies(Species<?> original) {
+ public CellDesignerComplexSpecies(CellDesignerSpecies<?> original) {
super(original);
- if (original instanceof ComplexSpecies) {
- ComplexSpecies complex = (ComplexSpecies) original;
+ if (original instanceof CellDesignerComplexSpecies) {
+ CellDesignerComplexSpecies complex = (CellDesignerComplexSpecies) original;
structuralState = complex.getStructuralState();
- for (Element<?> element : complex.getElements()) {
+ for (CellDesignerElement<?> element : complex.getElements()) {
addElement(element.copy());
}
}
@@ -66,16 +66,16 @@ public class ComplexSpecies extends Species<ComplexAlias> {
* Constructor with species id.
*
* @param complexId
- * {@link Species#idSpecies}
+ * {@link CellDesignerSpecies#idSpecies}
*/
- public ComplexSpecies(String complexId) {
+ public CellDesignerComplexSpecies(String complexId) {
super(complexId);
}
@Override
- public ComplexSpecies copy() {
- if (this.getClass() == ComplexSpecies.class) {
- return new ComplexSpecies(this);
+ public CellDesignerComplexSpecies copy() {
+ if (this.getClass() == CellDesignerComplexSpecies.class) {
+ return new CellDesignerComplexSpecies(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -92,10 +92,10 @@ public class ComplexSpecies extends Species<ComplexAlias> {
* @param element
* object to add
*/
- public void addElement(Element<?> element) {
- if (element instanceof Species) {
- for (Element<?> el : elements) {
- if (el instanceof Species) {
+ public void addElement(CellDesignerElement<?> element) {
+ if (element instanceof CellDesignerSpecies) {
+ for (CellDesignerElement<?> el : elements) {
+ if (el instanceof CellDesignerSpecies) {
if (el.getElementId().equals(element.getElementId())) {
throw new InvalidArgumentException("Cannot add two species with the same id: " + el.getElementId());
}
@@ -110,13 +110,13 @@ public class ComplexSpecies extends Species<ComplexAlias> {
*
* @return list of all elements in the complex.
*/
- public Set<Species<?>> getAllSimpleChildren() {
- Set<Species<?>> result = new HashSet<>();
- for (Element<?> element : getElements()) {
- if (element instanceof ComplexSpecies) {
- result.addAll(((ComplexSpecies) element).getAllSimpleChildren());
- } else if (element instanceof Species) {
- result.add((Species<?>) element);
+ public Set<CellDesignerSpecies<?>> getAllSimpleChildren() {
+ Set<CellDesignerSpecies<?>> result = new HashSet<>();
+ for (CellDesignerElement<?> element : getElements()) {
+ if (element instanceof CellDesignerComplexSpecies) {
+ result.addAll(((CellDesignerComplexSpecies) element).getAllSimpleChildren());
+ } else if (element instanceof CellDesignerSpecies) {
+ result.add((CellDesignerSpecies<?>) element);
}
}
return result;
@@ -146,7 +146,7 @@ public class ComplexSpecies extends Species<ComplexAlias> {
* @return the elements
* @see #elements
*/
- public Set<Element<?>> getElements() {
+ public Set<CellDesignerElement<?>> getElements() {
return elements;
}
@@ -155,12 +155,12 @@ public class ComplexSpecies extends Species<ComplexAlias> {
* the elements to set
* @see #elements
*/
- public void setElements(Set<Element<?>> elements) {
+ public void setElements(Set<CellDesignerElement<?>> elements) {
this.elements = elements;
}
- public ComplexAlias createAlias(String aliasId) {
- ComplexAlias result = new ComplexAlias(aliasId);
+ public Complex createAlias(String aliasId) {
+ Complex result = new Complex(aliasId);
super.setAliasFields(result);
if (elements.size() > 0) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpeciesComparator.java
similarity index 69%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpeciesComparator.java
index bf2c6f38dd..d0b0c10207 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpeciesComparator.java
@@ -15,11 +15,11 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
+public class CellDesignerComplexSpeciesComparator implements Comparator<CellDesignerComplexSpecies> {
/**
* Default class logger.
*/
- private Logger logger = Logger.getLogger(ComplexSpeciesComparator.class);
+ private Logger logger = Logger.getLogger(CellDesignerComplexSpeciesComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -32,19 +32,19 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
* @param epsilon
* {@link #epsilon}
*/
- public ComplexSpeciesComparator(double epsilon) {
+ public CellDesignerComplexSpeciesComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public ComplexSpeciesComparator() {
+ public CellDesignerComplexSpeciesComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(ComplexSpecies arg0, ComplexSpecies arg1) {
+ public int compare(CellDesignerComplexSpecies arg0, CellDesignerComplexSpecies arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -56,7 +56,7 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(ComplexSpecies.class)) {
+ if (arg0.getClass().equals(CellDesignerComplexSpecies.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -78,10 +78,10 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(ComplexSpecies arg0, ComplexSpecies arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
+ private int internalCompare(CellDesignerComplexSpecies arg0, CellDesignerComplexSpecies arg1) {
+ CellDesignerElementComparator elementComparator = new CellDesignerElementComparator(epsilon);
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
@@ -105,12 +105,12 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
}
- for (Element<?> element : arg0.getElements()) {
+ for (CellDesignerElement<?> element : arg0.getElements()) {
boolean found = false;
- if (element instanceof Species) {
- for (Element<?> element1 : arg1.getElements()) {
- if (element1 instanceof Species) {
+ if (element instanceof CellDesignerSpecies) {
+ for (CellDesignerElement<?> element1 : arg1.getElements()) {
+ if (element1 instanceof CellDesignerSpecies) {
if (element.getElementId().equals(element1.getElementId())) {
if (elementComparator.compare(element, element1) != 0) {
logger.debug("Species different: " + element.getElementId());
@@ -122,9 +122,9 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
}
}
- } else if (element instanceof Compartment) {
- for (Element<?> element1 : arg1.getElements()) {
- if (element1 instanceof Compartment) {
+ } else if (element instanceof CellDesignerCompartment) {
+ for (CellDesignerElement<?> element1 : arg1.getElements()) {
+ if (element1 instanceof CellDesignerCompartment) {
if (element.getElementId().equals(element1.getElementId())) {
if (elementComparator.compare(element, element1) != 0) {
logger.debug("Compartment different: " + element.getElementId());
@@ -139,9 +139,9 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
throw new NotImplementedException("Don't know how to compare: " + element.getClass());
}
if (!found) {
- if (element instanceof Species) {
+ if (element instanceof CellDesignerSpecies) {
logger.debug("Cannot find element: " + element.getElementId() + " in:");
- for (Element<?> el : arg1.getElements()) {
+ for (CellDesignerElement<?> el : arg1.getElements()) {
logger.debug(el.getElementId());
}
}
@@ -149,12 +149,12 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
}
}
- for (Element<?> element : arg1.getElements()) {
+ for (CellDesignerElement<?> element : arg1.getElements()) {
boolean found = false;
- if (element instanceof Species) {
- for (Element<?> element1 : arg0.getElements()) {
- if (element1 instanceof Species) {
+ if (element instanceof CellDesignerSpecies) {
+ for (CellDesignerElement<?> element1 : arg0.getElements()) {
+ if (element1 instanceof CellDesignerSpecies) {
if (element.getElementId().equals(element1.getElementId())) {
if (elementComparator.compare(element, element1) == 0) {
found = true;
@@ -163,9 +163,9 @@ public class ComplexSpeciesComparator implements Comparator<ComplexSpecies> {
}
}
- } else if (element instanceof Compartment) {
- for (Element<?> element1 : arg0.getElements()) {
- if (element1 instanceof Compartment) {
+ } else if (element instanceof CellDesignerCompartment) {
+ for (CellDesignerElement<?> element1 : arg0.getElements()) {
+ if (element1 instanceof CellDesignerCompartment) {
if (element.getElementId().equals(element1.getElementId())) {
if (elementComparator.compare(element, element1) == 0) {
found = true;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
similarity index 60%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
index 5d0ef0d4c4..2289b0707f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
+import lcsb.mapviewer.model.map.species.Degraded;
/**
* Class representing degraded objects in the model.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
* @author Piotr Gawron
*
*/
-public class Degraded extends Species<DegradedAlias> {
+public class CellDesignerDegraded extends CellDesignerSpecies<Degraded> {
/**
*
@@ -22,20 +22,20 @@ public class Degraded extends Species<DegradedAlias> {
* @param species
* parent species from which we want to copy data
*/
- public Degraded(Species species) {
+ public CellDesignerDegraded(CellDesignerSpecies<?> species) {
super(species);
}
/**
* Default constructor.
*/
- public Degraded() {
+ public CellDesignerDegraded() {
}
@Override
- public Degraded copy() {
- if (this.getClass() == Degraded.class) {
- return new Degraded(super.copy());
+ public CellDesignerDegraded copy() {
+ if (this.getClass() == CellDesignerDegraded.class) {
+ return new CellDesignerDegraded(super.copy());
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -47,8 +47,8 @@ public class Degraded extends Species<DegradedAlias> {
}
@Override
- public DegradedAlias createAlias(String aliasId) {
- DegradedAlias result = new DegradedAlias(aliasId);
+ public Degraded createAlias(String aliasId) {
+ Degraded result = new Degraded(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegradedComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegradedComparator.java
new file mode 100644
index 0000000000..a5e4b021fe
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegradedComparator.java
@@ -0,0 +1,82 @@
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.Comparator;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class implements comparator interface for Degraded.
+ *
+ * @author Piotr Gawron
+ *
+ * @see CellDesignerDegraded
+ */
+public class CellDesignerDegradedComparator implements Comparator<CellDesignerDegraded> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public CellDesignerDegradedComparator(double epsilon) {
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerDegradedComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public int compare(CellDesignerDegraded arg0, CellDesignerDegraded arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (arg0.getClass().equals(arg1.getClass())) {
+ if (arg0.getClass().equals(CellDesignerDegraded.class)) {
+ return internalCompare(arg0, arg1);
+ } else {
+ throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
+ }
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * This method compares only the fields that are defined in Degraded class in
+ * inheritence tree. It also calls the comparator for super class (Species).
+ *
+ * @param arg0
+ * first object to compare
+ * @param arg1
+ * second object to compare
+ * @return if all fields are qual then returns 0. If they are different then
+ * -1/1 is returned.
+ */
+ private int internalCompare(CellDesignerDegraded arg0, CellDesignerDegraded arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+
+ return 0;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
similarity index 62%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
index b3d86a5568..b0ea4d29f9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
+import lcsb.mapviewer.model.map.species.Drug;
/**
* Class representing drug in the model.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
* @author Piotr Gawron
*
*/
-public class Drug extends Species<DrugAlias> {
+public class CellDesignerDrug extends CellDesignerSpecies<Drug> {
/**
*
@@ -22,20 +22,20 @@ public class Drug extends Species<DrugAlias> {
* @param species
* parent species from which we want to copy data
*/
- public Drug(Species species) {
+ public CellDesignerDrug(CellDesignerSpecies<?> species) {
super(species);
}
/**
* Default constructor.
*/
- public Drug() {
+ public CellDesignerDrug() {
}
@Override
- public Drug copy() {
- if (this.getClass() == Drug.class) {
- return new Drug(this);
+ public CellDesignerDrug copy() {
+ if (this.getClass() == CellDesignerDrug.class) {
+ return new CellDesignerDrug(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -47,8 +47,8 @@ public class Drug extends Species<DrugAlias> {
}
@Override
- public DrugAlias createAlias(String aliasId) {
- DrugAlias result = new DrugAlias(aliasId);
+ public Drug createAlias(String aliasId) {
+ Drug result = new Drug(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrugComparator.java
similarity index 72%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrugComparator.java
index 46522e97af..b79fd9f364 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrugComparator.java
@@ -10,9 +10,9 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
* @author Piotr Gawron
*
- * @see Drug
+ * @see CellDesignerDrug
*/
-public class DrugComparator implements Comparator<Drug> {
+public class CellDesignerDrugComparator implements Comparator<CellDesignerDrug> {
/**
* Epsilon value used for comparison of doubles.
@@ -25,19 +25,19 @@ public class DrugComparator implements Comparator<Drug> {
* @param epsilon
* {@link #epsilon}
*/
- public DrugComparator(double epsilon) {
+ public CellDesignerDrugComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public DrugComparator() {
+ public CellDesignerDrugComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Drug arg0, Drug arg1) {
+ public int compare(CellDesignerDrug arg0, CellDesignerDrug arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -49,7 +49,7 @@ public class DrugComparator implements Comparator<Drug> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Drug.class)) {
+ if (arg0.getClass().equals(CellDesignerDrug.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -70,8 +70,8 @@ public class DrugComparator implements Comparator<Drug> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(Drug arg0, Drug arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerDrug arg0, CellDesignerDrug arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
similarity index 91%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
index fadaa2a653..77aaad3138 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
@@ -11,9 +11,9 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Generic element of the map. It is a root object in inheritence three for
@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.map.model.ModelData;
* @author Piotr Gawron
*
*/
-public abstract class Element<T extends Alias> implements Serializable {
+public abstract class CellDesignerElement<T extends Element> implements Serializable {
/**
*
@@ -37,7 +37,7 @@ public abstract class Element<T extends Alias> implements Serializable {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(Element.class);
+ private static Logger logger = Logger.getLogger(CellDesignerElement.class);
/**
* Notes describing this element.
@@ -82,12 +82,12 @@ public abstract class Element<T extends Alias> implements Serializable {
/**
* Where this element lies on.
*/
- private Compartment parent;
+ private CellDesignerCompartment parent;
/**
* In which complex this element is located.
*/
- private ComplexSpecies complex;
+ private CellDesignerComplexSpecies complex;
/**
* In which model this element is located.
@@ -106,7 +106,7 @@ public abstract class Element<T extends Alias> implements Serializable {
* @param element
* original object from which data should be initialized
*/
- protected Element(Element<?> element) {
+ protected CellDesignerElement(CellDesignerElement<?> element) {
this.parent = element.parent;
this.complex = element.complex;
this.notes = element.notes;
@@ -126,7 +126,7 @@ public abstract class Element<T extends Alias> implements Serializable {
/**
* Default constructor.
*/
- protected Element() {
+ protected CellDesignerElement() {
this.notes = "";
}
@@ -161,7 +161,7 @@ public abstract class Element<T extends Alias> implements Serializable {
*
* @return copy of the object
*/
- public abstract Element<T> copy();
+ public abstract CellDesignerElement<T> copy();
/**
* Adds synonyms to the element.
@@ -259,7 +259,7 @@ public abstract class Element<T extends Alias> implements Serializable {
* @return the parent
* @see #parent
*/
- public Compartment getParent() {
+ public CellDesignerCompartment getParent() {
return parent;
}
@@ -268,7 +268,7 @@ public abstract class Element<T extends Alias> implements Serializable {
* the parent to set
* @see #parent
*/
- public void setParent(Compartment parent) {
+ public void setParent(CellDesignerCompartment parent) {
this.parent = parent;
}
@@ -276,7 +276,7 @@ public abstract class Element<T extends Alias> implements Serializable {
* @return the complex
* @see #complex
*/
- public ComplexSpecies getComplex() {
+ public CellDesignerComplexSpecies getComplex() {
return complex;
}
@@ -285,7 +285,7 @@ public abstract class Element<T extends Alias> implements Serializable {
* the complex to set
* @see #complex
*/
- public void setComplex(ComplexSpecies complex) {
+ public void setComplex(CellDesignerComplexSpecies complex) {
this.complex = complex;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElementComparator.java
similarity index 82%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElementComparator.java
index a1167275a4..d56b62c7bc 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElementComparator.java
@@ -20,11 +20,11 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class ElementComparator implements Comparator<Element<?>> {
+public class CellDesignerElementComparator implements Comparator<CellDesignerElement<?>> {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ElementComparator.class);
+ private static Logger logger = Logger.getLogger(CellDesignerElementComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -37,14 +37,14 @@ public class ElementComparator implements Comparator<Element<?>> {
* @param epsilon
* {@link #epsilon}
*/
- public ElementComparator(double epsilon) {
+ public CellDesignerElementComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public ElementComparator() {
+ public CellDesignerElementComparator() {
this(Configuration.EPSILON);
}
@@ -60,7 +60,7 @@ public class ElementComparator implements Comparator<Element<?>> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- public int internalCompare(Element<?> arg0, Element<?> arg1) {
+ public int internalCompare(CellDesignerElement<?> arg0, CellDesignerElement<?> arg1) {
StringComparator stringComparator = new StringComparator();
if (arg0 == null) {
if (arg1 == null) {
@@ -152,7 +152,7 @@ public class ElementComparator implements Comparator<Element<?>> {
}
@Override
- public int compare(Element<?> arg0, Element<?> arg1) {
+ public int compare(CellDesignerElement<?> arg0, CellDesignerElement<?> arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -164,12 +164,12 @@ public class ElementComparator implements Comparator<Element<?>> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0 instanceof Species) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- return speciesComparator.compare((Species<?>) arg0, (Species<?>) arg1);
- } else if (arg0 instanceof Compartment) {
- CompartmentComparator compartmentComparator = new CompartmentComparator(epsilon);
- return compartmentComparator.compare((Compartment) arg0, (Compartment) arg1);
+ if (arg0 instanceof CellDesignerSpecies) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
+ return speciesComparator.compare((CellDesignerSpecies<?>) arg0, (CellDesignerSpecies<?>) arg1);
+ } else if (arg0 instanceof CellDesignerCompartment) {
+ CellDesignerCompartmentComparator compartmentComparator = new CellDesignerCompartmentComparator(epsilon);
+ return compartmentComparator.compare((CellDesignerCompartment) arg0, (CellDesignerCompartment) arg1);
} else {
throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
similarity index 51%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
index d573c97bc9..aae01214f4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
@@ -4,7 +4,8 @@ import java.util.ArrayList;
import java.util.List;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Gene;
/**
* Class representing gene in the model.
@@ -12,7 +13,7 @@ import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
* @author Piotr Gawron
*
*/
-public class Gene extends Species<GeneAlias> {
+public class CellDesignerGene extends CellDesignerSpecies<Gene> {
/**
*
@@ -22,7 +23,7 @@ public class Gene extends Species<GeneAlias> {
/**
* List of modifications for the Gene.
*/
- private List<ModificationResidue> modificationResidues = new ArrayList<>();
+ private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
/**
* Constructor that initializes gene with the data passed in the argument.
@@ -30,23 +31,23 @@ public class Gene extends Species<GeneAlias> {
* @param species
* original species used for data initialization
*/
- public Gene(Species species) {
+ public CellDesignerGene(CellDesignerSpecies<?> species) {
super(species);
- if (species instanceof Gene) {
- Gene gene = (Gene) species;
- for (ModificationResidue mr : gene.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
+ if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
+ for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
}
}
}
@Override
- public void update(Species species) {
+ public void update(CellDesignerSpecies<?> species) {
super.update(species);
- if (species instanceof Gene) {
- Gene gene = (Gene) species;
+ if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
- for (ModificationResidue mr : gene.getModificationResidues()) {
+ for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
addModificationResidue(mr);
}
}
@@ -55,14 +56,14 @@ public class Gene extends Species<GeneAlias> {
/**
* Default constructor.
*/
- public Gene() {
+ public CellDesignerGene() {
super();
}
@Override
- public Gene copy() {
- if (this.getClass() == Gene.class) {
- return new Gene(this);
+ public CellDesignerGene copy() {
+ if (this.getClass() == CellDesignerGene.class) {
+ return new CellDesignerGene(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -79,8 +80,8 @@ public class Gene extends Species<GeneAlias> {
* @param modificationResidue
* modifiaction to add
*/
- public void addModificationResidue(ModificationResidue modificationResidue) {
- for (ModificationResidue mr : modificationResidues) {
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
mr.update(modificationResidue);
return;
@@ -95,7 +96,7 @@ public class Gene extends Species<GeneAlias> {
* @return the modificationResidues
* @see #modificationResidues
*/
- public List<ModificationResidue> getModificationResidues() {
+ public List<CellDesignerModificationResidue> getModificationResidues() {
return modificationResidues;
}
@@ -104,15 +105,15 @@ public class Gene extends Species<GeneAlias> {
* the modificationResidues to set
* @see #modificationResidues
*/
- public void setModificationResidues(List<ModificationResidue> modificationResidues) {
+ public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
this.modificationResidues = modificationResidues;
}
@Override
- public GeneAlias createAlias(String aliasId) {
- GeneAlias result = new GeneAlias(aliasId);
+ public Gene createAlias(String aliasId) {
+ Gene result = new Gene(aliasId);
super.setAliasFields(result);
- for (ModificationResidue mr : modificationResidues) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
result.addModificationResidue(mr.createModificationResidueAlias());
}
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGeneComparator.java
similarity index 67%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGeneComparator.java
index 9f5ea4b31c..8e051533ed 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGeneComparator.java
@@ -7,15 +7,16 @@ import java.util.Set;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
/**
* This class implements comparator interface for Gene.
*
* @author Piotr Gawron
*
- * @see Gene
+ * @see CellDesignerGene
*/
-public class GeneComparator implements Comparator<Gene> {
+public class CellDesignerGeneComparator implements Comparator<CellDesignerGene> {
/**
* Epsilon value used for comparison of doubles.
@@ -28,19 +29,19 @@ public class GeneComparator implements Comparator<Gene> {
* @param epsilon
* {@link #epsilon}
*/
- public GeneComparator(double epsilon) {
+ public CellDesignerGeneComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public GeneComparator() {
+ public CellDesignerGeneComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Gene arg0, Gene arg1) {
+ public int compare(CellDesignerGene arg0, CellDesignerGene arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -52,7 +53,7 @@ public class GeneComparator implements Comparator<Gene> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Gene.class)) {
+ if (arg0.getClass().equals(CellDesignerGene.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -65,7 +66,7 @@ public class GeneComparator implements Comparator<Gene> {
/**
* This method compares only the fields that are defined in Gene class in
* inheritence tree. It also calls the comparator for the super class (
- * {@link Species}): {@link SpeciesComparator}.
+ * {@link CellDesignerSpecies}): {@link CellDesignerSpeciesComparator}.
*
* @param arg0
* first object to compare
@@ -74,8 +75,8 @@ public class GeneComparator implements Comparator<Gene> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(Gene arg0, Gene arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerGene arg0, CellDesignerGene arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
@@ -86,11 +87,11 @@ public class GeneComparator implements Comparator<Gene> {
Set<String> set1 = new HashSet<String>();
Set<String> set2 = new HashSet<String>();
- for (ModificationResidue region : arg0.getModificationResidues()) {
+ for (CellDesignerModificationResidue region : arg0.getModificationResidues()) {
set1.add(region.toString());
}
- for (ModificationResidue region : arg1.getModificationResidues()) {
+ for (CellDesignerModificationResidue region : arg1.getModificationResidues()) {
set2.add(region.toString());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
similarity index 51%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
index 54ba04d6a5..562f55a0e5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
/**
* Generic protein.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
* @author Piotr Gawron
*
*/
-public class GenericProtein extends Protein<GenericProteinAlias> {
+public class CellDesignerGenericProtein extends CellDesignerProtein<GenericProtein> {
/**
*
@@ -19,7 +19,7 @@ public class GenericProtein extends Protein<GenericProteinAlias> {
/**
* Default constructor.
*/
- public GenericProtein() {
+ public CellDesignerGenericProtein() {
super();
}
@@ -29,25 +29,25 @@ public class GenericProtein extends Protein<GenericProteinAlias> {
* @param species
* original species
*/
- public GenericProtein(Species<?> species) {
+ public CellDesignerGenericProtein(CellDesignerSpecies<?> species) {
super(species);
}
- public GenericProtein(String id) {
+ public CellDesignerGenericProtein(String id) {
setElementId(id);
}
@Override
- public GenericProtein copy() {
- if (this.getClass().equals(GenericProtein.class)) {
- return new GenericProtein(this);
+ public CellDesignerGenericProtein copy() {
+ if (this.getClass().equals(CellDesignerGenericProtein.class)) {
+ return new CellDesignerGenericProtein(this);
} else {
throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
}
}
- public GenericProteinAlias createAlias(String aliasId) {
- GenericProteinAlias result = new GenericProteinAlias(aliasId);
+ public GenericProtein createAlias(String aliasId) {
+ GenericProtein result = new GenericProtein(aliasId);
super.setAliasFields(result);
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
similarity index 63%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
index 7fc1abda1d..568bc61f13 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIon.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
+import lcsb.mapviewer.model.map.species.Ion;
/**
* Class representing ion in the model.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.IonAlias;
* @author Piotr Gawron
*
*/
-public class Ion extends Chemical<IonAlias> {
+public class CellDesignerIon extends CellDesignerChemical<Ion> {
/**
*
@@ -22,21 +22,21 @@ public class Ion extends Chemical<IonAlias> {
* @param species
* original species used for data initialization
*/
- public Ion(Species species) {
+ public CellDesignerIon(CellDesignerSpecies<?> species) {
super(species);
}
/**
* Default constructor.
*/
- public Ion() {
+ public CellDesignerIon() {
super();
}
@Override
- public Ion copy() {
- if (this.getClass() == Ion.class) {
- return new Ion(this);
+ public CellDesignerIon copy() {
+ if (this.getClass() == CellDesignerIon.class) {
+ return new CellDesignerIon(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -48,8 +48,8 @@ public class Ion extends Chemical<IonAlias> {
}
@Override
- public IonAlias createAlias(String aliasId) {
- IonAlias result = new IonAlias(aliasId);
+ public Ion createAlias(String aliasId) {
+ Ion result = new Ion(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
similarity index 51%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
index 9bfe21e7d8..d73d22cf5f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
/**
* Ion channel protein.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
* @author Piotr Gawron
*
*/
-public class IonChannelProtein extends Protein<IonChannelProteinAlias> {
+public class CellDesignerIonChannelProtein extends CellDesignerProtein<IonChannelProtein> {
/**
*
@@ -19,7 +19,7 @@ public class IonChannelProtein extends Protein<IonChannelProteinAlias> {
/**
* Default constructor.
*/
- public IonChannelProtein() {
+ public CellDesignerIonChannelProtein() {
super();
}
@@ -29,22 +29,22 @@ public class IonChannelProtein extends Protein<IonChannelProteinAlias> {
* @param species
* original species
*/
- public IonChannelProtein(Species species) {
+ public CellDesignerIonChannelProtein(CellDesignerSpecies<?> species) {
super(species);
}
@Override
- public IonChannelProtein copy() {
- if (this.getClass().equals(IonChannelProtein.class)) {
- return new IonChannelProtein(this);
+ public CellDesignerIonChannelProtein copy() {
+ if (this.getClass().equals(CellDesignerIonChannelProtein.class)) {
+ return new CellDesignerIonChannelProtein(this);
} else {
throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
}
}
@Override
- public IonChannelProteinAlias createAlias(String aliasId) {
- IonChannelProteinAlias result = new IonChannelProteinAlias(aliasId);
+ public IonChannelProtein createAlias(String aliasId) {
+ IonChannelProtein result = new IonChannelProtein(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonComparator.java
similarity index 62%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonComparator.java
index b0a691dc86..528dc4b2ed 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonComparator.java
@@ -2,23 +2,17 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
-import org.apache.log4j.Logger;
-
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
/**
- * This class implements comparator interface for Phenotype.
+ * This class implements comparator interface for Ion.
*
* @author Piotr Gawron
*
- * @see Phenotype
+ * @see CellDesignerIon
*/
-public class PhenotypeComparator implements Comparator<Phenotype> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PhenotypeComparator.class);
+public class CellDesignerIonComparator implements Comparator<CellDesignerIon> {
/**
* Epsilon value used for comparison of doubles.
@@ -31,19 +25,19 @@ public class PhenotypeComparator implements Comparator<Phenotype> {
* @param epsilon
* {@link #epsilon}
*/
- public PhenotypeComparator(double epsilon) {
+ public CellDesignerIonComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public PhenotypeComparator() {
+ public CellDesignerIonComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Phenotype arg0, Phenotype arg1) {
+ public int compare(CellDesignerIon arg0, CellDesignerIon arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -55,7 +49,7 @@ public class PhenotypeComparator implements Comparator<Phenotype> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Phenotype.class)) {
+ if (arg0.getClass().equals(CellDesignerIon.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -66,9 +60,9 @@ public class PhenotypeComparator implements Comparator<Phenotype> {
}
/**
- * This method compares only the fields that are defined in {@link Phenotype}
- * class in inheritence tree. It also calls the {@link SpeciesComparator} for
- * the super class ( {@link Species}).
+ * This method compares only the fields that are defined in {@link CellDesignerIon} class
+ * in inheritence tree. It also calls the {@link CellDesignerSpeciesComparator} for the
+ * super class ( {@link CellDesignerSpecies}).
*
* @param arg0
* first object to compare
@@ -77,13 +71,12 @@ public class PhenotypeComparator implements Comparator<Phenotype> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(Phenotype arg0, Phenotype arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerIon arg0, CellDesignerIon arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
-
return 0;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
similarity index 60%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
index ddb9639f1c..625a4f16b6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
+import lcsb.mapviewer.model.map.species.Phenotype;
/**
* Class representing phenotype in the model.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
* @author Piotr Gawron
*
*/
-public class Phenotype extends Species<PhenotypeAlias> {
+public class CellDesignerPhenotype extends CellDesignerSpecies<Phenotype> {
/**
*
@@ -23,20 +23,20 @@ public class Phenotype extends Species<PhenotypeAlias> {
* @param species
* original species used for data initialization
*/
- public Phenotype(Species species) {
+ public CellDesignerPhenotype(CellDesignerSpecies<?> species) {
super(species);
}
/**
* Default constructor.
*/
- public Phenotype() {
+ public CellDesignerPhenotype() {
}
@Override
- public Phenotype copy() {
- if (this.getClass() == Phenotype.class) {
- return new Phenotype(this);
+ public CellDesignerPhenotype copy() {
+ if (this.getClass() == CellDesignerPhenotype.class) {
+ return new CellDesignerPhenotype(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -48,8 +48,8 @@ public class Phenotype extends Species<PhenotypeAlias> {
}
@Override
- public PhenotypeAlias createAlias(String aliasId) {
- PhenotypeAlias result = new PhenotypeAlias(aliasId);
+ public Phenotype createAlias(String aliasId) {
+ Phenotype result = new Phenotype(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotypeComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotypeComparator.java
new file mode 100644
index 0000000000..e49f8cbb7f
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotypeComparator.java
@@ -0,0 +1,91 @@
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.Comparator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class implements comparator interface for Phenotype.
+ *
+ * @author Piotr Gawron
+ *
+ * @see CellDesignerPhenotype
+ */
+public class CellDesignerPhenotypeComparator implements Comparator<CellDesignerPhenotype> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(CellDesignerPhenotypeComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public CellDesignerPhenotypeComparator(double epsilon) {
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerPhenotypeComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public int compare(CellDesignerPhenotype arg0, CellDesignerPhenotype arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (arg0.getClass().equals(arg1.getClass())) {
+ if (arg0.getClass().equals(CellDesignerPhenotype.class)) {
+ return internalCompare(arg0, arg1);
+ } else {
+ throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
+ }
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * This method compares only the fields that are defined in {@link CellDesignerPhenotype}
+ * class in inheritence tree. It also calls the {@link CellDesignerSpeciesComparator} for
+ * the super class ( {@link CellDesignerSpecies}).
+ *
+ * @param arg0
+ * first object to compare
+ * @param arg1
+ * second object to compare
+ * @return if all fields are qual then returns 0. If they are different then
+ * -1/1 is returned.
+ */
+ private int internalCompare(CellDesignerPhenotype arg0, CellDesignerPhenotype arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
+ int result = speciesComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+
+ return 0;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
similarity index 61%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index afecc5eb38..4e94d37da3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -6,7 +6,8 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Protein;
/**
* Class representing protein in the model.
@@ -14,7 +15,7 @@ import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
* @author Piotr Gawron
*
*/
-public class Protein<T extends ProteinAlias> extends Species<T> {
+public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<T> {
/**
*
*/
@@ -23,7 +24,7 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(Protein.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesignerProtein.class.getName());
/**
* State of the protein.
@@ -33,7 +34,7 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
/**
* List of modifications for the Protein.
*/
- private List<ModificationResidue> modificationResidues = new ArrayList<ModificationResidue>();
+ private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<CellDesignerModificationResidue>();
/**
* Constructor that initializes protein with the data passed in the argument.
@@ -41,28 +42,28 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
* @param species
* original species used for data initialization
*/
- public Protein(Species<?> species) {
+ public CellDesignerProtein(CellDesignerSpecies<?> species) {
super(species);
- if (species instanceof Protein) {
- Protein<?> protein = (Protein) species;
+ if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
if (protein.getStructuralState() != null) {
setStructuralState(new String(protein.getStructuralState()));
}
- for (ModificationResidue mr : protein.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
+ for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
}
}
}
@Override
- public void update(Species<?> species) {
+ public void update(CellDesignerSpecies<?> species) {
super.update(species);
- if (species instanceof Protein) {
- Protein<?> protein = (Protein) species;
+ if (species instanceof CellDesignerProtein) {
+ CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
if (getStructuralState() == null || getStructuralState().equals("")) {
setStructuralState(protein.getStructuralState());
}
- for (ModificationResidue mr : protein.getModificationResidues()) {
+ for (CellDesignerModificationResidue mr : protein.getModificationResidues()) {
addModificationResidue(mr);
}
}
@@ -71,14 +72,14 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
/**
* Default constructor.
*/
- public Protein() {
+ public CellDesignerProtein() {
super();
}
@Override
- public Protein copy() {
- if (this.getClass().equals(Protein.class)) {
- return new Protein(this);
+ public CellDesignerProtein<T> copy() {
+ if (this.getClass().equals(CellDesignerProtein.class)) {
+ return new CellDesignerProtein<T>(this);
} else {
throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
}
@@ -95,8 +96,8 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
* @param modificationResidue
* modification to add
*/
- public void addModificationResidue(ModificationResidue modificationResidue) {
- for (ModificationResidue mr : modificationResidues) {
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
mr.update(modificationResidue);
return;
@@ -130,7 +131,7 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
* @return the modificationResidues
* @see #modificationResidues
*/
- public List<ModificationResidue> getModificationResidues() {
+ public List<CellDesignerModificationResidue> getModificationResidues() {
return modificationResidues;
}
@@ -139,7 +140,7 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
* the modificationResidues to set
* @see #modificationResidues
*/
- public void setModificationResidues(List<ModificationResidue> modificationResidues) {
+ public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
this.modificationResidues = modificationResidues;
}
@@ -152,7 +153,7 @@ public class Protein<T extends ProteinAlias> extends Species<T> {
protected void setAliasFields(T result) {
super.setAliasFields(result);
result.setStructuralState(structuralState);
- for (ModificationResidue mr : modificationResidues) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
result.addModificationResidue(mr.createModificationResidueAlias());
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProteinComparator.java
similarity index 70%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProteinComparator.java
index 0c3f33d7f0..681761fd54 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProteinComparator.java
@@ -10,19 +10,20 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
/**
* This class implements comparator interface for Protein.
*
* @author Piotr Gawron
*
- * @see Protein
+ * @see CellDesignerProtein
*/
-public class ProteinComparator implements Comparator<Protein<?>> {
+public class CellDesignerProteinComparator implements Comparator<CellDesignerProtein<?>> {
/**
* Default class logger.
*/
- private Logger logger = Logger.getLogger(ProteinComparator.class);
+ private Logger logger = Logger.getLogger(CellDesignerProteinComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -35,19 +36,19 @@ public class ProteinComparator implements Comparator<Protein<?>> {
* @param epsilon
* {@link #epsilon}
*/
- public ProteinComparator(double epsilon) {
+ public CellDesignerProteinComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public ProteinComparator() {
+ public CellDesignerProteinComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Protein arg0, Protein arg1) {
+ public int compare(CellDesignerProtein<?> arg0, CellDesignerProtein<?> arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -66,9 +67,9 @@ public class ProteinComparator implements Comparator<Protein<?>> {
}
/**
- * This method compares only the fields that are defined in {@link Protein}
- * class in inheritence tree. It also calls the {@link SpeciesComparator} for
- * the super class ( {@link Species}).
+ * This method compares only the fields that are defined in {@link CellDesignerProtein}
+ * class in inheritence tree. It also calls the {@link CellDesignerSpeciesComparator} for
+ * the super class ( {@link CellDesignerSpecies}).
*
* @param arg0
* first object to compare
@@ -77,8 +78,8 @@ public class ProteinComparator implements Comparator<Protein<?>> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(Protein<?> arg0, Protein<?> arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerProtein<?> arg0, CellDesignerProtein<?> arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
@@ -101,11 +102,11 @@ public class ProteinComparator implements Comparator<Protein<?>> {
Set<String> set1 = new HashSet<String>();
Set<String> set2 = new HashSet<String>();
- for (ModificationResidue region : arg0.getModificationResidues()) {
+ for (CellDesignerModificationResidue region : arg0.getModificationResidues()) {
set1.add(region.toString());
}
- for (ModificationResidue region : arg1.getModificationResidues()) {
+ for (CellDesignerModificationResidue region : arg1.getModificationResidues()) {
set2.add(region.toString());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
similarity index 52%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
index a3cb1b0446..8473383ecd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
/**
* Receptor protein.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
* @author Piotr Gawron
*
*/
-public class ReceptorProtein extends Protein<ReceptorProteinAlias> {
+public class CellDesignerReceptorProtein extends CellDesignerProtein<ReceptorProtein> {
/**
*
@@ -19,7 +19,7 @@ public class ReceptorProtein extends Protein<ReceptorProteinAlias> {
/**
* Default constructor.
*/
- public ReceptorProtein() {
+ public CellDesignerReceptorProtein() {
super();
}
@@ -29,22 +29,22 @@ public class ReceptorProtein extends Protein<ReceptorProteinAlias> {
* @param species
* original species
*/
- public ReceptorProtein(Species species) {
+ public CellDesignerReceptorProtein(CellDesignerSpecies<?> species) {
super(species);
}
@Override
- public ReceptorProtein copy() {
- if (this.getClass().equals(ReceptorProtein.class)) {
- return new ReceptorProtein(this);
+ public CellDesignerReceptorProtein copy() {
+ if (this.getClass().equals(CellDesignerReceptorProtein.class)) {
+ return new CellDesignerReceptorProtein(this);
} else {
throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
}
}
@Override
- public ReceptorProteinAlias createAlias(String aliasId) {
- ReceptorProteinAlias result = new ReceptorProteinAlias(aliasId);
+ public ReceptorProtein createAlias(String aliasId) {
+ ReceptorProtein result = new ReceptorProtein(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
similarity index 53%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index 95ad0b3e7f..4a59e2bc09 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -6,7 +6,7 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.species.Rna;
/**
* Class representing rna in the model.
@@ -14,7 +14,7 @@ import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
* @author Piotr Gawron
*
*/
-public class Rna extends Species<RnaAlias> {
+public class CellDesignerRna extends CellDesignerSpecies<Rna> {
/**
*
@@ -25,12 +25,12 @@ public class Rna extends Species<RnaAlias> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Rna.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesignerRna.class.getName());
/**
* List of rna regions (some rna sequences) in this object.
*/
- private List<RnaRegion> regions = new ArrayList<>();
+ private List<CellDesignerRnaRegion> regions = new ArrayList<>();
/**
* Constructor that initializes rna with the data passed in the argument.
@@ -38,12 +38,12 @@ public class Rna extends Species<RnaAlias> {
* @param species
* original species used for data initialization
*/
- public Rna(Species species) {
+ public CellDesignerRna(CellDesignerSpecies<?> species) {
super(species);
- if (species instanceof Rna) {
- Rna rna = (Rna) species;
- for (RnaRegion region : rna.getRegions()) {
- addRegion(new RnaRegion(region));
+ if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
+ for (CellDesignerRnaRegion region : rna.getRegions()) {
+ addRegion(new CellDesignerRnaRegion(region));
}
}
}
@@ -51,29 +51,29 @@ public class Rna extends Species<RnaAlias> {
/**
* Default constructor.
*/
- public Rna() {
+ public CellDesignerRna() {
super();
}
@Override
- public Rna copy() {
- if (this.getClass() == Rna.class) {
- return new Rna(this);
+ public CellDesignerRna copy() {
+ if (this.getClass() == CellDesignerRna.class) {
+ return new CellDesignerRna(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
}
@Override
- public void update(Species species) {
+ public void update(CellDesignerSpecies<?> species) {
super.update(species);
- if (species instanceof Rna) {
- Rna rna = (Rna) species;
- for (RnaRegion mr : getRegions()) {
+ if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
+ for (CellDesignerRnaRegion mr : getRegions()) {
mr.setState(null);
}
- for (RnaRegion region : rna.getRegions()) {
+ for (CellDesignerRnaRegion region : rna.getRegions()) {
updateRegion(region);
}
}
@@ -85,14 +85,14 @@ public class Rna extends Species<RnaAlias> {
* @param param
* region that with the data to update
*/
- private void updateRegion(RnaRegion param) {
- for (RnaRegion region : regions) {
+ private void updateRegion(CellDesignerRnaRegion param) {
+ for (CellDesignerRnaRegion region : regions) {
if (region.getIdRnaRegion().equals(param.getIdRnaRegion())) {
region.update(param);
return;
}
}
- addRegion(new RnaRegion(param));
+ addRegion(new CellDesignerRnaRegion(param));
}
@Override
@@ -102,13 +102,13 @@ public class Rna extends Species<RnaAlias> {
/**
* Adds region. If the region with given id exists then the data of this
- * region is copied to the one that is already in the {@link Rna}.
+ * region is copied to the one that is already in the {@link CellDesignerRna}.
*
* @param rnaRegion
* region to add
*/
- public void addRegion(RnaRegion rnaRegion) {
- for (RnaRegion region2 : regions) {
+ public void addRegion(CellDesignerRnaRegion rnaRegion) {
+ for (CellDesignerRnaRegion region2 : regions) {
if (region2.getIdRnaRegion().equals(rnaRegion.getIdRnaRegion())) {
region2.update(rnaRegion);
return;
@@ -124,7 +124,7 @@ public class Rna extends Species<RnaAlias> {
* @return the regions
* @see #regions
*/
- public List<RnaRegion> getRegions() {
+ public List<CellDesignerRnaRegion> getRegions() {
return regions;
}
@@ -133,15 +133,15 @@ public class Rna extends Species<RnaAlias> {
* the regions to set
* @see #regions
*/
- public void setRegions(List<RnaRegion> regions) {
+ public void setRegions(List<CellDesignerRnaRegion> regions) {
this.regions = regions;
}
@Override
- public RnaAlias createAlias(String aliasId) {
- RnaAlias result = new RnaAlias(aliasId);
+ public Rna createAlias(String aliasId) {
+ Rna result = new Rna(aliasId);
super.setAliasFields(result);
- for (RnaRegion region : regions) {
+ for (CellDesignerRnaRegion region : regions) {
result.addRegion(region.createRnaRegionAlias());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRnaComparator.java
similarity index 68%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRnaComparator.java
index d1982ef413..52b674dd77 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRnaComparator.java
@@ -13,9 +13,9 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
* @author Piotr Gawron
*
- * @see Rna
+ * @see CellDesignerRna
*/
-public class RnaComparator implements Comparator<Rna> {
+public class CellDesignerRnaComparator implements Comparator<CellDesignerRna> {
/**
* Epsilon value used for comparison of doubles.
@@ -28,19 +28,19 @@ public class RnaComparator implements Comparator<Rna> {
* @param epsilon
* {@link #epsilon}
*/
- public RnaComparator(double epsilon) {
+ public CellDesignerRnaComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public RnaComparator() {
+ public CellDesignerRnaComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Rna arg0, Rna arg1) {
+ public int compare(CellDesignerRna arg0, CellDesignerRna arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -52,7 +52,7 @@ public class RnaComparator implements Comparator<Rna> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Rna.class)) {
+ if (arg0.getClass().equals(CellDesignerRna.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -63,9 +63,9 @@ public class RnaComparator implements Comparator<Rna> {
}
/**
- * This method compares only the fields that are defined in {@link Rna} class
- * in inheritence tree. It also calls the {@link SpeciesComparator} for the
- * super class ({@link Species}).
+ * This method compares only the fields that are defined in {@link CellDesignerRna} class
+ * in inheritence tree. It also calls the {@link CellDesignerSpeciesComparator} for the
+ * super class ({@link CellDesignerSpecies}).
*
* @param arg0
* first object to compare
@@ -74,8 +74,8 @@ public class RnaComparator implements Comparator<Rna> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(Rna arg0, Rna arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerRna arg0, CellDesignerRna arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
@@ -86,11 +86,11 @@ public class RnaComparator implements Comparator<Rna> {
Set<String> set1 = new HashSet<String>();
Set<String> set2 = new HashSet<String>();
- for (RnaRegion region : arg0.getRegions()) {
+ for (CellDesignerRnaRegion region : arg0.getRegions()) {
set1.add(region.toString());
}
- for (RnaRegion region : arg1.getRegions()) {
+ for (CellDesignerRnaRegion region : arg1.getRegions()) {
set2.add(region.toString());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRnaRegion.java
similarity index 69%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRnaRegion.java
index ee5053a324..b67c6ec919 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRnaRegion.java
@@ -1,33 +1,22 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
/**
* This structure contains information about rna region (rna fragment of
* interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna Rna}.
*
* @author Piotr Gawron
*
*/
-@Entity
-@Table(name = "rna_region_table_new")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class RnaRegionAlias implements Serializable {
+public class CellDesignerRnaRegion implements Serializable {
/**
*
@@ -43,22 +32,14 @@ public class RnaRegionAlias implements Serializable {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaRegionAlias.class.getName());
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
+ private static Logger logger = Logger.getLogger(CellDesignerRnaRegion.class.getName());
/**
* Identifier of the region. Unique in the
* {@link lcsb.mapviewer.model.map.model.Model}.
*/
- @Column(name = "idrnaregion")
private String idRnaRegion = "";
+
/**
* Type of the region in the rna. There are three possible values:
* <ul>
@@ -67,8 +48,6 @@ public class RnaRegionAlias implements Serializable {
* <li>Modification site.</li>
* </ul>
*/
-
- @Column(name = "type")
private String type = "";
/**
@@ -76,38 +55,32 @@ public class RnaRegionAlias implements Serializable {
*
* @see ModificationState
*/
- @Column(name = "state")
private ModificationState state = null;
/**
* Name of the region.
*/
- @Column(name = "name")
private String name = "";
/**
* Size of the region in the graphic representation.
*/
- @Column(name = "size")
private double size = DEFAULT_SIZE;
/**
* Position on the species in graphic representation.
*/
- @Column(name = "pos")
private Double pos;
/**
* Defines a species where the region belongs to.
*/
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb")
- private RnaAlias species;
+ private CellDesignerRna species;
/**
* Default constructor.
*/
- public RnaRegionAlias() {
+ public CellDesignerRnaRegion() {
}
@@ -115,10 +88,9 @@ public class RnaRegionAlias implements Serializable {
* Creates object with the data taken from paramter region.
*
* @param mr
- * original {@link RnaRegionAlias}
+ * original {@link CellDesignerRnaRegion}
*/
- public RnaRegionAlias(RnaRegionAlias mr) {
- this.id = mr.id;
+ public CellDesignerRnaRegion(CellDesignerRnaRegion mr) {
this.idRnaRegion = mr.idRnaRegion;
this.size = mr.size;
setPos(mr.getPos());
@@ -162,9 +134,9 @@ public class RnaRegionAlias implements Serializable {
* region.
*
* @param mr
- * {@link RnaRegionAlias} from which data will be used to update
+ * {@link CellDesignerRnaRegion} from which data will be used to update
*/
- public void update(RnaRegionAlias mr) {
+ public void update(CellDesignerRnaRegion mr) {
if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
throw new InvalidArgumentException("Cannot update from mr with different id");
}
@@ -188,23 +160,6 @@ public class RnaRegionAlias implements Serializable {
}
- /**
- * @return the idRnaRegion
- * @see #idRnaRegion
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the idRnaRegion to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
/**
* @return the id
* @see #id
@@ -311,7 +266,7 @@ public class RnaRegionAlias implements Serializable {
* @return the species
* @see #species
*/
- public RnaAlias getSpecies() {
+ public CellDesignerRna getSpecies() {
return species;
}
@@ -320,8 +275,19 @@ public class RnaRegionAlias implements Serializable {
* the species to set
* @see #species
*/
- public void setSpecies(RnaAlias species) {
+ public void setSpecies(CellDesignerRna species) {
this.species = species;
}
+ public RnaRegion createRnaRegionAlias() {
+ RnaRegion result = new RnaRegion();
+ result.setIdRnaRegion(this.idRnaRegion);
+ result.setSize(this.size);
+ result.setPos(this.getPos());
+ result.setType(this.type);
+ result.setState(this.state);
+ result.setName(this.name);
+ return result;
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
similarity index 56%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
index 75f255eaa8..45521fc3ab 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
@@ -3,7 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
/**
* Class representing molecule in the model.
@@ -11,7 +11,7 @@ import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
* @author Piotr Gawron
*
*/
-public class SimpleMolecule extends Chemical<SimpleMoleculeAlias> {
+public class CellDesignerSimpleMolecule extends CellDesignerChemical<SimpleMolecule> {
/**
*
@@ -22,7 +22,7 @@ public class SimpleMolecule extends Chemical<SimpleMoleculeAlias> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SimpleMolecule.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesignerSimpleMolecule.class.getName());
/**
* Constructor that initializes molecule with the data passed in the argument.
@@ -30,20 +30,20 @@ public class SimpleMolecule extends Chemical<SimpleMoleculeAlias> {
* @param species
* original species used for data initialization
*/
- public SimpleMolecule(Species<?> species) {
+ public CellDesignerSimpleMolecule(CellDesignerSpecies<?> species) {
super(species);
}
/**
* Default constructor.
*/
- public SimpleMolecule() {
+ public CellDesignerSimpleMolecule() {
}
@Override
- public SimpleMolecule copy() {
- if (this.getClass() == SimpleMolecule.class) {
- return new SimpleMolecule(this);
+ public CellDesignerSimpleMolecule copy() {
+ if (this.getClass() == CellDesignerSimpleMolecule.class) {
+ return new CellDesignerSimpleMolecule(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -55,8 +55,8 @@ public class SimpleMolecule extends Chemical<SimpleMoleculeAlias> {
}
@Override
- public SimpleMoleculeAlias createAlias(String aliasId) {
- SimpleMoleculeAlias result = new SimpleMoleculeAlias(aliasId);
+ public SimpleMolecule createAlias(String aliasId) {
+ SimpleMolecule result = new SimpleMolecule(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMoleculeComparator.java
similarity index 72%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMoleculeComparator.java
index bb24f976d6..c6e47e7eee 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMoleculeComparator.java
@@ -13,13 +13,13 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
* @author Piotr Gawron
*
- * @see SimpleMolecule
+ * @see CellDesignerSimpleMolecule
*/
-public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
+public class CellDesignerSimpleMoleculeComparator implements Comparator<CellDesignerSimpleMolecule> {
/**
* Default class logger.
*/
- private Logger logger = Logger.getLogger(SimpleMoleculeComparator.class);
+ private Logger logger = Logger.getLogger(CellDesignerSimpleMoleculeComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -32,19 +32,19 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
* @param epsilon
* {@link #epsilon}
*/
- public SimpleMoleculeComparator(double epsilon) {
+ public CellDesignerSimpleMoleculeComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public SimpleMoleculeComparator() {
+ public CellDesignerSimpleMoleculeComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(SimpleMolecule arg0, SimpleMolecule arg1) {
+ public int compare(CellDesignerSimpleMolecule arg0, CellDesignerSimpleMolecule arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -56,7 +56,7 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(SimpleMolecule.class)) {
+ if (arg0.getClass().equals(CellDesignerSimpleMolecule.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -68,8 +68,8 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
/**
* This method compares only the fields that are defined in
- * {@link SimpleMolecule} class in inheritence tree. It also calls the
- * {@link SpeciesComparator} for the super class ( {@link Species}).
+ * {@link CellDesignerSimpleMolecule} class in inheritence tree. It also calls the
+ * {@link CellDesignerSpeciesComparator} for the super class ( {@link CellDesignerSpecies}).
*
* @param arg0
* first object to compare
@@ -78,8 +78,8 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(SimpleMolecule arg0, SimpleMolecule arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerSimpleMolecule arg0, CellDesignerSimpleMolecule arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
similarity index 91%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
index 0066fb92cc..f776c8f417 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
@@ -5,8 +5,8 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.PositionToCompartment;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
/**
* Generic species of the map.
@@ -14,7 +14,7 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
* @author Piotr Gawron
*
*/
-public class Species<T extends SpeciesAlias> extends Element<T> {
+public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<T> {
/**
*
*/
@@ -23,7 +23,7 @@ public class Species<T extends SpeciesAlias> extends Element<T> {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(Species.class.getName());
+ private static Logger logger = Logger.getLogger(CellDesignerSpecies.class.getName());
/**
* Identifier of the species. It must be unique within the model.
@@ -82,7 +82,7 @@ public class Species<T extends SpeciesAlias> extends Element<T> {
* @param species
* parent species from which we want to copy data
*/
- public Species(Species species) {
+ public CellDesignerSpecies(CellDesignerSpecies<?> species) {
super(species);
this.hypothetical = species.hypothetical;
this.idSpecies = species.idSpecies;
@@ -97,7 +97,7 @@ public class Species<T extends SpeciesAlias> extends Element<T> {
/**
* Default constructor.
*/
- public Species() {
+ public CellDesignerSpecies() {
super();
idSpecies = "";
}
@@ -108,14 +108,14 @@ public class Species<T extends SpeciesAlias> extends Element<T> {
* @param id
* species identifier
*/
- public Species(String id) {
+ public CellDesignerSpecies(String id) {
this();
this.idSpecies = id;
}
@Override
- public Species copy() {
- Species result = new Species(this);
+ public CellDesignerSpecies<T> copy() {
+ CellDesignerSpecies<T> result = new CellDesignerSpecies<T>(this);
result.idSpecies = idSpecies;
result.setNotes(getNotes());
@@ -139,7 +139,7 @@ public class Species<T extends SpeciesAlias> extends Element<T> {
* @param species
* object from which we are updating information
*/
- public void update(Species<?> species) {
+ public void update(CellDesignerSpecies<?> species) {
if (getName() == null || getName().equals("")) {
setName(species.getName());
} else if (!getName().trim().equals(species.getName().trim())) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpeciesComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpeciesComparator.java
new file mode 100644
index 0000000000..2604e8c88f
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpeciesComparator.java
@@ -0,0 +1,231 @@
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.Comparator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.BooleanComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+
+/**
+ * This class implements comparator interface for Species. It calls comparator
+ * implementation for all known subclases of Species class when necessary.
+ *
+ * @author Piotr Gawron
+ *
+ * @see CellDesignerSpecies
+ */
+public class CellDesignerSpeciesComparator implements Comparator<CellDesignerSpecies<?>> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerSpeciesComparator.class);
+
+ /**
+ * Comparator for {@link CellDesignerAntisenseRna}.
+ */
+ private CellDesignerAntisenseRnaComparator antisenseRnaComparator;
+
+ /**
+ * Comparator for {@link CellDesignerComplexSpecies}.
+ */
+ private CellDesignerComplexSpeciesComparator complexSpeciesComparator;
+
+ /**
+ * Comparator for {@link CellDesignerDegraded}.
+ */
+ private CellDesignerDegradedComparator degradedComparator;
+
+ /**
+ * Comparator for {@link CellDesignerDrug}.
+ */
+ private CellDesignerDrugComparator drugComparator;
+
+ /**
+ * Comparator for {@link CellDesignerGene}.
+ */
+ private CellDesignerGeneComparator geneComparator;
+
+ /**
+ * Comparator for {@link CellDesignerIon}.
+ */
+ private CellDesignerIonComparator ionComparator;
+
+ /**
+ * Comparator for {@link CellDesignerPhenotype}.
+ */
+ private CellDesignerPhenotypeComparator phenotypeComparator;
+
+ /**
+ * Comparator for {@link CellDesignerProtein}.
+ */
+ private CellDesignerProteinComparator proteinComparator;
+
+ /**
+ * Comparator for {@link CellDesignerRna}.
+ */
+ private CellDesignerRnaComparator rnaComparator;
+
+ /**
+ * Comparator for {@link CellDesignerSimpleMolecule}.
+ */
+ private CellDesignerSimpleMoleculeComparator simpleMoleculeComparator;
+
+ /**
+ * Comparator for {@link CellDesignerUnknown}.
+ */
+ private CellDesignerUnknownComparator unknownComparator;
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public CellDesignerSpeciesComparator(double epsilon) {
+ this.epsilon = epsilon;
+ antisenseRnaComparator = new CellDesignerAntisenseRnaComparator(epsilon);
+ complexSpeciesComparator = new CellDesignerComplexSpeciesComparator(epsilon);
+ degradedComparator = new CellDesignerDegradedComparator(epsilon);
+ drugComparator = new CellDesignerDrugComparator(epsilon);
+ geneComparator = new CellDesignerGeneComparator(epsilon);
+ ionComparator = new CellDesignerIonComparator(epsilon);
+ phenotypeComparator = new CellDesignerPhenotypeComparator(epsilon);
+ proteinComparator = new CellDesignerProteinComparator(epsilon);
+ rnaComparator = new CellDesignerRnaComparator(epsilon);
+ simpleMoleculeComparator = new CellDesignerSimpleMoleculeComparator(epsilon);
+ unknownComparator = new CellDesignerUnknownComparator(epsilon);
+
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerSpeciesComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public int compare(CellDesignerSpecies<?> arg0, CellDesignerSpecies<?> arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (arg0.getClass().equals(arg1.getClass())) {
+ if (arg0 instanceof CellDesignerAntisenseRna) {
+ return antisenseRnaComparator.compare((CellDesignerAntisenseRna) arg0, (CellDesignerAntisenseRna) arg1);
+ } else if (arg0 instanceof CellDesignerComplexSpecies) {
+ return complexSpeciesComparator.compare((CellDesignerComplexSpecies) arg0, (CellDesignerComplexSpecies) arg1);
+ } else if (arg0 instanceof CellDesignerDegraded) {
+ return degradedComparator.compare((CellDesignerDegraded) arg0, (CellDesignerDegraded) arg1);
+ } else if (arg0 instanceof CellDesignerDrug) {
+ return drugComparator.compare((CellDesignerDrug) arg0, (CellDesignerDrug) arg1);
+ } else if (arg0 instanceof CellDesignerGene) {
+ return geneComparator.compare((CellDesignerGene) arg0, (CellDesignerGene) arg1);
+ } else if (arg0 instanceof CellDesignerIon) {
+ return ionComparator.compare((CellDesignerIon) arg0, (CellDesignerIon) arg1);
+ } else if (arg0 instanceof CellDesignerPhenotype) {
+ return phenotypeComparator.compare((CellDesignerPhenotype) arg0, (CellDesignerPhenotype) arg1);
+ } else if (arg0 instanceof CellDesignerProtein) {
+ return proteinComparator.compare((CellDesignerProtein<?>) arg0, (CellDesignerProtein<?>) arg1);
+ } else if (arg0 instanceof CellDesignerRna) {
+ return rnaComparator.compare((CellDesignerRna) arg0, (CellDesignerRna) arg1);
+ } else if (arg0 instanceof CellDesignerSimpleMolecule) {
+ return simpleMoleculeComparator.compare((CellDesignerSimpleMolecule) arg0, (CellDesignerSimpleMolecule) arg1);
+ } else if (arg0 instanceof CellDesignerUnknown) {
+ return unknownComparator.compare((CellDesignerUnknown) arg0, (CellDesignerUnknown) arg1);
+ } else {
+ throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
+ }
+ } else {
+ logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
+ return -1;
+ }
+ }
+
+ /**
+ * This method compares only the fields that are defined in {@link CellDesignerSpecies}
+ * class in inheritence tree. It also calls the {@link CellDesignerElementComparator} for
+ * the super class ({@link lcsb.mapviewer.db.model.map.CellDesignerElement Element}).
+ *
+ * @param arg0
+ * first object to compare
+ * @param arg1
+ * second object to compare
+ * @return if all fields are qual then returns 0. If they are different then
+ * -1/1 is returned.
+ */
+ public int internalCompare(CellDesignerSpecies<?> arg0, CellDesignerSpecies<?> arg1) {
+ CellDesignerElementComparator elementComparator = new CellDesignerElementComparator(epsilon);
+ StringComparator stringComparator = new StringComparator();
+ IntegerComparator integerComparator = new IntegerComparator();
+ BooleanComparator booleanComparator = new BooleanComparator();
+
+ int result = elementComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+
+ if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
+ logger.debug("Id species different: " + arg0.getElementId() + ", " + arg1.getElementId());
+ return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
+ }
+
+ if (integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
+ logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
+ return integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
+ }
+
+ if (integerComparator.compare(arg0.getCharge(), arg1.getCharge()) != 0) {
+ logger.debug("Charge different: " + arg0.getCharge() + ", " + arg1.getCharge());
+ return integerComparator.compare(arg0.getCharge(), arg1.getCharge());
+ }
+
+ if (integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
+ logger.debug("Initial concentration different: " + arg0.getInitialConcentration() + ", " + arg1.getInitialConcentration());
+ return integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
+ }
+
+ if (booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits()) != 0) {
+ logger.debug("OnlySubstanceUnits different: " + arg0.hasOnlySubstanceUnits() + ", " + arg1.hasOnlySubstanceUnits());
+ return booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits());
+ }
+
+ if (arg0.getPositionToCompartment() != null || arg1.getPositionToCompartment() != null) {
+ Integer pos0 = null;
+ Integer pos1 = null;
+ if (arg0.getPositionToCompartment() != null) {
+ pos0 = arg0.getPositionToCompartment().ordinal();
+ }
+ if (arg1.getPositionToCompartment() != null) {
+ pos1 = arg1.getPositionToCompartment().ordinal();
+ }
+ if (integerComparator.compare(pos0, pos1) != 0) {
+ logger.debug("PositionToCompartment different: \"" + arg0.getPositionToCompartment() + "\", \"" + arg1.getPositionToCompartment() + "\"");
+ return integerComparator.compare(pos0, pos1);
+ }
+ }
+
+ if (booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical()) != 0) {
+ logger.debug("Hypothetical different: \"" + arg0.isHypothetical() + "\", \"" + arg1.isHypothetical() + "\"");
+ return booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
similarity index 52%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
index c05d481c5b..c26379a941 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
/**
* Truncated protein.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
* @author Piotr Gawron
*
*/
-public class TruncatedProtein extends Protein {
+public class CellDesignerTruncatedProtein extends CellDesignerProtein<TruncatedProtein> {
/**
*
@@ -19,7 +19,7 @@ public class TruncatedProtein extends Protein {
/**
* Default constructor.
*/
- public TruncatedProtein() {
+ public CellDesignerTruncatedProtein() {
super();
}
@@ -29,22 +29,22 @@ public class TruncatedProtein extends Protein {
* @param species
* original species
*/
- public TruncatedProtein(Species species) {
+ public CellDesignerTruncatedProtein(CellDesignerSpecies<?> species) {
super(species);
}
@Override
- public TruncatedProtein copy() {
- if (this.getClass().equals(TruncatedProtein.class)) {
- return new TruncatedProtein(this);
+ public CellDesignerTruncatedProtein copy() {
+ if (this.getClass().equals(CellDesignerTruncatedProtein.class)) {
+ return new CellDesignerTruncatedProtein(this);
} else {
throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
}
}
@Override
- public TruncatedProteinAlias createAlias(String aliasId) {
- TruncatedProteinAlias result = new TruncatedProteinAlias(aliasId);
+ public TruncatedProtein createAlias(String aliasId) {
+ TruncatedProtein result = new TruncatedProtein(aliasId);
super.setAliasFields(result);
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
similarity index 61%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
index 4fc711dffd..6e66e20ef8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.species.Unknown;
/**
* Class representing unknown element in the model.
@@ -9,7 +9,7 @@ import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
* @author Piotr Gawron
*
*/
-public class Unknown extends Species<UnknownAlias> {
+public class CellDesignerUnknown extends CellDesignerSpecies<Unknown> {
/**
*
*/
@@ -21,20 +21,20 @@ public class Unknown extends Species<UnknownAlias> {
* @param species
* original species used for data initialization
*/
- public Unknown(Species species) {
+ public CellDesignerUnknown(CellDesignerSpecies<?> species) {
super(species);
}
/**
* Default constructor.
*/
- public Unknown() {
+ public CellDesignerUnknown() {
}
@Override
- public Unknown copy() {
- if (this.getClass() == Unknown.class) {
- return new Unknown(this);
+ public CellDesignerUnknown copy() {
+ if (this.getClass() == CellDesignerUnknown.class) {
+ return new CellDesignerUnknown(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -46,8 +46,8 @@ public class Unknown extends Species<UnknownAlias> {
}
@Override
- public UnknownAlias createAlias(String aliasId) {
- UnknownAlias result = new UnknownAlias(aliasId);
+ public Unknown createAlias(String aliasId) {
+ Unknown result = new Unknown(aliasId);
super.setAliasFields(result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknownComparator.java
similarity index 64%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknownComparator.java
index 2e064d10ee..c80d46491c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknownComparator.java
@@ -10,9 +10,9 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
* @author Piotr Gawron
*
- * @see Unknown
+ * @see CellDesignerUnknown
*/
-public class UnknownComparator implements Comparator<Unknown> {
+public class CellDesignerUnknownComparator implements Comparator<CellDesignerUnknown> {
/**
* Epsilon value used for comparison of doubles.
*/
@@ -24,19 +24,19 @@ public class UnknownComparator implements Comparator<Unknown> {
* @param epsilon
* {@link #epsilon}
*/
- public UnknownComparator(double epsilon) {
+ public CellDesignerUnknownComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public UnknownComparator() {
+ public CellDesignerUnknownComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Unknown arg0, Unknown arg1) {
+ public int compare(CellDesignerUnknown arg0, CellDesignerUnknown arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -48,7 +48,7 @@ public class UnknownComparator implements Comparator<Unknown> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Unknown.class)) {
+ if (arg0.getClass().equals(CellDesignerUnknown.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -59,9 +59,9 @@ public class UnknownComparator implements Comparator<Unknown> {
}
/**
- * This method compares only the fields that are defined in {@link Unknown}
- * class in inheritence tree. It also calls the {@link SpeciesComparator} for
- * the super class ({@link Species}).
+ * This method compares only the fields that are defined in {@link CellDesignerUnknown}
+ * class in inheritence tree. It also calls the {@link CellDesignerSpeciesComparator} for
+ * the super class ({@link CellDesignerSpecies}).
*
* @param arg0
* first object to compare
@@ -70,8 +70,8 @@ public class UnknownComparator implements Comparator<Unknown> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(Unknown arg0, Unknown arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
+ private int internalCompare(CellDesignerUnknown arg0, CellDesignerUnknown arg1) {
+ CellDesignerSpeciesComparator speciesComparator = new CellDesignerSpeciesComparator(epsilon);
int result = speciesComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparator.java
deleted file mode 100644
index 486f9d6881..0000000000
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparator.java
+++ /dev/null
@@ -1,231 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.Comparator;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.BooleanComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-
-/**
- * This class implements comparator interface for Species. It calls comparator
- * implementation for all known subclases of Species class when necessary.
- *
- * @author Piotr Gawron
- *
- * @see Species
- */
-public class SpeciesComparator implements Comparator<Species> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(SpeciesComparator.class);
-
- /**
- * Comparator for {@link AntisenseRna}.
- */
- private AntisenseRnaComparator antisenseRnaComparator;
-
- /**
- * Comparator for {@link ComplexSpecies}.
- */
- private ComplexSpeciesComparator complexSpeciesComparator;
-
- /**
- * Comparator for {@link Degraded}.
- */
- private DegradedComparator degradedComparator;
-
- /**
- * Comparator for {@link Drug}.
- */
- private DrugComparator drugComparator;
-
- /**
- * Comparator for {@link Gene}.
- */
- private GeneComparator geneComparator;
-
- /**
- * Comparator for {@link Ion}.
- */
- private IonComparator ionComparator;
-
- /**
- * Comparator for {@link Phenotype}.
- */
- private PhenotypeComparator phenotypeComparator;
-
- /**
- * Comparator for {@link Protein}.
- */
- private ProteinComparator proteinComparator;
-
- /**
- * Comparator for {@link Rna}.
- */
- private RnaComparator rnaComparator;
-
- /**
- * Comparator for {@link SimpleMolecule}.
- */
- private SimpleMoleculeComparator simpleMoleculeComparator;
-
- /**
- * Comparator for {@link Unknown}.
- */
- private UnknownComparator unknownComparator;
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public SpeciesComparator(double epsilon) {
- this.epsilon = epsilon;
- antisenseRnaComparator = new AntisenseRnaComparator(epsilon);
- complexSpeciesComparator = new ComplexSpeciesComparator(epsilon);
- degradedComparator = new DegradedComparator(epsilon);
- drugComparator = new DrugComparator(epsilon);
- geneComparator = new GeneComparator(epsilon);
- ionComparator = new IonComparator(epsilon);
- phenotypeComparator = new PhenotypeComparator(epsilon);
- proteinComparator = new ProteinComparator(epsilon);
- rnaComparator = new RnaComparator(epsilon);
- simpleMoleculeComparator = new SimpleMoleculeComparator(epsilon);
- unknownComparator = new UnknownComparator(epsilon);
-
- }
-
- /**
- * Default constructor.
- */
- public SpeciesComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Species arg0, Species arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0 instanceof AntisenseRna) {
- return antisenseRnaComparator.compare((AntisenseRna) arg0, (AntisenseRna) arg1);
- } else if (arg0 instanceof ComplexSpecies) {
- return complexSpeciesComparator.compare((ComplexSpecies) arg0, (ComplexSpecies) arg1);
- } else if (arg0 instanceof Degraded) {
- return degradedComparator.compare((Degraded) arg0, (Degraded) arg1);
- } else if (arg0 instanceof Drug) {
- return drugComparator.compare((Drug) arg0, (Drug) arg1);
- } else if (arg0 instanceof Gene) {
- return geneComparator.compare((Gene) arg0, (Gene) arg1);
- } else if (arg0 instanceof Ion) {
- return ionComparator.compare((Ion) arg0, (Ion) arg1);
- } else if (arg0 instanceof Phenotype) {
- return phenotypeComparator.compare((Phenotype) arg0, (Phenotype) arg1);
- } else if (arg0 instanceof Protein) {
- return proteinComparator.compare((Protein) arg0, (Protein) arg1);
- } else if (arg0 instanceof Rna) {
- return rnaComparator.compare((Rna) arg0, (Rna) arg1);
- } else if (arg0 instanceof SimpleMolecule) {
- return simpleMoleculeComparator.compare((SimpleMolecule) arg0, (SimpleMolecule) arg1);
- } else if (arg0 instanceof Unknown) {
- return unknownComparator.compare((Unknown) arg0, (Unknown) arg1);
- } else {
- throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link Species}
- * class in inheritence tree. It also calls the {@link ElementComparator} for
- * the super class ({@link lcsb.mapviewer.db.model.map.Element Element}).
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(Species arg0, Species arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
- StringComparator stringComparator = new StringComparator();
- IntegerComparator integerComparator = new IntegerComparator();
- BooleanComparator booleanComparator = new BooleanComparator();
-
- int result = elementComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
- logger.debug("Id species different: " + arg0.getElementId() + ", " + arg1.getElementId());
- return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
- }
-
- if (integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
- logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
- return integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
- }
-
- if (integerComparator.compare(arg0.getCharge(), arg1.getCharge()) != 0) {
- logger.debug("Charge different: " + arg0.getCharge() + ", " + arg1.getCharge());
- return integerComparator.compare(arg0.getCharge(), arg1.getCharge());
- }
-
- if (integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
- logger.debug("Initial concentration different: " + arg0.getInitialConcentration() + ", " + arg1.getInitialConcentration());
- return integerComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
- }
-
- if (booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits()) != 0) {
- logger.debug("OnlySubstanceUnits different: " + arg0.hasOnlySubstanceUnits() + ", " + arg1.hasOnlySubstanceUnits());
- return booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits());
- }
-
- if (arg0.getPositionToCompartment() != null || arg1.getPositionToCompartment() != null) {
- Integer pos0 = null;
- Integer pos1 = null;
- if (arg0.getPositionToCompartment() != null) {
- pos0 = arg0.getPositionToCompartment().ordinal();
- }
- if (arg1.getPositionToCompartment() != null) {
- pos1 = arg1.getPositionToCompartment().ordinal();
- }
- if (integerComparator.compare(pos0, pos1) != 0) {
- logger.debug("PositionToCompartment different: \"" + arg0.getPositionToCompartment() + "\", \"" + arg1.getPositionToCompartment() + "\"");
- return integerComparator.compare(pos0, pos1);
- }
- }
-
- if (booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical()) != 0) {
- logger.debug("Hypothetical different: \"" + arg0.isHypothetical() + "\", \"" + arg1.isHypothetical() + "\"");
- return booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical());
- }
-
- return 0;
- }
-
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
similarity index 67%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
index 475464ccce..abd1d04166 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
@@ -1,21 +1,14 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.io.Serializable;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
* This class represent modification residue in protein and gene. However, it is
@@ -25,72 +18,59 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-@Entity
-@Table(name = "modification_residue_table_new")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class ModificationResidueAlias implements Serializable {
+public class CellDesignerModificationResidue implements Serializable {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ModificationResidueAlias.class.getName());
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
+ private static Logger logger = Logger.getLogger(CellDesignerModificationResidue.class.getName());
/**
* Identifier of the modification. Must be unique in single map model.
*/
- private String idModificationResidue = "";
+ private String idModificationResidue = "";
/**
* Name of the modification.
*/
- private String name = "";
+ private String name = "";
/**
* Some strange param in CellDesigner. No idea what is it for.
*/
- private String side = "";
+ private String side = "";
/**
* State in which this modification is.
*/
- private ModificationState state = null;
+ private ModificationState state = null;
/**
* Where this modification is located (on which side of the border).
*/
- private Double angle = null;
+ private Double angle = null;
/**
* How big is this modification (used only for some types of the
* modification).
*/
- private Double size = null;
+ private Double size = null;
/**
* Species to which this modification belong to.
*/
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb", nullable = false)
- private SpeciesAlias species;
+ private CellDesignerSpecies<?> species;
/**
* Default constructor.
*/
- public ModificationResidueAlias() {
+ public CellDesignerModificationResidue() {
}
/**
@@ -99,7 +79,7 @@ public class ModificationResidueAlias implements Serializable {
* @param mr
* original object from which data is taken
*/
- public ModificationResidueAlias(ModificationResidueAlias mr) {
+ public CellDesignerModificationResidue(CellDesignerModificationResidue mr) {
this.idModificationResidue = mr.idModificationResidue;
this.name = mr.name;
this.angle = mr.angle;
@@ -108,6 +88,15 @@ public class ModificationResidueAlias implements Serializable {
this.state = mr.state;
}
+ public CellDesignerModificationResidue(ModificationResidue mr) {
+ this.idModificationResidue = mr.getIdModificationResidue();
+ this.name = mr.getName();
+ this.angle = mr.getAngle();
+ this.size = mr.getSize();
+ this.side = mr.getSide();
+ this.state = mr.getState();
+ }
+
/**
* Updates fields in the object with the data given in the parameter
* modification.
@@ -115,7 +104,7 @@ public class ModificationResidueAlias implements Serializable {
* @param mr
* modification residue from which data will be used to update
*/
- public void update(ModificationResidueAlias mr) {
+ public void update(CellDesignerModificationResidue mr) {
if (mr.getName() != null && !mr.getName().equals("")) {
this.name = mr.name;
}
@@ -144,9 +133,9 @@ public class ModificationResidueAlias implements Serializable {
*
* @return copy of the object.
*/
- public ModificationResidueAlias copy() {
- if (this.getClass() == ModificationResidueAlias.class) {
- return new ModificationResidueAlias(this);
+ public CellDesignerModificationResidue copy() {
+ if (this.getClass() == CellDesignerModificationResidue.class) {
+ return new CellDesignerModificationResidue(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -189,23 +178,6 @@ public class ModificationResidueAlias implements Serializable {
}
}
- /**
- * @return the idModificationResidue
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the idModificationResidue to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
/**
* @return the id
* @see #idModificationResidue
@@ -312,7 +284,7 @@ public class ModificationResidueAlias implements Serializable {
* @return the species
* @see #species
*/
- public SpeciesAlias getSpecies() {
+ public CellDesignerSpecies<?> getSpecies() {
return species;
}
@@ -321,8 +293,20 @@ public class ModificationResidueAlias implements Serializable {
* the species to set
* @see #species
*/
- public void setSpecies(SpeciesAlias species) {
+ public void setSpecies(CellDesignerSpecies<?> species) {
this.species = species;
}
+ public ModificationResidue createModificationResidueAlias() {
+ ModificationResidue result = new ModificationResidue();
+
+ result.setIdModificationResidue(this.getIdModificationResidue());
+ result.setName(this.getName());
+ result.setAngle(this.getAngle());
+ result.setSize(this.getSize());
+ result.setSide(this.getSide());
+ result.setState(this.getState());
+ return result;
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectScheme.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ConnectScheme.java
similarity index 91%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectScheme.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ConnectScheme.java
index 76a7ed039a..b301451164 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectScheme.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ConnectScheme.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.util.HashMap;
import java.util.Map;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/EditPoints.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/EditPoints.java
similarity index 93%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/EditPoints.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/EditPoints.java
index 361675938d..a207ce0239 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/EditPoints.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/EditPoints.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.awt.geom.Point2D;
import java.util.ArrayList;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/LineProperties.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
similarity index 88%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/LineProperties.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
index d0d1da9452..c8c4203e2b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/LineProperties.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.awt.Color;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SingleLine.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SingleLine.java
similarity index 80%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SingleLine.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SingleLine.java
index 63defd059d..406d3d651c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SingleLine.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SingleLine.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-/**
- * Strange CellDEsigner structure to store width of single line...
- *
- * @author Piotr Gawron
- *
- */
-public class SingleLine {
-
- /**
- * Width of the line.
- */
- private Double width;
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+/**
+ * Strange CellDEsigner structure to store width of single line...
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SingleLine {
+
+ /**
+ * Width of the line.
+ */
+ private Double width;
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesState.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
similarity index 60%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesState.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
index 41f82d6aa0..c6a42cda6e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesState.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.util.ArrayList;
import java.util.List;
@@ -6,13 +6,13 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
/**
* Structure for storing the state of the Species in CellDesigner format.
@@ -41,7 +41,7 @@ public class SpeciesState {
/**
* List of species modification.
*/
- private List<ModificationResidue> modifications = new ArrayList<ModificationResidue>();
+ private List<CellDesignerModificationResidue> modifications = new ArrayList<CellDesignerModificationResidue>();
/**
* Adds modification to the state.
@@ -49,8 +49,8 @@ public class SpeciesState {
* @param modificationResidue
* modification to add
*/
- public void addModificationResidue(ModificationResidue modificationResidue) {
- for (ModificationResidue modification : modifications) {
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue modification : modifications) {
if (modification.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
modification.update(modificationResidue);
return;
@@ -71,30 +71,30 @@ public class SpeciesState {
* @param species
* object for which description is created
*/
- public SpeciesState(SpeciesAlias species) {
- if (species instanceof ProteinAlias) {
- ProteinAlias protein = (ProteinAlias) species;
+ public SpeciesState(Species species) {
+ if (species instanceof Protein) {
+ Protein protein = (Protein) species;
setStructuralState(protein.getStructuralState());
- for (ModificationResidueAlias mr : protein.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
}
- } else if (species instanceof ComplexAlias) {
- ComplexAlias complex = (ComplexAlias) species;
+ } else if (species instanceof Complex) {
+ Complex complex = (Complex) species;
setStructuralState(complex.getStructuralState());
- } else if (species instanceof RnaAlias) {
- RnaAlias rna = (RnaAlias) species;
- for (RnaRegionAlias region : rna.getRegions()) {
- ModificationResidue mr = new ModificationResidue();
+ } else if (species instanceof Rna) {
+ Rna rna = (Rna) species;
+ for (RnaRegion region : rna.getRegions()) {
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
mr.setIdModificationResidue(region.getIdRnaRegion());
mr.setSize(region.getSize());
mr.setState(region.getState());
addModificationResidue(mr);
}
- } else if (species instanceof GeneAlias) {
- GeneAlias gene = (GeneAlias) species;
- for (ModificationResidueAlias mr : gene.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
+ } else if (species instanceof Gene) {
+ Gene gene = (Gene) species;
+ for (ModificationResidue mr : gene.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
}
}
setHomodimer(species.getHomodimer());
@@ -151,7 +151,7 @@ public class SpeciesState {
* @return the modifications
* @see #modifications
*/
- public List<ModificationResidue> getModifications() {
+ public List<CellDesignerModificationResidue> getModifications() {
return modifications;
}
@@ -160,7 +160,7 @@ public class SpeciesState {
* the modifications to set
* @see #modifications
*/
- public void setModifications(List<ModificationResidue> modifications) {
+ public void setModifications(List<CellDesignerModificationResidue> modifications) {
this.modifications = modifications;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/View.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/View.java
similarity index 89%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/View.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/View.java
index 7cd66b3131..9960909347 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/View.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/View.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
import java.awt.Color;
import java.awt.Dimension;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
index 3ec3162c47..8f137652ac 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
@@ -10,11 +10,11 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Util class that helps in transformation of CellDesigner modifiers into
@@ -73,14 +73,14 @@ public class ModifierTypeUtils {
* alias to which modifier point to
* @return {@link Modifier} for the CellDesigner type
*/
- public Modifier createModifierForStringType(String type, SpeciesAlias alias) {
+ public Modifier createModifierForStringType(String type, Species alias) {
Modifier mod = null;
ModifierType modType = getModifierTypeForStringType(type);
if (modType == null) {
throw new InvalidArgumentException("Unknown modifier type: " + type);
}
try {
- mod = modType.getClazz().getConstructor(SpeciesAlias.class).newInstance(alias);
+ mod = modType.getClazz().getConstructor(Species.class).newInstance(alias);
} catch (Exception e) {
throw new InvalidStateException("Problem with instantiation of Modifier class: " + type);
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index c4dc7f4b95..5ae846b9b2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -28,11 +28,6 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
@@ -40,6 +35,11 @@ import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(CellDesignerXmlParserTest.class);
@@ -447,7 +447,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
model.setIdModel("as");
model.setWidth(10);
model.setHeight(10);
- SpeciesAlias speciesAlias = new GenericProteinAlias("id1");
+ Species speciesAlias = new GenericProtein("id1");
speciesAlias.setName("ROS");
RestAnnotationParser rap = new RestAnnotationParser();
rap.processNotes(
@@ -455,18 +455,18 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
speciesAlias);
model.addAlias(speciesAlias);
- GenericProteinAlias alias = new GenericProteinAlias("id");
+ GenericProtein alias = new GenericProtein("id");
alias.setName("ROS");
model.addAlias(alias);
- SimpleMoleculeAlias speciesAlias2 = new SimpleMoleculeAlias("id2");
+ SimpleMolecule speciesAlias2 = new SimpleMolecule("id2");
speciesAlias2.setName("PDK1");
rap.processNotes(
"Symbol: ROS1\r\nName: c-ros oncogene 1 , receptor tyrosine kinase\r\nDescription: RecName: Full=Proto-oncogene tyrosine-protein kinase ROS; EC=2.7.10.1; AltName: Full=Proto-oncogene c-Ros; AltName: Full=Proto-oncogene c-Ros-1; AltName: Full=Receptor tyrosine kinase c-ros oncogene 1; AltName: Full=c-Ros receptor tyrosine kinase; Flags: Precursor;\r\nPrevious Symbols:\r\nSynonyms: ROS, MCF3",
speciesAlias2);
model.addAlias(speciesAlias2);
- SimpleMoleculeAlias alias2 = new SimpleMoleculeAlias("id3");
+ SimpleMolecule alias2 = new SimpleMolecule("id3");
alias2.setName("PDK1");
model.addAlias(alias2);
@@ -519,7 +519,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
model.setHeight(20);
model.setNotes(null);
model.setIdModel("id");
- SpeciesAlias alias = new GenericProteinAlias("a");
+ Species alias = new GenericProtein("a");
alias.setName("AA");
model.addAlias(alias);
@@ -577,9 +577,9 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
FileInputStream fis = new FileInputStream("testFiles/homodimer.xml");
Model model = parser.createModel(new ConverterParams().inputStream(fis));
- for (Alias element : model.getAliases()) {
- if (element instanceof SpeciesAlias) {
- assertTrue("Homodimer value for class" + element.getClass() + " not upadted", ((SpeciesAlias) element).getHomodimer() > 1);
+ for (Element element : model.getAliases()) {
+ if (element instanceof Species) {
+ assertTrue("Homodimer value for class" + element.getClass() + " not upadted", ((Species) element).getHomodimer() > 1);
}
}
} catch (Exception e) {
@@ -646,7 +646,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = parser.createModel(new ConverterParams().filename("testFiles/notes_with_html_coding.xml"));
- Alias p = model.getAliasByAliasId("sa1");
+ Element p = model.getAliasByAliasId("sa1");
assertEquals(">symbol<", p.getSymbol());
@@ -804,7 +804,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
Model model = new ModelFullIndexed(null);
model.setWidth(100);
model.setHeight(100);
- GeneAlias gene = new GeneAlias("gene_id_1");
+ Gene gene = new Gene("gene_id_1");
gene.setName("geneNAME");
model.addAlias(gene);
String xmlString = parser.toXml(model);
@@ -938,7 +938,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
try {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = parser.createModel(new ConverterParams().filename("testFiles/problematic/problematic_notes.xml"));
- Alias element = model.getAliasByAliasId("sa2338");
+ Element element = model.getAliasByAliasId("sa2338");
assertFalse("Element note cannot contain head html tag", element.getNotes().contains("</head>"));
} catch (Exception e) {
e.printStackTrace();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index 7e4fd481ab..f8834afcbc 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -21,18 +21,18 @@ import org.junit.Test;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class ComplexParserTests extends CellDesignerTestFunctions {
@@ -68,9 +68,9 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/bubbles.xml");
- Alias species = model.getAliasByAliasId("sa6");
+ Element species = model.getAliasByAliasId("sa6");
assertNotNull(species);
- ProteinAlias protein = (ProteinAlias) species;
+ Protein protein = (Protein) species;
assertTrue(protein.getModificationResidues().size() > 0);
assertNotNull(protein.getStructuralState());
assertFalse(protein.getStructuralState().equals(""));
@@ -87,7 +87,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/problematic/elements_in_compartments.xml");
- List<Alias> aliases = new ArrayList<>();
+ List<Element> aliases = new ArrayList<>();
aliases.add(model.getAliasByAliasId("csa3"));
aliases.add(model.getAliasByAliasId("csa4"));
aliases.add(model.getAliasByAliasId("csa5"));
@@ -109,7 +109,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
aliases.add(model.getAliasByAliasId("sa18"));
aliases.add(model.getAliasByAliasId("sa19"));
aliases.add(model.getAliasByAliasId("sa20"));
- for (Alias alias : aliases) {
+ for (Element alias : aliases) {
assertNotNull(eu.getElementTag(alias) + " does not contain info about compartment", alias.getParent());
}
@@ -126,10 +126,10 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
model = getModelForFile("testFiles/problematic/acetyled_protein.xml");
Set<ModificationState> residues = new HashSet<ModificationState>();
- for (Alias element : model.getAliases()) {
- if (element instanceof SpeciesAlias) {
- ProteinAlias p = (ProteinAlias) element;
- for (ModificationResidueAlias mr : p.getModificationResidues()) {
+ for (Element element : model.getAliases()) {
+ if (element instanceof Species) {
+ Protein p = (Protein) element;
+ for (ModificationResidue mr : p.getModificationResidues()) {
residues.add(mr.getState());
}
}
@@ -138,7 +138,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
// of residues
assertEquals(2, residues.size());
- assertEquals(ModificationState.ACETYLATED, ((ProteinAlias) model.getAliasByAliasId("sa2")).getModificationResidues().get(0).getState());
+ assertEquals(ModificationState.ACETYLATED, ((Protein) model.getAliasByAliasId("sa2")).getModificationResidues().get(0).getState());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -150,7 +150,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
Model model;
try {
model = getModelForFile("testFiles/includedSpecies.xml");
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
assertNotNull(species);
assertNotNull(species.getNotes());
assertTrue("Wrong notes: " + species.getNotes(), species.getNotes().contains("hello world"));
@@ -165,7 +165,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
Model model;
try {
model = getModelForFile("testFiles/problematic/hypothetical_complex.xml");
- ComplexAlias species = (ComplexAlias) model.getAliasByAliasId("csa1");
+ Complex species = (Complex) model.getAliasByAliasId("csa1");
assertTrue(species.isHypothetical());
} catch (Exception e) {
e.printStackTrace();
@@ -178,8 +178,8 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
Model model;
try {
model = getModelForFile("testFiles/problematic/problematic_acetylation.xml");
- ProteinAlias p1 = (ProteinAlias) model.getAliasByAliasId("sa73");
- ProteinAlias p2 = (ProteinAlias) model.getAliasByAliasId("sa27");
+ Protein p1 = (Protein) model.getAliasByAliasId("sa73");
+ Protein p2 = (Protein) model.getAliasByAliasId("sa27");
assertEquals(ModificationState.ACETYLATED, p1.getModificationResidues().get(0).getState());
assertFalse(ModificationState.ACETYLATED.equals(p2.getModificationResidues().get(0).getState()));
@@ -194,7 +194,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
Model model;
try {
model = getModelForFile("testFiles/problematic/duplicated_miriam.xml");
- ProteinAlias p1 = (ProteinAlias) model.getAliasByAliasId("sa1");
+ Protein p1 = (Protein) model.getAliasByAliasId("sa1");
Set<String> ids = new HashSet<>();
assertTrue(p1.getMiriamData().size() > 0);
@@ -217,7 +217,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
Model model = getModelForFile("testFiles/problematic/kappa_example.xml");
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
assertFalse(species.getName().toLowerCase().contains("kappa"));
@@ -232,14 +232,14 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
try {
Model model = getModelForFile("testFiles/missing_xml_nodes.xml");
- assertTrue(((SpeciesAlias) model.getAliasByAliasId("sa3")).isHypothetical());
- assertTrue(((SpeciesAlias) model.getAliasByAliasId("sa4")).isHypothetical());
- assertTrue(((SpeciesAlias) model.getAliasByAliasId("sa5")).isHypothetical());
+ assertTrue(((Species) model.getAliasByAliasId("sa3")).isHypothetical());
+ assertTrue(((Species) model.getAliasByAliasId("sa4")).isHypothetical());
+ assertTrue(((Species) model.getAliasByAliasId("sa5")).isHypothetical());
- assertFalse(((SpeciesAlias) model.getAliasByAliasId("sa12")).isHypothetical());
- assertFalse(((SpeciesAlias) model.getAliasByAliasId("sa13")).isHypothetical());
- assertFalse(((SpeciesAlias) model.getAliasByAliasId("sa14")).isHypothetical());
- assertFalse(((SpeciesAlias) model.getAliasByAliasId("sa15")).isHypothetical());
+ assertFalse(((Species) model.getAliasByAliasId("sa12")).isHypothetical());
+ assertFalse(((Species) model.getAliasByAliasId("sa13")).isHypothetical());
+ assertFalse(((Species) model.getAliasByAliasId("sa14")).isHypothetical());
+ assertFalse(((Species) model.getAliasByAliasId("sa15")).isHypothetical());
} catch (Exception e) {
e.printStackTrace();
@@ -254,7 +254,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
model.setIdModel("as");
model.setWidth(100);
model.setHeight(100);
- GenericProteinAlias alias = new GenericProteinAlias("aid");
+ GenericProtein alias = new GenericProtein("aid");
alias.setName("name & no-name");
model.addAlias(alias);
@@ -284,7 +284,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
model.setIdModel("as");
model.setWidth(100);
model.setHeight(100);
- GenericProteinAlias alias = new GenericProteinAlias("aid");
+ GenericProtein alias = new GenericProtein("aid");
alias.setName("name\rno-name");
model.addAlias(alias);
@@ -322,8 +322,8 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
public void testRnaWithRegion() throws Exception {
try {
Model model = getModelForFile("testFiles/rnaWithRegion.xml");
- for (Alias species : model.getNotComplexSpeciesAliases()) {
- RnaAlias rna = (RnaAlias) species;
+ for (Element species : model.getNotComplexSpeciesAliases()) {
+ Rna rna = (Rna) species;
assertEquals(1, rna.getRegions().size());
}
} catch (Exception e) {
@@ -336,7 +336,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
public void testProtinWithModifications() throws Exception {
try {
Model model = getModelForFile("testFiles/proteinWithEverPossibleModification.xml");
- ProteinAlias protein = (ProteinAlias) model.getAliasByAliasId("sa1");
+ Protein protein = (Protein) model.getAliasByAliasId("sa1");
assertEquals(14, protein.getModificationResidues().size());
} catch (Exception e) {
e.printStackTrace();
@@ -348,8 +348,8 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
public void testAntisenseRnaWithRegion() throws Exception {
try {
Model model = getModelForFile("testFiles/antisenseRnaWithRegion.xml");
- for (SpeciesAlias species : model.getNotComplexSpeciesAliases()) {
- AntisenseRnaAlias rna = (AntisenseRnaAlias) species;
+ for (Species species : model.getNotComplexSpeciesAliases()) {
+ AntisenseRna rna = (AntisenseRna) species;
assertEquals(1, rna.getRegions().size());
}
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
index 6b8c0b31a8..2353bd3dc5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
@@ -17,9 +17,7 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.graphics.PolylineDataComparator;
-import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerComparator;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
@@ -30,6 +28,8 @@ import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.layout.graphics.LayerTextComparator;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class LayerXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(LayerXmlParserTest.class);
@@ -147,7 +147,7 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
public void testParseInvalidGroups3() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- GenericProteinAlias alias = new GenericProteinAlias("sa1");
+ GenericProtein alias = new GenericProtein("sa1");
model.addAlias(alias);
String xmlString = readFile("testFiles/invalid/group_collection3.xml");
@@ -408,21 +408,21 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
public void testGetAliasGroup() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- SpeciesAlias alias = new GenericProteinAlias("sa1035");
+ Species alias = new GenericProtein("sa1035");
model.addAlias(alias);
- alias = new GenericProteinAlias("sa1036");
+ alias = new GenericProtein("sa1036");
model.addAlias(alias);
- alias = new GenericProteinAlias("sa1037");
+ alias = new GenericProtein("sa1037");
model.addAlias(alias);
- alias = new GenericProteinAlias("sa1038");
+ alias = new GenericProtein("sa1038");
model.addAlias(alias);
String string = "<celldesigner:group id=\"g74\" members=\"sa1035,sa1036,sa1037,sa1038\"/>";
Node node = getNodeFromXmlString(string);
- AliasGroup group = parser.getAliasGroup(node, model);
+ ElementGroup group = parser.getAliasGroup(node, model);
assertNotNull(group);
assertEquals(4, group.getAliases().size());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
index 913a958c65..5c3a6edf02 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
@@ -8,9 +8,9 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
public class NestedComplexParsingTests extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(NestedComplexParsingTests.class);
@@ -29,30 +29,30 @@ public class NestedComplexParsingTests extends CellDesignerTestFunctions {
try {
model = getModelForFile("testFiles/xmlNodeTestExamples/nested_complex.xml");
- Alias s1 = model.getAliasByAliasId("csa1");
- Alias s2 = model.getAliasByAliasId("csa2");
- Alias s3 = model.getAliasByAliasId("csa3");
- Alias s4 = model.getAliasByAliasId("csa4");
- Alias s5 = model.getAliasByAliasId("csa5");
- Alias s6 = model.getAliasByAliasId("csa6");
- Alias s7 = model.getAliasByAliasId("sa1");
- Alias s8 = model.getAliasByAliasId("sa2");
- Alias s9 = model.getAliasByAliasId("sa3");
- Alias s10 = model.getAliasByAliasId("sa4");
- Alias s11 = model.getAliasByAliasId("sa5");
- Alias s12 = model.getAliasByAliasId("sa6");
- assertTrue(s1 instanceof ComplexAlias);
- assertTrue(s2 instanceof ComplexAlias);
- assertTrue(s3 instanceof ComplexAlias);
- assertTrue(s4 instanceof ComplexAlias);
- assertTrue(s5 instanceof ComplexAlias);
- assertTrue(s6 instanceof ComplexAlias);
- ComplexAlias cs1 = (ComplexAlias) s1;
- ComplexAlias cs2 = (ComplexAlias) s2;
- ComplexAlias cs3 = (ComplexAlias) s3;
- ComplexAlias cs4 = (ComplexAlias) s4;
- ComplexAlias cs5 = (ComplexAlias) s5;
- ComplexAlias cs6 = (ComplexAlias) s6;
+ Element s1 = model.getAliasByAliasId("csa1");
+ Element s2 = model.getAliasByAliasId("csa2");
+ Element s3 = model.getAliasByAliasId("csa3");
+ Element s4 = model.getAliasByAliasId("csa4");
+ Element s5 = model.getAliasByAliasId("csa5");
+ Element s6 = model.getAliasByAliasId("csa6");
+ Element s7 = model.getAliasByAliasId("sa1");
+ Element s8 = model.getAliasByAliasId("sa2");
+ Element s9 = model.getAliasByAliasId("sa3");
+ Element s10 = model.getAliasByAliasId("sa4");
+ Element s11 = model.getAliasByAliasId("sa5");
+ Element s12 = model.getAliasByAliasId("sa6");
+ assertTrue(s1 instanceof Complex);
+ assertTrue(s2 instanceof Complex);
+ assertTrue(s3 instanceof Complex);
+ assertTrue(s4 instanceof Complex);
+ assertTrue(s5 instanceof Complex);
+ assertTrue(s6 instanceof Complex);
+ Complex cs1 = (Complex) s1;
+ Complex cs2 = (Complex) s2;
+ Complex cs3 = (Complex) s3;
+ Complex cs4 = (Complex) s4;
+ Complex cs5 = (Complex) s5;
+ Complex cs6 = (Complex) s6;
assertEquals(2,cs1.getAliases().size());
assertEquals(2,cs2.getAliases().size());
assertEquals(0,cs3.getAliases().size());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java
index 45e1c12047..37e3ba1d29 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java
@@ -10,9 +10,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
public class ReconDataInCellDesignerXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ReconDataInCellDesignerXmlParserTest.class);
@@ -31,7 +31,7 @@ public class ReconDataInCellDesignerXmlParserTest extends CellDesignerTestFuncti
CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = parser.createModel(new ConverterParams().filename("testFiles/annotation/recon_annotation_example.xml"));
assertNotNull(model);
- SpeciesAlias species = (SpeciesAlias)model.getAliasByAliasId("sa1");
+ Species species = (Species)model.getAliasByAliasId("sa1");
assertNotNull(species);
assertEquals("S1_SYMB",species.getSymbol());
assertEquals("ABREVIATION",species.getAbbreviation());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
index a85efa5a63..9a2ac88f38 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
@@ -16,14 +16,14 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
@@ -49,21 +49,21 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testParseXmlSpeciesAliasCollection() throws Exception {
try {
- elements.addElement(new GenericProtein("s2594"));
- elements.addElement(new GenericProtein("s2595"));
- elements.addElement(new GenericProtein("s2596"));
- elements.addElement(new GenericProtein("s2506"));
+ elements.addElement(new CellDesignerGenericProtein("s2594"));
+ elements.addElement(new CellDesignerGenericProtein("s2595"));
+ elements.addElement(new CellDesignerGenericProtein("s2596"));
+ elements.addElement(new CellDesignerGenericProtein("s2506"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml");
Node node = getNodeFromXmlString(xmlString);
- List<SpeciesAlias> list = parser.parseXmlSpeciesAliasCollection(node);
+ List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
assertEquals(0, getWarnings().size());
assertNotNull(list);
assertEquals(4, list.size());
- SpeciesAlias aliasSa8 = null;
- SpeciesAlias aliasSa9 = null;
- SpeciesAlias aliasSa10 = null;
- SpeciesAlias aliasSa11 = null;
- for (SpeciesAlias alias : list) {
+ Species aliasSa8 = null;
+ Species aliasSa9 = null;
+ Species aliasSa10 = null;
+ Species aliasSa11 = null;
+ for (Species alias : list) {
if (alias.getAliasId().equals("sa8"))
aliasSa8 = alias;
if (alias.getAliasId().equals("sa9"))
@@ -132,21 +132,21 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testSpeciesAliasCollectionToXmlString() throws Exception {
try {
- elements.addElement(new GenericProtein("s2594"));
- elements.addElement(new GenericProtein("s2506"));
- elements.addElement(new GenericProtein("s2595"));
- elements.addElement(new GenericProtein("s2596"));
+ elements.addElement(new CellDesignerGenericProtein("s2594"));
+ elements.addElement(new CellDesignerGenericProtein("s2506"));
+ elements.addElement(new CellDesignerGenericProtein("s2595"));
+ elements.addElement(new CellDesignerGenericProtein("s2596"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml");
Node node = getNodeFromXmlString(xmlString);
- List<SpeciesAlias> list = parser.parseXmlSpeciesAliasCollection(node);
+ List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
assertEquals(0, getWarnings().size());
String xmlString2 = parser.speciesAliasCollectionToXmlString(list);
assertNotNull(xmlString2);
// add position to elements list, because parser forgot CD ids and created
// new for them
- for (SpeciesAlias alias : list) {
- elements.addElement(new GenericProtein(elements.getElementId(alias)));
+ for (Species alias : list) {
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
}
node = getNodeFromXmlString(xmlString2);
@@ -154,11 +154,11 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
assertEquals(0, getWarnings().size());
assertNotNull(list);
assertEquals(4, list.size());
- SpeciesAlias aliasSa8 = null;
- SpeciesAlias aliasSa9 = null;
- SpeciesAlias aliasSa10 = null;
- SpeciesAlias aliasSa11 = null;
- for (SpeciesAlias alias : list) {
+ Species aliasSa8 = null;
+ Species aliasSa9 = null;
+ Species aliasSa10 = null;
+ Species aliasSa11 = null;
+ for (Species alias : list) {
if (alias.getAliasId().equals("sa8"))
aliasSa8 = alias;
if (alias.getAliasId().equals("sa9"))
@@ -182,19 +182,19 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testParseXmlComplexAliasCollection() throws Exception {
try {
- elements.addElement(new ComplexSpecies("s2597"));
- elements.addElement(new ComplexSpecies("s2598"));
- elements.addElement(new ComplexSpecies("s2599"));
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
+ elements.addElement(new CellDesignerComplexSpecies("s2598"));
+ elements.addElement(new CellDesignerComplexSpecies("s2599"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml");
Node node = getNodeFromXmlString(xmlString);
- List<ComplexAlias> list = parser.parseXmlComplexAliasCollection(node);
+ List<Complex> list = parser.parseXmlComplexAliasCollection(node);
assertEquals(0, getWarnings().size());
assertNotNull(list);
assertEquals(3, list.size());
- ComplexAlias aliasSa1 = null;
- ComplexAlias aliasSa2 = null;
- ComplexAlias aliasSa3 = null;
- for (ComplexAlias alias : list) {
+ Complex aliasSa1 = null;
+ Complex aliasSa2 = null;
+ Complex aliasSa3 = null;
+ for (Complex alias : list) {
if (alias.getAliasId().equals("csa1"))
aliasSa1 = alias;
if (alias.getAliasId().equals("csa2"))
@@ -214,20 +214,20 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testComplexAliasCollectionToXmlString() throws Exception {
try {
- elements.addElement(new ComplexSpecies("s2597"));
- elements.addElement(new ComplexSpecies("s2598"));
- elements.addElement(new ComplexSpecies("s2599"));
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
+ elements.addElement(new CellDesignerComplexSpecies("s2598"));
+ elements.addElement(new CellDesignerComplexSpecies("s2599"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml");
Node node = getNodeFromXmlString(xmlString);
- List<ComplexAlias> list = parser.parseXmlComplexAliasCollection(node);
+ List<Complex> list = parser.parseXmlComplexAliasCollection(node);
assertEquals(0, getWarnings().size());
String xmlString2 = parser.complexAliasCollectionToXmlString(list);
assertNotNull(xmlString2);
// add position to elements list, because parser forgot CD ids and created
// new for them
- for (ComplexAlias complexAlias : list) {
- elements.addElement(new ComplexSpecies(elements.getElementId(complexAlias)));
+ for (Complex complexAlias : list) {
+ elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complexAlias)));
}
node = getNodeFromXmlString(xmlString2);
@@ -235,10 +235,10 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
assertEquals(0, getWarnings().size());
assertNotNull(list);
assertEquals(3, list.size());
- ComplexAlias aliasSa1 = null;
- ComplexAlias aliasSa2 = null;
- ComplexAlias aliasSa3 = null;
- for (ComplexAlias alias : list) {
+ Complex aliasSa1 = null;
+ Complex aliasSa2 = null;
+ Complex aliasSa3 = null;
+ for (Complex alias : list) {
if (alias.getAliasId().equals("csa1"))
aliasSa1 = alias;
if (alias.getAliasId().equals("csa2"))
@@ -258,20 +258,20 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testParseXmlCompartmentAliasCollection() throws Exception {
try {
- elements.addElement(new Compartment("c1"));
- elements.addElement(new Compartment("c2"));
- elements.addElement(new Compartment("c3"));
+ elements.addElement(new CellDesignerCompartment("c1"));
+ elements.addElement(new CellDesignerCompartment("c2"));
+ elements.addElement(new CellDesignerCompartment("c3"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml");
Node node = getNodeFromXmlString(xmlString);
- List<CompartmentAlias> list = parser.parseXmlCompartmentAliasCollection(node);
+ List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
assertEquals(0, getWarnings().size());
assertNotNull(list);
assertEquals(3, list.size());
- CompartmentAlias aliasCa1 = null;
- CompartmentAlias aliasCa2 = null;
- CompartmentAlias aliasCa3 = null;
- for (CompartmentAlias alias : list) {
+ Compartment aliasCa1 = null;
+ Compartment aliasCa2 = null;
+ Compartment aliasCa3 = null;
+ for (Compartment alias : list) {
if (alias.getAliasId().equals("ca1"))
aliasCa1 = alias;
if (alias.getAliasId().equals("ca2"))
@@ -291,13 +291,13 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testCompartmentAliasCollectionToXmlString() throws Exception {
try {
- elements.addElement(new Compartment("c1"));
- elements.addElement(new Compartment("c2"));
- elements.addElement(new Compartment("c3"));
+ elements.addElement(new CellDesignerCompartment("c1"));
+ elements.addElement(new CellDesignerCompartment("c2"));
+ elements.addElement(new CellDesignerCompartment("c3"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml");
Node node = getNodeFromXmlString(xmlString);
- List<CompartmentAlias> list = parser.parseXmlCompartmentAliasCollection(node);
+ List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
assertEquals(0, getWarnings().size());
String xmlString2 = parser.compartmentAliasCollectionToXmlString(list);
@@ -305,8 +305,8 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
// add position to elements list, because parser forgot CD ids and created
// new for them
- for (CompartmentAlias alias : list) {
- elements.addElement(new Compartment(elements.getElementId(alias)));
+ for (Compartment alias : list) {
+ elements.addElement(new CellDesignerCompartment(elements.getElementId(alias)));
}
node = getNodeFromXmlString(xmlString2);
@@ -315,10 +315,10 @@ public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
assertNotNull(list);
assertEquals(3, list.size());
- CompartmentAlias aliasSa1 = null;
- CompartmentAlias aliasSa2 = null;
- CompartmentAlias aliasSa3 = null;
- for (CompartmentAlias alias : list) {
+ Compartment aliasSa1 = null;
+ Compartment aliasSa2 = null;
+ Compartment aliasSa3 = null;
+ for (Compartment alias : list) {
if (alias.getAliasId().equals("ca1"))
aliasSa1 = alias;
if (alias.getAliasId().equals("ca2"))
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
index 52989043a4..39ec8b2440 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
@@ -16,13 +16,13 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.BottomSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.LeftSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.RightSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.TopSquareCompartmentAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -47,18 +47,18 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testToXml() throws Exception {
try {
- elements.addElement(new Compartment("c1"));
+ elements.addElement(new CellDesignerCompartment("c1"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
- CompartmentAlias alias = parser.parseXmlAlias(xmlString);
+ Compartment alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertEquals(0, getWarnings().size());
String xmlString2 = parser.toXml(alias);
assertNotNull(xmlString2);
- elements.addElement(new Compartment(elements.getElementId(alias)));
+ elements.addElement(new CellDesignerCompartment(elements.getElementId(alias)));
- CompartmentAlias alias2 = parser.parseXmlAlias(xmlString2);
+ Compartment alias2 = parser.parseXmlAlias(xmlString2);
assertEquals(0, getWarnings().size());
assertEquals(alias.getAliasId(), alias2.getAliasId());
@@ -96,7 +96,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
public void parseInvalidAlias2() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- Compartment comp = new Compartment();
+ CellDesignerCompartment comp = new CellDesignerCompartment();
comp.setElementId("c1");
elements.addElement(comp);
parser = new CompartmentAliasXmlParser(elements, model);
@@ -115,7 +115,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
public void parseInvalidAlias3() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- Compartment comp = new Compartment();
+ CellDesignerCompartment comp = new CellDesignerCompartment();
comp.setElementId("c1");
elements.addElement(comp);
parser = new CompartmentAliasXmlParser(elements, model);
@@ -134,7 +134,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
public void parseInvalidAlias4() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- Compartment comp = new Compartment();
+ CellDesignerCompartment comp = new CellDesignerCompartment();
comp.setElementId("c1");
elements.addElement(comp);
parser = new CompartmentAliasXmlParser(elements, model);
@@ -152,15 +152,15 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testParseXmlAliasNode() throws Exception {
try {
- elements.addElement(new Compartment("c1"));
+ elements.addElement(new CellDesignerCompartment("c1"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
- CompartmentAlias alias = (CompartmentAlias) parser.parseXmlAlias(xmlString);
+ Compartment alias = (Compartment) parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertNotNull(alias);
assertEquals("ca1", alias.getAliasId());
assertNotNull(alias.getName());
- assertTrue(alias instanceof SquareCompartmentAlias);
+ assertTrue(alias instanceof SquareCompartment);
assertEquals(139.0, alias.getX(), 1e-6);
assertEquals(55.0, alias.getY(), 1e-6);
assertEquals(522.0, alias.getWidth(), 1e-6);
@@ -189,7 +189,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testLeftToXml() throws Exception {
try {
- CompartmentAlias alias = new LeftSquareCompartmentAlias();
+ Compartment alias = new LeftSquareCompartment();
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
@@ -202,7 +202,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testRightToXml() throws Exception {
try {
- CompartmentAlias alias = new RightSquareCompartmentAlias();
+ Compartment alias = new RightSquareCompartment();
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
@@ -215,7 +215,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testTopToXml() throws Exception {
try {
- CompartmentAlias alias = new TopSquareCompartmentAlias();
+ Compartment alias = new TopSquareCompartment();
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
@@ -228,7 +228,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testBotttomToXml() throws Exception {
try {
- CompartmentAlias alias = new BottomSquareCompartmentAlias();
+ Compartment alias = new BottomSquareCompartment();
String xml = parser.toXml(alias);
assertNotNull(xml);
} catch (Exception e) {
@@ -241,7 +241,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testUnknownToXml() throws Exception {
try {
- CompartmentAlias alias = Mockito.mock(BottomSquareCompartmentAlias.class);
+ Compartment alias = Mockito.mock(BottomSquareCompartment.class);
parser.toXml(alias);
fail("Exception expected");
} catch (NotImplementedException e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
index 7d620bb070..f59f2c1826 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
@@ -9,10 +9,10 @@ import org.junit.Test;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
Model model;
@@ -33,15 +33,15 @@ public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testToXml() throws Exception {
try {
- elements.addElement(new ComplexSpecies("s2597"));
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias.xml");
- ComplexAlias alias = (ComplexAlias) parser.parseXmlAlias(xmlString);
+ Complex alias = (Complex) parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
String xmlString2 = parser.toXml(alias);
assertNotNull(xmlString2);
- elements.addElement(new ComplexSpecies(elements.getElementId(alias)));
- ComplexAlias alias2 = (ComplexAlias) parser.parseXmlAlias(xmlString2);
+ elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(alias)));
+ Complex alias2 = (Complex) parser.parseXmlAlias(xmlString2);
assertEquals(0, getWarnings().size());
assertEquals(alias.getAliasId(), alias2.getAliasId());
@@ -60,10 +60,10 @@ public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testParseXmlAliasNode() throws Exception {
try {
- elements.addElement(new ComplexSpecies("s2597"));
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias.xml");
- ComplexAlias alias = (ComplexAlias) parser.parseXmlAlias(xmlString);
+ Complex alias = (Complex) parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertEquals(false, alias.getActivity());
assertEquals("csa1", alias.getAliasId());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
index 3692a7f973..ec07f044b6 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
@@ -20,14 +20,14 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
static Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class);
@@ -35,8 +35,6 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
Model model;
private SpeciesAliasXmlParser parser;
- private String testCompartmentId2 = "s1";
- private String testCompartmentId = "s2";
private String testCompartmentAliasId2 = "s3";
private String testCompartmentAliasId = "s4";
private String testSpeciesId = "s5";
@@ -49,7 +47,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
model = createStubModel();
- GenericProtein species = new GenericProtein();
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein();
species.setElementId("s78");
elements.addElement(species);
@@ -58,7 +56,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
private Model createStubModel() {
Model model = new ModelFullIndexed(null);
- model.addAlias(new CompartmentAlias("ca1"));
+ model.addAlias(new Compartment("ca1"));
return model;
}
@@ -70,7 +68,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlAliasNode() throws Exception {
try {
String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias.xml");
- SpeciesAlias alias = parser.parseXmlAlias(xmlString);
+ Species alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertEquals(false, alias.getActivity());
assertEquals("sa36", alias.getAliasId());
@@ -90,7 +88,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlAliasFont() throws Exception {
try {
String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_font.xml");
- SpeciesAlias alias = parser.parseXmlAlias(xmlString);
+ Species alias = parser.parseXmlAlias(xmlString);
assertEquals(30.0, alias.getFontSize(), 1e-6);
} catch (Exception e) {
e.printStackTrace();
@@ -102,17 +100,17 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
public void testToXml() throws Exception {
try {
String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias.xml");
- SpeciesAlias alias = parser.parseXmlAlias(xmlString);
+ Species alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
String xmlString2 = parser.toXml(alias);
assertNotNull(xmlString2);
- elements.addElement(new GenericProtein(elements.getElementId(alias)));
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
Model model2 = createStubModel();
parser = new SpeciesAliasXmlParser(elements, model2);
- SpeciesAlias alias2 = parser.parseXmlAlias(xmlString2);
+ Species alias2 = parser.parseXmlAlias(xmlString2);
assertEquals(0, getWarnings().size());
assertEquals(alias.getActivity(), alias2.getActivity());
@@ -135,13 +133,13 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
public void testToXmlAliasWithStateNode() throws Exception {
try {
String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_state.xml");
- SpeciesAlias alias = parser.parseXmlAlias(xmlString);
+ Species alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
String xmlString2 = parser.toXml(alias);
assertNotNull(xmlString2);
- elements.addElement(new GenericProtein(elements.getElementId(alias)));
- SpeciesAlias alias2 = parser.parseXmlAlias(xmlString2);
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
+ Species alias2 = parser.parseXmlAlias(xmlString2);
assertEquals(0, getWarnings().size());
assertEquals("Alias state label different", alias.getAliasStateLabel(), alias2.getAliasStateLabel());
@@ -156,7 +154,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlAliasWithStateNode() throws Exception {
try {
String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_state.xml");
- SpeciesAlias alias = parser.parseXmlAlias(xmlString);
+ Species alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertNotNull(alias);
assertEquals("test", alias.getAliasStateLabel());
@@ -171,7 +169,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlAliasWithoutStateNode() throws Exception {
try {
String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_without_state.xml");
- SpeciesAlias alias = parser.parseXmlAlias(xmlString);
+ Species alias = parser.parseXmlAlias(xmlString);
assertEquals(0, getWarnings().size());
assertNotNull(alias);
assertNull(alias.getAliasStateLabel());
@@ -279,21 +277,21 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
ModelData md = new ModelData();
md.setModel(model);
- CompartmentAlias ca2 = new CompartmentAlias(testCompartmentAliasId2);
+ Compartment ca2 = new Compartment(testCompartmentAliasId2);
ca2.setAliasId(testCompartmentAliasId2);
ca2.setX(6);
ca2.setY(6);
ca2.setWidth(190);
ca2.setHeight(190);
- CompartmentAlias ca = new CompartmentAlias(testCompartmentAliasId);
+ Compartment ca = new Compartment(testCompartmentAliasId);
ca.setAliasId(testCompartmentAliasId);
ca.setX(5);
ca.setY(5);
ca.setWidth(200);
ca.setHeight(200);
- List<CompartmentAlias> list = new ArrayList<>();
+ List<Compartment> list = new ArrayList<>();
list.add(ca);
list.add(ca2);
@@ -301,7 +299,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
when(model.getCompartmentsAliases()).thenReturn(list);
when(model.getModelData()).thenReturn(md);
- SpeciesAlias alias = new ComplexAlias(testAliasId);
+ Species alias = new Complex(testAliasId);
alias.setX(10);
alias.setY(10);
alias.setWidth(100);
@@ -309,7 +307,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
alias.setModel(model);
alias.setActivity(true);
- elements.addElement(new ComplexSpecies(testSpeciesId));
+ elements.addElement(new CellDesignerComplexSpecies(testSpeciesId));
model.addAlias(alias);
SpeciesAliasXmlParser parser = new SpeciesAliasXmlParser(elements, model);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index bd02f9c653..473a5ba731 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -26,11 +26,11 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class RestAnnotationParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(RestAnnotationParserTest.class);
@@ -70,7 +70,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes.xml");
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
@@ -93,7 +93,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes3.xml");
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
assertNotNull(notes);
@@ -116,7 +116,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
proteinAlias.setNotes("text");
parser.processNotes(node.getFirstChild(), proteinAlias);
String notes = proteinAlias.getNotes();
@@ -141,7 +141,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes2.xml");
- GenericProteinAlias protein = new GenericProteinAlias("pr_id1");
+ GenericProtein protein = new GenericProtein("pr_id1");
protein.addSynonym("a1");
protein.addFormerSymbol("a1");
protein.setFullName("yyy");
@@ -166,7 +166,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes_invalid_charge.xml");
- SpeciesAlias proteinAlias = new GenericProteinAlias("id");
+ Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
assertEquals(1, getWarnings().size());
@@ -207,8 +207,8 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
try {
Model model = getModelForFile("testFiles/copyingAnnotationModel.xml");
- Set<Alias> elements = model.getAliases();
- for (Alias element : elements) {
+ Set<Element> elements = model.getAliases();
+ for (Element element : elements) {
if (element.getName().equals("blabla")) {
assertEquals(2, element.getMiriamData().size());
element.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "12345"));
@@ -228,7 +228,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
public void testProcessRdfDescription() throws Exception {
try {
RestAnnotationParser rap = new RestAnnotationParser();
- SpeciesAlias speciesAlias = new GenericProteinAlias("id");
+ Species speciesAlias = new GenericProtein("id");
speciesAlias.setNotes(
"begining\n" + "<rdf:RDF>" + "<rdf:Description rdf:about=\"#s2157\">\n" + "<bqmodel:is>\n" + "<rdf:Bag>\n"
+ "<rdf:li rdf:resource=\"urn:miriam:obo.chebi:CHEBI%3A17515\"/>\n" + "</rdf:Bag>\n" + "</bqmodel:is>\n" + "</rdf:Description>\n" + "</rdf:RDF>"
@@ -283,7 +283,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
String former1 = "form1";
String former2 = "form2";
- GenericProteinAlias element = new GenericProteinAlias("id");
+ GenericProtein element = new GenericProtein("id");
element.addFormerSymbol(former1);
element.addFormerSymbol(former2);
String str = rap.createAnnotationString(element);
@@ -420,7 +420,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
RestAnnotationParser parser = new RestAnnotationParser();
String str = super.readFile("testFiles/xmlNodeTestExamples/notes5.xml");
- parser.processNotes(str, new GenericProteinAlias("id"));
+ parser.processNotes(str, new GenericProtein("id"));
assertEquals(1, getWarnings().size());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java
index f85656e82b..caba87a708 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java
@@ -17,8 +17,8 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
public class CompartmentCollectionXmlParserTest extends CellDesignerTestFunctions {
static Logger logger = Logger.getLogger(CompartmentCollectionXmlParserTest.class);
@@ -44,7 +44,7 @@ public class CompartmentCollectionXmlParserTest extends CellDesignerTestFunction
String xmlString = readFile("testFiles/compartment/listOfCompartments.xml");
Node node = getNodeFromXmlString(xmlString);
- List<Compartment> compartments = parser.parseXmlCompartmentCollection(node);
+ List<CellDesignerCompartment> compartments = parser.parseXmlCompartmentCollection(node);
assertEquals(4, compartments.size());
@@ -75,10 +75,10 @@ public class CompartmentCollectionXmlParserTest extends CellDesignerTestFunction
String xmlString = readFile("testFiles/compartment/listOfCompartments.xml");
Node node = getNodeFromXmlString(xmlString);
- List<Compartment> compartments = parser.parseXmlCompartmentCollection(node);
+ List<CellDesignerCompartment> compartments = parser.parseXmlCompartmentCollection(node);
- List<CompartmentAlias> aliases = new ArrayList<>();
- for (Compartment compartment : compartments) {
+ List<Compartment> aliases = new ArrayList<>();
+ for (CellDesignerCompartment compartment : compartments) {
aliases.add(compartment.createAlias("ca" + aliasIdCounter));
}
@@ -87,10 +87,10 @@ public class CompartmentCollectionXmlParserTest extends CellDesignerTestFunction
node = getNodeFromXmlString(xmlString2);
- List<Compartment> compartments2 = parser.parseXmlCompartmentCollection(node);
+ List<CellDesignerCompartment> compartments2 = parser.parseXmlCompartmentCollection(node);
for (int i = 0; i < compartments.size(); i++) {
- Compartment compartmentA = compartments.get(i);
- Compartment compartmentB = compartments2.get(i);
+ CellDesignerCompartment compartmentA = compartments.get(i);
+ CellDesignerCompartment compartmentB = compartments2.get(i);
assertEquals(compartmentA.getName(), compartmentB.getName());
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
index 2286da47dc..fd6c3adb9f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
@@ -23,8 +23,8 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.species.ProteinXmlParserTest;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
protected Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
@@ -48,8 +48,8 @@ public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testProteinFile);
- Pair<String, Compartment> result = compartmentParser.parseXmlElement(xmlString);
- Compartment compartment = result.getRight();
+ Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
+ CellDesignerCompartment compartment = result.getRight();
assertNotNull(compartment);
assertEquals("c1", compartment.getElementId());
assertEquals(1, compartment.getMiriamData().size());
@@ -66,9 +66,9 @@ public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testProteinFile);
- Pair<String, Compartment> result = compartmentParser.parseXmlElement(xmlString);
- Compartment compartment = result.getRight();
- CompartmentAlias alias = compartment.createAlias("id");
+ Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
+ CellDesignerCompartment compartment = result.getRight();
+ Compartment alias = compartment.createAlias("id");
String transformedXml = compartmentParser.toXml(alias);
assertNotNull(transformedXml);
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -78,8 +78,8 @@ public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("compartment", root.item(0).getNodeName());
- Pair<String, Compartment> result2 = compartmentParser.parseXmlElement(compartmentParser.toXml(alias));
- Compartment compartment2 = result2.getRight();
+ Pair<String, CellDesignerCompartment> result2 = compartmentParser.parseXmlElement(compartmentParser.toXml(alias));
+ CellDesignerCompartment compartment2 = result2.getRight();
assertEquals(alias.getMiriamData().size(), compartment2.getMiriamData().size());
assertEquals(alias.getName(), compartment2.getName());
} catch (Exception e) {
@@ -133,8 +133,8 @@ public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testToXmlWithParent() throws Exception {
try {
- CompartmentAlias child = new CompartmentAlias("c_1");
- CompartmentAlias parent = new CompartmentAlias("p_1");
+ Compartment child = new Compartment("c_1");
+ Compartment parent = new Compartment("p_1");
parent.setName("PARENTNAME");
child.setParent(parent);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
index 6e7f4b63cb..a3d82e3f36 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
@@ -17,21 +17,21 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerA
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerEllipseTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPolygonTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerRectangleTransformation;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
public class AbstractCellDesignerAliasConverterTest {
- AbstractCellDesignerAliasConverter<SpeciesAlias> converter = new AbstractCellDesignerAliasConverter<SpeciesAlias>() {
+ AbstractCellDesignerAliasConverter<Species> converter = new AbstractCellDesignerAliasConverter<Species>() {
@Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
return null;
}
@Override
- protected PathIterator getBoundPathIterator(SpeciesAlias alias) {
+ protected PathIterator getBoundPathIterator(Species alias) {
return null;
}
};
@@ -53,7 +53,7 @@ public class AbstractCellDesignerAliasConverterTest {
EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
Logger.getRootLogger().addAppender(appender);
try {
- ProteinAlias alias = new GenericProteinAlias("id");
+ Protein alias = new GenericProtein("id");
alias.setWidth(1);
alias.setHeight(1);
converter.getAnchorPointCoordinates(alias, 0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java
index 44b126517b..b9f94cbb14 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java
@@ -11,10 +11,10 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class AntisenseRnaCellDesignerAliasConverterTest {
AntisenseRnaCellDesignerAliasConverter converter = new AntisenseRnaCellDesignerAliasConverter();
@@ -35,7 +35,7 @@ public class AntisenseRnaCellDesignerAliasConverterTest {
public void testGetPointCoordinatesForSbgn() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new GenericProteinAlias("id");
+ Species alias = new GenericProtein("id");
alias.setWidth(10);
alias.setHeight(10);
alias.setModel(model);
@@ -47,7 +47,7 @@ public class AntisenseRnaCellDesignerAliasConverterTest {
public void testGetAntisenseRnaPathForSbgn() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new GenericProteinAlias("id");
+ Species alias = new GenericProtein("id");
alias.setWidth(10);
alias.setHeight(10);
alias.setModel(model);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java
index 0d43ab1fa2..559e5c7ccc 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
public class CellDesignerAliasConverterTest {
@@ -39,7 +39,7 @@ public class CellDesignerAliasConverterTest {
@Test
public void testConstructorWithInvalidArg2() {
try {
- SpeciesAlias alias = Mockito.mock(SpeciesAlias.class);
+ Species alias = Mockito.mock(Species.class);
new CellDesignerAliasConverter(alias);
fail("Exception expected");
} catch (InvalidArgumentException e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java
index cb170f67bb..b62b4ffd3c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java
@@ -11,8 +11,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Species;
public class DegradedCellDesignerAliasConverterTest {
@@ -32,7 +32,7 @@ public class DegradedCellDesignerAliasConverterTest {
@Test
public void testGetAnchorPointCoordinatesForInvalidAlias() {
- DegradedAlias alias = new DegradedAlias("id");
+ Degraded alias = new Degraded("id");
alias.setWidth(-1);
Point2D point = converter.getAnchorPointCoordinates(alias, 0);
assertNotNull(point);
@@ -40,7 +40,7 @@ public class DegradedCellDesignerAliasConverterTest {
@Test
public void testGetAnchorPointCoordinatesForInvalidAlias2() {
- SpeciesAlias alias = new DegradedAlias("id");
+ Species alias = new Degraded("id");
Point2D point = converter.getAnchorPointCoordinates(alias, 0);
assertNotNull(point);
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
index 7c9ac6426b..67a112af5f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/GeneCellDesignerAliasConverterTest.java
@@ -9,10 +9,10 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Species;
public class GeneCellDesignerAliasConverterTest {
@@ -32,7 +32,7 @@ public class GeneCellDesignerAliasConverterTest {
@Test
public void testGetInvalidAliasPointCoordinates() {
- SpeciesAlias alias = new GeneAlias("id");
+ Species alias = new Gene("id");
alias.setX(1);
alias.setY(12);
alias.setWidth(10);
@@ -43,7 +43,7 @@ public class GeneCellDesignerAliasConverterTest {
@Test
public void testGetPath() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias alias = new GeneAlias("id");
+ Species alias = new Gene("id");
alias.setX(1);
alias.setY(12);
alias.setWidth(10);
@@ -59,7 +59,7 @@ public class GeneCellDesignerAliasConverterTest {
public void testGetPath2() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new GeneAlias("id");
+ Species alias = new Gene("id");
alias.setX(1);
alias.setY(12);
alias.setWidth(10);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
index 38bf992ff3..c43dd83f5e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverterTest.java
@@ -11,8 +11,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Species;
public class IonCellDesignerAliasConverterTest {
@@ -32,7 +32,7 @@ public class IonCellDesignerAliasConverterTest {
@Test
public void testGetAnchorPointCoordinatesForInvalidAlias() {
- SpeciesAlias alias = new IonAlias("id");
+ Species alias = new Ion("id");
alias.setWidth(-1);
Point2D point = converter.getAnchorPointCoordinates(alias, 0);
assertNotNull(point);
@@ -40,7 +40,7 @@ public class IonCellDesignerAliasConverterTest {
@Test
public void testGetAnchorPointCoordinatesForInvalidAlias2() {
- SpeciesAlias alias = new IonAlias("id");
+ Species alias = new Ion("id");
Point2D point = converter.getAnchorPointCoordinates(alias, 0);
assertNotNull(point);
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java
index e1c0b73dca..53505a973f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java
@@ -9,7 +9,7 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
public class ProteinCellDesignerAliasConverterTest {
@@ -30,7 +30,7 @@ public class ProteinCellDesignerAliasConverterTest {
@Test
public void testNotImplementedMethod() {
try {
- ProteinAlias alias = Mockito.mock(ProteinAlias.class);
+ Protein alias = Mockito.mock(Protein.class);
converter.getBoundPathIterator(alias);
} catch (NotImplementedException e) {
assertTrue(e.getMessage().contains("Not implemented protein converter for type"));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
index 33169890e6..8d1ba4016a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
@@ -11,7 +11,7 @@ import org.junit.Test;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class ProteinConverterTest extends CellDesignerTestFunctions {
static Logger logger = Logger.getLogger(ProteinConverterTest.class);
@@ -28,7 +28,7 @@ public class ProteinConverterTest extends CellDesignerTestFunctions {
public void testGetAnchorForAlias() throws Exception {
try {
- GenericProteinAlias alias = new GenericProteinAlias("id");
+ GenericProtein alias = new GenericProtein("id");
alias.setWidth(200);
alias.setHeight(300);
alias.setX(100.0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java
index 0441df9efe..51dd5de673 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java
@@ -11,10 +11,10 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class RnaCellDesignerAliasConverterTest {
RnaCellDesignerAliasConverter converter = new RnaCellDesignerAliasConverter();
@@ -35,7 +35,7 @@ public class RnaCellDesignerAliasConverterTest {
public void testGetPointCoordinatesForSbgn() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new GenericProteinAlias("id");
+ Species alias = new GenericProtein("id");
alias.setWidth(10);
alias.setHeight(10);
alias.setModel(model);
@@ -47,7 +47,7 @@ public class RnaCellDesignerAliasConverterTest {
public void testGetAntisebseRnaPathForSbgn() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new GenericProteinAlias("id");
+ Species alias = new GenericProtein("id");
alias.setWidth(10);
alias.setHeight(10);
alias.setModel(model);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
index b3ce0f3999..bf696af247 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverterTest.java
@@ -14,10 +14,10 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
public class SimpleMoleculeCellDesignerAliasConverterTest {
@@ -49,7 +49,7 @@ public class SimpleMoleculeCellDesignerAliasConverterTest {
public void testGetSbgnPointCoordinates() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new SimpleMoleculeAlias("id");
+ Species alias = new SimpleMolecule("id");
alias.setX(4);
alias.setY(5);
alias.setWidth(6);
@@ -65,7 +65,7 @@ public class SimpleMoleculeCellDesignerAliasConverterTest {
public void testGetSbgnAnchorPointCoordinates() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new SimpleMoleculeAlias("id");
+ Species alias = new SimpleMolecule("id");
alias.setX(4);
alias.setY(5);
alias.setWidth(6);
@@ -81,7 +81,7 @@ public class SimpleMoleculeCellDesignerAliasConverterTest {
public void testGetAnchorPointCoordinatesForEmptyAlias() {
Model model = new ModelFullIndexed(null);
model.setSbgnFormat(true);
- SpeciesAlias alias = new SimpleMoleculeAlias("id");
+ Species alias = new SimpleMolecule("id");
alias.setX(4);
alias.setY(5);
alias.setWidth(0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
index 4630f2acd9..d6c5a8a117 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/UnknownCellDesignerAliasConverterTest.java
@@ -11,8 +11,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class UnknownCellDesignerAliasConverterTest {
UnknownCellDesignerAliasConverter converter = new UnknownCellDesignerAliasConverter();
@@ -40,7 +40,7 @@ public class UnknownCellDesignerAliasConverterTest {
@Test
public void testGetAnchorPointCoordinates() {
- SpeciesAlias alias = new GenericProteinAlias("id");
+ Species alias = new GenericProtein("id");
alias.setWidth(0);
alias.setHeight(0);
Point2D point = converter.getAnchorPointCoordinates(alias, 0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java
index 1f606a0f4c..269ea1ad7b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java
@@ -14,11 +14,11 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ReactionCollectionXmlParserTest.class);
@@ -99,84 +99,84 @@ public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
private Model getModelFilledWithSpecies() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias sa1 = new GenericProteinAlias("sa1");
+ Species sa1 = new GenericProtein("sa1");
sa1.setX(100.0);
sa1.setY(200.0);
sa1.setWidth(300.0);
sa1.setHeight(400.0);
model.addAlias(sa1);
- SpeciesAlias sa2 = new GenericProteinAlias("sa2");
+ Species sa2 = new GenericProtein("sa2");
sa2.setX(1050.0);
sa2.setY(2050.0);
sa2.setWidth(300.0);
sa2.setHeight(450.0);
model.addAlias(sa2);
- SpeciesAlias sa3 = new GenericProteinAlias("sa3");
+ Species sa3 = new GenericProtein("sa3");
sa3.setX(600.0);
sa3.setY(250.0);
sa3.setWidth(300.0);
sa3.setHeight(400.0);
model.addAlias(sa3);
- SpeciesAlias sa4 = new GenericProteinAlias("sa4");
+ Species sa4 = new GenericProtein("sa4");
sa4.setX(550.0);
sa4.setY(350.0);
sa4.setWidth(300.0);
sa4.setHeight(450.0);
model.addAlias(sa4);
- SpeciesAlias sa5 = new GenericProteinAlias("sa5");
+ Species sa5 = new GenericProtein("sa5");
sa5.setX(10.0);
sa5.setY(250.0);
sa5.setWidth(300.0);
sa5.setHeight(450.0);
model.addAlias(sa5);
- SpeciesAlias sa6 = new GenericProteinAlias("sa6");
+ Species sa6 = new GenericProtein("sa6");
sa6.setX(10.0);
sa6.setY(250.0);
sa6.setWidth(300.0);
sa6.setHeight(450.0);
model.addAlias(sa6);
- SpeciesAlias sa10 = new GenericProteinAlias("sa10");
+ Species sa10 = new GenericProtein("sa10");
sa10.setX(210.0);
sa10.setY(220.0);
sa10.setWidth(320.0);
sa10.setHeight(250.0);
model.addAlias(sa10);
- SpeciesAlias sa11 = new GenericProteinAlias("sa11");
+ Species sa11 = new GenericProtein("sa11");
sa11.setX(11.0);
sa11.setY(320.0);
sa11.setWidth(321.0);
sa11.setHeight(150.0);
model.addAlias(sa11);
- SpeciesAlias sa12 = new GenericProteinAlias("sa12");
+ Species sa12 = new GenericProtein("sa12");
sa12.setX(12.0);
sa12.setY(20.0);
sa12.setWidth(321.0);
sa12.setHeight(150.0);
model.addAlias(sa12);
- SpeciesAlias sa13 = new GenericProteinAlias("sa13");
+ Species sa13 = new GenericProtein("sa13");
sa13.setX(513.0);
sa13.setY(20.0);
sa13.setWidth(321.0);
sa13.setHeight(150.0);
model.addAlias(sa13);
- SpeciesAlias sa14 = new GenericProteinAlias("sa14");
+ Species sa14 = new GenericProtein("sa14");
sa14.setX(14.0);
sa14.setY(820.0);
sa14.setWidth(321.0);
sa14.setHeight(150.0);
model.addAlias(sa14);
- SpeciesAlias sa15 = new GenericProteinAlias("sa15");
+ Species sa15 = new GenericProtein("sa15");
sa15.setX(815.0);
sa15.setY(620.0);
sa15.setWidth(321.0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
index 3c89a78565..9e568dd336 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
@@ -11,9 +11,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -21,6 +19,8 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ReactionFromXmlTest extends CellDesignerTestFunctions {
ReactionXmlParser parser;
@@ -37,22 +37,22 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
elements = new CellDesignerElementCollection();
parser = new ReactionXmlParser(elements);
- SpeciesAlias alias = new GenericProteinAlias("sa1");
+ Species alias = new GenericProtein("sa1");
model.addAlias(alias);
- alias = new GenericProteinAlias("sa2");
+ alias = new GenericProtein("sa2");
model.addAlias(alias);
- alias = new GenericProteinAlias("sa3");
+ alias = new GenericProtein("sa3");
model.addAlias(alias);
- alias = new GenericProteinAlias("sa4");
+ alias = new GenericProtein("sa4");
model.addAlias(alias);
- elements.addElement(new GenericProtein("s1"));
- elements.addElement(new GenericProtein("s2"));
- elements.addElement(new GenericProtein("s3"));
- elements.addElement(new GenericProtein("s4"));
+ elements.addElement(new CellDesignerGenericProtein("s1"));
+ elements.addElement(new CellDesignerGenericProtein("s2"));
+ elements.addElement(new CellDesignerGenericProtein("s3"));
+ elements.addElement(new CellDesignerGenericProtein("s4"));
}
@After
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
index aa91b51a14..a0fe14ccff 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
@@ -22,14 +22,10 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -56,6 +52,10 @@ import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
public class ReactionParserTests extends CellDesignerTestFunctions {
@@ -100,7 +100,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
Model model;
try {
model = getModelForFile("testFiles/problematic/pd_map_with_problematic_reaction_line.xml");
- assertTrue(model.getAliasByAliasId("sa5003") instanceof GenericProteinAlias);
+ assertTrue(model.getAliasByAliasId("sa5003") instanceof GenericProtein);
Set<Reaction> list = model.getReactions();
for (Reaction reaction : list) {
// reaction re1607 in this model was problematic, but in fact the
@@ -739,8 +739,8 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
reaction2 = reaction;
}
Reactant reactant = reaction1.getReactants().get(0);
- Alias alias1 = reaction1.getReactants().get(0).getAlias();
- Alias alias2 = reaction1.getProducts().get(0).getAlias();
+ Element alias1 = reaction1.getReactants().get(0).getAlias();
+ Element alias2 = reaction1.getProducts().get(0).getAlias();
Product product = reaction1.getProducts().get(0);
Point2D point = new Point2D.Double(alias1.getX() + alias1.getWidth() / 2, alias1.getY() + alias1.getHeight());
Point2D point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
@@ -1545,102 +1545,102 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
private Model getModelFilledWithSpecies() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias sa1 = new GenericProteinAlias("sa1");
+ Species sa1 = new GenericProtein("sa1");
sa1.setX(100.0);
sa1.setY(200.0);
sa1.setWidth(300.0);
sa1.setHeight(400.0);
model.addAlias(sa1);
- elements.addAlias(sa1, new GenericProtein("s1"));
+ elements.addAlias(sa1, new CellDesignerGenericProtein("s1"));
- SpeciesAlias sa2 = new GenericProteinAlias("sa2");
+ Species sa2 = new GenericProtein("sa2");
sa2.setX(1050.0);
sa2.setY(2050.0);
sa2.setWidth(300.0);
sa2.setHeight(450.0);
model.addAlias(sa2);
- elements.addAlias(sa2, new GenericProtein("s2"));
+ elements.addAlias(sa2, new CellDesignerGenericProtein("s2"));
- SpeciesAlias sa3 = new GenericProteinAlias("sa3");
+ Species sa3 = new GenericProtein("sa3");
sa3.setX(600.0);
sa3.setY(250.0);
sa3.setWidth(300.0);
sa3.setHeight(400.0);
model.addAlias(sa3);
- elements.addAlias(sa3, new GenericProtein("s3"));
+ elements.addAlias(sa3, new CellDesignerGenericProtein("s3"));
- SpeciesAlias sa4 = new GenericProteinAlias("sa4");
+ Species sa4 = new GenericProtein("sa4");
sa4.setX(550.0);
sa4.setY(350.0);
sa4.setWidth(300.0);
sa4.setHeight(450.0);
model.addAlias(sa4);
- elements.addElement(new GenericProtein("s4"));
+ elements.addElement(new CellDesignerGenericProtein("s4"));
- SpeciesAlias sa5 = new GenericProteinAlias("sa5");
+ Species sa5 = new GenericProtein("sa5");
sa5.setX(10.0);
sa5.setY(250.0);
sa5.setWidth(300.0);
sa5.setHeight(450.0);
model.addAlias(sa5);
- elements.addElement(new GenericProtein("s5"));
+ elements.addElement(new CellDesignerGenericProtein("s5"));
- SpeciesAlias sa6 = new GenericProteinAlias("sa6");
+ Species sa6 = new GenericProtein("sa6");
sa6.setX(10.0);
sa6.setY(250.0);
sa6.setWidth(300.0);
sa6.setHeight(450.0);
model.addAlias(sa6);
- elements.addElement(new GenericProtein("s6"));
+ elements.addElement(new CellDesignerGenericProtein("s6"));
- SpeciesAlias sa10 = new GenericProteinAlias("sa10");
+ Species sa10 = new GenericProtein("sa10");
sa10.setX(210.0);
sa10.setY(220.0);
sa10.setWidth(320.0);
sa10.setHeight(250.0);
model.addAlias(sa10);
- elements.addElement(new GenericProtein("s10"));
+ elements.addElement(new CellDesignerGenericProtein("s10"));
- SpeciesAlias sa11 = new GenericProteinAlias("sa11");
+ Species sa11 = new GenericProtein("sa11");
sa11.setX(11.0);
sa11.setY(320.0);
sa11.setWidth(321.0);
sa11.setHeight(150.0);
model.addAlias(sa11);
- elements.addElement(new GenericProtein("s11"));
+ elements.addElement(new CellDesignerGenericProtein("s11"));
- SpeciesAlias sa12 = new GenericProteinAlias("sa12");
+ Species sa12 = new GenericProtein("sa12");
sa12.setX(12.0);
sa12.setY(20.0);
sa12.setWidth(321.0);
sa12.setHeight(150.0);
model.addAlias(sa12);
- elements.addElement(new GenericProtein("s12"));
+ elements.addElement(new CellDesignerGenericProtein("s12"));
- SpeciesAlias sa13 = new GenericProteinAlias("sa13");
+ Species sa13 = new GenericProtein("sa13");
sa13.setX(513.0);
sa13.setY(20.0);
sa13.setWidth(321.0);
sa13.setHeight(150.0);
model.addAlias(sa13);
- elements.addElement(new GenericProtein("s13"));
+ elements.addElement(new CellDesignerGenericProtein("s13"));
- SpeciesAlias sa14 = new GenericProteinAlias("sa14");
+ Species sa14 = new GenericProtein("sa14");
sa14.setX(14.0);
sa14.setY(820.0);
sa14.setWidth(321.0);
sa14.setHeight(150.0);
model.addAlias(sa14);
- elements.addElement(new GenericProtein("s14"));
+ elements.addElement(new CellDesignerGenericProtein("s14"));
- SpeciesAlias sa15 = new GenericProteinAlias("sa15");
+ Species sa15 = new GenericProtein("sa15");
sa15.setX(815.0);
sa15.setY(620.0);
sa15.setWidth(321.0);
sa15.setHeight(150.0);
model.addAlias(sa15);
- elements.addElement(new GenericProtein("s15"));
+ elements.addElement(new CellDesignerGenericProtein("s15"));
return model;
}
@@ -1785,8 +1785,8 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
public void testProteinsInsideComplex() throws Exception {
try {
Model model = getModelForFile("testFiles/problematic/proteins_inside_complex.xml");
- for (Alias el : model.getAliases()) {
- assertFalse(el.getClass().equals(ProteinAlias.class));
+ for (Element el : model.getAliases()) {
+ assertFalse(el.getClass().equals(Protein.class));
}
} catch (Exception e) {
e.printStackTrace();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
index efc1a6ca89..09d2068026 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
@@ -18,9 +18,6 @@ import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Catalysis;
@@ -32,6 +29,9 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ReactionToXmlTest {
Logger logger = Logger.getLogger(ReactionToXmlTest.class);
@@ -56,7 +56,7 @@ public class ReactionToXmlTest {
@Test
public void testInvalidModification() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias alias = new GenericProteinAlias("2");
+ Species alias = new GenericProtein("2");
model.addAlias(alias);
@@ -113,11 +113,11 @@ public class ReactionToXmlTest {
public void testModificationFromInsideComplex() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias alias = new GenericProteinAlias("2");
+ Species alias = new GenericProtein("2");
model.addAlias(alias);
- ComplexAlias complex = new ComplexAlias("4");
+ Complex complex = new Complex("4");
complex.addAlias(alias);
alias.setParent(complex);
@@ -150,7 +150,7 @@ public class ReactionToXmlTest {
public void testInvalidReaction() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias alias = new GenericProteinAlias("2");
+ Species alias = new GenericProtein("2");
model.addAlias(alias);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
index 7fec98632d..d89c8ac115 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
@@ -21,9 +21,9 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion.AntisenseRnaRegionType;
public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
protected Logger logger = Logger.getLogger(AntisenseRnaXmlParserTest.class.getName());
@@ -47,13 +47,13 @@ public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpecies() throws Exception {
try {
String xmlString = readFile(testAntisenseRnaFile);
- Pair<String, AntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
- AntisenseRna antisenseRna = result.getRight();
+ Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna = result.getRight();
assertEquals("arn1", result.getLeft());
assertEquals("s1", antisenseRna.getName());
assertTrue(antisenseRna.getNotes().contains("some notes"));
assertEquals(1, antisenseRna.getRegions().size());
- AntisenseRnaRegion region = antisenseRna.getRegions().get(0);
+ CellDesignerAntisenseRnaRegion region = antisenseRna.getRegions().get(0);
assertEquals("tr1", region.getIdAntisenseRnaRegion());
assertEquals("zzz", region.getName());
assertEquals(0.3, region.getSize(), 1e-6);
@@ -125,8 +125,8 @@ public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
public void testToXml() throws Exception {
try {
String xmlString = readFile(testAntisenseRnaFile);
- Pair<String, AntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
- AntisenseRna antisenseRna = result.getRight();
+ Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna = result.getRight();
String transformedXml = antisenseRnaParser.toXml(antisenseRna.createAlias());
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -136,15 +136,15 @@ public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("celldesigner:AntisenseRNA", root.item(0).getNodeName());
- Pair<String, AntisenseRna> result2 = antisenseRnaParser.parseXmlElement(xmlString);
- AntisenseRna antisenseRna2 = result2.getRight();
+ Pair<String, CellDesignerAntisenseRna> result2 = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna2 = result2.getRight();
assertEquals(result.getLeft(), result2.getLeft());
assertEquals(antisenseRna.getName(), antisenseRna2.getName());
assertEquals(antisenseRna.getNotes().trim(), antisenseRna2.getNotes().trim());
assertEquals(1, antisenseRna2.getRegions().size());
- AntisenseRnaRegion region = antisenseRna.getRegions().get(0);
- AntisenseRnaRegion region2 = antisenseRna2.getRegions().get(0);
+ CellDesignerAntisenseRnaRegion region = antisenseRna.getRegions().get(0);
+ CellDesignerAntisenseRnaRegion region2 = antisenseRna2.getRegions().get(0);
assertEquals(region.getIdAntisenseRnaRegion(), region2.getIdAntisenseRnaRegion());
assertEquals(region.getName(), region2.getName());
assertEquals(region.getSize(), region2.getSize(), 1e-6);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
index 7cb2a41be7..fbaa3f2481 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
@@ -22,12 +22,12 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.alias.ComplexAliasXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
public class ComplexParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ComplexParserTest.class);
@@ -54,7 +54,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
public void testComplexState() throws Exception {
try {
Model model = getModelForFile("testFiles/problematic/complex_with_state.xml");
- ComplexAlias complex = (ComplexAlias) model.getAliasByAliasId("csa1");
+ Complex complex = (Complex) model.getAliasByAliasId("csa1");
assertEquals("test state", complex.getStructuralState());
} catch (Exception e) {
e.printStackTrace();
@@ -83,7 +83,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
public void testParseInvalidInputNode2() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- ComplexSpecies element = new ComplexSpecies();
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
element.setElementId("s3");
elements.addElement(element);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
@@ -103,7 +103,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
public void testParseInvalidInputNode3() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- ComplexSpecies element = new ComplexSpecies();
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
element.setElementId("s3");
elements.addElement(element);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
@@ -123,7 +123,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
public void testParseInvalidInputNode4() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- ComplexSpecies element = new ComplexSpecies();
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
element.setElementId("s3");
elements.addElement(element);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
@@ -143,7 +143,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
public void testParseInvalidInputNode5() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- ComplexSpecies element = new ComplexSpecies();
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
element.setElementId("s3");
elements.addElement(element);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
@@ -164,9 +164,9 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
try {
Model model = new ModelFullIndexed(null);
- CompartmentAlias ca = new CompartmentAlias(testCompartmentAliasId);
+ Compartment ca = new Compartment(testCompartmentAliasId);
- ComplexAlias alias = new ComplexAlias(testAliasId);
+ Complex alias = new Complex(testAliasId);
alias.setParent(ca);
@@ -189,9 +189,9 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
try {
Model model = new ModelFullIndexed(null);
- CompartmentAlias ca = new CompartmentAlias(testCompartmentAliasId);
+ Compartment ca = new Compartment(testCompartmentAliasId);
- ComplexAlias alias = new ComplexAlias(testAliasId);
+ Complex alias = new Complex(testAliasId);
alias.setCompartmentAlias(ca);
@@ -216,19 +216,19 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
ModelData md = new ModelData();
md.setModel(model);
- CompartmentAlias ca2 = new CompartmentAlias(testCompartmentAliasId2);
+ Compartment ca2 = new Compartment(testCompartmentAliasId2);
ca2.setX(6);
ca2.setY(6);
ca2.setWidth(190);
ca2.setHeight(190);
- CompartmentAlias ca = new CompartmentAlias(testCompartmentAliasId);
+ Compartment ca = new Compartment(testCompartmentAliasId);
ca.setX(5);
ca.setY(5);
ca.setWidth(200);
ca.setHeight(200);
- List<CompartmentAlias> list = new ArrayList<>();
+ List<Compartment> list = new ArrayList<>();
list.add(ca);
list.add(ca2);
@@ -236,7 +236,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
when(model.getCompartmentsAliases()).thenReturn(list);
when(model.getModelData()).thenReturn(md);
- ComplexAlias alias = new ComplexAlias(testAliasId);
+ Complex alias = new Complex(testAliasId);
alias.setX(10);
alias.setY(10);
alias.setWidth(100);
@@ -262,9 +262,9 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
try {
Model model = new ModelFullIndexed(null);
- ComplexAlias ca = new ComplexAlias(testCompartmentAliasId);
+ Complex ca = new Complex(testCompartmentAliasId);
- ComplexAlias alias = new ComplexAlias(testAliasId);
+ Complex alias = new Complex(testAliasId);
alias.setParent(ca);
@@ -287,7 +287,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
try {
Model model = new ModelFullIndexed(null);
- ComplexAlias alias = new ComplexAlias(testAliasId);
+ Complex alias = new Complex(testAliasId);
alias.setActivity(true);
@@ -309,13 +309,13 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
public void testAddInvalidReference() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- ComplexSpecies element = new ComplexSpecies();
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
element.setElementId("s2");
elements.addElement(element);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
- ComplexAlias child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml"));
+ Complex child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml"));
parser.addReference(child);
fail("Exception expected");
@@ -332,12 +332,12 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
public void testParseWithEmptyState() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- ComplexSpecies element = new ComplexSpecies("s2597");
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies("s2597");
elements.addElement(element);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
- ComplexAlias child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml"));
+ Complex child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml"));
assertNotNull(child);
assertNull(child.getAliasStateLabel());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
index f36a847416..6bbec67745 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
@@ -22,11 +22,11 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class GeneXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(GeneXmlParserTest.class.getName());
@@ -51,8 +51,8 @@ public class GeneXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpecies() {
try {
String xmlString = readFile(testGeneFile);
- Pair<String, Gene> result = geneParser.parseXmlElement(xmlString);
- Gene gene = result.getRight();
+ Pair<String, CellDesignerGene> result = geneParser.parseXmlElement(xmlString);
+ CellDesignerGene gene = result.getRight();
assertEquals("gn3", result.getLeft());
assertEquals("BCL6", gene.getName());
assertTrue(gene.getNotes().contains("B-cell CLL/lymphoma 6"));
@@ -66,8 +66,8 @@ public class GeneXmlParserTest extends CellDesignerTestFunctions {
public void testToXml() throws Exception {
try {
String xmlString = readFile(testGeneFile);
- Pair<String, Gene> result = geneParser.parseXmlElement(xmlString);
- Gene gene = result.getRight();
+ Pair<String, CellDesignerGene> result = geneParser.parseXmlElement(xmlString);
+ CellDesignerGene gene = result.getRight();
String transformedXml = geneParser.toXml(gene.createAlias());
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
@@ -76,8 +76,8 @@ public class GeneXmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("celldesigner:gene", root.item(0).getNodeName());
- Pair<String, Gene> result2 = geneParser.parseXmlElement(geneParser.toXml(gene.createAlias()));
- Gene gene2 = result2.getRight();
+ Pair<String, CellDesignerGene> result2 = geneParser.parseXmlElement(geneParser.toXml(gene.createAlias()));
+ CellDesignerGene gene2 = result2.getRight();
assertEquals(gene.getName(), gene2.getName());
assertTrue(gene2.getNotes().trim().contains(gene.getNotes().trim()));
} catch (Exception e) {
@@ -90,9 +90,9 @@ public class GeneXmlParserTest extends CellDesignerTestFunctions {
public void testParsePhosphorylatedGene() throws Exception {
try {
Model model = getModelForFile("testFiles/problematic/phosphorylated_gene.xml");
- GeneAlias gene = (GeneAlias) model.getAliasByAliasId("sa1");
+ Gene gene = (Gene) model.getAliasByAliasId("sa1");
assertEquals(1, gene.getModificationResidues().size());
- ModificationResidueAlias residue = gene.getModificationResidues().get(0);
+ ModificationResidue residue = gene.getModificationResidues().get(0);
assertEquals(ModificationState.PHOSPHORYLATED, residue.getState());
assertEquals("some name", residue.getName());
@@ -147,7 +147,7 @@ public class GeneXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testModificationResidueToXml() throws Exception {
try {
- ModificationResidueAlias mr = new ModificationResidueAlias();
+ ModificationResidue mr = new ModificationResidue();
mr.setIdModificationResidue("i");
mr.setName("a");
mr.setSide("2");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java
index c3277a4455..314077d9dc 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java
@@ -10,7 +10,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class InternalModelSpeciesDataTest {
@@ -40,7 +41,7 @@ public class InternalModelSpeciesDataTest {
public void testUpdateUnknownSpecies() {
InternalModelSpeciesData data = new InternalModelSpeciesData();
try {
- data.updateSpecies(new Species(), null);
+ data.updateSpecies(new CellDesignerSpecies<GenericProtein>(), null);
fail("Exception expected");
} catch (InvalidArgumentException e) {
assertTrue(e.getMessage().contains("Unknown species type"));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java
index 2ba1853a76..4404192113 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java
@@ -13,7 +13,8 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
public class ProteinMappingTest {
Logger logger = Logger.getLogger(ProteinMappingTest.class);
@@ -40,7 +41,7 @@ public class ProteinMappingTest {
@Test
public void testCreateInvalidProteinImpl() throws Exception {
// artificial implementation of Protein that is invalid
- class InvalidProtein extends Protein {
+ class InvalidProtein extends CellDesignerProtein<TruncatedProtein> {
private static final long serialVersionUID = 1L;
@SuppressWarnings("unused")
@@ -52,7 +53,7 @@ public class ProteinMappingTest {
// mopdify one of the elements of ProteinMapping so it will have invalid
// implementation
ProteinMapping typeToModify = ProteinMapping.GENERIC_PROTEIN;
- Class<? extends Protein> clazz = typeToModify.getCellDesignerClazz();
+ Class<? extends CellDesignerProtein<?>> clazz = typeToModify.getCellDesignerClazz();
try {
Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
index c411af0320..b09e9356c8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParserTest.java
@@ -23,9 +23,9 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.model.map.species.Protein;
public class ProteinXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
@@ -50,11 +50,11 @@ public class ProteinXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpecies() throws Exception {
try {
String xmlString = readFile(testProteinFile);
- Pair<String, Protein<?>> result = proteinParser.parseXmlElement(xmlString);
- Protein<?> protein = result.getRight();
+ Pair<String, CellDesignerProtein<?>> result = proteinParser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> protein = result.getRight();
assertEquals("pr23", result.getLeft());
assertEquals("SDHA", protein.getName());
- assertTrue(protein instanceof GenericProtein);
+ assertTrue(protein instanceof CellDesignerGenericProtein);
assertEquals(1, protein.getModificationResidues().size());
assertEquals("rs1", protein.getModificationResidues().get(0).getIdModificationResidue());
assertEquals("S176 bla bla", protein.getModificationResidues().get(0).getName());
@@ -72,8 +72,8 @@ public class ProteinXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testProteinFile);
- Pair<String, Protein<?>> result = proteinParser.parseXmlElement(xmlString);
- Protein<?> protein = result.getRight();
+ Pair<String, CellDesignerProtein<?>> result = proteinParser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> protein = result.getRight();
String transformedXml = proteinParser.toXml(protein.createAlias("id"));
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
@@ -82,8 +82,8 @@ public class ProteinXmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("celldesigner:protein", root.item(0).getNodeName());
- Pair<String, Protein<?>> result2 = proteinParser.parseXmlElement(proteinParser.toXml(protein.createAlias("id")));
- Protein<?> protein2 = result2.getRight();
+ Pair<String, CellDesignerProtein<?>> result2 = proteinParser.parseXmlElement(proteinParser.toXml(protein.createAlias("id")));
+ CellDesignerProtein<?> protein2 = result2.getRight();
assertEquals(protein.getName(), protein2.getName());
assertEquals(protein.getClass(), protein2.getClass());
assertEquals(protein.getModificationResidues().size(), protein2.getModificationResidues().size());
@@ -160,7 +160,7 @@ public class ProteinXmlParserTest extends CellDesignerTestFunctions {
@Test
public void testInvalidProteinToXml() throws Exception {
try {
- proteinParser.toXml(Mockito.mock(ProteinAlias.class));
+ proteinParser.toXml(Mockito.mock(Protein.class));
fail("Exception expected");
} catch (InvalidArgumentException e) {
assertTrue(e.getMessage().contains("Invalid protein class type"));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java
index 34757ada7c..e5624c6569 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParserTest.java
@@ -22,7 +22,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
public class RnaXmlParserTest extends CellDesignerTestFunctions {
protected Logger logger = Logger.getLogger(RnaXmlParserTest.class.getName());
@@ -49,8 +49,8 @@ public class RnaXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpecies() throws Exception {
try {
String xmlString = readFile(testRnaFile);
- Pair<String, Rna> result = rnaParser.parseXmlElement(xmlString);
- Rna rna = result.getRight();
+ Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
+ CellDesignerRna rna = result.getRight();
assertEquals("rn36", result.getLeft());
assertEquals("BCL6", rna.getName());
assertTrue(rna.getNotes().contains("B-cell CLL/lymphoma "));
@@ -64,8 +64,8 @@ public class RnaXmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesWithRegion() throws Exception {
try {
String xmlString = readFile(testRnaFile2);
- Pair<String, Rna> result = rnaParser.parseXmlElement(xmlString);
- Rna rna = result.getRight();
+ Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
+ CellDesignerRna rna = result.getRight();
assertNotNull(rna);
assertNotNull(rna.getRegions());
assertEquals(1, rna.getRegions().size());
@@ -80,8 +80,8 @@ public class RnaXmlParserTest extends CellDesignerTestFunctions {
public void testToXml() throws Exception {
try {
String xmlString = readFile(testRnaFile);
- Pair<String, Rna> result = rnaParser.parseXmlElement(xmlString);
- Rna rna = result.getRight();
+ Pair<String, CellDesignerRna> result = rnaParser.parseXmlElement(xmlString);
+ CellDesignerRna rna = result.getRight();
String transformedXml = rnaParser.toXml(rna.createAlias("id"));
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
@@ -91,8 +91,8 @@ public class RnaXmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("celldesigner:RNA", root.item(0).getNodeName());
- Pair<String, Rna> result2 = rnaParser.parseXmlElement(rnaParser.toXml(rna.createAlias("id")));
- Rna rna2 = result2.getRight();
+ Pair<String, CellDesignerRna> result2 = rnaParser.parseXmlElement(rnaParser.toXml(rna.createAlias("id")));
+ CellDesignerRna rna2 = result2.getRight();
assertEquals(rna.getName(), rna2.getName());
assertTrue(rna2.getNotes().trim().contains(rna.getNotes().trim()));
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java
index 7a59c5abe6..c44b0e7632 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java
@@ -12,10 +12,11 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Species;
public class SpeciesCollectionTest {
Logger logger = Logger.getLogger(SpeciesCollectionTest.class);
@@ -31,8 +32,8 @@ public class SpeciesCollectionTest {
@Test
public void testAdd() {
try {
- SpeciesCollection<Gene> coll = new SpeciesCollection<Gene>();
- Gene g = new Gene();
+ SpeciesCollection<CellDesignerGene> coll = new SpeciesCollection<CellDesignerGene>();
+ CellDesignerGene g = new CellDesignerGene();
g.setElementId("general Id");
coll.add(g, "geneId");
assertNotNull(coll.getSpeciesListByLocalId("geneId"));
@@ -46,16 +47,16 @@ public class SpeciesCollectionTest {
@Test
public void testUpdate() {
try {
- SpeciesCollection<Protein> coll = new SpeciesCollection<>();
- Protein protein = new GenericProtein();
+ SpeciesCollection<CellDesignerProtein<?>> coll = new SpeciesCollection<>();
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
protein.setElementId("");
coll.add(protein, "prot id");
- Protein p2 = new GenericProtein();
+ CellDesignerProtein<?> p2 = new CellDesignerGenericProtein();
p2.setElementId("id2");
coll.updateSpeciesByLocalId(p2, "prot id");
assertEquals(1, coll.getSpeciesListByLocalId("prot id").size());
- Protein p3 = coll.getSpeciesListByLocalId("prot id").get(0);
+ CellDesignerProtein<?> p3 = coll.getSpeciesListByLocalId("prot id").get(0);
assertEquals(protein, p3);
@@ -68,16 +69,16 @@ public class SpeciesCollectionTest {
@Test
public void testUpdateWithTypeChange() {
try {
- SpeciesCollection<Protein> coll = new SpeciesCollection<Protein>();
- Protein p = new Protein();
+ SpeciesCollection<CellDesignerProtein<?>> coll = new SpeciesCollection<>();
+ CellDesignerProtein<?> p = new CellDesignerProtein<>();
p.setElementId("");
coll.add(p, "prot id");
- GenericProtein p2 = new GenericProtein();
+ CellDesignerGenericProtein p2 = new CellDesignerGenericProtein();
p2.setElementId("id2");
coll.updateSpeciesByLocalId(p2, "prot id");
assertEquals(1, coll.getSpeciesListByLocalId("prot id").size());
- Protein p3 = coll.getSpeciesListByLocalId("prot id").get(0);
+ CellDesignerProtein<?> p3 = coll.getSpeciesListByLocalId("prot id").get(0);
// we don't have generic data anymore but new instance
assertFalse(p3.equals(p));
@@ -92,15 +93,15 @@ public class SpeciesCollectionTest {
@Test
public void testCreateNewInstance() {
try {
- SpeciesCollection<Species> coll = new SpeciesCollection<>();
- class InvalidSpecies extends Species {
+ SpeciesCollection<CellDesignerSpecies<?>> coll = new SpeciesCollection<>();
+ class InvalidSpecies extends CellDesignerSpecies<Species> {
private static final long serialVersionUID = 1L;
public InvalidSpecies() {
}
@SuppressWarnings("unused")
- public InvalidSpecies(final Species sp) {
+ public InvalidSpecies(final CellDesignerSpecies<?> sp) {
throw new NotImplementedException();
}
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java
index 67222b2161..ca6b5b5173 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java
@@ -20,21 +20,21 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
static Logger logger = Logger.getLogger(SpeciesCollectionXmlParserTest.class);
@@ -58,7 +58,7 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
@Before
public void setUp() throws Exception {
elements = new CellDesignerElementCollection();
- parser = new SpeciesCollectionXmlParser(model, elements);
+ parser = new SpeciesCollectionXmlParser(elements);
}
@After
@@ -70,9 +70,9 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testRnaListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlRnaCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlRnaCollection(node);
assertEquals(2, list.size());
- assertTrue(list.get(0).getRight() instanceof Rna);
+ assertTrue(list.get(0).getRight() instanceof CellDesignerRna);
} catch (Exception e) {
throw e;
}
@@ -139,16 +139,16 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testRnaListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlRnaCollection(node);
- List<RnaAlias> arList = new ArrayList<>();
- for (Pair<String, ? extends Species<?>> pair : list) {
- arList.add((RnaAlias) pair.getRight().createAlias());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlRnaCollection(node);
+ List<Rna> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((Rna) pair.getRight().createAlias());
}
String convertedString = parser.rnaCollectionToXmlString(arList);
assertNotNull(convertedString);
node = getNodeFromXmlString(convertedString);
assertEquals("celldesigner:listOfRNAs", node.getNodeName());
- List<Pair<String, ? extends Species<?>>> list2 = parser.parseXmlRnaCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlRnaCollection(node);
assertNotNull(list2);
assertEquals(list.size(), list2.size());
assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
@@ -162,9 +162,9 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testGeneListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlGeneCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlGeneCollection(node);
assertEquals(2, list.size());
- assertTrue(list.get(0).getRight() instanceof Gene);
+ assertTrue(list.get(0).getRight() instanceof CellDesignerGene);
} catch (Exception exception) {
fail("Unexpected exception occurred");
}
@@ -175,16 +175,16 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testGeneListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlGeneCollection(node);
- List<GeneAlias> arList = new ArrayList<>();
- for (Pair<String, ? extends Species> pair : list) {
- arList.add((GeneAlias) pair.getRight().createAlias());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlGeneCollection(node);
+ List<Gene> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((Gene) pair.getRight().createAlias());
}
String convertedString = parser.geneCollectionToXmlString(arList);
assertNotNull(convertedString);
node = getNodeFromXmlString(convertedString);
assertEquals("celldesigner:listOfGenes", node.getNodeName());
- List<Pair<String, ? extends Species<?>>> list2 = parser.parseXmlGeneCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlGeneCollection(node);
assertNotNull(list2);
assertEquals(list.size(), list2.size());
assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
@@ -198,9 +198,9 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testProteinListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlProteinCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlProteinCollection(node);
assertEquals(4, list.size());
- assertTrue(list.get(0).getRight() instanceof Protein);
+ assertTrue(list.get(0).getRight() instanceof CellDesignerProtein);
} catch (Exception exception) {
fail("Unexpected exception occurred");
}
@@ -211,16 +211,16 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testProteinListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlProteinCollection(node);
- List<ProteinAlias> arList = new ArrayList<>();
- for (Pair<String, ? extends Species<?>> pair : list) {
- arList.add((ProteinAlias) pair.getRight().createAlias("" + idCounter++));
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlProteinCollection(node);
+ List<Protein> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((Protein) pair.getRight().createAlias("" + idCounter++));
}
String convertedString = parser.proteinCollectionToXmlString(arList);
assertNotNull(convertedString);
node = getNodeFromXmlString(convertedString);
assertEquals("celldesigner:listOfProteins", node.getNodeName());
- List<Pair<String, ? extends Species<?>>> list2 = parser.parseXmlProteinCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlProteinCollection(node);
assertNotNull(list2);
assertEquals(list.size(), list2.size());
assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
@@ -235,9 +235,9 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testAntisenseRnaListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
assertEquals(2, list.size());
- assertTrue(list.get(0).getRight() instanceof AntisenseRna);
+ assertTrue(list.get(0).getRight() instanceof CellDesignerAntisenseRna);
} catch (Exception exception) {
fail("Unexpected exception occurred");
}
@@ -248,16 +248,16 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testAntisenseRnaListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
- List<AntisenseRnaAlias> arList = new ArrayList<>();
- for (Pair<String, ? extends Species<?>> pair : list) {
- arList.add((AntisenseRnaAlias) pair.getRight().createAlias());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
+ List<AntisenseRna> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((AntisenseRna) pair.getRight().createAlias());
}
String convertedString = parser.antisenseRnaCollectionToXmlString(arList);
assertNotNull(convertedString);
node = getNodeFromXmlString(convertedString);
assertEquals("celldesigner:listOfAntisenseRNAs", node.getNodeName());
- List<Pair<String, ? extends Species<?>>> list2 = parser.parseXmlAntisenseRnaCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlAntisenseRnaCollection(node);
assertNotNull(list2);
assertEquals(list.size(), list2.size());
assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
@@ -272,7 +272,7 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testSbmlListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseSbmlSpeciesCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseSbmlSpeciesCollection(node);
assertEquals(9, list.size());
} catch (Exception e) {
e.printStackTrace();
@@ -299,27 +299,27 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testSbmlListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseSbmlSpeciesCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseSbmlSpeciesCollection(node);
Model model = new ModelFullIndexed(null);
int x = 0;
- List<SpeciesAlias> speciesList = new ArrayList<>();
- for (Pair<String, ? extends Species<?>> el : list) {
- Species<?> species = el.getRight();
- if (species.getClass() == Protein.class) {
- species = new GenericProtein(species);
+ List<Species> speciesList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> el : list) {
+ CellDesignerSpecies<?> species = el.getRight();
+ if (species.getClass() == CellDesignerProtein.class) {
+ species = new CellDesignerGenericProtein(species);
}
species.setModel(model);
- SpeciesAlias alias = species.createAlias("alias" + (x++));
+ Species alias = species.createAlias("alias" + (x++));
model.addAlias(alias);
speciesList.add(alias);
}
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
String convertedString = parser.speciesCollectionToSbmlString(speciesList);
assertNotNull(convertedString);
node = getNodeFromXmlString(convertedString);
assertEquals("listOfSpecies", node.getNodeName());
- List<Pair<String, ? extends Species<?>>> list2 = parser.parseSbmlSpeciesCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseSbmlSpeciesCollection(node);
assertNotNull(list2);
assertEquals(list.size(), list2.size());
assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
@@ -334,14 +334,14 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
try {
String xmlString = readFile(testDirectory + testIncludedListXmlFile);
Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends Species<?>>> list = parser.parseIncludedSpeciesCollection(node);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseIncludedSpeciesCollection(node);
assertEquals(3, list.size());
int complexes = 0;
int proteins = 0;
- for (Pair<String, ? extends Species<?>> species : list) {
- if (species.getRight() instanceof ComplexSpecies)
+ for (Pair<String, ? extends CellDesignerSpecies<?>> species : list) {
+ if (species.getRight() instanceof CellDesignerComplexSpecies)
complexes++;
- if (species.getRight() instanceof Protein)
+ if (species.getRight() instanceof CellDesignerProtein)
proteins++;
}
assertEquals(1, complexes);
@@ -435,7 +435,7 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
// this is only for test coverage puropse
- SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(new ModelFullIndexed(null), elements);
+ SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
Field field = SpeciesCollectionXmlParser.class.getDeclaredField("helpParser");
field.setAccessible(true);
try {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
index 1d70306270..c4a2530988 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesMappingTest.java
@@ -11,7 +11,8 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Protein;
public class SpeciesMappingTest {
@@ -38,7 +39,7 @@ public class SpeciesMappingTest {
@Test
public void testCreateInvalidSpeciesImpl() throws Exception {
// artificial implementation of Species that is invalid
- class InvalidSpecies extends Species {
+ class InvalidSpecies extends CellDesignerSpecies<Protein> {
private static final long serialVersionUID = 1L;
@SuppressWarnings("unused")
@@ -50,7 +51,7 @@ public class SpeciesMappingTest {
// mopdify one of the elements of SpeciesMapping so it will have invalid
// implementation
SpeciesMapping typeToModify = SpeciesMapping.ANTISENSE_RNA;
- Class<? extends Species> clazz = typeToModify.getCellDesignerClazz();
+ Class<? extends CellDesignerSpecies> clazz = typeToModify.getCellDesignerClazz();
try {
Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
@@ -59,7 +60,7 @@ public class SpeciesMappingTest {
// and check if we catch properly information about problematic
// implementation
- typeToModify.createSpecies(new Species());
+ typeToModify.createSpecies(new CellDesignerSpecies<Protein>());
fail("Exceptione expected");
} catch (InvalidStateException e) {
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
index a9f75e8ea8..5e35e8399e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
@@ -26,26 +26,26 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRnaRegion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.RnaRegion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SpeciesState;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@SuppressWarnings("unused")
@@ -85,8 +85,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesAntisenseRna() throws Exception {
try {
String xmlString = readFile(testDirectory + testAntisenseRnaFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- AntisenseRna species = (AntisenseRna) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
assertEquals("s2", species.getElementId());
assertEquals("s3", species.getName());
assertEquals(new Integer(2), species.getInitialAmount());
@@ -102,8 +102,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlAntisenseRna() throws Exception {
try {
String xmlString = readFile(testDirectory + testAntisenseRnaFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- AntisenseRna species = (AntisenseRna) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -114,8 +114,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- AntisenseRna species2 = (AntisenseRna) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerAntisenseRna species2 = (CellDesignerAntisenseRna) result2.getRight();
assertEquals(species.getName(), species2.getName());
assertEquals(species.getParent(), species2.getParent());
@@ -134,8 +134,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesComplex() throws Exception {
try {
String xmlString = readFile(testDirectory + testComplexFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- ComplexSpecies species = (ComplexSpecies) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
assertNotNull(species);
assertEquals("s6549", species.getElementId());
assertEquals("LC3-II", species.getName());
@@ -150,8 +150,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlComplex() throws Exception {
try {
String xmlString = readFile(testDirectory + testComplexFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- ComplexSpecies species = (ComplexSpecies) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -162,8 +162,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- ComplexSpecies species2 = (ComplexSpecies) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerComplexSpecies species2 = (CellDesignerComplexSpecies) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -182,8 +182,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesDegraded() throws Exception {
try {
String xmlString = readFile(testDirectory + testDegradedFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Degraded species = (Degraded) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
assertNotNull(species);
assertEquals("s1275", species.getElementId());
assertEquals("s1275", species.getName());
@@ -199,8 +199,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlDegraded() throws Exception {
try {
String xmlString = readFile(testDirectory + testDegradedFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Degraded species = (Degraded) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -211,8 +211,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- Degraded species2 = (Degraded) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerDegraded species2 = (CellDesignerDegraded) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -230,8 +230,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesDrug() throws Exception {
try {
String xmlString = readFile(testDirectory + testDrugFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Drug species = (Drug) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDrug species = (CellDesignerDrug) result.getRight();
assertEquals("s6104", species.getElementId());
assertEquals("geldanamycin", species.getName());
assertEquals(new Integer(0), species.getCharge());
@@ -245,8 +245,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlDrug() throws Exception {
try {
String xmlString = readFile(testDirectory + testDrugFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Drug species = (Drug) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDrug species = (CellDesignerDrug) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -257,8 +257,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- Drug species2 = (Drug) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerDrug species2 = (CellDesignerDrug) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -276,8 +276,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesGene() throws Exception {
try {
String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Gene species = (Gene) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
assertEquals("s5916", species.getElementId());
assertEquals("Ptgr1", species.getName());
@@ -292,20 +292,20 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@Test
public void testParseXmlSpeciesGeneWithModelUpdate() throws Exception {
try {
- Species gene = new Gene();
+ CellDesignerSpecies<?> gene = new CellDesignerGene();
gene.setElementId("s5916");
InternalModelSpeciesData modelData = new InternalModelSpeciesData();
modelData.updateSpecies(gene, "");
SpeciesSbmlParser complexParser = new SpeciesSbmlParser(elements);
- Gene oldGene = new Gene();
+ CellDesignerGene oldGene = new CellDesignerGene();
oldGene.setElementId("s5916");
oldGene.setName("Ptgr1");
modelData.updateSpecies(oldGene, "gn95");
String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends Species> result = complexParser.parseXmlElement(xmlString);
- Gene species = (Gene) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = complexParser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
modelData.updateSpecies(species, result.getLeft());
assertEquals("s5916", species.getElementId());
@@ -321,8 +321,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlGene() throws Exception {
try {
String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Gene species = (Gene) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -333,8 +333,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- Gene species2 = (Gene) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerGene species2 = (CellDesignerGene) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -355,8 +355,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesIon() throws Exception {
try {
String xmlString = readFile(testDirectory + testIonFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Ion species = (Ion) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerIon species = (CellDesignerIon) result.getRight();
assertEquals("s6029", species.getElementId());
assertEquals("Pi", species.getName());
@@ -372,8 +372,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlIon() throws Exception {
try {
String xmlString = readFile(testDirectory + testIonFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Ion species = (Ion) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerIon species = (CellDesignerIon) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -384,8 +384,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(xmlString);
- Ion species2 = (Ion) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(xmlString);
+ CellDesignerIon species2 = (CellDesignerIon) result2.getRight();
assertNotNull(species2);
assertEquals(species.getElementId(), species2.getElementId());
@@ -408,8 +408,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesPhenotype() throws Exception {
try {
String xmlString = readFile(testDirectory + testPhenotypeFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Phenotype species = (Phenotype) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
assertEquals("s5462", species.getElementId());
assertEquals("Neuronal damage and death", species.getName());
@@ -424,8 +424,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlPhenotype() throws Exception {
try {
String xmlString = readFile(testDirectory + testPhenotypeFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Phenotype species = (Phenotype) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -436,8 +436,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- Phenotype species2 = (Phenotype) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerPhenotype species2 = (CellDesignerPhenotype) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -458,8 +458,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesProtein() throws Exception {
try {
String xmlString = readFile(testDirectory + testProteinFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Protein species = (Protein) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
assertEquals("s5456", species.getElementId());
assertEquals("PTPRC", species.getName());
@@ -477,8 +477,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlProtein() throws Exception {
try {
String xmlString = readFile(testDirectory + testProteinFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- GenericProtein species = new GenericProtein(result.getRight());
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein(result.getRight());
String transformedXml = parser.toXml(species.createAlias("" + idCounter++));
assertNotNull(transformedXml);
@@ -489,8 +489,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias("" + idCounter++)));
- Protein species2 = (Protein) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias("" + idCounter++)));
+ CellDesignerProtein<?> species2 = (CellDesignerProtein<?>) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -511,8 +511,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesRna() throws Exception {
try {
String xmlString = readFile(testDirectory + testRnaFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Rna species = (Rna) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerRna species = (CellDesignerRna) result.getRight();
assertEquals("s5914", species.getElementId());
assertEquals("Fmo3", species.getName());
@@ -529,8 +529,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlRna() throws Exception {
try {
String xmlString = readFile(testDirectory + testRnaFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Rna species = (Rna) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerRna species = (CellDesignerRna) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -541,8 +541,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- Rna species2 = (Rna) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerRna species2 = (CellDesignerRna) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -563,8 +563,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesSimpleMolecule() throws Exception {
try {
String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- SimpleMolecule species = (SimpleMolecule) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
assertEquals("s5463", species.getElementId());
assertEquals("Peroxides", species.getName());
assertEquals(new Integer(0), species.getInitialAmount());
@@ -578,8 +578,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlSimpleMolecule() throws Exception {
try {
String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- SimpleMolecule species = (SimpleMolecule) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
String transformedXml = parser.toXml(species.createAlias("" + idCounter++));
assertNotNull(transformedXml);
@@ -590,8 +590,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias("" + idCounter++)));
- SimpleMolecule species2 = (SimpleMolecule) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias("" + idCounter++)));
+ CellDesignerSimpleMolecule species2 = (CellDesignerSimpleMolecule) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -612,8 +612,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testParseXmlSpeciesUnknown() throws Exception {
try {
String xmlString = readFile(testDirectory + testUnknownFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Unknown species = (Unknown) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
assertEquals("s1356", species.getElementId());
assertEquals("unidentified caspase acting on Occludin", species.getName());
assertEquals(new Integer(0), species.getInitialAmount());
@@ -628,8 +628,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testToXmlUnknown() throws Exception {
try {
String xmlString = readFile(testDirectory + testUnknownFile);
- Pair<String, ? extends Species> result = parser.parseXmlElement(xmlString);
- Unknown species = (Unknown) result.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
String transformedXml = parser.toXml(species.createAlias());
assertNotNull(transformedXml);
@@ -640,8 +640,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
NodeList root = doc.getChildNodes();
assertEquals("species", root.item(0).getNodeName());
- Pair<String, ? extends Species> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
- Unknown species2 = (Unknown) result2.getRight();
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(parser.toXml(species.createAlias()));
+ CellDesignerUnknown species2 = (CellDesignerUnknown) result2.getRight();
assertNotNull(species2);
assertEquals(species.getName(), species2.getName());
@@ -857,7 +857,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@Test
public void testToXmlWithDefaultCompartment() throws Exception {
try {
- GenericProtein species = new GenericProtein();
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein();
String xml = parser.toXml(species.createAlias("EL_ID"));
assertTrue(xml.contains("EL_ID"));
} catch (Exception e) {
@@ -869,7 +869,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@Test
public void testInvalidSpeciesIdentityToXml() throws Exception {
try {
- SpeciesAlias species = Mockito.mock(SpeciesAlias.class);
+ Species species = Mockito.mock(Species.class);
parser.speciesIdentityToXml(species);
fail("Excepiton expected");
} catch (InvalidArgumentException e) {
@@ -883,7 +883,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@Test
public void testSpeciesIdentityToXml() throws Exception {
try {
- GenericProteinAlias species = new GenericProteinAlias("xx");
+ GenericProtein species = new GenericProtein("xx");
species.setHypothetical(true);
String xml = parser.speciesIdentityToXml(species);
assertTrue(xml.contains("<celldesigner:hypothetical>true</celldesigner:hypothetical>"));
@@ -912,8 +912,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testProcessInvalidStateDataInSpecies() throws Exception {
try {
SpeciesState state = new SpeciesState();
- state.addModificationResidue(new ModificationResidue());
- Species species = new ComplexSpecies();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -930,7 +930,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
try {
SpeciesState state = new SpeciesState();
state.setStructuralState("state");
- Species species = new Gene();
+ CellDesignerGene species = new CellDesignerGene();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -947,7 +947,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
try {
SpeciesState state = new SpeciesState();
state.setStructuralState("state");
- Species species = new Rna();
+ CellDesignerRna species = new CellDesignerRna();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -963,8 +963,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testProcessInvalidStateDataInSpecies4() throws Exception {
try {
SpeciesState state = new SpeciesState();
- state.addModificationResidue(new ModificationResidue());
- Species species = new SimpleMolecule();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -981,7 +981,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
try {
SpeciesState state = new SpeciesState();
state.setStructuralState("state");
- Species species = new SimpleMolecule();
+ CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -998,7 +998,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
try {
SpeciesState state = new SpeciesState();
state.setStructuralState("state");
- Species species = new AntisenseRna();
+ CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -1015,7 +1015,7 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
try {
SpeciesState state = new SpeciesState();
state.setStructuralState("state");
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -1031,8 +1031,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testProcessInvalidStateDataInSpecies8() throws Exception {
try {
SpeciesState state = new SpeciesState();
- state.addModificationResidue(new ModificationResidue());
- Species species = new Species();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
parser.processStateDataInSpecies(species, state);
fail("Exception expected");
@@ -1048,8 +1048,8 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
public void testProcessAntisenseRnaStateDataInSpecies() throws Exception {
try {
SpeciesState state = new SpeciesState();
- state.addModificationResidue(new ModificationResidue());
- AntisenseRna species = new AntisenseRna();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
parser.processStateDataInSpecies(species, state);
@@ -1064,11 +1064,11 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@Test
public void testCreateRnaRegion() throws Exception {
try {
- ModificationResidue mr = new ModificationResidue();
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
mr.setSize(1.0);
mr.setAngle(1.0);
- RnaRegion region = parser.createRnaRegion(mr);
+ CellDesignerRnaRegion region = parser.createRnaRegion(mr);
assertNotNull(region.getPos());
} catch (Exception e) {
@@ -1080,11 +1080,11 @@ public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@Test
public void testCreateAntisenseRnaRegion() throws Exception {
try {
- ModificationResidue mr = new ModificationResidue();
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
mr.setSize(1.0);
mr.setAngle(1.0);
- AntisenseRnaRegion region = parser.createAntisenseRnaRegion(mr);
+ CellDesignerAntisenseRnaRegion region = parser.createAntisenseRnaRegion(mr);
assertNotNull(region.getPos());
} catch (Exception e) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
index 842bdd559e..0b09958461 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
@@ -9,14 +9,14 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRnaComparator;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRnaComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion.AntisenseRnaRegionType;
public class AntisenseRnaComparatorTest {
- AntisenseRnaComparator comparator = new AntisenseRnaComparator();
+ CellDesignerAntisenseRnaComparator comparator = new CellDesignerAntisenseRnaComparator();
@Before
public void setUp() throws Exception {
@@ -29,18 +29,14 @@ public class AntisenseRnaComparatorTest {
@Test
public void testEquals() {
try {
- AntisenseRna aRna1 = createAntisenseRna();
- AntisenseRna aRna2 = createAntisenseRna();
+ CellDesignerAntisenseRna aRna1 = createAntisenseRna();
+ CellDesignerAntisenseRna aRna2 = createAntisenseRna();
assertEquals(0, comparator.compare(aRna1, aRna1));
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setElementId("AAA");
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -50,8 +46,8 @@ public class AntisenseRnaComparatorTest {
@Test
public void testDifferent() {
try {
- AntisenseRna aRna1 = createAntisenseRna();
- AntisenseRna aRna2 = createAntisenseRna();
+ CellDesignerAntisenseRna aRna1 = createAntisenseRna();
+ CellDesignerAntisenseRna aRna2 = createAntisenseRna();
aRna1.getRegions().get(0).setName("bla");
assertTrue(comparator.compare(aRna1, aRna2) != 0);
assertTrue(comparator.compare(aRna2, aRna1) != 0);
@@ -68,11 +64,11 @@ public class AntisenseRnaComparatorTest {
assertTrue(comparator.compare(aRna2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- AntisenseRna unknown = createAntisenseRna();
+ CellDesignerAntisenseRna unknown = createAntisenseRna();
unknown.setName("n");
assertTrue(comparator.compare(unknown, aRna2) != 0);
- assertTrue(comparator.compare(unknown, new AntisenseRna() {
+ assertTrue(comparator.compare(unknown, new CellDesignerAntisenseRna() {
private static final long serialVersionUID = 1L;
}) != 0);
} catch (Exception e) {
@@ -81,10 +77,10 @@ public class AntisenseRnaComparatorTest {
}
}
- public AntisenseRna createAntisenseRna() {
- AntisenseRna result = new AntisenseRna();
+ public CellDesignerAntisenseRna createAntisenseRna() {
+ CellDesignerAntisenseRna result = new CellDesignerAntisenseRna();
- AntisenseRnaRegion region1 = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion region1 = new CellDesignerAntisenseRnaRegion();
result.addRegion(region1);
region1.setIdAntisenseRnaRegion("a");
region1.setName("name");
@@ -98,7 +94,7 @@ public class AntisenseRnaComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends AntisenseRna {
+ class Tmp extends CellDesignerAntisenseRna {
private static final long serialVersionUID = 1L;
}
Tmp object = new Tmp();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
index 12841cda2a..ac90daa015 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
@@ -13,8 +13,8 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion.AntisenseRnaRegionType;
public class AntisenseRnaRegionTest {
@@ -29,7 +29,7 @@ public class AntisenseRnaRegionTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new AntisenseRnaRegion());
+ SerializationUtils.serialize(new CellDesignerAntisenseRnaRegion());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -67,8 +67,8 @@ public class AntisenseRnaRegionTest {
@Test
public void testConstructor1() {
try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion(antisenseRna);
+ CellDesignerAntisenseRnaRegion antisenseRna = new CellDesignerAntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion antisenseRna2 = new CellDesignerAntisenseRnaRegion(antisenseRna);
assertNotNull(antisenseRna2);
} catch (Exception e) {
e.printStackTrace();
@@ -79,11 +79,11 @@ public class AntisenseRnaRegionTest {
@Test
public void testUpdate() {
try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion antisenseRna = new CellDesignerAntisenseRnaRegion();
antisenseRna.setState(ModificationState.EMPTY);
antisenseRna.setName("as");
antisenseRna.setPos(3.0);
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion antisenseRna2 = new CellDesignerAntisenseRnaRegion();
antisenseRna2.update(antisenseRna);
assertEquals(antisenseRna.getState(), antisenseRna2.getState());
} catch (Exception e) {
@@ -95,8 +95,8 @@ public class AntisenseRnaRegionTest {
@Test
public void testInvalidUpdate() {
try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion antisenseRna = new CellDesignerAntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion antisenseRna2 = new CellDesignerAntisenseRnaRegion();
antisenseRna.setIdAntisenseRnaRegion("@1");
antisenseRna2.setIdAntisenseRnaRegion("@");
antisenseRna2.update(antisenseRna);
@@ -111,9 +111,9 @@ public class AntisenseRnaRegionTest {
@Test
public void testGetters() {
try {
- AntisenseRnaRegion region = new AntisenseRnaRegion(new AntisenseRnaRegion());
+ CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion(new CellDesignerAntisenseRnaRegion());
int id = 91;
- AntisenseRna species = new AntisenseRna();
+ CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
double pos = 4.6;
double size = 5.3;
AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
@@ -164,7 +164,7 @@ public class AntisenseRnaRegionTest {
@Test
public void testToString() {
try {
- assertNotNull(new AntisenseRnaRegion().toString());
+ assertNotNull(new CellDesignerAntisenseRnaRegion().toString());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -174,7 +174,7 @@ public class AntisenseRnaRegionTest {
@Test
public void testCopy() {
try {
- AntisenseRnaRegion degraded = new AntisenseRnaRegion().copy();
+ CellDesignerAntisenseRnaRegion degraded = new CellDesignerAntisenseRnaRegion().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -185,7 +185,7 @@ public class AntisenseRnaRegionTest {
@Test
public void testInvalidCopy() {
try {
- new AntisenseRnaRegion() {
+ new CellDesignerAntisenseRnaRegion() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
index 4e4b7fa223..c6b3142eae 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
@@ -14,7 +14,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class AntisenseRnaTest {
@@ -29,7 +30,7 @@ public class AntisenseRnaTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new AntisenseRna());
+ SerializationUtils.serialize(new CellDesignerAntisenseRna());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -39,9 +40,9 @@ public class AntisenseRnaTest {
@Test
public void testConstructor1() {
try {
- AntisenseRna original = new AntisenseRna();
- original.addRegion(new AntisenseRnaRegion());
- AntisenseRna aRna = new AntisenseRna(original);
+ CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
+ original.addRegion(new CellDesignerAntisenseRnaRegion());
+ CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna(original);
assertNotNull(aRna);
} catch (Exception e) {
e.printStackTrace();
@@ -52,12 +53,12 @@ public class AntisenseRnaTest {
@Test
public void testAddRnaRegion() {
try {
- AntisenseRna original = new AntisenseRna();
- AntisenseRnaRegion region = new AntisenseRnaRegion();
+ CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
+ CellDesignerAntisenseRnaRegion region = new CellDesignerAntisenseRnaRegion();
region.setIdAntisenseRnaRegion("id1");
original.addRegion(region);
- AntisenseRnaRegion region2 = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion region2 = new CellDesignerAntisenseRnaRegion();
region2.setIdAntisenseRnaRegion("id1");
region2.setName("nam");
original.addRegion(region2);
@@ -66,7 +67,7 @@ public class AntisenseRnaTest {
assertEquals("nam", original.getRegions().get(0).getName());
- AntisenseRnaRegion region3 = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion region3 = new CellDesignerAntisenseRnaRegion();
region3.setIdAntisenseRnaRegion("id2");
region3.setName("nam");
original.addRegion(region3);
@@ -81,24 +82,24 @@ public class AntisenseRnaTest {
@Test
public void testUpdate() {
try {
- AntisenseRna original = new AntisenseRna();
- AntisenseRnaRegion region2 = new AntisenseRnaRegion();
+ CellDesignerAntisenseRna original = new CellDesignerAntisenseRna();
+ CellDesignerAntisenseRnaRegion region2 = new CellDesignerAntisenseRnaRegion();
region2.setIdAntisenseRnaRegion("id1");
region2.setName("nam");
original.addRegion(region2);
- AntisenseRnaRegion region3 = new AntisenseRnaRegion();
+ CellDesignerAntisenseRnaRegion region3 = new CellDesignerAntisenseRnaRegion();
region3.setIdAntisenseRnaRegion("id2");
region3.setName("nam");
original.addRegion(region3);
- AntisenseRna copy = new AntisenseRna(original);
- copy.addRegion(new AntisenseRnaRegion());
+ CellDesignerAntisenseRna copy = new CellDesignerAntisenseRna(original);
+ copy.addRegion(new CellDesignerAntisenseRnaRegion());
copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
original.update(copy);
boolean acetylatedFound = false;
- for (AntisenseRnaRegion region : copy.getRegions()) {
+ for (CellDesignerAntisenseRnaRegion region : copy.getRegions()) {
if (ModificationState.ACETYLATED.equals(region.getState())) {
acetylatedFound = true;
}
@@ -106,7 +107,7 @@ public class AntisenseRnaTest {
assertTrue(acetylatedFound);
assertEquals(3, copy.getRegions().size());
- original.update(new GenericProtein());
+ original.update(new CellDesignerGenericProtein());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -116,10 +117,10 @@ public class AntisenseRnaTest {
@Test
public void testGetters() {
try {
- AntisenseRna aRna = new AntisenseRna(new Species());
+ CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna(new CellDesignerSpecies<AntisenseRna>());
assertNotNull(aRna.getStringType());
- List<AntisenseRnaRegion> regions = new ArrayList<>();
+ List<CellDesignerAntisenseRnaRegion> regions = new ArrayList<>();
aRna.setRegions(regions);
@@ -133,7 +134,7 @@ public class AntisenseRnaTest {
@Test
public void testCopy() {
try {
- AntisenseRna aRna = new AntisenseRna().copy();
+ CellDesignerAntisenseRna aRna = new CellDesignerAntisenseRna().copy();
assertNotNull(aRna);
} catch (Exception e) {
e.printStackTrace();
@@ -144,7 +145,7 @@ public class AntisenseRnaTest {
@Test
public void testInvalidCopy() {
try {
- new AntisenseRna() {
+ new CellDesignerAntisenseRna() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
index 2bd397c337..28971eabb4 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.common.exception.InvalidClassException;
public class CompartmentComparatorTest {
- CompartmentComparator comparator = new CompartmentComparator();
+ CellDesignerCompartmentComparator comparator = new CellDesignerCompartmentComparator();
@Before
public void setUp() throws Exception {
@@ -25,18 +25,14 @@ public class CompartmentComparatorTest {
@Test
public void testEquals() {
try {
- Compartment comp1 = createCompartment();
- Compartment comp2 = createCompartment();
+ CellDesignerCompartment comp1 = createCompartment();
+ CellDesignerCompartment comp2 = createCompartment();
assertEquals(0, comparator.compare(comp1, comp1));
assertEquals(0, comparator.compare(comp1, comp2));
assertEquals(0, comparator.compare(comp2, comp1));
- comp1.setElementId("AAA");
- assertEquals(0, comparator.compare(comp1, comp2));
- assertEquals(0, comparator.compare(comp2, comp1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -46,8 +42,8 @@ public class CompartmentComparatorTest {
@Test
public void testDifferent() {
try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
+ CellDesignerCompartment compartment1 = createCompartment();
+ CellDesignerCompartment compartment2 = createCompartment();
compartment1.setElementId("id2");
assertTrue(comparator.compare(compartment1, compartment2) != 0);
assertTrue(comparator.compare(compartment2, compartment1) != 0);
@@ -70,8 +66,8 @@ public class CompartmentComparatorTest {
}
}
- public Compartment createCompartment() {
- Compartment result = new Compartment();
+ public CellDesignerCompartment createCompartment() {
+ CellDesignerCompartment result = new CellDesignerCompartment();
result.setElementId("id1");
result.setName("bla");
return result;
@@ -80,8 +76,8 @@ public class CompartmentComparatorTest {
@Test
public void testInvalid() {
try {
- Compartment compartment1 = new Compartment();
- Compartment compartment2 = new Compartment() {
+ CellDesignerCompartment compartment1 = new CellDesignerCompartment();
+ CellDesignerCompartment compartment2 = new CellDesignerCompartment() {
/**
*
@@ -100,7 +96,7 @@ public class CompartmentComparatorTest {
@Test
public void testInvalid2() {
try {
- Compartment compartment2 = new Compartment() {
+ CellDesignerCompartment compartment2 = new CellDesignerCompartment() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
index f1f04aa3f3..683467964a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
@@ -26,7 +26,7 @@ public class CompartmentTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Compartment());
+ SerializationUtils.serialize(new CellDesignerCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -36,9 +36,9 @@ public class CompartmentTest {
@Test
public void testConstructor1() {
try {
- Compartment original = new Compartment();
- original.addElement(new GenericProtein());
- Compartment compartment = new Compartment(original);
+ CellDesignerCompartment original = new CellDesignerCompartment();
+ original.addElement(new CellDesignerGenericProtein());
+ CellDesignerCompartment compartment = new CellDesignerCompartment(original);
assertNotNull(compartment);
} catch (Exception e) {
@@ -50,12 +50,12 @@ public class CompartmentTest {
@Test
public void testEquals() {
try {
- Compartment original = new Compartment();
+ CellDesignerCompartment original = new CellDesignerCompartment();
original.setName("anme");
- Compartment compartment = new Compartment(original);
- Compartment compartment2 = new Compartment();
+ CellDesignerCompartment compartment = new CellDesignerCompartment(original);
+ CellDesignerCompartment compartment2 = new CellDesignerCompartment();
- Compartment compartment3 = new Compartment();
+ CellDesignerCompartment compartment3 = new CellDesignerCompartment();
compartment3.setElementId("q");
assertEquals(0, compartment.compareTo(original));
@@ -80,7 +80,7 @@ public class CompartmentTest {
@Test
public void testCopy() {
try {
- Compartment compartment = new Compartment().copy();
+ CellDesignerCompartment compartment = new CellDesignerCompartment().copy();
assertNotNull(compartment);
} catch (Exception e) {
e.printStackTrace();
@@ -93,7 +93,7 @@ public class CompartmentTest {
try {
String elementId = "id";
- Compartment compartment = new Compartment();
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
compartment.setElementId(elementId);
assertEquals(elementId, compartment.getElementId());
@@ -108,9 +108,9 @@ public class CompartmentTest {
@Test
public void testAddElements() {
try {
- GenericProtein protein = new GenericProtein();
+ CellDesignerGenericProtein protein = new CellDesignerGenericProtein();
- Compartment compartment = new Compartment();
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
assertEquals(0, compartment.getElements().size());
compartment.addElement(protein);
@@ -127,7 +127,7 @@ public class CompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new Compartment() {
+ new CellDesignerCompartment() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
index 0f9d38dd02..2d12d5c292 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
@@ -11,17 +11,17 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpeciesComparator;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpeciesComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
public class ComplexSpeciesComparatorTest {
Logger logger = Logger.getLogger(ComplexSpeciesComparatorTest.class);
- ComplexSpeciesComparator comparator = new ComplexSpeciesComparator();
+ CellDesignerComplexSpeciesComparator comparator = new CellDesignerComplexSpeciesComparator();
@Before
public void setUp() throws Exception {
@@ -34,20 +34,16 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testEquals() {
try {
- ComplexSpecies complex1 = createComplexSpecies();
- ComplexSpecies complex2 = createComplexSpecies();
+ CellDesignerComplexSpecies complex1 = createComplexSpecies();
+ CellDesignerComplexSpecies complex2 = createComplexSpecies();
assertEquals(0, comparator.compare(complex1, complex1));
assertEquals(0, comparator.compare(complex1, complex2));
assertEquals(0, comparator.compare(complex2, complex1));
- complex1.setElementId("AAA");
- assertEquals(0, comparator.compare(complex1, complex2));
- assertEquals(0, comparator.compare(complex2, complex1));
-
- complex2.addElement(new Compartment("test"));
- complex1.addElement(new Compartment("test"));
+ complex2.addElement(new CellDesignerCompartment("test"));
+ complex1.addElement(new CellDesignerCompartment("test"));
assertEquals(0, comparator.compare(complex1, complex2));
assertEquals(0, comparator.compare(complex2, complex1));
} catch (Exception e) {
@@ -59,7 +55,7 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testInvalidComp() throws Exception {
try {
- class Tmp extends ComplexSpecies {
+ class Tmp extends CellDesignerComplexSpecies {
private static final long serialVersionUID = 1L;
}
@@ -76,11 +72,11 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testInvalidComp2() throws Exception {
try {
- ComplexSpecies complex1 = createComplexSpecies();
- ComplexSpecies complex2 = createComplexSpecies();
+ CellDesignerComplexSpecies complex1 = createComplexSpecies();
+ CellDesignerComplexSpecies complex2 = createComplexSpecies();
- complex2.addElement(new Compartment("test"));
- complex1.addElement(Mockito.mock(Element.class));
+ complex2.addElement(new CellDesignerCompartment("test"));
+ complex1.addElement(Mockito.mock(CellDesignerElement.class));
comparator.compare(complex1, complex2);
comparator.compare(complex2, complex1);
fail("Exception expected");
@@ -95,15 +91,15 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testInvalidComp3() throws Exception {
try {
- ComplexSpecies complex1 = createComplexSpecies();
- ComplexSpecies complex2 = createComplexSpecies();
- Compartment c = new Compartment("test");
+ CellDesignerComplexSpecies complex1 = createComplexSpecies();
+ CellDesignerComplexSpecies complex2 = createComplexSpecies();
+ CellDesignerCompartment c = new CellDesignerCompartment("test");
c.setName("a");
complex2.addElement(c);
c.setName("");
- complex2.addElement(new Compartment("test"));
- complex1.addElement(new Compartment("test"));
- complex1.addElement(Mockito.mock(Element.class));
+ complex2.addElement(new CellDesignerCompartment("test"));
+ complex1.addElement(new CellDesignerCompartment("test"));
+ complex1.addElement(Mockito.mock(CellDesignerElement.class));
comparator.compare(complex2, complex1);
fail("Exception expected");
} catch (NotImplementedException e) {
@@ -117,8 +113,8 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testDifferent() throws Exception {
try {
- ComplexSpecies complex1 = createComplexSpecies();
- ComplexSpecies complex2 = createComplexSpecies();
+ CellDesignerComplexSpecies complex1 = createComplexSpecies();
+ CellDesignerComplexSpecies complex2 = createComplexSpecies();
complex1.setHomodimer(123);
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -143,14 +139,14 @@ public class ComplexSpeciesComparatorTest {
complex1 = createComplexSpecies();
complex2 = createComplexSpecies();
- ComplexSpecies child = (ComplexSpecies) complex1.getElements().iterator().next();
+ CellDesignerComplexSpecies child = (CellDesignerComplexSpecies) complex1.getElements().iterator().next();
child.getElements().iterator().next().setNotes("grand child notes");
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
complex1 = createComplexSpecies();
complex2 = createComplexSpecies();
- Protein prot = new GenericProtein();
+ CellDesignerProtein<?> prot = new CellDesignerGenericProtein();
prot.setElementId("test");
complex1.addElement(prot);
assertTrue(comparator.compare(complex1, complex2) != 0);
@@ -162,7 +158,7 @@ public class ComplexSpeciesComparatorTest {
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
- assertTrue(comparator.compare(new ComplexSpecies(), new ComplexSpecies() {
+ assertTrue(comparator.compare(new CellDesignerComplexSpecies(), new CellDesignerComplexSpecies() {
/**
*
@@ -179,12 +175,12 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testDifferent3() throws Exception {
try {
- ComplexSpecies complex1 = createComplexSpecies();
- ComplexSpecies complex2 = createComplexSpecies();
- Protein prot = new GenericProtein();
+ CellDesignerComplexSpecies complex1 = createComplexSpecies();
+ CellDesignerComplexSpecies complex2 = createComplexSpecies();
+ CellDesignerGenericProtein prot = new CellDesignerGenericProtein();
prot.setElementId("test");
complex1.addElement(prot);
- prot = new GenericProtein();
+ prot = new CellDesignerGenericProtein();
prot.setElementId("test2");
complex2.addElement(prot);
assertTrue(comparator.compare(complex1, complex2) != 0);
@@ -199,16 +195,16 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testDifferent4() throws Exception {
try {
- ComplexSpecies complex1 = createComplexSpecies();
- ComplexSpecies complex2 = createComplexSpecies();
- Compartment c = new Compartment("test");
+ CellDesignerComplexSpecies complex1 = createComplexSpecies();
+ CellDesignerComplexSpecies complex2 = createComplexSpecies();
+ CellDesignerCompartment c = new CellDesignerCompartment("test");
c.setName("a");
complex2.addElement(c);
- complex2.addElement(new Compartment("test"));
+ complex2.addElement(new CellDesignerCompartment("test"));
c.setName("");
- complex1.addElement(new Compartment("test"));
- Compartment d = new Compartment("test2");
+ complex1.addElement(new CellDesignerCompartment("test"));
+ CellDesignerCompartment d = new CellDesignerCompartment("test2");
d.setName("a");
complex1.addElement(d);
assertTrue(comparator.compare(complex1, complex2) != 0);
@@ -223,13 +219,13 @@ public class ComplexSpeciesComparatorTest {
@Test
public void testDifferent2() throws Exception {
try {
- ComplexSpecies complex1 = createComplexSpecies();
- ComplexSpecies complex2 = createComplexSpecies();
- Compartment comp = new Compartment();
+ CellDesignerComplexSpecies complex1 = createComplexSpecies();
+ CellDesignerComplexSpecies complex2 = createComplexSpecies();
+ CellDesignerCompartment comp = new CellDesignerCompartment();
comp.setElementId("test");
comp.setFullName("X");
complex1.addElement(comp);
- complex2.addElement(new Compartment("test"));
+ complex2.addElement(new CellDesignerCompartment("test"));
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
@@ -239,19 +235,19 @@ public class ComplexSpeciesComparatorTest {
}
}
- public ComplexSpecies createComplexSpecies() {
- ComplexSpecies result = new ComplexSpecies();
+ public CellDesignerComplexSpecies createComplexSpecies() {
+ CellDesignerComplexSpecies result = new CellDesignerComplexSpecies();
result.setHypothetical(true);
result.setHomodimer(3);
- ComplexSpecies child = new ComplexSpecies();
+ CellDesignerComplexSpecies child = new CellDesignerComplexSpecies();
result.addElement(child);
child.setCharge(12);
child.setName("buu");
child.setNotes("hey, hi, hello");
- ComplexSpecies grandChild = new ComplexSpecies();
+ CellDesignerComplexSpecies grandChild = new CellDesignerComplexSpecies();
child.addElement(grandChild);
child.setCharge(123);
child.setName("buus");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
index 1c15f8cf5a..d4a46a3bce 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
@@ -14,9 +14,10 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
public class ComplexSpeciesTest {
@@ -31,7 +32,7 @@ public class ComplexSpeciesTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new ComplexSpecies());
+ SerializationUtils.serialize(new CellDesignerComplexSpecies());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -41,7 +42,7 @@ public class ComplexSpeciesTest {
@Test
public void testConstructor1() {
try {
- ComplexSpecies degraded = new ComplexSpecies(new Species());
+ CellDesignerComplexSpecies degraded = new CellDesignerComplexSpecies(new CellDesignerSpecies<AntisenseRna>());
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -52,12 +53,12 @@ public class ComplexSpeciesTest {
@Test
public void testGetters() {
try {
- ComplexSpecies species = new ComplexSpecies();
- species.addElement(new Species());
- ComplexSpecies complex = new ComplexSpecies(species);
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies(species);
assertNotNull(complex.getStringType());
- Set<Element<?>> elements = new HashSet<>();
+ Set<CellDesignerElement<?>> elements = new HashSet<>();
complex.setElements(elements);
assertEquals(elements, complex.getElements());
} catch (Exception e) {
@@ -69,9 +70,9 @@ public class ComplexSpeciesTest {
@Test
public void testAddElement() {
try {
- ComplexSpecies species = new ComplexSpecies();
- species.addElement(new Species());
- species.addElement(new Species());
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
fail("Exception expected");
} catch (InvalidArgumentException e) {
} catch (Exception e) {
@@ -83,7 +84,7 @@ public class ComplexSpeciesTest {
@Test
public void testSetStructuralState() {
try {
- ComplexSpecies species = new ComplexSpecies();
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
species.setStructuralState("a");
species.setStructuralState("b");
assertEquals("b", species.getStructuralState());
@@ -96,11 +97,11 @@ public class ComplexSpeciesTest {
@Test
public void testGetAllSimpleChildren() {
try {
- ComplexSpecies species = new ComplexSpecies();
- species.addElement(new Species());
- ComplexSpecies complex = new ComplexSpecies("a");
- complex.addElement(new Species("s"));
- complex.addElement(new Species("d"));
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies("a");
+ complex.addElement(new CellDesignerSpecies<AntisenseRna>("s"));
+ complex.addElement(new CellDesignerSpecies<AntisenseRna>("d"));
species.addElement(complex);
assertEquals(3, species.getAllSimpleChildren().size());
} catch (Exception e) {
@@ -112,7 +113,7 @@ public class ComplexSpeciesTest {
@Test
public void testCopy() {
try {
- ComplexSpecies degraded = new ComplexSpecies().copy();
+ CellDesignerComplexSpecies degraded = new CellDesignerComplexSpecies().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -123,7 +124,7 @@ public class ComplexSpeciesTest {
@Test
public void testInvalidCopy() {
try {
- new ComplexSpecies() {
+ new CellDesignerComplexSpecies() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java
index 1a5ebdc15a..e427ca6477 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java
@@ -10,6 +10,8 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
+
public class ConnectSchemeTest {
@AfterClass
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
index 50364bb452..5725351d96 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
@@ -9,12 +9,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.DegradedComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegradedComparator;
public class DegradedComparatorTest {
- DegradedComparator comparator = new DegradedComparator();
+ CellDesignerDegradedComparator comparator = new CellDesignerDegradedComparator();
@Before
public void setUp() throws Exception {
@@ -27,18 +27,14 @@ public class DegradedComparatorTest {
@Test
public void testEquals() {
try {
- Degraded degraded1 = createDegraded();
- Degraded degraded2 = createDegraded();
+ CellDesignerDegraded degraded1 = createDegraded();
+ CellDesignerDegraded degraded2 = createDegraded();
assertEquals(0, comparator.compare(degraded1, degraded1));
assertEquals(0, comparator.compare(degraded1, degraded2));
assertEquals(0, comparator.compare(degraded2, degraded1));
- degraded1.setElementId("AAA");
- assertEquals(0, comparator.compare(degraded1, degraded2));
- assertEquals(0, comparator.compare(degraded2, degraded1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -48,8 +44,8 @@ public class DegradedComparatorTest {
@Test
public void testDifferent() {
try {
- Degraded degraded1 = createDegraded();
- Degraded degraded2 = createDegraded();
+ CellDesignerDegraded degraded1 = createDegraded();
+ CellDesignerDegraded degraded2 = createDegraded();
degraded1 = createDegraded();
degraded2 = createDegraded();
degraded1.setCharge(54);
@@ -62,11 +58,11 @@ public class DegradedComparatorTest {
assertTrue(comparator.compare(degraded2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- Degraded degraded = createDegraded();
+ CellDesignerDegraded degraded = createDegraded();
degraded.setName("n");
assertTrue(comparator.compare(degraded, degraded1) != 0);
- assertTrue(comparator.compare(degraded, new Degraded() {
+ assertTrue(comparator.compare(degraded, new CellDesignerDegraded() {
private static final long serialVersionUID = 1L;
}) != 0);
} catch (Exception e) {
@@ -75,8 +71,8 @@ public class DegradedComparatorTest {
}
}
- public Degraded createDegraded() {
- Degraded result = new Degraded();
+ public CellDesignerDegraded createDegraded() {
+ CellDesignerDegraded result = new CellDesignerDegraded();
result.setCharge(12);
return result;
}
@@ -84,7 +80,7 @@ public class DegradedComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Degraded{
+ class Tmp extends CellDesignerDegraded{
private static final long serialVersionUID = 1L;
}
Tmp object = new Tmp();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
index fafbfa6f55..245d441ac1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
@@ -9,8 +9,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Degraded;
public class DegradedTest {
@@ -25,7 +26,7 @@ public class DegradedTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Degraded());
+ SerializationUtils.serialize(new CellDesignerDegraded());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -35,7 +36,7 @@ public class DegradedTest {
@Test
public void testConstructor1() {
try {
- Degraded degraded = new Degraded(new Species());
+ CellDesignerDegraded degraded = new CellDesignerDegraded(new CellDesignerSpecies<Degraded>());
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +47,7 @@ public class DegradedTest {
@Test
public void testGetters() {
try {
- Degraded degraded = new Degraded(new Species());
+ CellDesignerDegraded degraded = new CellDesignerDegraded(new CellDesignerSpecies<Degraded>());
assertNotNull(degraded.getStringType());
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +58,7 @@ public class DegradedTest {
@Test
public void testCopy() {
try {
- Degraded degraded = new Degraded().copy();
+ CellDesignerDegraded degraded = new CellDesignerDegraded().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -68,7 +69,7 @@ public class DegradedTest {
@Test
public void testInvalidCopy() {
try {
- new Degraded() {
+ new CellDesignerDegraded() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
index c478814faa..90c5337753 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
@@ -9,12 +9,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.DrugComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrugComparator;
public class DrugComparatorTest {
- DrugComparator comparator = new DrugComparator();
+ CellDesignerDrugComparator comparator = new CellDesignerDrugComparator();
@Before
public void setUp() throws Exception {
@@ -27,18 +27,14 @@ public class DrugComparatorTest {
@Test
public void testEquals() {
try {
- Drug drug1 = createDrug();
- Drug drug2 = createDrug();
+ CellDesignerDrug drug1 = createDrug();
+ CellDesignerDrug drug2 = createDrug();
assertEquals(0, comparator.compare(drug1, drug1));
assertEquals(0, comparator.compare(drug1, drug2));
assertEquals(0, comparator.compare(drug2, drug1));
- drug1.setElementId("AAA");
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -48,16 +44,16 @@ public class DrugComparatorTest {
@Test
public void testDifferent() {
try {
- Drug drug2 = createDrug();
+ CellDesignerDrug drug2 = createDrug();
assertTrue(comparator.compare(null, drug2) != 0);
assertTrue(comparator.compare(drug2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- Drug drug = createDrug();
+ CellDesignerDrug drug = createDrug();
drug.setName("n");
assertTrue(comparator.compare(drug, drug2) != 0);
- assertTrue(comparator.compare(drug, new Drug() {
+ assertTrue(comparator.compare(drug, new CellDesignerDrug() {
private static final long serialVersionUID = 1L;
}) != 0);
@@ -67,15 +63,15 @@ public class DrugComparatorTest {
}
}
- public Drug createDrug() {
- Drug result = new Drug();
+ public CellDesignerDrug createDrug() {
+ CellDesignerDrug result = new CellDesignerDrug();
return result;
}
@Test
public void testInvalid() {
try {
- class Tmp extends Drug{
+ class Tmp extends CellDesignerDrug{
private static final long serialVersionUID = 1L;
}
Tmp object = new Tmp();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
index 381663e7c4..67068e7b80 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
@@ -9,8 +9,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Drug;
public class DrugTest {
@@ -25,7 +26,7 @@ public class DrugTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Drug());
+ SerializationUtils.serialize(new CellDesignerDrug());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -36,7 +37,7 @@ public class DrugTest {
@Test
public void testConstructor1() {
try {
- Drug degraded = new Drug(new Species());
+ CellDesignerDrug degraded = new CellDesignerDrug(new CellDesignerSpecies<Drug>());
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -47,7 +48,7 @@ public class DrugTest {
@Test
public void testGetters() {
try {
- Drug degraded = new Drug(new Species());
+ CellDesignerDrug degraded = new CellDesignerDrug(new CellDesignerSpecies<Drug>());
assertNotNull(degraded.getStringType());
} catch (Exception e) {
e.printStackTrace();
@@ -58,7 +59,7 @@ public class DrugTest {
@Test
public void testCopy() {
try {
- Drug degraded = new Drug().copy();
+ CellDesignerDrug degraded = new CellDesignerDrug().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -69,7 +70,7 @@ public class DrugTest {
@Test
public void testInvalidCopy() {
try {
- new Drug() {
+ new CellDesignerDrug() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparatorTest.java
index d3517fcfe4..2682e00a74 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparatorTest.java
@@ -13,11 +13,11 @@ import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.PositionToCompartment;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
public class ElementComparatorTest {
- ElementComparator comparator = new ElementComparator();
+ CellDesignerElementComparator comparator = new CellDesignerElementComparator();
@Before
public void setUp() throws Exception {
@@ -30,7 +30,7 @@ public class ElementComparatorTest {
@Test
public void testException() {
try {
- Element<?> el = Mockito.mock(Element.class);
+ CellDesignerElement<?> el = Mockito.mock(CellDesignerElement.class);
comparator.compare(el, el);
fail("Exception should occur");
@@ -45,7 +45,7 @@ public class ElementComparatorTest {
@Test
public void testException2() {
try {
- assertEquals(0, comparator.compare(new Compartment(), new Compartment()));
+ assertEquals(0, comparator.compare(new CellDesignerCompartment(), new CellDesignerCompartment()));
} catch (Exception e) {
e.printStackTrace();
@@ -56,8 +56,8 @@ public class ElementComparatorTest {
@Test
public void testEquals() {
try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species2 = createSimpleMolecule();
assertEquals(0, comparator.compare(species1, species2));
assertEquals(0, comparator.compare(null, null));
@@ -73,7 +73,7 @@ public class ElementComparatorTest {
@Test
public void testInternalCompare() {
try {
- SimpleMolecule species1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species1 = createSimpleMolecule();
assertTrue(comparator.internalCompare(species1, null) != 0);
assertTrue(comparator.internalCompare(null, species1) != 0);
@@ -90,8 +90,8 @@ public class ElementComparatorTest {
@Test
public void testDifferent() {
try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species2 = createSimpleMolecule();
species1.setCharge(99);
assertTrue(comparator.compare(species1, species2) != 0);
@@ -158,8 +158,8 @@ public class ElementComparatorTest {
@Test
public void testDifferentNewFields() throws Exception {
try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species2 = createSimpleMolecule();
species1.setSymbol("some symbol");
assertTrue(comparator.compare(species1, species2) != 0);
@@ -192,8 +192,8 @@ public class ElementComparatorTest {
}
}
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule();
+ public CellDesignerSimpleMolecule createSimpleMolecule() {
+ CellDesignerSimpleMolecule result = new CellDesignerSimpleMolecule();
result.setHomodimer(12);
result.setElementId("id");
result.setName("id");
@@ -211,9 +211,9 @@ public class ElementComparatorTest {
@Test
public void testDifferentNewReconFields() throws Exception {
try {
- SimpleMolecule element1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule element1 = createSimpleMolecule();
- SimpleMolecule element2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule element2 = createSimpleMolecule();
element2.setAbbreviation("ABRR");
assertTrue(comparator.compare(element1, element2) != 0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
index 7eac4d04d4..290c5f552d 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
@@ -35,9 +35,9 @@ public class ElementTest extends CellDesignerTestFunctions {
@Test
public void testConstructor() {
try {
- Species<?> element = Mockito.spy(Species.class);
+ CellDesignerSpecies<?> element = Mockito.spy(CellDesignerSpecies.class);
element.addMiriamData(new MiriamData());
- Element<?> copy = new GenericProtein(element);
+ CellDesignerElement<?> copy = new CellDesignerGenericProtein(element);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -51,7 +51,7 @@ public class ElementTest extends CellDesignerTestFunctions {
List<MiriamData> list = new ArrayList<>();
list.add(new MiriamData(MiriamType.CAS, "1"));
list.add(new MiriamData(MiriamType.CAS, "1"));
- Element<?> element = Mockito.spy(Element.class);
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
element.addMiriamData(list);
assertEquals(1, element.getMiriamData().size());
assertEquals(1, getWarnings().size());
@@ -67,7 +67,7 @@ public class ElementTest extends CellDesignerTestFunctions {
@Test
public void testSetNotes() {
try {
- Element<?> element = Mockito.spy(Element.class);
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
element.setNotes("</html>");
fail("Exception epxected");
} catch (InvalidArgumentException e) {
@@ -80,7 +80,7 @@ public class ElementTest extends CellDesignerTestFunctions {
@Test
public void testAddSynonym() {
try {
- Element<?> element = Mockito.spy(Element.class);
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
List<String> synonyms = new ArrayList<>();
synonyms.add("syn");
element.addSynonyms(synonyms);
@@ -103,10 +103,10 @@ public class ElementTest extends CellDesignerTestFunctions {
@Test
public void testGetters() {
try {
- Element<?> element = Mockito.spy(Element.class);
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
List<String> synonyms = new ArrayList<>();
List<String> formerSymbols = new ArrayList<>();
- ComplexSpecies complex = new ComplexSpecies();
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies();
Model model = new ModelFullIndexed(null);
String formula = "str";
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
index 7e4ded16e3..b671da3858 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
@@ -9,11 +9,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class GeneComparatorTest {
- GeneComparator comparator = new GeneComparator();
+ CellDesignerGeneComparator comparator = new CellDesignerGeneComparator();
@Before
public void setUp() throws Exception {
@@ -26,18 +27,14 @@ public class GeneComparatorTest {
@Test
public void testEquals() {
try {
- Gene gene1 = createGene();
- Gene gene2 = createGene();
+ CellDesignerGene gene1 = createGene();
+ CellDesignerGene gene2 = createGene();
assertEquals(0, comparator.compare(gene1, gene1));
assertEquals(0, comparator.compare(gene1, gene2));
assertEquals(0, comparator.compare(gene2, gene1));
- gene1.setElementId("AAA");
- assertEquals(0, comparator.compare(gene1, gene2));
- assertEquals(0, comparator.compare(gene2, gene1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -47,8 +44,8 @@ public class GeneComparatorTest {
@Test
public void testDifferent() {
try {
- Gene gene1 = createGene();
- Gene gene2 = createGene();
+ CellDesignerGene gene1 = createGene();
+ CellDesignerGene gene2 = createGene();
gene1.getModificationResidues().get(0).setName("bla");
assertTrue(comparator.compare(gene1, gene2) != 0);
assertTrue(comparator.compare(gene2, gene1) != 0);
@@ -65,11 +62,11 @@ public class GeneComparatorTest {
assertTrue(comparator.compare(gene2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- Gene gene = createGene();
+ CellDesignerGene gene = createGene();
gene.setName("n");
assertTrue(comparator.compare(gene, gene2) != 0);
- assertTrue(comparator.compare(gene, new Gene() {
+ assertTrue(comparator.compare(gene, new CellDesignerGene() {
private static final long serialVersionUID = 1L;
}) != 0);
@@ -79,11 +76,11 @@ public class GeneComparatorTest {
}
}
- public Gene createGene() {
- Gene result = new Gene();
+ public CellDesignerGene createGene() {
+ CellDesignerGene result = new CellDesignerGene();
result.setHypothetical(true);
- ModificationResidue residue = new ModificationResidue();
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
result.addModificationResidue(residue);
residue.setIdModificationResidue("a");
@@ -97,7 +94,7 @@ public class GeneComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Gene{
+ class Tmp extends CellDesignerGene{
private static final long serialVersionUID = 1L;
}
Tmp object = new Tmp();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
index 9cd00ce899..3615ade99b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
@@ -13,9 +13,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Gene;
public class GeneTest {
@@ -30,7 +29,7 @@ public class GeneTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Gene());
+ SerializationUtils.serialize(new CellDesignerGene());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -40,9 +39,9 @@ public class GeneTest {
@Test
public void testConstructor1() {
try {
- Gene original = new Gene();
- original.addModificationResidue(new ModificationResidue());
- Gene gene = new Gene(original);
+ CellDesignerGene original = new CellDesignerGene();
+ original.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerGene gene = new CellDesignerGene(original);
assertNotNull(gene);
} catch (Exception e) {
e.printStackTrace();
@@ -53,8 +52,8 @@ public class GeneTest {
@Test
public void testGetters() {
try {
- List<ModificationResidue> modificationResidues = new ArrayList<>();
- Gene gene = new Gene(new Species());
+ List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
+ CellDesignerGene gene = new CellDesignerGene(new CellDesignerSpecies<Gene>());
assertNotNull(gene.getStringType());
gene.setModificationResidues(modificationResidues);
assertEquals(modificationResidues, gene.getModificationResidues());
@@ -67,7 +66,7 @@ public class GeneTest {
@Test
public void testCopy() {
try {
- Gene degraded = new Gene().copy();
+ CellDesignerGene degraded = new CellDesignerGene().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -78,7 +77,7 @@ public class GeneTest {
@Test
public void testInvalidCopy() {
try {
- new Gene() {
+ new CellDesignerGene() {
/**
*
@@ -96,10 +95,10 @@ public class GeneTest {
@Test
public void testUpdate() {
try {
- Gene gene = new Gene();
- Gene gene2 = new Gene();
- List<ModificationResidue> residues = new ArrayList<>();
- residues.add(new ModificationResidue());
+ CellDesignerGene gene = new CellDesignerGene();
+ CellDesignerGene gene2 = new CellDesignerGene();
+ List<CellDesignerModificationResidue> residues = new ArrayList<>();
+ residues.add(new CellDesignerModificationResidue());
gene2.setModificationResidues(residues);
@@ -114,11 +113,11 @@ public class GeneTest {
@Test
public void testAddModificationResidue() {
try {
- Gene gene = new Gene();
- ModificationResidue mr = new ModificationResidue();
+ CellDesignerGene gene = new CellDesignerGene();
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
mr.setIdModificationResidue("id1");
- ModificationResidue mr2 = new ModificationResidue();
+ CellDesignerModificationResidue mr2 = new CellDesignerModificationResidue();
mr2.setIdModificationResidue("id1");
gene.addModificationResidue(mr);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
index 308a7a8341..40507f0dce 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
@@ -9,8 +9,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class GenericProteinTest {
@@ -25,7 +26,7 @@ public class GenericProteinTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new GenericProtein());
+ SerializationUtils.serialize(new CellDesignerGenericProtein());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -35,7 +36,7 @@ public class GenericProteinTest {
@Test
public void testConstructor() {
try {
- GenericProtein species = new GenericProtein(new Species());
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein(new CellDesignerSpecies<GenericProtein>());
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +47,7 @@ public class GenericProteinTest {
@Test
public void testCopy1() {
try {
- GenericProtein species = new GenericProtein(new Species()).copy();
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein(new CellDesignerSpecies<GenericProtein>()).copy();
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +58,7 @@ public class GenericProteinTest {
@Test
public void testCopy2() {
try {
- new GenericProtein() {
+ new CellDesignerGenericProtein() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
index df94d86afb..927e254d89 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
@@ -9,8 +9,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.IonChannelProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIonChannelProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
public class IonChannelProteinTest {
@@ -25,7 +26,7 @@ public class IonChannelProteinTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new IonChannelProtein());
+ SerializationUtils.serialize(new CellDesignerIonChannelProtein());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -35,7 +36,7 @@ public class IonChannelProteinTest {
@Test
public void testConstructor() {
try {
- IonChannelProtein species = new IonChannelProtein(new Species());
+ CellDesignerIonChannelProtein species = new CellDesignerIonChannelProtein(new CellDesignerSpecies<IonChannelProtein>());
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +47,7 @@ public class IonChannelProteinTest {
@Test
public void testCopy1() {
try {
- IonChannelProtein species = new IonChannelProtein(new Species()).copy();
+ CellDesignerIonChannelProtein species = new CellDesignerIonChannelProtein(new CellDesignerSpecies<IonChannelProtein>()).copy();
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +58,7 @@ public class IonChannelProteinTest {
@Test
public void testCopy2() {
try {
- new IonChannelProtein() {
+ new CellDesignerIonChannelProtein() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
index d30536e668..d0c3eae081 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
@@ -9,12 +9,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.IonComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIonComparator;
public class IonComparatorTest {
- IonComparator comparator = new IonComparator();
+ CellDesignerIonComparator comparator = new CellDesignerIonComparator();
@Before
public void setUp() throws Exception {
@@ -27,18 +27,14 @@ public class IonComparatorTest {
@Test
public void testEquals() {
try {
- Ion ion1 = createIon();
- Ion ion2 = createIon();
+ CellDesignerIon ion1 = createIon();
+ CellDesignerIon ion2 = createIon();
assertEquals(0, comparator.compare(ion1, ion1));
assertEquals(0, comparator.compare(ion1, ion2));
assertEquals(0, comparator.compare(ion2, ion1));
- ion1.setElementId("AAA");
- assertEquals(0, comparator.compare(ion1, ion2));
- assertEquals(0, comparator.compare(ion2, ion1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Ione exception occurred");
@@ -48,16 +44,16 @@ public class IonComparatorTest {
@Test
public void testDifferent() {
try {
- Ion ion2 = createIon();
+ CellDesignerIon ion2 = createIon();
assertTrue(comparator.compare(null, ion2) != 0);
assertTrue(comparator.compare(ion2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- Ion ion = createIon();
+ CellDesignerIon ion = createIon();
ion.setName("n");
assertTrue(comparator.compare(ion, ion2) != 0);
- assertTrue(comparator.compare(ion, new Ion() {
+ assertTrue(comparator.compare(ion, new CellDesignerIon() {
private static final long serialVersionUID = 1L;
}) != 0);
} catch (Exception e) {
@@ -66,15 +62,15 @@ public class IonComparatorTest {
}
}
- public Ion createIon() {
- Ion result = new Ion();
+ public CellDesignerIon createIon() {
+ CellDesignerIon result = new CellDesignerIon();
return result;
}
@Test
public void testInvalid() {
try {
- class Tmp extends Ion {
+ class Tmp extends CellDesignerIon {
private static final long serialVersionUID = 1L;
}
Tmp object = new Tmp();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
index d97de2bcb6..6e234ae978 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
@@ -9,8 +9,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
public class IonTest {
@@ -25,7 +26,7 @@ public class IonTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Ion());
+ SerializationUtils.serialize(new CellDesignerIon());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -36,7 +37,7 @@ public class IonTest {
@Test
public void testConstructor1() {
try {
- Ion degraded = new Ion(new Species());
+ CellDesignerIon degraded = new CellDesignerIon(new CellDesignerSpecies<IonChannelProtein>());
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -47,7 +48,7 @@ public class IonTest {
@Test
public void testGetters() {
try {
- Ion degraded = new Ion(new Species());
+ CellDesignerIon degraded = new CellDesignerIon(new CellDesignerSpecies<IonChannelProtein>());
assertNotNull(degraded.getStringType());
} catch (Exception e) {
e.printStackTrace();
@@ -58,7 +59,7 @@ public class IonTest {
@Test
public void testCopy() {
try {
- Ion degraded = new Ion().copy();
+ CellDesignerIon degraded = new CellDesignerIon().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -69,7 +70,7 @@ public class IonTest {
@Test
public void testInvalidCopy() {
try {
- new Ion() {
+ new CellDesignerIon() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java
index 86d86e31c3..501161070d 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java
@@ -7,6 +7,8 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
+
public class LinePropertiesTest {
@AfterClass
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
index 9f3f99119e..992af01828 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
@@ -13,7 +13,9 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class ModificationResidueTest {
@@ -28,7 +30,7 @@ public class ModificationResidueTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new ModificationResidue());
+ SerializationUtils.serialize(new CellDesignerModificationResidue());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -38,8 +40,8 @@ public class ModificationResidueTest {
@Test
public void testConstructor() {
try {
- ModificationResidue original = new ModificationResidue();
- ModificationResidue copy = new ModificationResidue(original);
+ CellDesignerModificationResidue original = new CellDesignerModificationResidue();
+ CellDesignerModificationResidue copy = new CellDesignerModificationResidue(original);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -50,8 +52,8 @@ public class ModificationResidueTest {
@Test
public void testUpdate() {
try {
- ModificationResidue original = new ModificationResidue();
- ModificationResidue update = new ModificationResidue();
+ CellDesignerModificationResidue original = new CellDesignerModificationResidue();
+ CellDesignerModificationResidue update = new CellDesignerModificationResidue();
String name = "n";
String side = "s";
@@ -81,13 +83,13 @@ public class ModificationResidueTest {
@Test
public void testGetters() {
try {
- ModificationResidue original = new ModificationResidue();
+ CellDesignerModificationResidue original = new CellDesignerModificationResidue();
String doubleStr = "2.0";
String invalidDoubleStr = "a2.0";
String nullStr = null;
Double angle = 2.0;
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<IonChannelProtein>();
original.setAngle(doubleStr);
assertEquals(angle, original.getAngle(), Configuration.EPSILON);
@@ -122,7 +124,7 @@ public class ModificationResidueTest {
@Test
public void testCopy() {
try {
- ModificationResidue degraded = new ModificationResidue().copy();
+ CellDesignerModificationResidue degraded = new CellDesignerModificationResidue().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -133,7 +135,7 @@ public class ModificationResidueTest {
@Test
public void testInvalidCopy() {
try {
- new ModificationResidue() {
+ new CellDesignerModificationResidue() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
index 11e30dd99c..f2af6d00a9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
public class PhenotypeComparatorTest {
- PhenotypeComparator comparator = new PhenotypeComparator();
+ CellDesignerPhenotypeComparator comparator = new CellDesignerPhenotypeComparator();
@Before
public void setUp() throws Exception {
@@ -25,18 +25,14 @@ public class PhenotypeComparatorTest {
@Test
public void testEquals() {
try {
- Phenotype phenotype1 = createPhenotype();
- Phenotype phenotype2 = createPhenotype();
+ CellDesignerPhenotype phenotype1 = createPhenotype();
+ CellDesignerPhenotype phenotype2 = createPhenotype();
assertEquals(0, comparator.compare(phenotype1, phenotype1));
assertEquals(0, comparator.compare(phenotype1, phenotype2));
assertEquals(0, comparator.compare(phenotype2, phenotype1));
- phenotype1.setElementId("AAA");
- assertEquals(0, comparator.compare(phenotype1, phenotype2));
- assertEquals(0, comparator.compare(phenotype2, phenotype1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -46,7 +42,7 @@ public class PhenotypeComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Phenotype {
+ class Tmp extends CellDesignerPhenotype {
private static final long serialVersionUID = 1L;
}
Tmp phenotype1 = new Tmp();
@@ -66,16 +62,16 @@ public class PhenotypeComparatorTest {
@Test
public void testDifferent() {
try {
- Phenotype phenotype2 = createPhenotype();
+ CellDesignerPhenotype phenotype2 = createPhenotype();
assertTrue(comparator.compare(null, phenotype2) != 0);
assertTrue(comparator.compare(phenotype2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- assertTrue(comparator.compare(phenotype2, new Phenotype() {
+ assertTrue(comparator.compare(phenotype2, new CellDesignerPhenotype() {
private static final long serialVersionUID = 1L;
}) != 0);
- Phenotype phenotype = createPhenotype();
+ CellDesignerPhenotype phenotype = createPhenotype();
phenotype2 = createPhenotype();
phenotype.setName("n");
assertTrue(comparator.compare(phenotype, phenotype2) != 0);
@@ -86,8 +82,8 @@ public class PhenotypeComparatorTest {
}
}
- public Phenotype createPhenotype() {
- Phenotype result = new Phenotype();
+ public CellDesignerPhenotype createPhenotype() {
+ CellDesignerPhenotype result = new CellDesignerPhenotype();
return result;
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
index f137ee4d62..2c29ccafb2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
@@ -23,7 +23,7 @@ public class PhenotypeTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Phenotype());
+ SerializationUtils.serialize(new CellDesignerPhenotype());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -33,8 +33,8 @@ public class PhenotypeTest {
@Test
public void testConstructor1() {
try {
- Phenotype original = new Phenotype();
- Phenotype copy = new Phenotype(original);
+ CellDesignerPhenotype original = new CellDesignerPhenotype();
+ CellDesignerPhenotype copy = new CellDesignerPhenotype(original);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -45,7 +45,7 @@ public class PhenotypeTest {
@Test
public void testCopy() {
try {
- Phenotype degraded = new Phenotype().copy();
+ CellDesignerPhenotype degraded = new CellDesignerPhenotype().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -56,7 +56,7 @@ public class PhenotypeTest {
@Test
public void testInvalidCopy() {
try {
- new Phenotype() {
+ new CellDesignerPhenotype() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
index 48bdfbb22e..1fef8ac670 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
@@ -8,11 +8,12 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class ProteinComparatorTest {
- ProteinComparator comparator = new ProteinComparator();
+ CellDesignerProteinComparator comparator = new CellDesignerProteinComparator();
@Before
public void setUp() throws Exception {
@@ -25,18 +26,14 @@ public class ProteinComparatorTest {
@Test
public void testEquals() {
try {
- Protein aRna1 = createProtein();
- Protein aRna2 = createProtein();
+ CellDesignerGenericProtein aRna1 = createProtein();
+ CellDesignerGenericProtein aRna2 = createProtein();
assertEquals(0, comparator.compare(aRna1, aRna1));
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setElementId("AAA");
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -46,8 +43,8 @@ public class ProteinComparatorTest {
@Test
public void testDifferent() {
try {
- GenericProtein aRna1 = createProtein();
- GenericProtein aRna2 = createProtein();
+ CellDesignerGenericProtein aRna1 = createProtein();
+ CellDesignerGenericProtein aRna2 = createProtein();
aRna1.getModificationResidues().get(0).setName("bla");
assertTrue(comparator.compare(aRna1, aRna2) != 0);
assertTrue(comparator.compare(aRna2, aRna1) != 0);
@@ -64,7 +61,7 @@ public class ProteinComparatorTest {
assertTrue(comparator.compare(aRna2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- assertTrue(comparator.compare(aRna2, new GenericProtein()) != 0);
+ assertTrue(comparator.compare(aRna2, new CellDesignerGenericProtein()) != 0);
aRna1 = createProtein();
aRna2 = createProtein();
@@ -90,13 +87,13 @@ public class ProteinComparatorTest {
}
}
- public GenericProtein createProtein() {
- GenericProtein result = new GenericProtein();
+ public CellDesignerGenericProtein createProtein() {
+ CellDesignerGenericProtein result = new CellDesignerGenericProtein();
result.setHomodimer(12);
result.setStructuralState("id1");
result.setHypothetical(true);
- ModificationResidue residue = new ModificationResidue();
+ CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
result.addModificationResidue(residue);
residue.setIdModificationResidue("a");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
index 6c7acf7e88..abfd04f7e1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
@@ -11,12 +11,11 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Protein;
public class ProteinTest {
@@ -31,24 +30,23 @@ public class ProteinTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new GenericProtein());
+ SerializationUtils.serialize(new CellDesignerGenericProtein());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
@Test
public void testConstructor1() {
try {
- Protein protein = new GenericProtein();
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
protein.setStructuralState("srt");
- List<ModificationResidue> residues = new ArrayList<>();
- residues.add(new ModificationResidue());
-
+ List<CellDesignerModificationResidue> residues = new ArrayList<>();
+ residues.add(new CellDesignerModificationResidue());
+
protein.setModificationResidues(residues);
- Protein protein2 = new GenericProtein(protein);
+ CellDesignerProtein<?> protein2 = new CellDesignerGenericProtein(protein);
assertNotNull(protein2);
} catch (Exception e) {
e.printStackTrace();
@@ -59,17 +57,17 @@ public class ProteinTest {
@Test
public void testUpdate() {
try {
- Protein protein = new GenericProtein();
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
protein.setStructuralState("");
- Protein protein2 = new GenericProtein();
+ CellDesignerProtein<?> protein2 = new CellDesignerGenericProtein();
protein2.setStructuralState("srt");
- List<ModificationResidue> residues = new ArrayList<>();
- residues.add(new ModificationResidue());
-
+ List<CellDesignerModificationResidue> residues = new ArrayList<>();
+ residues.add(new CellDesignerModificationResidue());
+
protein2.setModificationResidues(residues);
-
+
protein.update(protein2);
- assertEquals(protein2.getStructuralState(),protein.getStructuralState());
+ assertEquals(protein2.getStructuralState(), protein.getStructuralState());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -79,13 +77,13 @@ public class ProteinTest {
@Test
public void testAddModificationResidue() {
try {
- Protein protein = new GenericProtein();
- ModificationResidue mr = new ModificationResidue();
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
mr.setIdModificationResidue("id1");
-
- ModificationResidue mr2 = new ModificationResidue();
+
+ CellDesignerModificationResidue mr2 = new CellDesignerModificationResidue();
mr2.setIdModificationResidue("id1");
-
+
protein.addModificationResidue(mr);
assertEquals(1, protein.getModificationResidues().size());
protein.addModificationResidue(mr2);
@@ -99,10 +97,10 @@ public class ProteinTest {
@Test
public void testSetStructuralState() {
try {
- Protein protein = new GenericProtein();
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
protein.setStructuralState("str");
protein.setStructuralState("str1");
-
+
assertEquals("str1", protein.getStructuralState());
} catch (Exception e) {
e.printStackTrace();
@@ -113,7 +111,7 @@ public class ProteinTest {
@Test
public void testGetters() {
try {
- Protein protein = new GenericProtein(new Species());
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein(new CellDesignerSpecies<Protein>());
assertNotNull(protein.getStringType());
} catch (Exception e) {
e.printStackTrace();
@@ -124,7 +122,7 @@ public class ProteinTest {
@Test
public void testCopy() {
try {
- Protein protein = new GenericProtein().copy();
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein().copy();
assertNotNull(protein);
} catch (Exception e) {
e.printStackTrace();
@@ -135,13 +133,8 @@ public class ProteinTest {
@Test
public void testInvalidCopy() {
try {
- new Protein() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ CellDesignerProtein<?> mock = Mockito.spy(CellDesignerProtein.class);
+ mock.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
@@ -150,5 +143,4 @@ public class ProteinTest {
}
}
-
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
index 0f9fad6249..6f0c2b58b8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
@@ -9,8 +9,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.ReceptorProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
public class ReceptorProteinTest {
@@ -25,17 +24,17 @@ public class ReceptorProteinTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new ReceptorProtein());
+ SerializationUtils.serialize(new CellDesignerReceptorProtein());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void testConstructor() {
try {
- ReceptorProtein species = new ReceptorProtein(new Species());
+ CellDesignerReceptorProtein species = new CellDesignerReceptorProtein(new CellDesignerSpecies<ReceptorProtein>());
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +45,7 @@ public class ReceptorProteinTest {
@Test
public void testCopy1() {
try {
- ReceptorProtein species = new ReceptorProtein(new Species()).copy();
+ CellDesignerReceptorProtein species = new CellDesignerReceptorProtein(new CellDesignerSpecies<ReceptorProtein>()).copy();
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +56,7 @@ public class ReceptorProteinTest {
@Test
public void testCopy2() {
try {
- new ReceptorProtein() {
+ new CellDesignerReceptorProtein() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
index e2aca98f8e..5fd31da294 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
@@ -9,11 +9,11 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class RnaComparatorTest {
- RnaComparator comparator = new RnaComparator();
+ CellDesignerRnaComparator comparator = new CellDesignerRnaComparator();
@Before
public void setUp() throws Exception {
@@ -26,18 +26,14 @@ public class RnaComparatorTest {
@Test
public void testEquals() {
try {
- Rna aRna1 = createRna();
- Rna aRna2 = createRna();
+ CellDesignerRna aRna1 = createRna();
+ CellDesignerRna aRna2 = createRna();
assertEquals(0, comparator.compare(aRna1, aRna1));
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setElementId("AAA");
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -47,8 +43,8 @@ public class RnaComparatorTest {
@Test
public void testDifferent() {
try {
- Rna aRna1 = createRna();
- Rna aRna2 = createRna();
+ CellDesignerRna aRna1 = createRna();
+ CellDesignerRna aRna2 = createRna();
aRna1.getRegions().get(0).setState(ModificationState.ACETYLATED);
assertTrue(comparator.compare(aRna1, aRna2) != 0);
assertTrue(comparator.compare(aRna2, aRna1) != 0);
@@ -65,11 +61,11 @@ public class RnaComparatorTest {
assertTrue(comparator.compare(aRna2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- Rna rna = createRna();
+ CellDesignerRna rna = createRna();
rna.setName("n");
assertTrue(comparator.compare(rna, aRna2) != 0);
- assertTrue(comparator.compare(rna, new Rna() {
+ assertTrue(comparator.compare(rna, new CellDesignerRna() {
private static final long serialVersionUID = 1L;
}) != 0);
@@ -79,11 +75,11 @@ public class RnaComparatorTest {
}
}
- public Rna createRna() {
- Rna result = new Rna();
+ public CellDesignerRna createRna() {
+ CellDesignerRna result = new CellDesignerRna();
result.setHypothetical(true);
- RnaRegion region1 = new RnaRegion();
+ CellDesignerRnaRegion region1 = new CellDesignerRnaRegion();
result.addRegion(region1);
region1.setIdRnaRegion("a");
region1.setState(ModificationState.DONT_CARE);
@@ -96,7 +92,7 @@ public class RnaComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Rna {
+ class Tmp extends CellDesignerRna {
private static final long serialVersionUID = 1L;
}
Tmp object = new Tmp();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
index fe45169fc0..ac16a87425 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
@@ -11,7 +11,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class RnaRegionTest {
@@ -26,7 +26,7 @@ public class RnaRegionTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new RnaRegion());
+ SerializationUtils.serialize(new CellDesignerRnaRegion());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -36,7 +36,7 @@ public class RnaRegionTest {
@Test
public void testConstructor() {
try {
- RnaRegion region = new RnaRegion(new RnaRegion());
+ CellDesignerRnaRegion region = new CellDesignerRnaRegion(new CellDesignerRnaRegion());
assertNotNull(region);
} catch (Exception e) {
e.printStackTrace();
@@ -47,7 +47,7 @@ public class RnaRegionTest {
@Test
public void testSetSize() {
try {
- RnaRegion region = new RnaRegion();
+ CellDesignerRnaRegion region = new CellDesignerRnaRegion();
try {
region.setSize("as");
fail("Exception expected");
@@ -64,7 +64,7 @@ public class RnaRegionTest {
@Test
public void testSetPos() {
try {
- RnaRegion region = new RnaRegion();
+ CellDesignerRnaRegion region = new CellDesignerRnaRegion();
try {
region.setPos("as");
fail("Exception expected");
@@ -81,8 +81,8 @@ public class RnaRegionTest {
@Test
public void testUpdate() {
try {
- RnaRegion region = new RnaRegion();
- RnaRegion region2 = new RnaRegion();
+ CellDesignerRnaRegion region = new CellDesignerRnaRegion();
+ CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
region2.setState(ModificationState.ACETYLATED);
region2.setName("asd");
region2.setPos(2.2);
@@ -99,9 +99,9 @@ public class RnaRegionTest {
@Test
public void testUpdate2() {
try {
- RnaRegion region = new RnaRegion();
+ CellDesignerRnaRegion region = new CellDesignerRnaRegion();
region.setIdRnaRegion("1");
- RnaRegion region2 = new RnaRegion();
+ CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
region2.setIdRnaRegion("2");
region.update(region2);
fail("Exception expected");
@@ -115,9 +115,9 @@ public class RnaRegionTest {
@Test
public void testGetters() {
try {
- RnaRegion region = new RnaRegion();
+ CellDesignerRnaRegion region = new CellDesignerRnaRegion();
double size = 2.5;
- Rna species = new Rna();
+ CellDesignerRna species = new CellDesignerRna();
region.setSize(size);
region.setSpecies(species);
assertEquals(size, region.getSize(), Configuration.EPSILON);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
index 56e0c936a5..6ec2c5cb3c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
@@ -15,7 +15,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
public class RnaTest {
Logger logger = Logger.getLogger(RnaTest.class);
@@ -31,18 +32,17 @@ public class RnaTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Rna());
+ SerializationUtils.serialize(new CellDesignerRna());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
@Test
public void testConstructor1() {
try {
- Rna rna = new Rna(new Species());
+ CellDesignerRna rna = new CellDesignerRna(new CellDesignerSpecies<Rna>());
assertNotNull(rna);
} catch (Exception e) {
e.printStackTrace();
@@ -53,9 +53,9 @@ public class RnaTest {
@Test
public void testGetters() {
try {
- Rna rna = new Rna(new Species());
+ CellDesignerRna rna = new CellDesignerRna(new CellDesignerSpecies<Rna>());
assertNotNull(rna.getStringType());
- List<RnaRegion> regions = new ArrayList<>();
+ List<CellDesignerRnaRegion> regions = new ArrayList<>();
rna.setRegions(regions);
@@ -69,7 +69,7 @@ public class RnaTest {
@Test
public void testCopy() {
try {
- Rna rna = new Rna().copy();
+ CellDesignerRna rna = new CellDesignerRna().copy();
assertNotNull(rna);
} catch (Exception e) {
e.printStackTrace();
@@ -80,7 +80,7 @@ public class RnaTest {
@Test
public void testInvalidCopy() {
try {
- new Rna() {
+ new CellDesignerRna() {
/**
*
@@ -95,16 +95,15 @@ public class RnaTest {
}
}
-
@Test
public void testAddRnaRegion() {
try {
- Rna original = new Rna();
- RnaRegion region = new RnaRegion();
+ CellDesignerRna original = new CellDesignerRna();
+ CellDesignerRnaRegion region = new CellDesignerRnaRegion();
region.setIdRnaRegion("id1");
original.addRegion(region);
- RnaRegion region2 = new RnaRegion();
+ CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
region2.setIdRnaRegion("id1");
region2.setName("nam");
original.addRegion(region2);
@@ -113,7 +112,7 @@ public class RnaTest {
assertEquals("nam", original.getRegions().get(0).getName());
- RnaRegion region3 = new RnaRegion();
+ CellDesignerRnaRegion region3 = new CellDesignerRnaRegion();
region3.setIdRnaRegion("id2");
region3.setName("nam");
original.addRegion(region3);
@@ -128,26 +127,26 @@ public class RnaTest {
@Test
public void testUpdate() {
try {
- Rna original = new Rna();
- RnaRegion region2 = new RnaRegion();
+ CellDesignerRna original = new CellDesignerRna();
+ CellDesignerRnaRegion region2 = new CellDesignerRnaRegion();
region2.setIdRnaRegion("id1");
region2.setName("nam");
original.addRegion(region2);
- RnaRegion region3 = new RnaRegion();
+ CellDesignerRnaRegion region3 = new CellDesignerRnaRegion();
region3.setIdRnaRegion("id2");
region3.setName("nam");
original.addRegion(region3);
- Rna copy = new Rna(original);
- copy.addRegion(new RnaRegion());
+ CellDesignerRna copy = new CellDesignerRna(original);
+ copy.addRegion(new CellDesignerRnaRegion());
copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
-
+
logger.debug(copy.getRegions().size());
original.update(copy);
boolean acetylatedFound = false;
- for (RnaRegion region : copy.getRegions()) {
+ for (CellDesignerRnaRegion region : copy.getRegions()) {
if (ModificationState.ACETYLATED.equals(region.getState())) {
acetylatedFound = true;
}
@@ -156,7 +155,7 @@ public class RnaTest {
assertEquals(3, original.getRegions().size());
assertEquals(3, copy.getRegions().size());
- original.update(new GenericProtein());
+ original.update(new CellDesignerGenericProtein());
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
index 05dbd82998..65e44068bb 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
@@ -9,12 +9,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMoleculeComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMoleculeComparator;
public class SimpleMoleculeComparatorTest {
- SimpleMoleculeComparator comparator = new SimpleMoleculeComparator();
+ CellDesignerSimpleMoleculeComparator comparator = new CellDesignerSimpleMoleculeComparator();
@Before
public void setUp() throws Exception {
@@ -27,18 +27,14 @@ public class SimpleMoleculeComparatorTest {
@Test
public void testEquals() {
try {
- SimpleMolecule simpleMolecule1 = createSimpleMolecule();
- SimpleMolecule simpleMolecule2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule simpleMolecule1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule simpleMolecule2 = createSimpleMolecule();
assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule1));
assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
- simpleMolecule1.setElementId("AAA");
- assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
- assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -48,8 +44,8 @@ public class SimpleMoleculeComparatorTest {
@Test
public void testDifferent() {
try {
- SimpleMolecule simpleMolecule1 = createSimpleMolecule();
- SimpleMolecule simpleMolecule2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule simpleMolecule1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule simpleMolecule2 = createSimpleMolecule();
simpleMolecule1.setHomodimer(3);
assertTrue(comparator.compare(simpleMolecule1, simpleMolecule2) != 0);
assertTrue(comparator.compare(simpleMolecule2, simpleMolecule1) != 0);
@@ -72,7 +68,7 @@ public class SimpleMoleculeComparatorTest {
assertTrue(comparator.compare(simpleMolecule2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- assertTrue(comparator.compare(simpleMolecule1, new SimpleMolecule() {
+ assertTrue(comparator.compare(simpleMolecule1, new CellDesignerSimpleMolecule() {
private static final long serialVersionUID = 1L;
}) != 0);
@@ -85,7 +81,7 @@ public class SimpleMoleculeComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends SimpleMolecule {
+ class Tmp extends CellDesignerSimpleMolecule {
private static final long serialVersionUID = 1L;
}
;
@@ -103,8 +99,8 @@ public class SimpleMoleculeComparatorTest {
@Test
public void testDifferentNewFields() throws Exception {
try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species2 = createSimpleMolecule();
species1.setSmiles("some symbol");
assertTrue(comparator.compare(species1, species2) != 0);
@@ -123,8 +119,8 @@ public class SimpleMoleculeComparatorTest {
}
}
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule();
+ public CellDesignerSimpleMolecule createSimpleMolecule() {
+ CellDesignerSimpleMolecule result = new CellDesignerSimpleMolecule();
result.setHomodimer(12);
return result;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
index 82db2cc5d4..6b819c24c4 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
@@ -9,8 +9,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
public class SimpleMoleculeTest {
@@ -25,7 +24,7 @@ public class SimpleMoleculeTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new SimpleMolecule());
+ SerializationUtils.serialize(new CellDesignerSimpleMolecule());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -36,7 +35,7 @@ public class SimpleMoleculeTest {
@Test
public void testConstructor1() {
try {
- SimpleMolecule degraded = new SimpleMolecule(new Species());
+ CellDesignerSimpleMolecule degraded = new CellDesignerSimpleMolecule(new CellDesignerSpecies<SimpleMolecule>());
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -47,7 +46,7 @@ public class SimpleMoleculeTest {
@Test
public void testGetters() {
try {
- SimpleMolecule degraded = new SimpleMolecule(new Species());
+ CellDesignerSimpleMolecule degraded = new CellDesignerSimpleMolecule(new CellDesignerSpecies<SimpleMolecule>());
assertNotNull(degraded.getStringType());
} catch (Exception e) {
e.printStackTrace();
@@ -58,7 +57,7 @@ public class SimpleMoleculeTest {
@Test
public void testCopy() {
try {
- SimpleMolecule degraded = new SimpleMolecule().copy();
+ CellDesignerSimpleMolecule degraded = new CellDesignerSimpleMolecule().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -69,7 +68,7 @@ public class SimpleMoleculeTest {
@Test
public void testInvalidCopy() {
try {
- new SimpleMolecule() {
+ new CellDesignerSimpleMolecule() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparatorTest.java
index 1f6cc0aea6..fb7c885891 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparatorTest.java
@@ -4,41 +4,24 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import org.junit.After;
-import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.PositionToCompartment;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
public class SpeciesComparatorTest {
- SpeciesComparator comparator = new SpeciesComparator();
-
- class Mock extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
+ CellDesignerSpeciesComparator comparator = new CellDesignerSpeciesComparator();
@Test
public void testException() {
try {
- comparator.compare(new Mock(), new Mock());
+ CellDesignerSpecies<?> mock = Mockito.mock(CellDesignerSpecies.class);
+ comparator.compare(mock, mock);
fail("Exception should occur");
} catch (InvalidClassException e) {
@@ -52,18 +35,18 @@ public class SpeciesComparatorTest {
@Test
public void testEquals() {
try {
- Species species1 = createSimpleMolecule();
- Species species2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species2 = createSimpleMolecule();
assertEquals(0, comparator.compare(species1, species2));
assertEquals(0, comparator.compare(null, null));
- assertEquals(0, comparator.compare(new AntisenseRna(), new AntisenseRna()));
- assertEquals(0, comparator.compare(new Degraded(), new Degraded()));
- assertEquals(0, comparator.compare(new Drug(), new Drug()));
- assertEquals(0, comparator.compare(new Ion(), new Ion()));
- assertEquals(0, comparator.compare(new Phenotype(), new Phenotype()));
- assertEquals(0, comparator.compare(new Rna(), new Rna()));
+ assertEquals(0, comparator.compare(new CellDesignerAntisenseRna(), new CellDesignerAntisenseRna()));
+ assertEquals(0, comparator.compare(new CellDesignerDegraded(), new CellDesignerDegraded()));
+ assertEquals(0, comparator.compare(new CellDesignerDrug(), new CellDesignerDrug()));
+ assertEquals(0, comparator.compare(new CellDesignerIon(), new CellDesignerIon()));
+ assertEquals(0, comparator.compare(new CellDesignerPhenotype(), new CellDesignerPhenotype()));
+ assertEquals(0, comparator.compare(new CellDesignerRna(), new CellDesignerRna()));
} catch (Exception e) {
e.printStackTrace();
@@ -74,8 +57,8 @@ public class SpeciesComparatorTest {
@Test
public void testDifferent() {
try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species1 = createSimpleMolecule();
+ CellDesignerSimpleMolecule species2 = createSimpleMolecule();
species1.setCharge(99);
assertTrue(comparator.compare(species1, species2) != 0);
@@ -138,7 +121,6 @@ public class SpeciesComparatorTest {
assertTrue(comparator.compare(species1, species2) != 0);
assertTrue(comparator.compare(species2, species1) != 0);
-
species1 = createSimpleMolecule();
species2 = createSimpleMolecule();
species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_IS);
@@ -151,7 +133,7 @@ public class SpeciesComparatorTest {
assertTrue(comparator.compare(species1, species2) != 0);
assertTrue(comparator.compare(species2, species1) != 0);
- assertTrue(comparator.compare(new Rna(), new Drug()) != 0);
+ assertTrue(comparator.compare(new CellDesignerRna(), new CellDesignerDrug()) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -159,8 +141,8 @@ public class SpeciesComparatorTest {
}
}
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule();
+ public CellDesignerSimpleMolecule createSimpleMolecule() {
+ CellDesignerSimpleMolecule result = new CellDesignerSimpleMolecule();
result.setHomodimer(12);
result.setElementId("id");
result.setName("id");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
index 882a0b0e68..b8814cdb37 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
@@ -11,10 +11,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
public class SpeciesStateTest {
@@ -28,7 +30,7 @@ public class SpeciesStateTest {
@Test
public void testGetters() {
- List<ModificationResidue> modifications = new ArrayList<>();
+ List<CellDesignerModificationResidue> modifications = new ArrayList<>();
SpeciesState state = new SpeciesState();
state.setModifications(modifications);
assertEquals(modifications, state.getModifications());
@@ -48,16 +50,16 @@ public class SpeciesStateTest {
@Test
public void testConstructorFromRna() {
- RnaAlias rna = new RnaAlias("1");
- rna.addRegion(new RnaRegionAlias());
+ Rna rna = new Rna("1");
+ rna.addRegion(new RnaRegion());
SpeciesState state = new SpeciesState(rna);
assertEquals(1, state.getModifications().size());
}
@Test
public void testConstructorFromGene() {
- GeneAlias gene = new GeneAlias("2");
- gene.addModificationResidue(new ModificationResidueAlias());
+ Gene gene = new Gene("2");
+ gene.addModificationResidue(new ModificationResidue());
SpeciesState state = new SpeciesState(gene);
assertEquals(1, state.getModifications().size());
}
@@ -65,8 +67,8 @@ public class SpeciesStateTest {
@Test
public void testAddModifResidue() {
SpeciesState state = new SpeciesState();
- state.addModificationResidue(new ModificationResidue());
- ModificationResidue mr = new ModificationResidue();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
mr.setName("a");
state.addModificationResidue(mr);
assertEquals(1, state.getModifications().size());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
index fbb1662a5b..14a1f22989 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
@@ -15,6 +15,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class SpeciesTest extends CellDesignerTestFunctions {
@@ -29,7 +30,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Species());
+ SerializationUtils.serialize(new CellDesignerSpecies<GenericProtein>());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -39,7 +40,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testGetters() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
String elementId = "51";
Integer initialAmount = 54;
Integer initialConcentration = 58;
@@ -77,7 +78,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
public void testConstructor() {
try {
String id = "as_id";
- Species species = new Species(id);
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>(id);
assertEquals(id, species.getElementId());
} catch (Exception e) {
e.printStackTrace();
@@ -88,7 +89,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testSetId() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setElementId("");
species.setElementId("xx");
try {
@@ -108,10 +109,10 @@ public class SpeciesTest extends CellDesignerTestFunctions {
public void testUpdate1() {
try {
int warningsCount = getWarnings().size();
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setName("A");
species.setNotes("XXX");
- Species species2 = new Species();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
species2.setName("B");
species.update(species2);
int warningsCount2 = getWarnings().size();
@@ -126,9 +127,9 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testUpdate2() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setNotes("XXX");
- Species species2 = new Species();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
species2.addMiriamData(new MiriamData());
species.update(species2);
int warningsCount = getWarnings().size();
@@ -143,9 +144,9 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testUpdate3() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setNotes("XXX");
- Species species2 = new Species();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
species2.setNotes("xx");
species.update(species2);
int warningsCount = getWarnings().size();
@@ -160,9 +161,9 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testUpdate4() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setNotes("XX");
- Species species2 = new Species();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
species2.setNotes("xxX");
species.update(species2);
int warningsCount = getWarnings().size();
@@ -178,9 +179,9 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testUpdate5() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setNotes("XX");
- Species species2 = new Species();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
species2.setNotes("a as x");
species2.setHypothetical(true);
species2.setSymbol("sym");
@@ -198,10 +199,10 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testUpdate6() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setSymbol("sym1");
species.setFullName("a_sym1");
- Species species2 = new Species();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
species2.setSymbol("sym2");
species2.setFullName("b_sym1");
species.update(species2);
@@ -217,8 +218,8 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testUpdate7() {
try {
- Species species = new Species();
- Species species2 = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
species2.addSynonym("syn");
species2.addFormerSymbol("sym");
species.update(species2);
@@ -234,7 +235,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testSetInitialAmount() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setInitialAmount("1");
assertEquals((Integer) 1, species.getInitialAmount());
try {
@@ -255,7 +256,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testSetCharge() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setCharge("1");
assertEquals((Integer) 1, species.getCharge());
try {
@@ -276,7 +277,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testSetOnlySubstanceUnits() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setOnlySubstanceUnits("true");
assertTrue(species.getOnlySubstanceUnits());
try {
@@ -298,7 +299,7 @@ public class SpeciesTest extends CellDesignerTestFunctions {
@Test
public void testSetInitialConcentration() {
try {
- Species species = new Species();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
species.setInitialConcentration("1");
assertEquals((Integer) 1, species.getInitialConcentration());
try {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
index 90ebc9489c..6f3882334d 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
@@ -9,8 +9,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.converter.model.celldesigner.structure.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
public class TruncatedProteinTest {
@@ -25,17 +24,17 @@ public class TruncatedProteinTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new TruncatedProtein());
+ SerializationUtils.serialize(new CellDesignerTruncatedProtein());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void testConstructor() {
try {
- TruncatedProtein species = new TruncatedProtein(new Species());
+ CellDesignerTruncatedProtein species = new CellDesignerTruncatedProtein(new CellDesignerSpecies<TruncatedProtein>());
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +45,7 @@ public class TruncatedProteinTest {
@Test
public void testCopy1() {
try {
- TruncatedProtein species = new TruncatedProtein(new Species()).copy();
+ CellDesignerTruncatedProtein species = new CellDesignerTruncatedProtein(new CellDesignerSpecies<TruncatedProtein>()).copy();
assertNotNull(species);
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +56,7 @@ public class TruncatedProteinTest {
@Test
public void testCopy2() {
try {
- new TruncatedProtein() {
+ new CellDesignerTruncatedProtein() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
index f09907eb61..6eb492e927 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
@@ -9,12 +9,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
-import lcsb.mapviewer.converter.model.celldesigner.structure.UnknownComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknownComparator;
public class UnknownComparatorTest {
- UnknownComparator comparator = new UnknownComparator();
+ CellDesignerUnknownComparator comparator = new CellDesignerUnknownComparator();
@Before
public void setUp() throws Exception {
@@ -27,18 +27,14 @@ public class UnknownComparatorTest {
@Test
public void testEquals() {
try {
- Unknown aRna1 = createUnknown();
- Unknown aRna2 = createUnknown();
+ CellDesignerUnknown aRna1 = createUnknown();
+ CellDesignerUnknown aRna2 = createUnknown();
assertEquals(0, comparator.compare(aRna1, aRna1));
assertEquals(0, comparator.compare(aRna1, aRna2));
assertEquals(0, comparator.compare(aRna2, aRna1));
- aRna1.setElementId("AAA");
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -48,16 +44,16 @@ public class UnknownComparatorTest {
@Test
public void testDifferent() {
try {
- Unknown unknown2 = createUnknown();
+ CellDesignerUnknown unknown2 = createUnknown();
assertTrue(comparator.compare(null, unknown2) != 0);
assertTrue(comparator.compare(unknown2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- Unknown unknown = createUnknown();
+ CellDesignerUnknown unknown = createUnknown();
unknown.setName("n");
assertTrue(comparator.compare(unknown, unknown2) != 0);
- assertTrue(comparator.compare(unknown, new Unknown() {
+ assertTrue(comparator.compare(unknown, new CellDesignerUnknown() {
private static final long serialVersionUID = 1L;
}) != 0);
@@ -67,15 +63,15 @@ public class UnknownComparatorTest {
}
}
- public Unknown createUnknown() {
- Unknown result = new Unknown();
+ public CellDesignerUnknown createUnknown() {
+ CellDesignerUnknown result = new CellDesignerUnknown();
return result;
}
@Test
public void testInvalid() {
try {
- class Tmp extends Unknown{
+ class Tmp extends CellDesignerUnknown{
private static final long serialVersionUID = 1L;
}
Tmp object = new Tmp();
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
index 24ac6f9abf..8ed1e0bc65 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
@@ -9,8 +9,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
+import lcsb.mapviewer.model.map.species.Unknown;
public class UnknownTest {
@@ -25,7 +26,7 @@ public class UnknownTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new Unknown());
+ SerializationUtils.serialize(new CellDesignerUnknown());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -35,7 +36,7 @@ public class UnknownTest {
@Test
public void testConstructor1() {
try {
- Unknown degraded = new Unknown(new Species());
+ CellDesignerUnknown degraded = new CellDesignerUnknown(new CellDesignerSpecies<Unknown>());
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +47,7 @@ public class UnknownTest {
@Test
public void testGetters() {
try {
- Unknown degraded = new Unknown(new Species());
+ CellDesignerUnknown degraded = new CellDesignerUnknown(new CellDesignerSpecies<Unknown>());
assertNotNull(degraded.getStringType());
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +58,7 @@ public class UnknownTest {
@Test
public void testCopy() {
try {
- Unknown degraded = new Unknown().copy();
+ CellDesignerUnknown degraded = new CellDesignerUnknown().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -68,7 +69,7 @@ public class UnknownTest {
@Test
public void testInvalidCopy() {
try {
- new Unknown() {
+ new CellDesignerUnknown() {
/**
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java
index 9050c16045..818365ca41 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java
@@ -9,6 +9,8 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+
public class ViewTest {
@AfterClass
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
index c8e441ead6..47c055254a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
@@ -16,16 +16,16 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.AndOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ModifierTypeUtilsTest {
@@ -218,7 +218,7 @@ public class ModifierTypeUtilsTest {
}
@SuppressWarnings("unused")
- public InvalidModifier(SpeciesAlias alias, Element<?> element) {
+ public InvalidModifier(Species alias, CellDesignerElement<?> element) {
throw new NotImplementedException();
}
}
@@ -235,7 +235,7 @@ public class ModifierTypeUtilsTest {
// and check if we catch properly information about problematic
// implementation
- utils.createModifierForStringType(typeToModify.getStringName(), new GenericProteinAlias("id"));
+ utils.createModifierForStringType(typeToModify.getStringName(), new GenericProtein("id"));
fail("Exceptione expected");
} catch (InvalidStateException e) {
assertTrue(e.getMessage().contains("Problem with instantiation of Modifier class"));
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 5a6f1927fb..551f51b2af 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -29,21 +29,7 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.modifier.Catalysis;
import lcsb.mapviewer.model.map.modifier.Inhibition;
@@ -70,6 +56,20 @@ import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction
import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -156,9 +156,9 @@ public class SbgnmlXmlExporter {
map.setLanguage(Language.PD.getName());
Sbgn sbgnData = new Sbgn();
- List<SpeciesAlias> aliases = model.getSpeciesAliases();
+ List<Species> aliases = model.getSpeciesAliases();
- for (SpeciesAlias a : aliases) {
+ for (Species a : aliases) {
if (a.getComplexAlias() == null) {
Glyph newGlyph = aliasToGlyph(a);
map.getGlyph().add(newGlyph);
@@ -194,7 +194,7 @@ public class SbgnmlXmlExporter {
* alias with all parameters for the glyph
* @return newly created glyph
*/
- private Glyph aliasToGlyph(Alias alias) {
+ private Glyph aliasToGlyph(Element alias) {
Glyph newGlyph = new Glyph();
boolean idIsANumber = true;
try {
@@ -219,8 +219,8 @@ public class SbgnmlXmlExporter {
if (GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE)
|| GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE_MULTIMER)) {
- ProteinAlias protein = (ProteinAlias) alias;
- for (ModificationResidueAlias mr : protein.getModificationResidues()) {
+ Protein protein = (Protein) alias;
+ for (ModificationResidue mr : protein.getModificationResidues()) {
Glyph stateVariableGlyph = parseStateVariable(mr, newGlyph);
stateVariableGlyph.setId(newGlyph.getId().concat("-").concat(stateVariableGlyph.getId()));
newGlyph.getGlyph().add(stateVariableGlyph);
@@ -232,9 +232,9 @@ public class SbgnmlXmlExporter {
newGlyph.getGlyph().add(unitOfInformationGlyph);
}
- if (alias instanceof ComplexAlias) {
- ComplexAlias complexAlias = (ComplexAlias) alias;
- for (SpeciesAlias a : complexAlias.getAliases()) {
+ if (alias instanceof Complex) {
+ Complex complexAlias = (Complex) alias;
+ for (Species a : complexAlias.getAliases()) {
Glyph childGlyph = aliasToGlyph(a);
newGlyph.getGlyph().add(childGlyph);
}
@@ -315,9 +315,9 @@ public class SbgnmlXmlExporter {
* element to extract GlyphCLazz from
* @return GlyphClazz adequate for given alias
*/
- private GlyphClazz getGlyphClazzFromElement(Alias element) {
- if (element instanceof ProteinAlias) {
- ProteinAlias protein = (ProteinAlias) element;
+ private GlyphClazz getGlyphClazzFromElement(Element element) {
+ if (element instanceof Protein) {
+ Protein protein = (Protein) element;
if (protein.getHomodimer() == 1) {
return GlyphClazz.MACROMOLECULE;
} else {
@@ -325,8 +325,8 @@ public class SbgnmlXmlExporter {
}
}
- if (element instanceof SimpleMoleculeAlias) {
- SimpleMoleculeAlias simpleMolecule = (SimpleMoleculeAlias) element;
+ if (element instanceof SimpleMolecule) {
+ SimpleMolecule simpleMolecule = (SimpleMolecule) element;
if (simpleMolecule.getHomodimer() == 1) {
return GlyphClazz.SIMPLE_CHEMICAL;
} else {
@@ -334,8 +334,8 @@ public class SbgnmlXmlExporter {
}
}
- if (element instanceof IonAlias) {
- IonAlias ion = (IonAlias) element;
+ if (element instanceof Ion) {
+ Ion ion = (Ion) element;
if (ion.getHomodimer() == 1) {
return GlyphClazz.SIMPLE_CHEMICAL;
} else {
@@ -343,8 +343,8 @@ public class SbgnmlXmlExporter {
}
}
- if (element instanceof GeneAlias) {
- GeneAlias gene = (GeneAlias) element;
+ if (element instanceof Gene) {
+ Gene gene = (Gene) element;
if (gene.getHomodimer() == 1) {
return GlyphClazz.NUCLEIC_ACID_FEATURE;
} else {
@@ -352,8 +352,8 @@ public class SbgnmlXmlExporter {
}
}
- if (element instanceof RnaAlias) {
- RnaAlias rna = (RnaAlias) element;
+ if (element instanceof Rna) {
+ Rna rna = (Rna) element;
if (rna.getHomodimer() == 1) {
return GlyphClazz.NUCLEIC_ACID_FEATURE;
} else {
@@ -361,8 +361,8 @@ public class SbgnmlXmlExporter {
}
}
- if (element instanceof AntisenseRnaAlias) {
- AntisenseRnaAlias rna = (AntisenseRnaAlias) element;
+ if (element instanceof AntisenseRna) {
+ AntisenseRna rna = (AntisenseRna) element;
if (rna.getHomodimer() == 1) {
return GlyphClazz.NUCLEIC_ACID_FEATURE;
} else {
@@ -370,8 +370,8 @@ public class SbgnmlXmlExporter {
}
}
- if (element instanceof ComplexAlias) {
- ComplexAlias complexSpecies = (ComplexAlias) element;
+ if (element instanceof Complex) {
+ Complex complexSpecies = (Complex) element;
if (complexSpecies.getHomodimer() == 1) {
return GlyphClazz.COMPLEX;
} else {
@@ -379,18 +379,18 @@ public class SbgnmlXmlExporter {
}
}
- if (element instanceof DegradedAlias) {
+ if (element instanceof Degraded) {
return GlyphClazz.SOURCE_AND_SINK;
}
- if (element instanceof PhenotypeAlias) {
+ if (element instanceof Phenotype) {
return GlyphClazz.PHENOTYPE;
}
- if (element instanceof CompartmentAlias) {
+ if (element instanceof Compartment) {
return GlyphClazz.COMPARTMENT;
}
- if (element instanceof UnknownAlias) {
+ if (element instanceof Unknown) {
return GlyphClazz.UNSPECIFIED_ENTITY;
}
@@ -405,22 +405,22 @@ public class SbgnmlXmlExporter {
* element with the name
* @return label for a glyph
*/
- private Label getGlyphLabelFromAlias(Alias element) {
+ private Label getGlyphLabelFromAlias(Element element) {
Label label = new Label();
label.setText(element.getName());
return label;
}
/**
- * Returns state variable glyph parsed from {@link ModificationResidueAlias}.
+ * Returns state variable glyph parsed from {@link ModificationResidue}.
*
* @param mr
- * {@link ModificationResidueAlias} to be parsed
+ * {@link ModificationResidue} to be parsed
* @param parentGlyph
* parent glyph for the state variable
* @return state variable glyph
*/
- private Glyph parseStateVariable(ModificationResidueAlias mr, Glyph parentGlyph) {
+ private Glyph parseStateVariable(ModificationResidue mr, Glyph parentGlyph) {
Glyph glyph = new Glyph();
glyph.setId(mr.getIdModificationResidue());
glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
@@ -484,27 +484,27 @@ public class SbgnmlXmlExporter {
* @return glyph with unit of information extracted from the alias or null if
* no unit of information was found
*/
- private Glyph getUnitOfInformationGlyph(Alias alias) {
+ private Glyph getUnitOfInformationGlyph(Element alias) {
Glyph uoiGlyph = null;
String uoiText = "";
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias species = (SpeciesAlias) alias;
+ if (alias instanceof Species) {
+ Species species = (Species) alias;
int homodir = species.getHomodimer();
if (homodir > 1) {
uoiText = "N:".concat(Integer.toString(homodir));
}
}
- if (alias instanceof TruncatedProteinAlias) {
+ if (alias instanceof TruncatedProtein) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:truncatedProtein");
}
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias speciesAlias = (SpeciesAlias) alias;
+ if (alias instanceof Species) {
+ Species speciesAlias = (Species) alias;
if ((speciesAlias.getAliasStateLabel() != null) && (speciesAlias.getAliasStatePrefix() != null)) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
@@ -517,19 +517,19 @@ public class SbgnmlXmlExporter {
}
if (!uoiText.contains("ct:")) {
- if (alias instanceof RnaAlias) {
+ if (alias instanceof Rna) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:RNA");
}
- if (alias instanceof AntisenseRnaAlias) {
+ if (alias instanceof AntisenseRna) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:antisenseRNA");
}
- if (alias instanceof GeneAlias) {
+ if (alias instanceof Gene) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
@@ -716,7 +716,7 @@ public class SbgnmlXmlExporter {
throw new InvalidArgumentException();
}
- if (reaction.getProducts().get(0).getAlias() instanceof PhenotypeAlias) {
+ if (reaction.getProducts().get(0).getAlias() instanceof Phenotype) {
logger.warn("Found Phenotype being a reactant in process. That is discouraged");
}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index 30617c76de..521f433ccf 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -36,21 +36,8 @@ import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Catalysis;
@@ -73,6 +60,19 @@ import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction
import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
* This class is a parser for SBGN-ML files.
@@ -352,7 +352,7 @@ public class SbgnmlXmlParser {
* @throws Exception
*/
private void parseGlyph(Glyph g, Model model) {
- SpeciesAlias newSpecies = null;
+ Species newSpecies = null;
switch (GlyphClazz.fromClazz(g.getClazz())) {
case AND:
case NOT:
@@ -369,35 +369,35 @@ public class SbgnmlXmlParser {
parseComplex(g, null, false, model);
break;
case MACROMOLECULE:
- newSpecies = new GenericProteinAlias(g.getId());
+ newSpecies = new GenericProtein(g.getId());
parseSpecies(g, newSpecies, true, model);
break;
case MACROMOLECULE_MULTIMER:
- newSpecies = new GenericProteinAlias(g.getId());
+ newSpecies = new GenericProtein(g.getId());
parseSpecies(g, newSpecies, false, model);
break;
case NUCLEIC_ACID_FEATURE:
if (isRNA(g)) {
- newSpecies = new RnaAlias(g.getId());
+ newSpecies = new Rna(g.getId());
} else {
- newSpecies = new GeneAlias(g.getId());
+ newSpecies = new Gene(g.getId());
}
parseSpecies(g, newSpecies, true, model);
break;
case NUCLEIC_ACID_FEATURE_MULTIMER:
if (isRNA(g)) {
- newSpecies = new RnaAlias(g.getId());
+ newSpecies = new Rna(g.getId());
} else {
- newSpecies = new GeneAlias(g.getId());
+ newSpecies = new Gene(g.getId());
}
parseSpecies(g, newSpecies, false, model);
break;
case PERTURBING_AGENT:
- newSpecies = new PhenotypeAlias(g.getId());
+ newSpecies = new Phenotype(g.getId());
parseSpecies(g, newSpecies, true, model);
break;
case PHENOTYPE:
- newSpecies = new PhenotypeAlias(g.getId());
+ newSpecies = new Phenotype(g.getId());
parseSpecies(g, newSpecies, true, model);
break;
case ASSOCIATION:
@@ -408,22 +408,22 @@ public class SbgnmlXmlParser {
processes.add(new Process(g));
break;
case SIMPLE_CHEMICAL:
- newSpecies = new SimpleMoleculeAlias(g.getId());
+ newSpecies = new SimpleMolecule(g.getId());
parseSpecies(g, newSpecies, true, model);
break;
case SIMPLE_CHEMICAL_MULTIMER:
- newSpecies = new SimpleMoleculeAlias(g.getId());
+ newSpecies = new SimpleMolecule(g.getId());
parseSpecies(g, newSpecies, false, model);
break;
case SOURCE_AND_SINK:
- newSpecies = new DegradedAlias(g.getId());
+ newSpecies = new Degraded(g.getId());
parseSpecies(g, newSpecies, true, model);
break;
case TAG:
case SUBMAP:
logger.warn("Submaps are not supported. Glyph: " + g.getId() + " has not been parsed.");
case UNSPECIFIED_ENTITY:
- newSpecies = new UnknownAlias(g.getId());
+ newSpecies = new Unknown(g.getId());
parseSpecies(g, newSpecies, true, model);
break;
default:
@@ -487,7 +487,7 @@ public class SbgnmlXmlParser {
if (a.getSource() instanceof Glyph) {
Glyph sourceGlyph = (Glyph) a.getSource();
if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)
- && (model.getAliasByAliasId(targetGlyph.getId()) instanceof SpeciesAlias)) {
+ && (model.getAliasByAliasId(targetGlyph.getId()) instanceof Species)) {
try {
parsePhenotypeArc(a, model);
} catch (InvalidArgumentException ex) {
@@ -579,7 +579,7 @@ public class SbgnmlXmlParser {
* @param model
* model to be updated
*/
- private void parseSpecies(Glyph g, SpeciesAlias newSpecies, boolean isHomodimer, Model model) {
+ private void parseSpecies(Glyph g, Species newSpecies, boolean isHomodimer, Model model) {
newSpecies.setModel(model);
// If Glyph has label with a name, set it as Species name. If not, set
// Id as name.
@@ -613,11 +613,11 @@ public class SbgnmlXmlParser {
}
} else {
String structuralState = child.getState().getValue();
- if (newSpecies instanceof ProteinAlias) {
- ProteinAlias protein = (ProteinAlias) newSpecies;
+ if (newSpecies instanceof Protein) {
+ Protein protein = (Protein) newSpecies;
protein.setStructuralState(structuralState);
- } else if (newSpecies instanceof ComplexAlias) {
- ComplexAlias complex = (ComplexAlias) newSpecies;
+ } else if (newSpecies instanceof Complex) {
+ Complex complex = (Complex) newSpecies;
complex.setStructuralState(structuralState);
}
}
@@ -637,7 +637,7 @@ public class SbgnmlXmlParser {
* @param model
* model to be updated
*/
- private void parseAlias(Glyph g, SpeciesAlias newAlias, Model model) {
+ private void parseAlias(Glyph g, Species newAlias, Model model) {
newAlias.setHeight(new Double(g.getBbox().getH()));
newAlias.setWidth(new Double(g.getBbox().getW()));
newAlias.setX(new Double(g.getBbox().getX()));
@@ -645,13 +645,13 @@ public class SbgnmlXmlParser {
if (g.getCompartmentRef() != null) {
Glyph compartmentGlyph = (Glyph) g.getCompartmentRef();
- CompartmentAlias compartmentAlias = model.getCompartmentAliasByCompartmentAliasId(compartmentGlyph.getId());
+ Compartment compartmentAlias = model.getCompartmentAliasByCompartmentAliasId(compartmentGlyph.getId());
newAlias.setParent(compartmentAlias);
newAlias.setCompartmentAlias(compartmentAlias);
compartmentAlias.addAlias(newAlias);
} else if (newAlias.getComplexAlias() == null) {
// If the alias is in any compartment, assign it to that compartment
- for (CompartmentAlias compartmentAlias : model.getCompartmentsAliases()) {
+ for (Compartment compartmentAlias : model.getCompartmentsAliases()) {
boolean dx1 = compartmentAlias.getX() + compartmentAlias.getWidth() - newAlias.getX() >= 0;
boolean dx2 = compartmentAlias.getX() - (newAlias.getX() + newAlias.getWidth()) <= 0;
boolean dy1 = compartmentAlias.getY() + compartmentAlias.getHeight() - newAlias.getY() >= 0;
@@ -739,12 +739,12 @@ public class SbgnmlXmlParser {
* Exception is thrown if state variable is parsed for species other
* than Protein
*/
- private void parseStateVariable(Glyph unitOfInformationGlyph, Glyph speciesGlyph, SpeciesAlias newSpecies) throws Exception {
- if (!(newSpecies instanceof ProteinAlias)) {
+ private void parseStateVariable(Glyph unitOfInformationGlyph, Glyph speciesGlyph, Species newSpecies) throws Exception {
+ if (!(newSpecies instanceof Protein)) {
throw new Exception("Only macromolecule elements can have state variables.");
}
- ProteinAlias protein = (ProteinAlias) newSpecies;
- ModificationResidueAlias mr = new ModificationResidueAlias();
+ Protein protein = (Protein) newSpecies;
+ ModificationResidue mr = new ModificationResidue();
mr.setSpecies(protein);
mr.setIdModificationResidue(unitOfInformationGlyph.getId());
@@ -804,7 +804,7 @@ public class SbgnmlXmlParser {
* @param alias
* alias that the unit of information concerns
*/
- private void parseUnitOfInformation(Glyph unitOfInformationGlyph, SpeciesAlias alias) {
+ private void parseUnitOfInformation(Glyph unitOfInformationGlyph, Species alias) {
String unitOfInformationText = unitOfInformationGlyph.getLabel().getText();
if (unitOfInformationText.contains(":") && !unitOfInformationText.startsWith("N:")) {
String unitOfInformationPrefix = unitOfInformationText.substring(0, unitOfInformationText.indexOf(':'));
@@ -829,49 +829,49 @@ public class SbgnmlXmlParser {
* @param model
* model to update with the parsed complex species
*/
- private void parseComplex(Glyph complexGlyph, ComplexAlias parentComplexSpecies, boolean isHomodimer, Model model) {
- ComplexAlias complexSpecies = new ComplexAlias(complexGlyph.getId());
+ private void parseComplex(Glyph complexGlyph, Complex parentComplexSpecies, boolean isHomodimer, Model model) {
+ Complex complexSpecies = new Complex(complexGlyph.getId());
if (parentComplexSpecies != null) {
complexSpecies.setComplexAlias(parentComplexSpecies);
}
parseSpecies(complexGlyph, complexSpecies, isHomodimer, model);
- ComplexAlias complexAlias = (ComplexAlias) model.getAliasByAliasId(complexGlyph.getId());
+ Complex complexAlias = (Complex) model.getAliasByAliasId(complexGlyph.getId());
for (Glyph child : complexGlyph.getGlyph()) {
- SpeciesAlias newSpecies;
+ Species newSpecies;
switch (GlyphClazz.fromClazz(child.getClazz())) {
case UNSPECIFIED_ENTITY:
- newSpecies = new UnknownAlias(child.getId());
+ newSpecies = new Unknown(child.getId());
newSpecies.setComplexAlias(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case SIMPLE_CHEMICAL:
- newSpecies = new SimpleMoleculeAlias(child.getId());
+ newSpecies = new SimpleMolecule(child.getId());
newSpecies.setComplexAlias(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case MACROMOLECULE:
- newSpecies = new GenericProteinAlias(child.getId());
+ newSpecies = new GenericProtein(child.getId());
newSpecies.setComplexAlias(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case NUCLEIC_ACID_FEATURE:
- newSpecies = new GeneAlias(child.getId());
+ newSpecies = new Gene(child.getId());
newSpecies.setComplexAlias(complexSpecies);
parseSpecies(child, newSpecies, true, model);
break;
case SIMPLE_CHEMICAL_MULTIMER:
- newSpecies = new SimpleMoleculeAlias(child.getId());
+ newSpecies = new SimpleMolecule(child.getId());
newSpecies.setComplexAlias(complexSpecies);
parseSpecies(child, newSpecies, false, model);
break;
case MACROMOLECULE_MULTIMER:
- newSpecies = new GenericProteinAlias(child.getId());
+ newSpecies = new GenericProtein(child.getId());
newSpecies.setComplexAlias(complexSpecies);
parseSpecies(child, newSpecies, false, model);
break;
case NUCLEIC_ACID_FEATURE_MULTIMER:
- newSpecies = new GeneAlias(child.getId());
+ newSpecies = new Gene(child.getId());
newSpecies.setComplexAlias(complexSpecies);
parseSpecies(child, newSpecies, false, model);
break;
@@ -884,10 +884,10 @@ public class SbgnmlXmlParser {
default:
break;
}
- Alias newAlias = model.getAliasByAliasId(child.getId());
+ Element newAlias = model.getAliasByAliasId(child.getId());
if (newAlias != null) {
newAlias.setParent(complexAlias);
- complexAlias.addAlias((SpeciesAlias) newAlias);
+ complexAlias.addAlias((Species) newAlias);
}
}
}
@@ -1265,7 +1265,7 @@ public class SbgnmlXmlParser {
}
if (a.getSource() instanceof Glyph) {
Glyph sourceGlyph = (Glyph) a.getSource();
- SpeciesAlias modifierAlias = (SpeciesAlias) model.getAliasByAliasId(sourceGlyph.getId());
+ Species modifierAlias = (Species) model.getAliasByAliasId(sourceGlyph.getId());
modifier.setAlias(modifierAlias);
List<Point2D> pointList = getLinePoints(a);
pointList.remove(pointList.size() - 1);
@@ -1459,7 +1459,7 @@ public class SbgnmlXmlParser {
}
Glyph sourceGlyph = (Glyph) logicArc.getSource();
- SpeciesAlias modifierAlias = (SpeciesAlias) model.getAliasByAliasId(sourceGlyph.getId());
+ Species modifierAlias = (Species) model.getAliasByAliasId(sourceGlyph.getId());
modifier.setAlias(modifierAlias);
List<Point2D> pointList = getLinePoints(logicArc);
pointList.add(operatorCenterPoint);
@@ -1485,7 +1485,7 @@ public class SbgnmlXmlParser {
*/
private void parseCompartment(Glyph g, Model model) {
- CompartmentAlias compAlias = new SquareCompartmentAlias(g.getId());
+ Compartment compAlias = new SquareCompartment(g.getId());
if (g.getLabel() != null) {
compAlias.setName(g.getLabel().getText());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index c67e4e2ff6..33a4974fe4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -15,15 +15,15 @@ import java.util.Map;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -164,7 +164,7 @@ public abstract class AbstractImageGenerator {
/**
* List of objects containging information about layouts visualized in the
* javascript (on client side). Every object (map) represents data for
- * single layout. In this map we have pairs between {@link Alias}/
+ * single layout. In this map we have pairs between {@link Element}/
* {@link Reaction} and {@link ColorSchema} used to visualize the element.
*
*/
@@ -442,11 +442,11 @@ public abstract class AbstractImageGenerator {
/**
* Adds layout data that is visualized on the client side. Layout data
- * contains mapping between {@link Alias}/{@link Reaction} and
+ * contains mapping between {@link Element}/{@link Reaction} and
* {@link ColorSchema} used for coloring specific element.
*
* @param map
- * layout data containing mapping between {@link Alias}/
+ * layout data containing mapping between {@link Element}/
* {@link Reaction} and {@link ColorSchema} used for coloring
* specific element
*/
@@ -467,7 +467,7 @@ public abstract class AbstractImageGenerator {
* object in layouts visualized in the javascript.
*
* @param object
- * object ({@link Alias} or {@link Reaction}) for which we return
+ * object ({@link Element} or {@link Reaction}) for which we return
* list of {@link ColorSchema} in different layouts
* @return list with {@link ColorSchema} used to visualize the specific
* object in layouts visualized in the javascript
@@ -562,12 +562,12 @@ public abstract class AbstractImageGenerator {
// or layers if they should be solid and hide complexity behind it
// draw all aliases
- for (Alias alias : params.getModel().getSortedAliases()) {
+ for (Element alias : params.getModel().getSortedAliases()) {
// draw only aliases that don't have parents (aren't included in any
// compartment/complexes)
- if (alias.getParent() == null && alias instanceof SpeciesAlias) {
+ if (alias.getParent() == null && alias instanceof Species) {
- drawAlias((SpeciesAlias) alias, params.getVisibleLayoutsForElement(alias));
+ drawAlias((Species) alias, params.getVisibleLayoutsForElement(alias));
}
}
// draw all reactions
@@ -575,7 +575,7 @@ public abstract class AbstractImageGenerator {
drawReaction(reaction, params.getVisibleLayoutsForElement(reaction));
}
// draw all compartments
- for (CompartmentAlias ca : params.getModel().getSortedCompartmentsAliases()) {
+ for (Compartment ca : params.getModel().getSortedCompartmentsAliases()) {
// draw only aliases that don't have parents (aren't included in any
// compartment/complexes)
if (ca.getParent() == null) {
@@ -623,7 +623,7 @@ public abstract class AbstractImageGenerator {
* @throws DrawingException
* thrown when there was a problem with drawing compartment alias
*/
- protected void drawCompartmentAlias(final CompartmentAlias compAlias, final boolean nested, List<ColorSchema> visibleLayouts, Params params)
+ protected void drawCompartmentAlias(final Compartment compAlias, final boolean nested, List<ColorSchema> visibleLayouts, Params params)
throws DrawingException {
// If 'compAlias' has not the big enough visibility level then should not be
// visible.
@@ -653,7 +653,7 @@ public abstract class AbstractImageGenerator {
// we draw compartment alias only when we have hierarchical view or it's
// standard compartment (not the artifital pathway)
- if (nested || !(compAlias instanceof ArtifitialCompartmentAlias)) {
+ if (nested || !(compAlias instanceof PathwayCompartment)) {
try {
converter.drawAlias(compAlias, graphics, compartmentParams, visibleLayouts);
} catch (Exception e) {
@@ -667,17 +667,17 @@ public abstract class AbstractImageGenerator {
if (fill) {
return;
}
- List<Alias> result = new ArrayList<Alias>();
+ List<Element> result = new ArrayList<Element>();
result.addAll(compAlias.getAliases());
- Collections.sort(result, Alias.SIZE_COMPARATOR);
+ Collections.sort(result, Element.SIZE_COMPARATOR);
// draw all children of this compartment
- for (Alias alias : result) {
+ for (Element alias : result) {
// if a child is a standard alias
- if (alias instanceof SpeciesAlias) {
- drawAlias((SpeciesAlias) alias, params.getVisibleLayoutsForElement(alias));
- } else if (alias instanceof CompartmentAlias) {
- drawCompartmentAlias((CompartmentAlias) alias, nested, params.getVisibleLayoutsForElement(alias), params);
+ if (alias instanceof Species) {
+ drawAlias((Species) alias, params.getVisibleLayoutsForElement(alias));
+ } else if (alias instanceof Compartment) {
+ drawCompartmentAlias((Compartment) alias, nested, params.getVisibleLayoutsForElement(alias), params);
} else {
// if a child is not a compartment or an alias then we have a
// problem
@@ -686,7 +686,7 @@ public abstract class AbstractImageGenerator {
}
if (!compAlias.containsIdenticalSpecies()) {
- if (!(compAlias instanceof ArtifitialCompartmentAlias)) {
+ if (!(compAlias instanceof PathwayCompartment)) {
converter.drawText(compAlias, graphics, compartmentParams);
}
}
@@ -702,7 +702,7 @@ public abstract class AbstractImageGenerator {
* @throws DrawingException
* thrown when there was a problem with drawing an alias
*/
- protected void drawAlias(final SpeciesAlias alias, List<ColorSchema> visibleLayouts) throws DrawingException {
+ protected void drawAlias(final Species alias, List<ColorSchema> visibleLayouts) throws DrawingException {
// The displaying of alias is indicated by values of VisibilityLevel. If
// VisibilityLevel is big enough, then it is
@@ -722,10 +722,10 @@ public abstract class AbstractImageGenerator {
}
boolean rescale = false;
- if (alias instanceof ComplexAlias) {
- if (((ComplexAlias) alias).getAliases().size() == 0) {
+ if (alias instanceof Complex) {
+ if (((Complex) alias).getAliases().size() == 0) {
rescale = true;
- } else if (((ComplexAlias) alias).getAliases().get(0).getVisibilityLevel() > level) {
+ } else if (((Complex) alias).getAliases().get(0).getVisibilityLevel() > level) {
rescale = true;
}
}
@@ -744,14 +744,14 @@ public abstract class AbstractImageGenerator {
// if the alias is a complex alias then we may want to draw children
// objects
- if (alias instanceof ComplexAlias) {
- ComplexAlias complex = (ComplexAlias) alias;
+ if (alias instanceof Complex) {
+ Complex complex = (Complex) alias;
// before drawing children check if the view is not set to brief
// mode
if (!complex.getState().equalsIgnoreCase("brief")) {
// depending on current zoom level, children are drawn or not
if (complex.getTransparencyLevel() <= level) {
- for (SpeciesAlias a : complex.getAliases()) {
+ for (Species a : complex.getAliases()) {
drawAlias(a, visibleLayouts);
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AliasConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AliasConverter.java
index 43255ebac4..a60ff0cd60 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AliasConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AliasConverter.java
@@ -27,29 +27,29 @@ import lcsb.mapviewer.converter.graphics.species.RnaConverter;
import lcsb.mapviewer.converter.graphics.species.SBGNNucleicAcidFeatureConverter;
import lcsb.mapviewer.converter.graphics.species.SimpleMoleculeConverter;
import lcsb.mapviewer.converter.graphics.species.UnknownConverter;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.BottomSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.LeftSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.OvalCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RightSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.TopSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.Unknown;
/**
* This class is designed to convert any type of alias into a graphic glyph that
@@ -60,7 +60,7 @@ import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
* @author Piotr Gawron
*
*/
-public class AliasConverter implements IAliasConverter<Alias> {
+public class AliasConverter implements IAliasConverter<Element> {
/**
* Default class logger.
*/
@@ -77,35 +77,35 @@ public class AliasConverter implements IAliasConverter<Alias> {
* in this map is a class of alias. Value is the converter that can process
* this type of alias.
*/
- private static Map<Class<? extends Alias>, IAliasConverter<?>> aliasConverters = new HashMap<Class<? extends Alias>, IAliasConverter<?>>();
+ private static Map<Class<? extends Element>, IAliasConverter<?>> aliasConverters = new HashMap<Class<? extends Element>, IAliasConverter<?>>();
static {
// at the beginning lets add all implemented aliases
// for element reference
- addAliasConverter(GenericProteinAlias.class, new ProteinConverter());
- addAliasConverter(IonChannelProteinAlias.class, new ProteinConverter());
- addAliasConverter(ReceptorProteinAlias.class, new ProteinConverter());
- addAliasConverter(TruncatedProteinAlias.class, new ProteinConverter());
- addAliasConverter(DegradedAlias.class, new DegradedConverter());
- addAliasConverter(ComplexAlias.class, new ComplexConverter());
- addAliasConverter(SimpleMoleculeAlias.class, new SimpleMoleculeConverter());
- addAliasConverter(DrugAlias.class, new DrugConverter());
- addAliasConverter(IonAlias.class, new IonConverter());
- addAliasConverter(PhenotypeAlias.class, new PhenotypeConverter());
- addAliasConverter(RnaAlias.class, new RnaConverter());
- addAliasConverter(AntisenseRnaAlias.class, new AntisenseRnaConverter());
- addAliasConverter(GeneAlias.class, new GeneConverter());
- addAliasConverter(UnknownAlias.class, new UnknownConverter());
+ addAliasConverter(GenericProtein.class, new ProteinConverter());
+ addAliasConverter(IonChannelProtein.class, new ProteinConverter());
+ addAliasConverter(ReceptorProtein.class, new ProteinConverter());
+ addAliasConverter(TruncatedProtein.class, new ProteinConverter());
+ addAliasConverter(Degraded.class, new DegradedConverter());
+ addAliasConverter(Complex.class, new ComplexConverter());
+ addAliasConverter(SimpleMolecule.class, new SimpleMoleculeConverter());
+ addAliasConverter(Drug.class, new DrugConverter());
+ addAliasConverter(Ion.class, new IonConverter());
+ addAliasConverter(Phenotype.class, new PhenotypeConverter());
+ addAliasConverter(Rna.class, new RnaConverter());
+ addAliasConverter(AntisenseRna.class, new AntisenseRnaConverter());
+ addAliasConverter(Gene.class, new GeneConverter());
+ addAliasConverter(Unknown.class, new UnknownConverter());
// for compartment aliases
- addAliasConverter(SquareCompartmentAlias.class, new SquareCompartmentConverter());
- addAliasConverter(OvalCompartmentAlias.class, new OvalCompartmentConverter());
- addAliasConverter(ArtifitialCompartmentAlias.class, new ArtifitialCompartmentConverter());
- addAliasConverter(BottomSquareCompartmentAlias.class, new BottomSquareCompartmentConverter());
- addAliasConverter(TopSquareCompartmentAlias.class, new TopSquareCompartmentConverter());
- addAliasConverter(LeftSquareCompartmentAlias.class, new LeftSquareCompartmentConverter());
- addAliasConverter(RightSquareCompartmentAlias.class, new RightSquareCompartmentConverter());
+ addAliasConverter(SquareCompartment.class, new SquareCompartmentConverter());
+ addAliasConverter(OvalCompartment.class, new OvalCompartmentConverter());
+ addAliasConverter(PathwayCompartment.class, new ArtifitialCompartmentConverter());
+ addAliasConverter(BottomSquareCompartment.class, new BottomSquareCompartmentConverter());
+ addAliasConverter(TopSquareCompartment.class, new TopSquareCompartmentConverter());
+ addAliasConverter(LeftSquareCompartment.class, new LeftSquareCompartmentConverter());
+ addAliasConverter(RightSquareCompartment.class, new RightSquareCompartmentConverter());
}
@@ -117,7 +117,7 @@ public class AliasConverter implements IAliasConverter<Alias> {
* @param converter
* converter that should be used for conversion of this alias
*/
- protected static void addAliasConverter(final Class<? extends Alias> clazz, final IAliasConverter<?> converter) {
+ protected static void addAliasConverter(final Class<? extends Element> clazz, final IAliasConverter<?> converter) {
if (aliasConverters.get(clazz) != null) {
logger.warn("Converter for " + clazz + " has been already added");
}
@@ -133,7 +133,7 @@ public class AliasConverter implements IAliasConverter<Alias> {
* @return converter that can be applied for the given alias; null if such
* converter doesn't exist
*/
- private static IAliasConverter<? extends Alias> getConverterForAlias(final Alias alias) {
+ private static IAliasConverter<? extends Element> getConverterForAlias(final Element alias) {
if (alias == null) {
throw new InvalidArgumentException("alias cannot be null");
}
@@ -161,10 +161,10 @@ public class AliasConverter implements IAliasConverter<Alias> {
* @param sbgnFormat
* boolean value indicating if SBGN display format should be used
*/
- public AliasConverter(final Alias alias, final boolean sbgnFormat) {
+ public AliasConverter(final Element alias, final boolean sbgnFormat) {
// If alias is a nucleic acid feature to be displayed in SBGN
- if (sbgnFormat && (alias instanceof AntisenseRnaAlias || alias instanceof RnaAlias || alias instanceof GeneAlias)) {
+ if (sbgnFormat && (alias instanceof AntisenseRna || alias instanceof Rna || alias instanceof Gene)) {
aliasConverter = new SBGNNucleicAcidFeatureConverter();
} else {
// If not, at the beginning try to find an appropriate converter
@@ -183,25 +183,25 @@ public class AliasConverter implements IAliasConverter<Alias> {
* @param alias
* alias for which this converter will be used
*/
- public AliasConverter(final Alias alias) {
+ public AliasConverter(final Element alias) {
this(alias, false);
}
@SuppressWarnings("unchecked")
@Override
- public void drawAlias(final Alias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Element alias, final Graphics2D graphics, final ConverterParams params) {
aliasConverter.drawAlias(alias, graphics, params);
}
@SuppressWarnings("unchecked")
@Override
- public void drawText(final Alias compAlias, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ public void drawText(final Element compAlias, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
aliasConverter.drawText(compAlias, graphics, params);
}
@SuppressWarnings("unchecked")
@Override
- public void drawAlias(Alias alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ public void drawAlias(Element alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
aliasConverter.drawAlias(alias, graphics, params, visualizedLayoutsColorSchemas);
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/IAliasConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/IAliasConverter.java
index bfb089af4f..d06ea04b21 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/IAliasConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/IAliasConverter.java
@@ -4,18 +4,18 @@ import java.awt.Graphics2D;
import java.util.List;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This interface defines what operations should be possible to convert
- * {@link Alias} into a graphics on Graphics2D object.
+ * {@link Element} into a graphics on Graphics2D object.
*
* @author Piotr Gawron
*
* @param <T>
* class of alias to convert
*/
-public interface IAliasConverter<T extends Alias> {
+public interface IAliasConverter<T extends Element> {
/**
* Alpha value (0..255) used for visualizing layout data that are normally
* visualized in javascript.
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/ArtifitialCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/ArtifitialCompartmentConverter.java
index 021a918f00..17dd4f37e2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/ArtifitialCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/ArtifitialCompartmentConverter.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.converter.graphics.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-
-/**
- * This class allows to draw ArtifitialCompartment on the Graphics2D class.
- *
- * @author Piotr Gawron
- *
- */
-public class ArtifitialCompartmentConverter extends CompartmentConverter<ArtifitialCompartmentAlias> {
- /**
- * Background color of drawn compartments.
- */
- private Color backgroundColor = Color.LIGHT_GRAY;
-
- @Override
- public void drawAlias(final ArtifitialCompartmentAlias alias, final Graphics2D graphics, final ConverterParams params) {
- // keep the old values of colors and line
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- Shape shape = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
-
- Color color = alias.getColor();
-
- // fill the background
- if (params.isFill()) {
- graphics.setColor(backgroundColor);
- } else {
- Color bgAlphaColor = new Color(0, 0, 0, getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(shape);
-
- // draw the border
- graphics.setColor(color);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(shape);
-
- // restore old color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description of the compartment
- if (params.isFill()) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
- } else {
- if (!alias.containsIdenticalSpecies()) {
- drawText(alias, graphics, params);
- }
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+
+/**
+ * This class allows to draw ArtifitialCompartment on the Graphics2D class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ArtifitialCompartmentConverter extends CompartmentConverter<PathwayCompartment> {
+ /**
+ * Background color of drawn compartments.
+ */
+ private Color backgroundColor = Color.LIGHT_GRAY;
+
+ @Override
+ public void drawAlias(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ // keep the old values of colors and line
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ Shape shape = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+
+ Color color = alias.getColor();
+
+ // fill the background
+ if (params.isFill()) {
+ graphics.setColor(backgroundColor);
+ } else {
+ Color bgAlphaColor = new Color(0, 0, 0, getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(shape);
+
+ // draw the border
+ graphics.setColor(color);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(shape);
+
+ // restore old color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description of the compartment
+ if (params.isFill()) {
+ Point2D tmpPoint = alias.getNamePoint();
+ alias.setNamePoint(alias.getCenter());
+ drawText(alias, graphics, params);
+ alias.setNamePoint(tmpPoint);
+ } else {
+ if (!alias.containsIdenticalSpecies()) {
+ drawText(alias, graphics, params);
+ }
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
index e3108042dd..25d9cdd4f3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.converter.graphics.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.BottomSquareCompartmentAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing BottomSquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class BottomSquareCompartmentConverter extends CompartmentConverter<BottomSquareCompartmentAlias> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(BottomSquareCompartmentConverter.class.getName());
-
- @Override
- public void drawAlias(final BottomSquareCompartmentAlias alias, final Graphics2D graphics, final ConverterParams params) {
- // keep the old values of colors and line
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = new Line2D.Double(0, alias.getY(), alias.getWidth(), alias.getY());
- Shape s3 = new Line2D.Double(0, alias.getY() + alias.getThickness(), alias.getWidth(), alias.getY() + alias.getThickness());
- Area a1 = new Area(new Rectangle2D.Double(0.0, alias.getY(), alias.getWidth(), alias.getHeight()));
-
- Color c1 = alias.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- // fill the background
- if (params.isFill()) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (params.isFill()) {
- graphics.fill(a1);
- }
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (params.isFill()) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing BottomSquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BottomSquareCompartmentConverter extends CompartmentConverter<BottomSquareCompartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(BottomSquareCompartmentConverter.class.getName());
+
+ @Override
+ public void drawAlias(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ // keep the old values of colors and line
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = new Line2D.Double(0, alias.getY(), alias.getWidth(), alias.getY());
+ Shape s3 = new Line2D.Double(0, alias.getY() + alias.getThickness(), alias.getWidth(), alias.getY() + alias.getThickness());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, alias.getY(), alias.getWidth(), alias.getHeight()));
+
+ Color c1 = alias.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ // fill the background
+ if (params.isFill()) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (params.isFill()) {
+ graphics.fill(a1);
+ }
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (params.isFill()) {
+ Point2D tmpPoint = alias.getNamePoint();
+ alias.setNamePoint(alias.getCenter());
+ drawText(alias, graphics, params);
+ alias.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
index ea1699fcb9..cf4088bb9b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
@@ -17,8 +17,8 @@ import lcsb.mapviewer.converter.graphics.IAliasConverter;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
import lcsb.mapviewer.converter.graphics.placefinder.PlaceFinder;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
/**
* Abstract class responsible for common methods to draw compartmentAliases on
@@ -30,7 +30,7 @@ import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
* class for which the comparator is created
*
*/
-public abstract class CompartmentConverter<T extends CompartmentAlias> implements IAliasConverter<T> {
+public abstract class CompartmentConverter<T extends Compartment> implements IAliasConverter<T> {
/**
* Default class logger.
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
index 146d977a7b..5d3f1a7fa5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.converter.graphics.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.LeftSquareCompartmentAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing LeftSquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSquareCompartmentAlias> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LeftSquareCompartmentConverter.class.getName());
-
- @Override
- public void drawAlias(final LeftSquareCompartmentAlias alias, final Graphics2D graphics, final ConverterParams params) {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = new Line2D.Double(alias.getWidth(), alias.getHeight(), alias.getWidth(), 0);
- Shape s3 = new Line2D.Double(alias.getWidth() - alias.getThickness(), 0, alias.getWidth() - alias.getThickness(), alias.getHeight());
- Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, alias.getWidth(), alias.getHeight()));
-
- Color c1 = alias.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- // fill the background
- if (params.isFill()) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (params.isFill()) {
- graphics.fill(a1);
- }
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (params.isFill()) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing LeftSquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSquareCompartment> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LeftSquareCompartmentConverter.class.getName());
+
+ @Override
+ public void drawAlias(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = new Line2D.Double(alias.getWidth(), alias.getHeight(), alias.getWidth(), 0);
+ Shape s3 = new Line2D.Double(alias.getWidth() - alias.getThickness(), 0, alias.getWidth() - alias.getThickness(), alias.getHeight());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, alias.getWidth(), alias.getHeight()));
+
+ Color c1 = alias.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ // fill the background
+ if (params.isFill()) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (params.isFill()) {
+ graphics.fill(a1);
+ }
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (params.isFill()) {
+ Point2D tmpPoint = alias.getNamePoint();
+ alias.setNamePoint(alias.getCenter());
+ drawText(alias, graphics, params);
+ alias.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
index 3ece516ee3..e13e233558 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
@@ -1,91 +1,91 @@
-package lcsb.mapviewer.converter.graphics.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.OvalCompartmentAlias;
-
-/**
- * Class responsible for drawing OvalCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartmentAlias> {
-
- /**
- * Returns shape representing alias.
- *
- * @param alias
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
- */
- private Shape getShape(final Alias alias) {
- return new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
- }
-
- @Override
- public void drawAlias(final OvalCompartmentAlias alias, final Graphics2D graphics, final ConverterParams params) {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = getShape(alias);
- alias.increaseBorder(-alias.getThickness());
- Shape s3 = getShape(alias);
- alias.increaseBorder(alias.getThickness());
-
- Color c1 = alias.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- Area a1 = new Area(s1);
- a1.subtract(new Area(s3));
-
- // fill the background
- if (params.isFill()) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- graphics.fill(a1);
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (params.isFill()) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
- } else {
- if (!alias.containsIdenticalSpecies()) {
- drawText(alias, graphics, params);
- }
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class responsible for drawing OvalCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartment> {
+
+ /**
+ * Returns shape representing alias.
+ *
+ * @param alias
+ * alias for which we are looking for a Shape
+ * @return Shape object that represents alias
+ */
+ private Shape getShape(final Element alias) {
+ return new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ }
+
+ @Override
+ public void drawAlias(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = getShape(alias);
+ alias.increaseBorder(-alias.getThickness());
+ Shape s3 = getShape(alias);
+ alias.increaseBorder(alias.getThickness());
+
+ Color c1 = alias.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ Area a1 = new Area(s1);
+ a1.subtract(new Area(s3));
+
+ // fill the background
+ if (params.isFill()) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ graphics.fill(a1);
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (params.isFill()) {
+ Point2D tmpPoint = alias.getNamePoint();
+ alias.setNamePoint(alias.getCenter());
+ drawText(alias, graphics, params);
+ alias.setNamePoint(tmpPoint);
+ } else {
+ if (!alias.containsIdenticalSpecies()) {
+ drawText(alias, graphics, params);
+ }
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
index 5c8237d3d6..5fa37bec8f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.converter.graphics.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.RightSquareCompartmentAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing RightSquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class RightSquareCompartmentConverter extends CompartmentConverter<RightSquareCompartmentAlias> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RightSquareCompartmentConverter.class.getName());
-
- @Override
- public void drawAlias(final RightSquareCompartmentAlias alias, final Graphics2D graphics, final ConverterParams params) {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = new Line2D.Double(alias.getX(), alias.getHeight(), alias.getX(), 0);
- Shape s3 = new Line2D.Double(alias.getX() + alias.getThickness(), alias.getHeight(), alias.getX(), 0);
- Area a1 = new Area(new Rectangle2D.Double(alias.getX(), 0.0, alias.getWidth(), alias.getHeight()));
-
- Color c1 = alias.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- // fill the background
- if (params.isFill()) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (params.isFill()) {
- graphics.fill(a1);
- }
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // three lines below are only temporary fix...
- double x = alias.getNamePoint().getX() - alias.getX();
- double y = alias.getNamePoint().getY();
- alias.getNamePoint().setLocation(x, y);
-
- // draw description
- if (params.isFill()) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
- }
- x += alias.getX();
- alias.getNamePoint().setLocation(x, y);
- }
-}
+package lcsb.mapviewer.converter.graphics.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing RightSquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RightSquareCompartmentConverter extends CompartmentConverter<RightSquareCompartment> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RightSquareCompartmentConverter.class.getName());
+
+ @Override
+ public void drawAlias(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = new Line2D.Double(alias.getX(), alias.getHeight(), alias.getX(), 0);
+ Shape s3 = new Line2D.Double(alias.getX() + alias.getThickness(), alias.getHeight(), alias.getX(), 0);
+ Area a1 = new Area(new Rectangle2D.Double(alias.getX(), 0.0, alias.getWidth(), alias.getHeight()));
+
+ Color c1 = alias.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ // fill the background
+ if (params.isFill()) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (params.isFill()) {
+ graphics.fill(a1);
+ }
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // three lines below are only temporary fix...
+ double x = alias.getNamePoint().getX() - alias.getX();
+ double y = alias.getNamePoint().getY();
+ alias.getNamePoint().setLocation(x, y);
+
+ // draw description
+ if (params.isFill()) {
+ Point2D tmpPoint = alias.getNamePoint();
+ alias.setNamePoint(alias.getCenter());
+ drawText(alias, graphics, params);
+ alias.setNamePoint(tmpPoint);
+ }
+ x += alias.getX();
+ alias.getNamePoint().setLocation(x, y);
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
index e379687c91..d07657464f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.converter.graphics.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing SquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class SquareCompartmentConverter extends CompartmentConverter<SquareCompartmentAlias> {
- /**
- * How big is the arc in the corner of rectangle that represents square
- * compartment.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 20;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SquareCompartmentConverter.class.getName());
-
- /**
- * Returns shape representing alias.
- *
- * @param alias
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
- */
- private Shape getShape(final Alias alias) {
- return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
- }
-
- @Override
- public void drawAlias(final SquareCompartmentAlias alias, final Graphics2D graphics, final ConverterParams params) {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = getShape(alias);
- alias.increaseBorder(-alias.getThickness());
- Shape s3 = getShape(alias);
- alias.increaseBorder(alias.getThickness());
-
- Color c1 = alias.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- Area a1 = new Area(s1);
- a1.subtract(new Area(s3));
-
- // fill the background
- if (params.isFill()) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- graphics.fill(a1);
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (params.isFill()) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing SquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SquareCompartmentConverter extends CompartmentConverter<SquareCompartment> {
+ /**
+ * How big is the arc in the corner of rectangle that represents square
+ * compartment.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 20;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SquareCompartmentConverter.class.getName());
+
+ /**
+ * Returns shape representing alias.
+ *
+ * @param alias
+ * alias for which we are looking for a Shape
+ * @return Shape object that represents alias
+ */
+ private Shape getShape(final Element alias) {
+ return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+ @Override
+ public void drawAlias(final SquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = getShape(alias);
+ alias.increaseBorder(-alias.getThickness());
+ Shape s3 = getShape(alias);
+ alias.increaseBorder(alias.getThickness());
+
+ Color c1 = alias.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ Area a1 = new Area(s1);
+ a1.subtract(new Area(s3));
+
+ // fill the background
+ if (params.isFill()) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ graphics.fill(a1);
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (params.isFill()) {
+ Point2D tmpPoint = alias.getNamePoint();
+ alias.setNamePoint(alias.getCenter());
+ drawText(alias, graphics, params);
+ alias.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
index e9bc9a55c7..afc5febcff 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.converter.graphics.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.TopSquareCompartmentAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing TopSquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquareCompartmentAlias> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(TopSquareCompartmentConverter.class.getName());
-
- @Override
- public void drawAlias(final TopSquareCompartmentAlias alias, final Graphics2D graphics, final ConverterParams params) {
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- Shape s1 = new Line2D.Double(0, alias.getHeight(), alias.getWidth(), alias.getHeight());
- Shape s3 = new Line2D.Double(0, alias.getHeight() - alias.getThickness(), alias.getWidth(), alias.getHeight() - alias.getThickness());
- Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, alias.getWidth(), alias.getHeight()));
-
- Color c1 = alias.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- if (params.isFill()) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (params.isFill()) {
- graphics.fill(a1);
- }
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
- // draw description
- if (params.isFill()) {
- Point2D tmpPoint = alias.getNamePoint();
- alias.setNamePoint(alias.getCenter());
- drawText(alias, graphics, params);
- alias.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing TopSquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquareCompartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(TopSquareCompartmentConverter.class.getName());
+
+ @Override
+ public void drawAlias(final TopSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ Shape s1 = new Line2D.Double(0, alias.getHeight(), alias.getWidth(), alias.getHeight());
+ Shape s3 = new Line2D.Double(0, alias.getHeight() - alias.getThickness(), alias.getWidth(), alias.getHeight() - alias.getThickness());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, alias.getWidth(), alias.getHeight()));
+
+ Color c1 = alias.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ if (params.isFill()) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (params.isFill()) {
+ graphics.fill(a1);
+ }
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+ // draw description
+ if (params.isFill()) {
+ Point2D tmpPoint = alias.getNamePoint();
+ alias.setNamePoint(alias.getCenter());
+ drawText(alias, graphics, params);
+ alias.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/package-info.java
index ac04e1c815..238015b528 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/package-info.java
@@ -1,7 +1,5 @@
-/**
- * Provides classes that draws different implemention of
- * {@link lcsb.mapviewer.db.model.map.layout.alias.CompartmentAlias
- * CompartmentAlias} on the {@link java.awt.Graphics2D Graphics2D}.
- */
-package lcsb.mapviewer.converter.graphics.compartment;
-
+/**
+ * Provides classes that draws different implemention of
+ * {@link Compartment} on the {@link Graphics2D}.
+ */
+package lcsb.mapviewer.converter.graphics.compartment;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
index 210333ea16..06b52123ff 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
@@ -1,466 +1,466 @@
-package lcsb.mapviewer.converter.graphics.placefinder;
-
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class allows to find free space where description should appear for the
- * alias in hierarchical view.
- *
- * @author Piotr Gawron
- *
- */
-public class PlaceFinder {
-
- /**
- * Represents small part of the map (enclosed by cuting lines) where something
- * can be put. Contains borders (height, weight, location etc). Informatin if
- * it can be used or no and range (magic field that describes how much to the
- * bottom rectangle can be extended).
- *
- * @author Piotr Gawron
- *
- */
- private class Field {
- /**
- * Border of the field.
- */
- private Rectangle2D border;
- /**
- * Can the field be used for something or is occupied?
- */
- private boolean available = true;
- /**
- * How many fields to the bottom are free (how much could we extend empty
- * rectangle.
- */
- private int range = -1;
-
- /**
- * @return the border
- * @see #border
- */
- Rectangle2D getBorder() {
- return border;
- }
-
- /**
- * @param border
- * the border to set
- * @see #border
- */
- void setBorder(Rectangle2D border) {
- this.border = border;
- }
-
- /**
- * @return the available
- * @see #available
- */
- public boolean isAvailable() {
- return available;
- }
-
- /**
- * @param available
- * the available to set
- * @see #available
- */
- public void setAvailable(boolean available) {
- this.available = available;
- }
-
- /**
- * @return the range
- * @see #range
- */
- public int getRange() {
- return range;
- }
-
- /**
- * @param range
- * the range to set
- * @see #range
- */
- public void setRange(int range) {
- this.range = range;
- }
- }
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PlaceFinder.class.getName());
- /**
- * Whole surface is split into rectangular regions. The lines that cut the
- * surface correspond to borders of aliases that overlap current alias. This
- * matrix defines which of these regions can be used for description.
- */
- private Field[][] matrix;
-
- /**
- * List of {@link CompartmentAlias compartment aliases} that split surface
- * into regions.
- */
- private List<CompartmentAlias> aliases;
-
- /**
- * Alias for which computation is done.
- */
- private Alias mainAlias;
-
- /**
- * Left boundary of the rectangle in which we want to fit our description.
- */
- private double leftBound;
- /**
- * Right boundary of the rectangle in which we want to fit our description.
- */
- private double rightBound;
- /**
- * Top boundary of the rectangle in which we want to fit our description.
- */
- private double upBound;
- /**
- * Bottom boundary of the rectangle in which we want to fit our description.
- */
- private double bottomBound;
-
- /**
- * Model for which this {@link PlaceFinder} was created.
- */
- private Model model;
-
- /**
- * Map with aliases that should be considered when looking for a place to put
- * text.
- */
- private Map<Alias, List<CompartmentAlias>> otherAliases = new HashMap<Alias, List<CompartmentAlias>>();
-
- /**
- * Default constructor for place finder in a model.
- *
- * @param model
- * model
- *
- */
- public PlaceFinder(Model model) {
- this.model = model;
- }
-
- /**
- * Finds the biggest rectangle.
- *
- * @return the biggest rectangle
- */
- private Rectangle2D findRectangle() {
- Rectangle2D biggestRectangle = new Rectangle2D.Double();
- Rectangle2D temporaryRectangle = null;
- for (int y = 0; y < getSizeY(); y++) {
- for (int x = 0; x < getSizeX(); x++) {
- temporaryRectangle = computeRectangleMaxArea(x, y);
- double newArea = temporaryRectangle.getWidth() * temporaryRectangle.getHeight();
- double oldArea = biggestRectangle.getWidth() * biggestRectangle.getHeight();
- if (newArea > oldArea) {
- biggestRectangle = temporaryRectangle;
- }
- }
- }
-
- return biggestRectangle;
- }
-
- /**
- * Computes the biggest rectangle that starts in the region on the position
- * [x,y].
- *
- * @param x
- * x index of the region
- * @param y
- * y index of the region
- * @return the biggest rectangle that starts in the region on the given
- * position
- */
- private Rectangle2D computeRectangleMaxArea(int x, int y) {
- Rectangle2D result = new Rectangle2D.Double();
- int possibleMaximumOfHeight = matrix[x][y].getRange();
- for (int k = x; k >= 0 && matrix[k][y].isAvailable(); k--) {
- if (matrix[k][y].getRange() < possibleMaximumOfHeight) {
- possibleMaximumOfHeight = matrix[k][y].getRange();
- }
- Rectangle2D temporary = computeRectangle(x, y, k, possibleMaximumOfHeight);
- double newArea = temporary.getWidth() * temporary.getHeight();
- double oldArea = result.getWidth() * result.getHeight();
- if (newArea > oldArea) {
- result = temporary;
- }
- }
- return result;
- }
-
- /**
- * Computes rectangle in region range [k..x][y..y+height].
- *
- * @param x
- * end x coordinate
- * @param y
- * start y coordinate
- * @param k
- * start x coordinate
- * @param height
- * height in y coordinate
- * @return rectangle in region range
- */
- private Rectangle2D computeRectangle(int x, int y, int k, int height) {
- double resX = matrix[k][y].getBorder().getX();
- double resY = matrix[k][y].getBorder().getY();
- double resWidth = matrix[x][y + height - 1].getBorder().getX() - resX + matrix[x][y + height - 1].getBorder().getWidth();
- double resHeight = matrix[x][y + height - 1].getBorder().getY() - resY + matrix[x][y + height - 1].getBorder().getHeight();
-
- return new Rectangle2D.Double(resX, resY, resWidth, resHeight);
- }
-
- /**
- * Computes how deep in y axis can regions be extended from starting x,y
- * region.
- */
- private void findRanges() {
- for (int i = 0; i < getSizeX(); i++) {
- for (int j = 0; j < getSizeY(); j++) {
- if (!matrix[i][j].isAvailable()) {
- int k = j;
- int temporaryRange = 0;
- while (k >= 0 && matrix[i][k].getRange() == -1) {
- matrix[i][k--].setRange(temporaryRange++);
- }
- }
- }
- if (matrix[i][getSizeY() - 1].isAvailable()) {
- int k = getSizeY() - 1;
- int temporaryRange = 1;
- while (k >= 0 && matrix[i][k].getRange() == -1) {
- matrix[i][k--].setRange(temporaryRange++);
- }
- }
-
- }
- }
-
- /**
- * Disables regions for all aliases.
- */
- private void fillMatrixWithAliases() {
- for (Alias alias : aliases) {
- if (alias != mainAlias) {
- fillMatrixWithAlias(alias);
- }
- }
- }
-
- /**
- * Disable regions for given alias.
- *
- * @param alias
- * alias that should disable regions
- */
- private void fillMatrixWithAlias(Alias alias) {
- Double a, b, c, d;
-
- a = alias.getX();
- b = alias.getX() + alias.getWidth();
- c = alias.getY() + alias.getHeight();
- d = alias.getY();
-
- fillWithPoints(a, b, c, d);
- }
-
- /**
- * Disable regions between given coordinates.
- *
- * @param x
- * starting x coordinate
- * @param xw
- * ending x coordinate
- * @param yh
- * ending y coordinate
- * @param y
- * starting y coordinate
- */
- private void fillWithPoints(Double x, Double xw, Double yh, Double y) {
- Integer widthStart = 0;
- Integer widthEnd = matrix.length;
- Integer heightStart = 0;
- Integer heightEnd = matrix[0].length;
-
- for (int i = 0; i < matrix.length; i++) {
- if (matrix[i][0].getBorder().getX() <= x) {
- widthStart = i;
- }
- if (matrix[i][0].getBorder().getX() <= xw) {
- widthEnd = i;
- }
- }
- if (matrix[matrix.length - 1][0].getBorder().getX() + matrix[matrix.length - 1][0].getBorder().getWidth() <= xw) {
- widthEnd = matrix.length;
- }
- for (int i = 0; i < matrix[0].length; i++) {
- if (matrix[0][i].getBorder().getY() <= y) {
- heightStart = i;
- }
- if (matrix[0][i].getBorder().getY() <= yh) {
- heightEnd = i;
- }
- }
- if (matrix[0][matrix[0].length - 1].getBorder().getY() + matrix[0][matrix[0].length - 1].getBorder().getHeight() <= yh) {
- heightEnd = matrix[0].length;
- }
-
- for (int i = widthStart; i < widthEnd; i++) {
- for (int j = heightStart; j < heightEnd; j++) {
- matrix[i][j].setAvailable(false);
- }
- }
- }
-
- /**
- * This method looks for a place to put description of the alias on the map.
- *
- * @param alias
- * alias for which we try to determine text position
- * @return bounds where text could be put
- */
- public Rectangle2D getRetangle(CompartmentAlias alias) {
- List<CompartmentAlias> list = otherAliases.get(alias);
- if (list == null) {
- list = new ArrayList<CompartmentAlias>();
- for (CompartmentAlias compAlias : model.getCompartmentsAliases()) {
- if (compAlias.getVisibilityLevel() <= alias.getVisibilityLevel() && compAlias.getTransparencyLevel() > alias.getVisibilityLevel()) {
- if (compAlias.cross(alias) && compAlias.getSize() <= alias.getSize()) {
- list.add(compAlias);
- }
- }
- }
- otherAliases.put(alias, list);
- }
-
- this.mainAlias = alias;
- this.aliases = list;
-
- leftBound = alias.getX();
- rightBound = (alias.getX() + alias.getWidth());
- upBound = alias.getY();
- bottomBound = (alias.getY() + alias.getHeight());
-
- createMatrix();
-
- fillMatrixWithAliases();
-
- findRanges(); // 2*O(n^2)
-
- return findRectangle();
- }
-
- /**
- * Create empty matrix with fields.
- *
- * @see #matrix
- */
- protected void createMatrix() {
- Set<Double> xs = new TreeSet<Double>();
- Set<Double> ys = new TreeSet<Double>();
- List<Double> widths = new ArrayList<Double>();
- List<Double> xCoordsOfBegginingOfRectangle = new ArrayList<Double>();
- List<Double> heights = new ArrayList<Double>();
- List<Double> yCoordsOfBegginingOfRectangle = new ArrayList<Double>();
-
- for (Alias alias : aliases) {
- double x1 = alias.getX();
- double x2 = alias.getX() + alias.getWidth();
- double y1 = alias.getY();
- double y2 = alias.getY() + alias.getHeight();
- if (x1 >= leftBound && x1 <= rightBound) {
- xs.add(x1);
- }
- if (x2 >= leftBound && x2 <= rightBound) {
- xs.add(x2);
- }
-
- if (y1 >= upBound && y1 <= bottomBound) {
- ys.add(y1);
- }
- if (y2 >= upBound && y2 <= bottomBound) {
- ys.add(y2);
- }
- }
- Double previous = null;
- for (Double width : xs) {
- if (previous != null) {
- widths.add(width - previous);
- }
- xCoordsOfBegginingOfRectangle.add(width);
- previous = width;
- }
- previous = null;
- for (Double height : ys) {
- if (previous != null) {
- heights.add(height - previous);
- }
- yCoordsOfBegginingOfRectangle.add(height);
- previous = height;
- }
-
- matrix = new Field[xs.size() - 1][ys.size() - 1];
-
- for (int i = 0; i < getSizeX(); i++) {
- for (int j = 0; j < getSizeY(); j++) {
- Field field = new Field();
- xCoordsOfBegginingOfRectangle.get(i);
- yCoordsOfBegginingOfRectangle.get(j);
- widths.get(i);
- heights.get(j);
- field.setBorder(new Rectangle2D.Double(xCoordsOfBegginingOfRectangle.get(i), yCoordsOfBegginingOfRectangle.get(j), widths.get(i), heights.get(j)));
- matrix[i][j] = field;
- }
- }
- }
-
- /**
- *
- * @return {@link #model}
- */
- public Model getModel() {
- return model;
- }
-
- /**
- * Returns width of the {@link #matrix}.
- *
- * @return width of the {@link #matrix}
- */
- private int getSizeX() {
- return matrix.length;
- }
-
- /**
- * Returns height of the {@link #matrix}.
- *
- * @return height of the {@link #matrix}
- */
- private int getSizeY() {
- return matrix[0].length;
- }
-
-}
+package lcsb.mapviewer.converter.graphics.placefinder;
+
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class allows to find free space where description should appear for the
+ * alias in hierarchical view.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PlaceFinder {
+
+ /**
+ * Represents small part of the map (enclosed by cuting lines) where something
+ * can be put. Contains borders (height, weight, location etc). Informatin if
+ * it can be used or no and range (magic field that describes how much to the
+ * bottom rectangle can be extended).
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private class Field {
+ /**
+ * Border of the field.
+ */
+ private Rectangle2D border;
+ /**
+ * Can the field be used for something or is occupied?
+ */
+ private boolean available = true;
+ /**
+ * How many fields to the bottom are free (how much could we extend empty
+ * rectangle.
+ */
+ private int range = -1;
+
+ /**
+ * @return the border
+ * @see #border
+ */
+ Rectangle2D getBorder() {
+ return border;
+ }
+
+ /**
+ * @param border
+ * the border to set
+ * @see #border
+ */
+ void setBorder(Rectangle2D border) {
+ this.border = border;
+ }
+
+ /**
+ * @return the available
+ * @see #available
+ */
+ public boolean isAvailable() {
+ return available;
+ }
+
+ /**
+ * @param available
+ * the available to set
+ * @see #available
+ */
+ public void setAvailable(boolean available) {
+ this.available = available;
+ }
+
+ /**
+ * @return the range
+ * @see #range
+ */
+ public int getRange() {
+ return range;
+ }
+
+ /**
+ * @param range
+ * the range to set
+ * @see #range
+ */
+ public void setRange(int range) {
+ this.range = range;
+ }
+ }
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(PlaceFinder.class.getName());
+ /**
+ * Whole surface is split into rectangular regions. The lines that cut the
+ * surface correspond to borders of aliases that overlap current alias. This
+ * matrix defines which of these regions can be used for description.
+ */
+ private Field[][] matrix;
+
+ /**
+ * List of {@link Compartment compartment aliases} that split surface
+ * into regions.
+ */
+ private List<Compartment> aliases;
+
+ /**
+ * Alias for which computation is done.
+ */
+ private Element mainAlias;
+
+ /**
+ * Left boundary of the rectangle in which we want to fit our description.
+ */
+ private double leftBound;
+ /**
+ * Right boundary of the rectangle in which we want to fit our description.
+ */
+ private double rightBound;
+ /**
+ * Top boundary of the rectangle in which we want to fit our description.
+ */
+ private double upBound;
+ /**
+ * Bottom boundary of the rectangle in which we want to fit our description.
+ */
+ private double bottomBound;
+
+ /**
+ * Model for which this {@link PlaceFinder} was created.
+ */
+ private Model model;
+
+ /**
+ * Map with aliases that should be considered when looking for a place to put
+ * text.
+ */
+ private Map<Element, List<Compartment>> otherAliases = new HashMap<Element, List<Compartment>>();
+
+ /**
+ * Default constructor for place finder in a model.
+ *
+ * @param model
+ * model
+ *
+ */
+ public PlaceFinder(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * Finds the biggest rectangle.
+ *
+ * @return the biggest rectangle
+ */
+ private Rectangle2D findRectangle() {
+ Rectangle2D biggestRectangle = new Rectangle2D.Double();
+ Rectangle2D temporaryRectangle = null;
+ for (int y = 0; y < getSizeY(); y++) {
+ for (int x = 0; x < getSizeX(); x++) {
+ temporaryRectangle = computeRectangleMaxArea(x, y);
+ double newArea = temporaryRectangle.getWidth() * temporaryRectangle.getHeight();
+ double oldArea = biggestRectangle.getWidth() * biggestRectangle.getHeight();
+ if (newArea > oldArea) {
+ biggestRectangle = temporaryRectangle;
+ }
+ }
+ }
+
+ return biggestRectangle;
+ }
+
+ /**
+ * Computes the biggest rectangle that starts in the region on the position
+ * [x,y].
+ *
+ * @param x
+ * x index of the region
+ * @param y
+ * y index of the region
+ * @return the biggest rectangle that starts in the region on the given
+ * position
+ */
+ private Rectangle2D computeRectangleMaxArea(int x, int y) {
+ Rectangle2D result = new Rectangle2D.Double();
+ int possibleMaximumOfHeight = matrix[x][y].getRange();
+ for (int k = x; k >= 0 && matrix[k][y].isAvailable(); k--) {
+ if (matrix[k][y].getRange() < possibleMaximumOfHeight) {
+ possibleMaximumOfHeight = matrix[k][y].getRange();
+ }
+ Rectangle2D temporary = computeRectangle(x, y, k, possibleMaximumOfHeight);
+ double newArea = temporary.getWidth() * temporary.getHeight();
+ double oldArea = result.getWidth() * result.getHeight();
+ if (newArea > oldArea) {
+ result = temporary;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Computes rectangle in region range [k..x][y..y+height].
+ *
+ * @param x
+ * end x coordinate
+ * @param y
+ * start y coordinate
+ * @param k
+ * start x coordinate
+ * @param height
+ * height in y coordinate
+ * @return rectangle in region range
+ */
+ private Rectangle2D computeRectangle(int x, int y, int k, int height) {
+ double resX = matrix[k][y].getBorder().getX();
+ double resY = matrix[k][y].getBorder().getY();
+ double resWidth = matrix[x][y + height - 1].getBorder().getX() - resX + matrix[x][y + height - 1].getBorder().getWidth();
+ double resHeight = matrix[x][y + height - 1].getBorder().getY() - resY + matrix[x][y + height - 1].getBorder().getHeight();
+
+ return new Rectangle2D.Double(resX, resY, resWidth, resHeight);
+ }
+
+ /**
+ * Computes how deep in y axis can regions be extended from starting x,y
+ * region.
+ */
+ private void findRanges() {
+ for (int i = 0; i < getSizeX(); i++) {
+ for (int j = 0; j < getSizeY(); j++) {
+ if (!matrix[i][j].isAvailable()) {
+ int k = j;
+ int temporaryRange = 0;
+ while (k >= 0 && matrix[i][k].getRange() == -1) {
+ matrix[i][k--].setRange(temporaryRange++);
+ }
+ }
+ }
+ if (matrix[i][getSizeY() - 1].isAvailable()) {
+ int k = getSizeY() - 1;
+ int temporaryRange = 1;
+ while (k >= 0 && matrix[i][k].getRange() == -1) {
+ matrix[i][k--].setRange(temporaryRange++);
+ }
+ }
+
+ }
+ }
+
+ /**
+ * Disables regions for all aliases.
+ */
+ private void fillMatrixWithAliases() {
+ for (Element alias : aliases) {
+ if (alias != mainAlias) {
+ fillMatrixWithAlias(alias);
+ }
+ }
+ }
+
+ /**
+ * Disable regions for given alias.
+ *
+ * @param alias
+ * alias that should disable regions
+ */
+ private void fillMatrixWithAlias(Element alias) {
+ Double a, b, c, d;
+
+ a = alias.getX();
+ b = alias.getX() + alias.getWidth();
+ c = alias.getY() + alias.getHeight();
+ d = alias.getY();
+
+ fillWithPoints(a, b, c, d);
+ }
+
+ /**
+ * Disable regions between given coordinates.
+ *
+ * @param x
+ * starting x coordinate
+ * @param xw
+ * ending x coordinate
+ * @param yh
+ * ending y coordinate
+ * @param y
+ * starting y coordinate
+ */
+ private void fillWithPoints(Double x, Double xw, Double yh, Double y) {
+ Integer widthStart = 0;
+ Integer widthEnd = matrix.length;
+ Integer heightStart = 0;
+ Integer heightEnd = matrix[0].length;
+
+ for (int i = 0; i < matrix.length; i++) {
+ if (matrix[i][0].getBorder().getX() <= x) {
+ widthStart = i;
+ }
+ if (matrix[i][0].getBorder().getX() <= xw) {
+ widthEnd = i;
+ }
+ }
+ if (matrix[matrix.length - 1][0].getBorder().getX() + matrix[matrix.length - 1][0].getBorder().getWidth() <= xw) {
+ widthEnd = matrix.length;
+ }
+ for (int i = 0; i < matrix[0].length; i++) {
+ if (matrix[0][i].getBorder().getY() <= y) {
+ heightStart = i;
+ }
+ if (matrix[0][i].getBorder().getY() <= yh) {
+ heightEnd = i;
+ }
+ }
+ if (matrix[0][matrix[0].length - 1].getBorder().getY() + matrix[0][matrix[0].length - 1].getBorder().getHeight() <= yh) {
+ heightEnd = matrix[0].length;
+ }
+
+ for (int i = widthStart; i < widthEnd; i++) {
+ for (int j = heightStart; j < heightEnd; j++) {
+ matrix[i][j].setAvailable(false);
+ }
+ }
+ }
+
+ /**
+ * This method looks for a place to put description of the alias on the map.
+ *
+ * @param alias
+ * alias for which we try to determine text position
+ * @return bounds where text could be put
+ */
+ public Rectangle2D getRetangle(Compartment alias) {
+ List<Compartment> list = otherAliases.get(alias);
+ if (list == null) {
+ list = new ArrayList<Compartment>();
+ for (Compartment compAlias : model.getCompartmentsAliases()) {
+ if (compAlias.getVisibilityLevel() <= alias.getVisibilityLevel() && compAlias.getTransparencyLevel() > alias.getVisibilityLevel()) {
+ if (compAlias.cross(alias) && compAlias.getSize() <= alias.getSize()) {
+ list.add(compAlias);
+ }
+ }
+ }
+ otherAliases.put(alias, list);
+ }
+
+ this.mainAlias = alias;
+ this.aliases = list;
+
+ leftBound = alias.getX();
+ rightBound = (alias.getX() + alias.getWidth());
+ upBound = alias.getY();
+ bottomBound = (alias.getY() + alias.getHeight());
+
+ createMatrix();
+
+ fillMatrixWithAliases();
+
+ findRanges(); // 2*O(n^2)
+
+ return findRectangle();
+ }
+
+ /**
+ * Create empty matrix with fields.
+ *
+ * @see #matrix
+ */
+ protected void createMatrix() {
+ Set<Double> xs = new TreeSet<Double>();
+ Set<Double> ys = new TreeSet<Double>();
+ List<Double> widths = new ArrayList<Double>();
+ List<Double> xCoordsOfBegginingOfRectangle = new ArrayList<Double>();
+ List<Double> heights = new ArrayList<Double>();
+ List<Double> yCoordsOfBegginingOfRectangle = new ArrayList<Double>();
+
+ for (Element alias : aliases) {
+ double x1 = alias.getX();
+ double x2 = alias.getX() + alias.getWidth();
+ double y1 = alias.getY();
+ double y2 = alias.getY() + alias.getHeight();
+ if (x1 >= leftBound && x1 <= rightBound) {
+ xs.add(x1);
+ }
+ if (x2 >= leftBound && x2 <= rightBound) {
+ xs.add(x2);
+ }
+
+ if (y1 >= upBound && y1 <= bottomBound) {
+ ys.add(y1);
+ }
+ if (y2 >= upBound && y2 <= bottomBound) {
+ ys.add(y2);
+ }
+ }
+ Double previous = null;
+ for (Double width : xs) {
+ if (previous != null) {
+ widths.add(width - previous);
+ }
+ xCoordsOfBegginingOfRectangle.add(width);
+ previous = width;
+ }
+ previous = null;
+ for (Double height : ys) {
+ if (previous != null) {
+ heights.add(height - previous);
+ }
+ yCoordsOfBegginingOfRectangle.add(height);
+ previous = height;
+ }
+
+ matrix = new Field[xs.size() - 1][ys.size() - 1];
+
+ for (int i = 0; i < getSizeX(); i++) {
+ for (int j = 0; j < getSizeY(); j++) {
+ Field field = new Field();
+ xCoordsOfBegginingOfRectangle.get(i);
+ yCoordsOfBegginingOfRectangle.get(j);
+ widths.get(i);
+ heights.get(j);
+ field.setBorder(new Rectangle2D.Double(xCoordsOfBegginingOfRectangle.get(i), yCoordsOfBegginingOfRectangle.get(j), widths.get(i), heights.get(j)));
+ matrix[i][j] = field;
+ }
+ }
+ }
+
+ /**
+ *
+ * @return {@link #model}
+ */
+ public Model getModel() {
+ return model;
+ }
+
+ /**
+ * Returns width of the {@link #matrix}.
+ *
+ * @return width of the {@link #matrix}
+ */
+ private int getSizeX() {
+ return matrix.length;
+ }
+
+ /**
+ * Returns height of the {@link #matrix}.
+ *
+ * @return height of the {@link #matrix}
+ */
+ private int getSizeY() {
+ return matrix[0].length;
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
index ebfb0c2dcc..1bbb52b6c3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
@@ -14,10 +14,10 @@ import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
* This class defines methods used for drawing Antisense Rna SpeciesAlias on the
@@ -27,7 +27,7 @@ import lcsb.mapviewer.model.map.layout.alias.ModificationState;
*
*/
-public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRnaAlias> {
+public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
/**
* Default class logger.
*/
@@ -35,7 +35,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRnaAlias> {
private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
@Override
- public void drawAlias(final AntisenseRnaAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final AntisenseRna alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getAntisenseRnaPath(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
@@ -46,7 +46,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRnaAlias> {
graphics.draw(path);
graphics.setStroke(stroke);
- for (AntisenseRnaRegionAlias mr : alias.getRegions()) {
+ for (AntisenseRnaRegion mr : alias.getRegions()) {
drawRegion(alias, mr, graphics, false, false);
}
@@ -60,7 +60,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRnaAlias> {
* alias for which we want to get border
* @return border of the alias
*/
- private GeneralPath getAntisenseRnaPath(final Alias alias) {
+ private GeneralPath getAntisenseRnaPath(final Element alias) {
// CHECKSTYLE:OFF
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
path.moveTo(alias.getX(), alias.getY());
@@ -73,7 +73,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRnaAlias> {
}
@Override
- public PathIterator getBoundPathIterator(final AntisenseRnaAlias alias) {
+ public PathIterator getBoundPathIterator(final AntisenseRna alias) {
return getAntisenseRnaPath(alias).getPathIterator(new AffineTransform());
}
@@ -91,7 +91,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRnaAlias> {
* @param drawDescription
* flag determining if we want to draw description as well
*/
- private void drawRegion(final AntisenseRnaAlias alias, final AntisenseRnaRegionAlias mr, final Graphics2D graphics, final boolean drawEmptyRegion,
+ private void drawRegion(final AntisenseRna alias, final AntisenseRnaRegion mr, final Graphics2D graphics, final boolean drawEmptyRegion,
final boolean drawDescription) {
if ((!drawEmptyRegion) && (mr.getState() == null)) {
return;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
index 5cc49ba923..c9ac29e527 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
@@ -15,8 +15,8 @@ import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
/**
* This class defines methods used for drawing ComplexAlias on the graphics2d
@@ -25,7 +25,7 @@ import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
* @author Piotr Gawron
*
*/
-public class ComplexConverter extends SpeciesConverter<ComplexAlias> {
+public class ComplexConverter extends SpeciesConverter<Complex> {
/**
* How big is the triangle trimmed part of the complex.
@@ -43,7 +43,7 @@ public class ComplexConverter extends SpeciesConverter<ComplexAlias> {
private static Logger logger = Logger.getLogger(ComplexConverter.class.getName());
@Override
- public void drawAlias(final ComplexAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getState().equalsIgnoreCase("complexnoborder")) {
return;
}
@@ -128,8 +128,8 @@ public class ComplexConverter extends SpeciesConverter<ComplexAlias> {
}
@Override
- public void drawText(final ComplexAlias alias, final Graphics2D graphics, final ConverterParams params) {
- if (((ComplexAlias) alias).getAliases().size() > 0) {
+ public void drawText(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
+ if (((Complex) alias).getAliases().size() > 0) {
if (alias.getTransparencyLevel() <= params.getLevel()) {
super.drawText(alias, graphics, params);
return;
@@ -156,7 +156,7 @@ public class ComplexConverter extends SpeciesConverter<ComplexAlias> {
* exact object for which we want to get a border
* @return border of the alias
*/
- private GeneralPath getAliasPath(final Alias alias) {
+ private GeneralPath getAliasPath(final Element alias) {
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
path.moveTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY());
path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY());
@@ -171,7 +171,7 @@ public class ComplexConverter extends SpeciesConverter<ComplexAlias> {
}
@Override
- public PathIterator getBoundPathIterator(final ComplexAlias alias) {
+ public PathIterator getBoundPathIterator(final Complex alias) {
return getAliasPath(alias).getPathIterator(new AffineTransform());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
index 30dd8db319..44c0b254b2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
@@ -1,121 +1,121 @@
-package lcsb.mapviewer.converter.graphics.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class defines methods used for drawing Degraded SpeciesAlias on the
- * graphics2d object.
- *
- * @author Piotr Gawron
- *
- */
-public class DegradedConverter extends SpeciesConverter<SpeciesAlias> {
- /**
- * Part of height of the line used to cross degraded circle that goes behind
- * this circle.
- */
- private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(DegradedConverter.class.getName());
-
- @Override
- public void drawAlias(final SpeciesAlias alias, final Graphics2D graphics, final ConverterParams params) {
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- Area a1 = new Area(new Ellipse2D.Double(x, y, diameter, diameter));
-
- double lineX1 = alias.getX() + alias.getWidth() / 2 + CROSS_LINE_EXTENDED_LENGTH;
- double lineY1 = alias.getY();
-
- double lineX2 = alias.getX() + alias.getWidth() / 2 - CROSS_LINE_EXTENDED_LENGTH;
- double lineY2 = alias.getY() + diameter + 2 * CROSS_LINE_EXTENDED_LENGTH;
-
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 2);
- path.moveTo(lineX1, lineY1);
- path.lineTo(lineX1 + 1, lineY1);
- path.lineTo(lineX2 + 1, lineY2);
- path.lineTo(lineX2, lineY2);
- path.closePath();
-
- a1.exclusiveOr(new Area(path));
- Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
- graphics.fill(a1);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
- graphics.draw(a1);
- graphics.setStroke(stroke);
- drawText(alias, graphics, params);
- }
-
- /**
- * Returns transformed y coordinate for the degraded alias.
- *
- * @param alias
- * object alias to to which we are looking for y coordinate
- * @return y coordinate of the alias
- */
- private double getYCoord(final Alias alias) {
- double y = alias.getY() + CROSS_LINE_EXTENDED_LENGTH;
- return y;
- }
-
- /**
- * Returns transformed x coordinate for the degraded alias.
- *
- * @param alias
- * object alias to to which we are looking for x coordinate
- * @param diameter
- * diameter of cross line used in this alias
- * @return x coordinate of the alias
- */
- private double getXCoord(final Alias alias, final double diameter) {
- double x = alias.getX() + (alias.getWidth() - diameter) / 2;
- return x;
- }
-
- /**
- * Computes diameter of cross line for the degraded alias.
- *
- * @param alias
- * object alias to to which we are looking for diameter.
- * @return diameter of the cross line
- */
- private double getDiameter(final Alias alias) {
- double diameter = Math.min(alias.getWidth(), alias.getHeight()) - 2 * CROSS_LINE_EXTENDED_LENGTH;
- if (diameter < 0) {
- logger.warn("Diameter cannot be negative...");
- diameter = 0;
- }
- return diameter;
- }
-
- @Override
- public String getText(final SpeciesAlias alias) {
- return "";
- }
-
- @Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
- throw new InvalidStateException("This class doesn't have bound");
- }
-
-}
+package lcsb.mapviewer.converter.graphics.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class defines methods used for drawing Degraded SpeciesAlias on the
+ * graphics2d object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DegradedConverter extends SpeciesConverter<Species> {
+ /**
+ * Part of height of the line used to cross degraded circle that goes behind
+ * this circle.
+ */
+ private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(DegradedConverter.class.getName());
+
+ @Override
+ public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ Area a1 = new Area(new Ellipse2D.Double(x, y, diameter, diameter));
+
+ double lineX1 = alias.getX() + alias.getWidth() / 2 + CROSS_LINE_EXTENDED_LENGTH;
+ double lineY1 = alias.getY();
+
+ double lineX2 = alias.getX() + alias.getWidth() / 2 - CROSS_LINE_EXTENDED_LENGTH;
+ double lineY2 = alias.getY() + diameter + 2 * CROSS_LINE_EXTENDED_LENGTH;
+
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 2);
+ path.moveTo(lineX1, lineY1);
+ path.lineTo(lineX1 + 1, lineY1);
+ path.lineTo(lineX2 + 1, lineY2);
+ path.lineTo(lineX2, lineY2);
+ path.closePath();
+
+ a1.exclusiveOr(new Area(path));
+ Color c = graphics.getColor();
+ graphics.setColor(alias.getColor());
+ graphics.fill(a1);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(alias));
+ graphics.draw(a1);
+ graphics.setStroke(stroke);
+ drawText(alias, graphics, params);
+ }
+
+ /**
+ * Returns transformed y coordinate for the degraded alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for y coordinate
+ * @return y coordinate of the alias
+ */
+ private double getYCoord(final Element alias) {
+ double y = alias.getY() + CROSS_LINE_EXTENDED_LENGTH;
+ return y;
+ }
+
+ /**
+ * Returns transformed x coordinate for the degraded alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for x coordinate
+ * @param diameter
+ * diameter of cross line used in this alias
+ * @return x coordinate of the alias
+ */
+ private double getXCoord(final Element alias, final double diameter) {
+ double x = alias.getX() + (alias.getWidth() - diameter) / 2;
+ return x;
+ }
+
+ /**
+ * Computes diameter of cross line for the degraded alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for diameter.
+ * @return diameter of the cross line
+ */
+ private double getDiameter(final Element alias) {
+ double diameter = Math.min(alias.getWidth(), alias.getHeight()) - 2 * CROSS_LINE_EXTENDED_LENGTH;
+ if (diameter < 0) {
+ logger.warn("Diameter cannot be negative...");
+ diameter = 0;
+ }
+ return diameter;
+ }
+
+ @Override
+ public String getText(final Species alias) {
+ return "";
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final Species alias) {
+ throw new InvalidStateException("This class doesn't have bound");
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
index a186c8ea4d..f737787cac 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
@@ -1,106 +1,106 @@
-package lcsb.mapviewer.converter.graphics.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class defines methods used for drawing Drug SpeciesAlias on the
- * graphics2d object.
- *
- * @author Piotr Gawron
- *
- */
-public class DrugConverter extends SpeciesConverter<SpeciesAlias> {
- /**
- * Distance between internal and external border of drug graphical
- * representation.
- */
- private static final int OFFSET_BETWEEN_BORDERS = 4;
- /**
- * How big should be the arc in rectangle for drug representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DrugConverter.class.getName());
-
- /**
- * Returns shape of the Drug .
- *
- * @param alias
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- private Shape getDrugShape(final Alias alias) {
- return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
- }
-
- @Override
- public void drawAlias(final SpeciesAlias alias, final Graphics2D graphics, final ConverterParams params) {
- Shape a1 = getDrugShape(alias);
- double offset = OFFSET_BETWEEN_BORDERS;
- Shape a2 = new RoundRectangle2D.Double(
- alias.getX() + offset, alias.getY() + offset, alias.getWidth() - 2 * offset, alias.getHeight() - 2 * offset, RECTANGLE_CORNER_ARC_SIZE,
- RECTANGLE_CORNER_ARC_SIZE);
- Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
- graphics.fill(a1);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
- graphics.draw(a1);
- graphics.draw(a2);
- graphics.setStroke(stroke);
- drawText(alias, graphics, params);
- }
-
- /**
- * Returns shape of the Drug as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- protected ArrayList<Point2D> getDrugPoints(final SpeciesAlias alias) {
- ArrayList<Point2D> list = new ArrayList<Point2D>();
-
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
-
- // CHECKSTYLE:OFF
- list.add(new Point2D.Double(x, y + height / 2));
- list.add(new Point2D.Double(x + width / 12, y));
- list.add(new Point2D.Double(x + width / 2, y));
- list.add(new Point2D.Double(x + width * 11 / 12, y));
- list.add(new Point2D.Double(x + width, y + height / 2));
- list.add(new Point2D.Double(x + width * 11 / 12, y + height));
- list.add(new Point2D.Double(x + width / 2, y + height));
- list.add(new Point2D.Double(x + width / 12, y + height));
- // CHECKSTYLE:ON
-
- return list;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
- return getDrugShape(alias).getPathIterator(new AffineTransform());
- }
-
-}
+package lcsb.mapviewer.converter.graphics.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class defines methods used for drawing Drug SpeciesAlias on the
+ * graphics2d object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugConverter extends SpeciesConverter<Species> {
+ /**
+ * Distance between internal and external border of drug graphical
+ * representation.
+ */
+ private static final int OFFSET_BETWEEN_BORDERS = 4;
+ /**
+ * How big should be the arc in rectangle for drug representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DrugConverter.class.getName());
+
+ /**
+ * Returns shape of the Drug .
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ private Shape getDrugShape(final Element alias) {
+ return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+ @Override
+ public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
+ Shape a1 = getDrugShape(alias);
+ double offset = OFFSET_BETWEEN_BORDERS;
+ Shape a2 = new RoundRectangle2D.Double(
+ alias.getX() + offset, alias.getY() + offset, alias.getWidth() - 2 * offset, alias.getHeight() - 2 * offset, RECTANGLE_CORNER_ARC_SIZE,
+ RECTANGLE_CORNER_ARC_SIZE);
+ Color c = graphics.getColor();
+ graphics.setColor(alias.getColor());
+ graphics.fill(a1);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(alias));
+ graphics.draw(a1);
+ graphics.draw(a2);
+ graphics.setStroke(stroke);
+ drawText(alias, graphics, params);
+ }
+
+ /**
+ * Returns shape of the Drug as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ protected ArrayList<Point2D> getDrugPoints(final Species alias) {
+ ArrayList<Point2D> list = new ArrayList<Point2D>();
+
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+
+ // CHECKSTYLE:OFF
+ list.add(new Point2D.Double(x, y + height / 2));
+ list.add(new Point2D.Double(x + width / 12, y));
+ list.add(new Point2D.Double(x + width / 2, y));
+ list.add(new Point2D.Double(x + width * 11 / 12, y));
+ list.add(new Point2D.Double(x + width, y + height / 2));
+ list.add(new Point2D.Double(x + width * 11 / 12, y + height));
+ list.add(new Point2D.Double(x + width / 2, y + height));
+ list.add(new Point2D.Double(x + width / 12, y + height));
+ // CHECKSTYLE:ON
+
+ return list;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final Species alias) {
+ return getDrugShape(alias).getPathIterator(new AffineTransform());
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
index fecd7d7777..195dd99d7c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
@@ -14,10 +14,10 @@ import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
* This class defines methods used for drawing Gene SpeciesAlias on the
@@ -26,7 +26,7 @@ import lcsb.mapviewer.model.map.layout.alias.ModificationState;
* @author Piotr Gawron
*
*/
-public class GeneConverter extends SpeciesConverter<GeneAlias> {
+public class GeneConverter extends SpeciesConverter<Gene> {
/**
* Default class logger.
*/
@@ -34,7 +34,7 @@ public class GeneConverter extends SpeciesConverter<GeneAlias> {
private static Logger logger = Logger.getLogger(GeneConverter.class.getName());
@Override
- public void drawAlias(final GeneAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Gene alias, final Graphics2D graphics, final ConverterParams params) {
Shape shape = getGeneShape(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
@@ -45,7 +45,7 @@ public class GeneConverter extends SpeciesConverter<GeneAlias> {
graphics.draw(shape);
graphics.setStroke(stroke);
- for (ModificationResidueAlias mr : alias.getModificationResidues()) {
+ for (ModificationResidue mr : alias.getModificationResidues()) {
drawModification(alias, mr, graphics, false, false);
}
@@ -70,7 +70,7 @@ public class GeneConverter extends SpeciesConverter<GeneAlias> {
* flag that indicates if we should draw description of the
* modification
*/
- private void drawModification(final GeneAlias alias, final ModificationResidueAlias mr, final Graphics2D graphics, final boolean drawEmptyModification,
+ private void drawModification(final Gene alias, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
final boolean drawDescription) {
if ((!drawEmptyModification) && (mr.getState() == null)) {
return;
@@ -118,14 +118,14 @@ public class GeneConverter extends SpeciesConverter<GeneAlias> {
* alias for which we are looking for a Shape
* @return Shape object that represents alias
*/
- private Shape getGeneShape(final Alias alias) {
+ private Shape getGeneShape(final Element alias) {
Shape shape;
shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
return shape;
}
@Override
- public PathIterator getBoundPathIterator(final GeneAlias alias) {
+ public PathIterator getBoundPathIterator(final Gene alias) {
return getGeneShape(alias).getPathIterator(new AffineTransform());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
index 1b0dd1ac47..34f5a147c0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
@@ -10,8 +10,8 @@ import java.awt.geom.Point2D;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -23,14 +23,14 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class IonConverter extends SpeciesConverter<SpeciesAlias> {
+public class IonConverter extends SpeciesConverter<Species> {
/**
* Default class logger.
*/
private static Logger logger = Logger.getLogger(IonConverter.class.getName());
@Override
- public void drawAlias(final SpeciesAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
double diameter = getDiameter(alias);
double x = getXCoord(alias, diameter);
double y = getYCoord(alias);
@@ -53,7 +53,7 @@ public class IonConverter extends SpeciesConverter<SpeciesAlias> {
* object alias to to which we are looking for y coordinate
* @return y coordinate of the alias
*/
- private double getYCoord(final Alias alias) {
+ private double getYCoord(final Element alias) {
double y = alias.getY();
return y;
}
@@ -67,7 +67,7 @@ public class IonConverter extends SpeciesConverter<SpeciesAlias> {
* diameter of circle representation of ion
* @return x coordinate of the alias
*/
- private double getXCoord(final Alias alias, final double diameter) {
+ private double getXCoord(final Element alias, final double diameter) {
double x = alias.getX() + (alias.getWidth() - diameter) / 2;
return x;
}
@@ -79,7 +79,7 @@ public class IonConverter extends SpeciesConverter<SpeciesAlias> {
* object alias to to which we are looking for diameter.
* @return diameter of ion circle representation
*/
- private double getDiameter(final Alias alias) {
+ private double getDiameter(final Element alias) {
double diameter = Math.min(alias.getWidth(), alias.getHeight());
if (diameter < 0) {
logger.warn("Something is wrong. Size cannot be negative");
@@ -90,12 +90,12 @@ public class IonConverter extends SpeciesConverter<SpeciesAlias> {
}
@Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
+ public PathIterator getBoundPathIterator(final Species alias) {
throw new InvalidStateException("This class doesn't have bound");
}
@Override
- public Point2D getPointCoordinatesOnBorder(final SpeciesAlias alias, final double angle) {
+ public Point2D getPointCoordinatesOnBorder(final Species alias, final double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
logger.warn("Looking for coordinates for the alias with 0 size");
return alias.getCenter();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
index 217c3f630d..6dba03ff81 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
@@ -9,8 +9,8 @@ import java.awt.geom.Path2D;
import java.awt.geom.PathIterator;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -22,7 +22,7 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class PhenotypeConverter extends SpeciesConverter<SpeciesAlias> {
+public class PhenotypeConverter extends SpeciesConverter<Species> {
/**
* Default class logger.
*/
@@ -30,7 +30,7 @@ public class PhenotypeConverter extends SpeciesConverter<SpeciesAlias> {
private static Logger logger = Logger.getLogger(PhenotypeConverter.class.getName());
@Override
- public void drawAlias(final SpeciesAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getPhenotypePath(alias);
Color c = graphics.getColor();
@@ -51,7 +51,7 @@ public class PhenotypeConverter extends SpeciesConverter<SpeciesAlias> {
* alias for which we are looking for a border
* @return GeneralPath object defining border of the given alias
*/
- private GeneralPath getPhenotypePath(final Alias alias) {
+ private GeneralPath getPhenotypePath(final Element alias) {
// CHECKSTYLE:OFF
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 6);
path.moveTo(alias.getX() + alias.getWidth() / 6, alias.getY());
@@ -66,7 +66,7 @@ public class PhenotypeConverter extends SpeciesConverter<SpeciesAlias> {
}
@Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
+ public PathIterator getBoundPathIterator(final Species alias) {
return getPhenotypePath(alias).getPathIterator(new AffineTransform());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
index 7816899e08..b3e3343d98 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
@@ -21,26 +21,25 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.db.model.map.species.Protein Protein} on the
+ * This class defines methods used for drawing {@link Protein} on the
* {@link Graphics2D} object.
*
* @author Piotr Gawron
*
*/
-public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
+public class ProteinConverter extends SpeciesConverter<Protein> {
/**
* Width of the ion part in the open channel representation.
*/
@@ -59,7 +58,7 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
*/
private static Logger logger = Logger.getLogger(ProteinConverter.class.getName());
- private ElementUtils eu = new ElementUtils();
+ private ElementUtils eu = new ElementUtils();
/**
* Returns shape of generic protein.
@@ -68,12 +67,12 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- private Shape getGenericShape(final Alias alias) {
+ private Shape getGenericShape(final Element alias) {
return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
}
@Override
- public void drawAlias(final ProteinAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Protein alias, final Graphics2D graphics, final ConverterParams params) {
// Local variable setting the SBGN visualization
boolean sbgnFormat = params.isSbgnFormat();
@@ -112,12 +111,12 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
Shape shape = null;
- if (alias instanceof GenericProteinAlias || sbgnFormat) {
+ if (alias instanceof GenericProtein || sbgnFormat) {
shape = getGenericShape(alias);
if (alias.getActivity() && !sbgnFormat) {
drawActivityGenericProtein(alias, graphics);
}
- } else if (alias instanceof IonChannelProteinAlias) {
+ } else if (alias instanceof IonChannelProtein) {
Area a1;
if (!alias.getActivity()) {
a1 = new Area(
@@ -136,12 +135,12 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
RECTANGLE_CORNER_ARC_SIZE));
a1.add(a2);
shape = a1;
- } else if (alias instanceof TruncatedProteinAlias) {
+ } else if (alias instanceof TruncatedProtein) {
shape = getTruncatedShape(alias);
if (alias.getActivity()) {
drawActivityTruncatedShape(alias, graphics);
}
- } else if (alias instanceof ReceptorProteinAlias) {
+ } else if (alias instanceof ReceptorProtein) {
shape = getReceptorShape(alias);
if (alias.getActivity()) {
drawActivityReceptorProtein(alias, graphics);
@@ -162,14 +161,14 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
// SBGN display mode - units of information and state variables are
// printed on the top element only
if (!sbgnFormat || (homodimerId == homodir - 1)) {
- for (ModificationResidueAlias mr : alias.getModificationResidues()) {
+ for (ModificationResidue mr : alias.getModificationResidues()) {
// SBGN display mode - print empty state variables
drawModification(alias, mr, graphics, sbgnFormat, false);
}
if (sbgnFormat) {
// SBGN display mode - ion channel's state is marked as a unit of
// information
- if (alias instanceof IonChannelProteinAlias) {
+ if (alias instanceof IonChannelProtein) {
if (!unitOfInformationText.equals("")) {
unitOfInformationText = unitOfInformationText.concat("; ");
}
@@ -205,14 +204,14 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
}
/**
- * Draws activity border of {@link GenericProtein} alias.
+ * Draws activity border of {@link GenericProtein}.
*
* @param alias
- * {@link SpeciesAlias} that will be drawn
+ * {@link Species} that will be drawn
* @param graphics
* where we are drawing
*/
- private void drawActivityGenericProtein(final SpeciesAlias alias, final Graphics2D graphics) {
+ private void drawActivityGenericProtein(final Protein alias, final Graphics2D graphics) {
int border = ACTIVITY_BORDER_DISTANCE;
alias.increaseBorder(border);
Shape shape2 = getGenericShape(alias);
@@ -224,14 +223,14 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
}
/**
- * Draws activity border of {@link ReceptorProtein} alias.
+ * Draws activity border of {@link ReceptorProtein}.
*
* @param alias
- * {@link SpeciesAlias} that will be drawn
+ * {@link Species} that will be drawn
* @param graphics
* where we are drawing
*/
- public void drawActivityReceptorProtein(final SpeciesAlias alias, final Graphics2D graphics) {
+ public void drawActivityReceptorProtein(final Protein alias, final Graphics2D graphics) {
int border = ACTIVITY_BORDER_DISTANCE;
alias.setX(alias.getX() - border);
alias.setY(alias.getY() - border);
@@ -249,14 +248,14 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
}
/**
- * Draws activity border of {@link TruncatedProtein} alias.
+ * Draws activity border of {@link TruncatedProtein}.
*
* @param alias
- * {@link SpeciesAlias} that will be drawn
+ * {@link Species} that will be drawn
* @param graphics
* where we are drawing
*/
- public void drawActivityTruncatedShape(final SpeciesAlias alias, final Graphics2D graphics) {
+ public void drawActivityTruncatedShape(final Protein alias, final Graphics2D graphics) {
int border = ACTIVITY_BORDER_DISTANCE;
alias.setX(alias.getX() - border);
alias.setY(alias.getY() - border);
@@ -291,7 +290,7 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
* flag that indicates if we should draw description of the
* modification
*/
- private void drawModification(final ProteinAlias alias, final ModificationResidueAlias mr, final Graphics2D graphics, final boolean drawEmptyModification,
+ private void drawModification(final Protein alias, final ModificationResidue mr, final Graphics2D graphics, final boolean drawEmptyModification,
final boolean drawDescription) {
if ((!drawEmptyModification) && (mr.getState() == null)) {
return;
@@ -356,7 +355,7 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- protected Shape getReceptorShape(final Alias alias) {
+ protected Shape getReceptorShape(final Element alias) {
Shape shape;
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
ArrayList<Point2D> points = getReceptorPoints(alias);
@@ -376,7 +375,7 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- protected Shape getTruncatedShape(final Alias alias) {
+ protected Shape getTruncatedShape(final Element alias) {
Shape shape;
GeneralPath path = new GeneralPath();
// CHECKSTYLE:OFF
@@ -405,7 +404,7 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
* alias for which we are looking for a border
* @return list of points defining border of the given alias
*/
- private ArrayList<Point2D> getReceptorPoints(final Alias alias) {
+ private ArrayList<Point2D> getReceptorPoints(final Element alias) {
double x = alias.getX();
double y = alias.getY();
double width = alias.getWidth();
@@ -427,14 +426,14 @@ public class ProteinConverter extends SpeciesConverter<ProteinAlias> {
}
@Override
- public PathIterator getBoundPathIterator(final ProteinAlias alias) {
- if (alias instanceof GenericProteinAlias) {
+ public PathIterator getBoundPathIterator(final Protein alias) {
+ if (alias instanceof GenericProtein) {
return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof ReceptorProteinAlias) {
+ } else if (alias instanceof ReceptorProtein) {
return getReceptorShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof IonChannelProteinAlias) {
+ } else if (alias instanceof IonChannelProtein) {
return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof TruncatedProteinAlias) {
+ } else if (alias instanceof TruncatedProtein) {
return getTruncatedShape(alias).getPathIterator(new AffineTransform());
} else {
throw new InvalidArgumentException("Not implemented protein converter for type: " + alias.getClass());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
index 0e0c06e2b3..67e92e517f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
@@ -14,20 +14,19 @@ import java.awt.geom.Point2D;
import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Rna
- * Rna} on the {@link Graphics2D} object.
+ * This class defines methods used for drawing {@link Rna} on the
+ * {@link Graphics2D} object.
*
* @author Piotr Gawron
*
*/
-public class RnaConverter extends SpeciesConverter<RnaAlias> {
+public class RnaConverter extends SpeciesConverter<Rna> {
/**
* Default class logger.
*/
@@ -35,7 +34,7 @@ public class RnaConverter extends SpeciesConverter<RnaAlias> {
private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
@Override
- public void drawAlias(final RnaAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Rna alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getRnaPath(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
@@ -46,7 +45,7 @@ public class RnaConverter extends SpeciesConverter<RnaAlias> {
graphics.draw(path);
graphics.setStroke(stroke);
- for (RnaRegionAlias mr : alias.getRegions()) {
+ for (RnaRegion mr : alias.getRegions()) {
drawModification(alias, mr, graphics, false, false);
}
@@ -60,7 +59,7 @@ public class RnaConverter extends SpeciesConverter<RnaAlias> {
* alias for which we are looking for a border
* @return GeneralPath object defining border of the given alias
*/
- private GeneralPath getRnaPath(final Alias alias) {
+ private GeneralPath getRnaPath(final Element alias) {
// CHECKSTYLE:OFF
GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
path.moveTo(alias.getX() + alias.getWidth() / 4, alias.getY());
@@ -73,7 +72,7 @@ public class RnaConverter extends SpeciesConverter<RnaAlias> {
}
@Override
- public PathIterator getBoundPathIterator(final RnaAlias alias) {
+ public PathIterator getBoundPathIterator(final Rna alias) {
return getRnaPath(alias).getPathIterator(new AffineTransform());
}
@@ -95,7 +94,7 @@ public class RnaConverter extends SpeciesConverter<RnaAlias> {
* flag that indicates if we should draw description of the
* modification
*/
- private void drawModification(final RnaAlias alias, final RnaRegionAlias mr, final Graphics2D graphics, final boolean drawEmptyModification,
+ private void drawModification(final Rna alias, final RnaRegion mr, final Graphics2D graphics, final boolean drawEmptyModification,
final boolean drawDescription) {
if ((!drawEmptyModification) && (mr.getState() == null)) {
return;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
index 25252c4945..599c7023d1 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
@@ -9,8 +9,8 @@ import java.awt.geom.GeneralPath;
import java.awt.geom.PathIterator;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines methods used for drawing SpeciesAlias of nucleic acid
@@ -20,7 +20,7 @@ import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
*
*/
-public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAlias> {
+public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
/**
* How big should be the arc in rectangle for nucleic acid feature
@@ -35,7 +35,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAli
* alias for which the shape should be returned
* @return shape of the SBGN Nucleic acid feature for given alias
*/
- private Shape getShape(final Alias alias) {
+ private Shape getShape(final Element alias) {
GeneralPath bottomRoundedRectangle = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
@@ -51,7 +51,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAli
}
@Override
- public void drawAlias(SpeciesAlias alias, Graphics2D graphics, ConverterParams params) {
+ public void drawAlias(Species alias, Graphics2D graphics, ConverterParams params) {
// Unit of information text - multimer cardinality
String unitOfInformationText = null;
if (alias.getAliasStatePrefix() != null && alias.getAliasStateLabel() != null) {
@@ -113,7 +113,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAli
}
@Override
- protected PathIterator getBoundPathIterator(SpeciesAlias alias) {
+ protected PathIterator getBoundPathIterator(Species alias) {
return getShape(alias).getPathIterator(new AffineTransform());
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
index 35fed2b238..fd4c02aa19 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
@@ -12,24 +12,23 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.SimpleMolecule
- * SimpleMolecule} on the {@link Graphics2D} object.
+ * This class defines methods used for drawing {@link SimpleMolecule} on
+ * the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
*/
-public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMoleculeAlias> {
+public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
/**
* Default class logger.
*/
private static Logger logger = Logger.getLogger(SimpleMoleculeConverter.class.getName());
@Override
- public void drawAlias(final SimpleMoleculeAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final SimpleMolecule alias, final Graphics2D graphics, final ConverterParams params) {
int homodir;
if (params.isSbgnFormat()) {
// If the SBGN display mode is set, multimer is shown as two stacked
@@ -93,12 +92,12 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMoleculeAlia
}
@Override
- public PathIterator getBoundPathIterator(final SimpleMoleculeAlias alias) {
+ public PathIterator getBoundPathIterator(final SimpleMolecule alias) {
throw new InvalidStateException("This class doesn't provide boundPath");
}
@Override
- public Point2D getPointCoordinatesOnBorder(final SimpleMoleculeAlias alias, final double angle) {
+ public Point2D getPointCoordinatesOnBorder(final SimpleMolecule alias, final double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
logger.warn("Looking for coordinates on border of alias of size 0");
return alias.getCenter();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
index 7e546fc818..6413599429 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
@@ -23,21 +23,21 @@ import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.converter.graphics.IAliasConverter;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
- * This class defines basics used for drawing aliases of
- * {@link lcsb.mapviewer.db.model.map.species.Species Species} (node in the
- * graph representation) on the graphics2d object.
+ * This class defines basics used for drawing aliases of {@link Species}
+ * (node in the graph representation) on the graphics2d object.
*
* @param <T>
* alias class that can be drawn with this converter
* @author Piotr Gawron
*
*/
-public abstract class SpeciesConverter<T extends Alias> implements IAliasConverter<T> {
+public abstract class SpeciesConverter<T extends Species> implements IAliasConverter<T> {
+
/**
* PI value.
*/
@@ -240,7 +240,7 @@ public abstract class SpeciesConverter<T extends Alias> implements IAliasConvert
* alias for which we are looking for a border
* @return Shape object defining given alias
*/
- protected Shape getDefaultAliasShape(final Alias alias) {
+ protected Shape getDefaultAliasShape(final Element alias) {
Shape shape;
shape = new Rectangle(alias.getX().intValue(), alias.getY().intValue(), alias.getWidth().intValue(), alias.getHeight().intValue());
return shape;
@@ -255,7 +255,7 @@ public abstract class SpeciesConverter<T extends Alias> implements IAliasConvert
* specific drawing parameters (like scale)
* @return Font that should be used for drawing alias description
*/
- protected Font getFont(final Alias alias, ConverterParams params) {
+ protected Font getFont(final Element alias, ConverterParams params) {
double fontSize = DEFAULT_SPECIES_FONT_SIZE;
if (alias.getFontSize() != null) {
fontSize = alias.getFontSize();
@@ -288,8 +288,8 @@ public abstract class SpeciesConverter<T extends Alias> implements IAliasConvert
graphics.setFont(font);
Point2D point = alias.getCenter();
- if (alias instanceof ComplexAlias) {
- if (((ComplexAlias) alias).getAliases().size() > 0) {
+ if (alias instanceof Complex) {
+ if (((Complex) alias).getAliases().size() > 0) {
if (alias.getTransparencyLevel() <= params.getLevel()) {
point.setLocation(point.getX(), alias.getY() + alias.getHeight() - graphics.getFontMetrics().getAscent());
}
@@ -392,15 +392,15 @@ public abstract class SpeciesConverter<T extends Alias> implements IAliasConvert
* alias to be drawn
* @return style of the line used to draw alias
*/
- protected Stroke getBorderLine(final SpeciesAlias alias) {
+ protected Stroke getBorderLine(final Species alias) {
if (!alias.isHypothetical()) {
- if (alias instanceof ComplexAlias) {
+ if (alias instanceof Complex) {
return LineType.SOLID_BOLD.getStroke();
} else {
return LineType.SOLID.getStroke();
}
} else {
- if (alias instanceof ComplexAlias) {
+ if (alias instanceof Complex) {
return LineType.DASHED_BOLD.getStroke();
} else {
return LineType.DASHED.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
index 4337fe9367..7063ad399c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
@@ -11,7 +11,7 @@ import java.awt.geom.Point2D;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -23,14 +23,14 @@ import org.apache.log4j.Logger;
* @author Piotr Gawron
*
*/
-public class UnknownConverter extends SpeciesConverter<SpeciesAlias> {
+public class UnknownConverter extends SpeciesConverter<Species> {
/**
* Default class logger.
*/
private static Logger logger = Logger.getLogger(UnknownConverter.class.getName());
@Override
- public void drawAlias(final SpeciesAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ public void drawAlias(final Species alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getActivity()) {
int border = ACTIVITY_BORDER_DISTANCE;
alias.increaseBorder(border);
@@ -51,12 +51,12 @@ public class UnknownConverter extends SpeciesConverter<SpeciesAlias> {
}
@Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
+ public PathIterator getBoundPathIterator(final Species alias) {
throw new InvalidStateException("This class doesn't provide boundPath");
}
@Override
- public Point2D getPointCoordinatesOnBorder(final SpeciesAlias alias, final double angle) {
+ public Point2D getPointCoordinatesOnBorder(final Species alias, final double angle) {
if (alias.getWidth() == 0 && alias.getHeight() == 0) {
logger.warn("Looking for coordinates for unknown of 0 size");
return alias.getCenter();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index fbc8c4b21d..02e0979c11 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -1,36 +1,37 @@
-package lcsb.mapviewer.converter.graphics;
-
-import static org.junit.Assert.fail;
-import lcsb.mapviewer.model.map.layout.alias.BottomSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.LeftSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.RightSquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.TopSquareCompartmentAlias;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ConverterTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- new AliasConverter(new BottomSquareCompartmentAlias());
- new AliasConverter(new TopSquareCompartmentAlias());
- new AliasConverter(new LeftSquareCompartmentAlias());
- new AliasConverter(new RightSquareCompartmentAlias());
- }catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+
+public class ConverterTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ new AliasConverter(new BottomSquareCompartment());
+ new AliasConverter(new TopSquareCompartment());
+ new AliasConverter(new LeftSquareCompartment());
+ new AliasConverter(new RightSquareCompartment());
+ }catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index 59817921e0..96d8113bbb 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -18,14 +18,14 @@ import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.converter.graphics.compartment.ArtifitialCompartmentConverter;
import lcsb.mapviewer.converter.graphics.species.ComplexConverter;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class NormalImageGeneratorTest {
static Logger logger = Logger.getLogger(NormalImageGenerator.class);
@@ -52,7 +52,7 @@ public class NormalImageGeneratorTest {
class TmpComplexConverter extends ComplexConverter {
@Override
- public void drawText(ComplexAlias compAlias, Graphics2D graphics, ConverterParams params) {
+ public void drawText(Complex compAlias, Graphics2D graphics, ConverterParams params) {
setScale(params.getScale());
setCentered(params.isTextCentered());
super.drawText(compAlias, graphics, params);
@@ -64,7 +64,7 @@ public class NormalImageGeneratorTest {
public void testComplexConversion() throws Exception {
scale = null;
try {
- AliasConverter.addAliasConverter(ComplexAlias.class, new TmpComplexConverter());
+ AliasConverter.addAliasConverter(Complex.class, new TmpComplexConverter());
Model model = createComplexModel();
new CreateHierarchyCommand(model, 2, 2).execute();
@@ -84,7 +84,7 @@ public class NormalImageGeneratorTest {
model.setWidth(600);
model.setHeight(600);
- ComplexAlias alias = new ComplexAlias("1");
+ Complex alias = new Complex("1");
alias.setName("a");
alias.setX(10);
alias.setY(10);
@@ -92,7 +92,7 @@ public class NormalImageGeneratorTest {
alias.setHeight(50);
model.addAlias(alias);
- SpeciesAlias a2 = new GenericProteinAlias("2");
+ Species a2 = new GenericProtein("2");
a2.setName("b");
a2.setX(10);
a2.setY(100);
@@ -105,7 +105,7 @@ public class NormalImageGeneratorTest {
class TmpArtifitialConverter extends ArtifitialCompartmentConverter {
@Override
- public void drawText(ArtifitialCompartmentAlias compAlias, Graphics2D graphics, ConverterParams params) {
+ public void drawText(PathwayCompartment compAlias, Graphics2D graphics, ConverterParams params) {
setScale(params.getScale());
setCentered(params.isTextCentered());
setArtifitialCalled(true);
@@ -118,7 +118,7 @@ public class NormalImageGeneratorTest {
public void testNestedCompartmentsConversion() throws Exception {
scale = null;
try {
- AliasConverter.addAliasConverter(ArtifitialCompartmentAlias.class, new TmpArtifitialConverter());
+ AliasConverter.addAliasConverter(PathwayCompartment.class, new TmpArtifitialConverter());
Model model = createCompartmentModel();
new CreateHierarchyCommand(model, 2, 2).execute();
new PngImageGenerator(new Params().scale(2).width(600).height(600).model(model).level(0).nested(true));
@@ -149,7 +149,7 @@ public class NormalImageGeneratorTest {
layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
- ComplexAlias alias = new ComplexAlias("1");
+ Complex alias = new Complex("1");
alias.setName("a");
alias.setX(300);
alias.setY(90);
@@ -164,7 +164,7 @@ public class NormalImageGeneratorTest {
public void testArtifitialInNonHierarchicalView() throws Exception {
scale = null;
try {
- AliasConverter.addAliasConverter(ArtifitialCompartmentAlias.class, new TmpArtifitialConverter());
+ AliasConverter.addAliasConverter(PathwayCompartment.class, new TmpArtifitialConverter());
setArtifitialCalled(false);
Model model = createCompartmentModel();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
index eeef94d0f5..a69271674f 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
@@ -15,11 +15,11 @@ import org.junit.Test;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
public class PdfImageGeneratorTest {
@@ -88,7 +88,7 @@ public class PdfImageGeneratorTest {
layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
- ComplexAlias alias = new ComplexAlias("1");
+ Complex alias = new Complex("1");
alias.setName("a");
alias.setX(300);
alias.setY(90);
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
index 4acd4cebfd..d9d071ebc1 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
@@ -11,8 +11,8 @@ import org.apache.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -29,7 +29,7 @@ public class AllPlaceFinderTest {
Model model = new ModelFullIndexed(null);
model.addAlias(createCompartmentAlias(94.0, 70.0, 355.0, 173.0));
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
actual = pf.getRetangle(alias).toString();
}
@@ -47,7 +47,7 @@ public class AllPlaceFinderTest {
model.addAlias(createCompartmentAlias(332.0, 66.0, 188.0, 255.0));
String expected = "";
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
actual = pf.getRetangle(alias).toString();
Rectangle2D result = alias.getBorder();
@@ -59,9 +59,9 @@ public class AllPlaceFinderTest {
@Test
public void twoIntersectingCompartments() throws InvalidXmlSchemaException, IOException {
Model model = new ModelFullIndexed(null);
- CompartmentAlias alias = createCompartmentAlias(87.0, 56.0, 235.0, 219.0);
+ Compartment alias = createCompartmentAlias(87.0, 56.0, 235.0, 219.0);
model.addAlias(alias);
- CompartmentAlias alias2 = createCompartmentAlias(227.0, 17.0, 290.0, 317.0);
+ Compartment alias2 = createCompartmentAlias(227.0, 17.0, 290.0, 317.0);
model.addAlias(alias2);
PlaceFinder pf = new PlaceFinder(model);
@@ -77,7 +77,7 @@ public class AllPlaceFinderTest {
model.addAlias(createCompartmentAlias(45.0, 38.0, 174.0, 169.0));
model.addAlias(createCompartmentAlias(118.0, 85.0, 60.0, 68.0));
double actual = 0.0;
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
Rectangle2D rect = pf.getRetangle(alias);
actual = rect.getWidth() * rect.getHeight();
@@ -93,7 +93,7 @@ public class AllPlaceFinderTest {
model.addAlias(createCompartmentAlias(88.0, 70.0, 138.0, 112.0));
double actual = 0.0;
Rectangle2D result = null;
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
Rectangle2D rect = pf.getRetangle(alias);
actual += rect.getWidth() * rect.getHeight();
@@ -118,8 +118,8 @@ public class AllPlaceFinderTest {
return tru;
}
- private CompartmentAlias createCompartmentAlias(double x, double y, double width, double height) {
- CompartmentAlias result = new SquareCompartmentAlias();
+ private Compartment createCompartmentAlias(double x, double y, double width, double height) {
+ Compartment result = new SquareCompartment();
result.setAliasId("" + id++);
result.setX(x);
result.setY(y);
@@ -137,7 +137,7 @@ public class AllPlaceFinderTest {
model.addAlias(createCompartmentAlias(4521.0, 0.0, 10000.0, 6000.0));
model.addAlias(createCompartmentAlias(4828.0, 0.0, 5172.0, 6000.0));
double actual = 0.0;
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
Rectangle2D rect = pf.getRetangle(alias);
actual = rect.getWidth() * rect.getHeight();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
index 1f93051927..64c6307dd4 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
@@ -17,8 +17,8 @@ import org.junit.Test;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
public class SpeciesConverterTest {
@@ -34,11 +34,11 @@ public class SpeciesConverterTest {
public void testGetResidueCoords() throws Exception {
try {
final class Conv extends ProteinConverter {
- public Point2D getCoordinate(ProteinAlias alias, double angle) {
+ public Point2D getCoordinate(Protein alias, double angle) {
return super.getResidueCoordinates(alias, angle);
}
}
- GenericProteinAlias alias = new GenericProteinAlias("id");
+ GenericProtein alias = new GenericProtein("id");
alias.setX(135);
alias.setY(194.0);
alias.setWidth(130);
@@ -68,12 +68,12 @@ public class SpeciesConverterTest {
Graphics2D graphics = bi.createGraphics();
ProteinConverter rc = new ProteinConverter();
- GenericProteinAlias alias = createAlias();
+ GenericProtein alias = createAlias();
rc.drawAlias(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
- GenericProteinAlias alias2 = createAlias();
+ GenericProtein alias2 = createAlias();
bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
graphics = bi.createGraphics();
@@ -101,12 +101,12 @@ public class SpeciesConverterTest {
Graphics2D graphics = bi.createGraphics();
ProteinConverter rc = new ProteinConverter();
- GenericProteinAlias alias = createAlias();
+ GenericProtein alias = createAlias();
rc.drawAlias(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
- GenericProteinAlias alias2 = createAlias();
+ GenericProtein alias2 = createAlias();
bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
graphics = bi.createGraphics();
@@ -142,12 +142,12 @@ public class SpeciesConverterTest {
Graphics2D graphics = bi.createGraphics();
ProteinConverter rc = new ProteinConverter();
- GenericProteinAlias alias = createAlias();
+ GenericProtein alias = createAlias();
rc.drawAlias(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
- GenericProteinAlias alias2 = createAlias();
+ GenericProtein alias2 = createAlias();
bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
graphics = bi.createGraphics();
@@ -176,8 +176,8 @@ public class SpeciesConverterTest {
}
}
- private GenericProteinAlias createAlias() {
- GenericProteinAlias alias = new GenericProteinAlias("id");
+ private GenericProtein createAlias() {
+ GenericProtein alias = new GenericProtein("id");
alias.setName("NAME_OF_THE_ELEMENT");
alias.setX(10);
alias.setY(20);
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index e004c14c8a..ab1c2c2f80 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -31,16 +31,16 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class allows to create complex {@link Model} that contains submaps. It's
@@ -211,26 +211,26 @@ public class ComplexZipConverter<T extends IConverter> {
topModel
.addCreationWarning("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains modifiers. Skipped");
} else {
- Alias fromAlias = reaction.getReactants().get(0).getAlias();
- Alias toAlias = reaction.getProducts().get(0).getAlias();
- if (!(fromAlias instanceof SpeciesAlias)) {
+ Element fromAlias = reaction.getReactants().get(0).getAlias();
+ Element toAlias = reaction.getProducts().get(0).getAlias();
+ if (!(fromAlias instanceof Species)) {
topModel.addCreationWarning(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start in species. Skipped");
- } else if (!(toAlias instanceof SpeciesAlias)) {
+ } else if (!(toAlias instanceof Species)) {
topModel.addCreationWarning(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end in species. Skipped");
} else {
- ComplexAlias complexFrom = ((SpeciesAlias) fromAlias).getComplexAlias();
- ComplexAlias complexTo = ((SpeciesAlias) toAlias).getComplexAlias();
+ Complex complexFrom = ((Species) fromAlias).getComplexAlias();
+ Complex complexTo = ((Species) toAlias).getComplexAlias();
if (complexFrom == null) {
topModel.addCreationWarning(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't start inside complex. Skipped");
- } else if (complexTo == null && (!(toAlias instanceof ComplexAlias))) {
+ } else if (complexTo == null && (!(toAlias instanceof Complex))) {
topModel.addCreationWarning(
"[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping + ") contains doesn't end inside complex. Skipped");
} else {
if (complexTo == null) {
- complexTo = (ComplexAlias) toAlias;
+ complexTo = (Complex) toAlias;
}
String fromName = complexFrom.getName();
String toName = complexTo.getName();
@@ -241,18 +241,18 @@ public class ComplexZipConverter<T extends IConverter> {
} else if (toModel == null) {
throw new InvalidArgumentException("Mapping file references to " + toName + " submodel. But such model doesn't exist");
}
- Alias source = fromModel.getAliasByAliasId(fromAlias.getName());
+ Element source = fromModel.getAliasByAliasId(fromAlias.getName());
if (source == null) {
throw new InvalidArgumentException("Mapping file references to element with alias: " + fromAlias.getName() + ". But such element doesn't exist");
}
- Alias dest = null;
- if (!(toAlias instanceof ComplexAlias)) {
+ Element dest = null;
+ if (!(toAlias instanceof Complex)) {
dest = fromModel.getAliasByAliasId(toAlias.getName());
}
SubmodelType type = SubmodelType.UNKNOWN;
- if (fromAlias instanceof ProteinAlias) {
+ if (fromAlias instanceof Protein) {
type = SubmodelType.DOWNSTREAM_TARGETS;
- } else if (fromAlias instanceof PhenotypeAlias) {
+ } else if (fromAlias instanceof Phenotype) {
type = SubmodelType.PATHWAY;
}
AliasSubmodelConnection connection = new AliasSubmodelConnection(toModel, type);
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index f959a49748..84e13e4ee8 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -28,11 +28,6 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewLink;
import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -41,6 +36,11 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Species;
public class ComplexZipConverterTest {
private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
@@ -59,43 +59,43 @@ public class ComplexZipConverterTest {
public Model createModel(ConverterParams params) {
Model result = new ModelFullIndexed(null);
- SpeciesAlias sa1 = new GenericProteinAlias("sa1");
+ Species sa1 = new GenericProtein("sa1");
result.addAlias(sa1);
- SpeciesAlias sa2 = new GenericProteinAlias("sa2");
+ Species sa2 = new GenericProtein("sa2");
result.addAlias(sa2);
- SpeciesAlias sa3 = new GenericProteinAlias("sa3");
+ Species sa3 = new GenericProtein("sa3");
result.addAlias(sa3);
- SpeciesAlias sa4 = new PhenotypeAlias("sa4");
+ Species sa4 = new Phenotype("sa4");
result.addAlias(sa4);
- ComplexAlias ca1 = new ComplexAlias("ca1");
+ Complex ca1 = new Complex("ca1");
ca1.setName("main");
result.addAlias(ca1);
- SpeciesAlias sa5 = new GenericProteinAlias("sa5");
+ Species sa5 = new GenericProtein("sa5");
sa5.setName("sa1");
result.addAlias(sa5);
ca1.addAlias(sa5);
- SpeciesAlias sa6 = new PhenotypeAlias("sa6");
+ Species sa6 = new Phenotype("sa6");
sa6.setName("sa4");
result.addAlias(sa6);
ca1.addAlias(sa6);
- ComplexAlias ca2 = new ComplexAlias("ca2");
+ Complex ca2 = new Complex("ca2");
ca2.setName("s1");
result.addAlias(ca2);
- SpeciesAlias sa7 = new GenericProteinAlias("sa7");
+ Species sa7 = new GenericProtein("sa7");
sa7.setName("sa1");
result.addAlias(sa7);
ca2.addAlias(sa7);
- ComplexAlias ca3 = new ComplexAlias("cs3");
+ Complex ca3 = new Complex("cs3");
ca3.setName("s2");
result.addAlias(ca3);
- ComplexAlias ca4 = new ComplexAlias("cs4");
+ Complex ca4 = new Complex("cs4");
ca4.setName("s3");
result.addAlias(ca4);
@@ -234,20 +234,20 @@ public class ComplexZipConverterTest {
assertNotNull(s2Model);
assertNotNull(s3Model);
- Alias al1 = model.getAliasByAliasId("sa1");
+ Element al1 = model.getAliasByAliasId("sa1");
assertNotNull(al1.getSubmodel());
assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
- Alias al2 = model.getAliasByAliasId("sa2");
+ Element al2 = model.getAliasByAliasId("sa2");
assertNull(al2.getSubmodel());
- Alias al4 = model.getAliasByAliasId("sa4");
+ Element al4 = model.getAliasByAliasId("sa4");
assertNotNull(al4.getSubmodel());
assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
- Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
+ Element s1_al1 = s1Model.getAliasByAliasId("sa1");
assertNotNull(s1_al1.getSubmodel());
assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
@@ -294,20 +294,20 @@ public class ComplexZipConverterTest {
assertNotNull(s2Model);
assertNotNull(s3Model);
- Alias al1 = model.getAliasByAliasId("sa1");
+ Element al1 = model.getAliasByAliasId("sa1");
assertNotNull(al1.getSubmodel());
assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
- Alias al2 = model.getAliasByAliasId("sa2");
+ Element al2 = model.getAliasByAliasId("sa2");
assertNull(al2.getSubmodel());
- Alias al4 = model.getAliasByAliasId("sa4");
+ Element al4 = model.getAliasByAliasId("sa4");
assertNotNull(al4.getSubmodel());
assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
- Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
+ Element s1_al1 = s1Model.getAliasByAliasId("sa1");
assertNotNull(s1_al1.getSubmodel());
assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/SelectedPoint.java b/editor/src/main/java/lcsb/mapviewer/editor/SelectedPoint.java
index 17db3f35fd..28caa05a55 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/SelectedPoint.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/SelectedPoint.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.editor;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Class represeting selected {@link Point2D} on {@link Alias} or
- * {@link Reaction}.
- *
- * @author Piotr Gawron
- *
- */
-public class SelectedPoint {
-
- /**
- * Point that is selected.
- */
- private Point2D point;
-
- /**
- * Object where the point is located.
- */
- private Object container;
-
- /**
- * Default constructor.
- *
- * @param container
- * {@link #container}
- * @param point
- * {@link #point}
- */
- public SelectedPoint(Object container, Point2D point) {
- if (!(container instanceof Alias) && !(container instanceof Reaction)) {
- throw new InvalidArgumentException("Unknown container class: " + container);
- }
- this.container = container;
- this.point = point;
- }
-
- /**
- * @return the point
- * @see #point
- */
- public Point2D getPoint() {
- return point;
- }
-
- /**
- * @return the container
- * @see #container
- */
- public Object getContainer() {
- return container;
- }
-}
+package lcsb.mapviewer.editor;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class represeting selected {@link Point2D} on {@link Element} or
+ * {@link Reaction}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SelectedPoint {
+
+ /**
+ * Point that is selected.
+ */
+ private Point2D point;
+
+ /**
+ * Object where the point is located.
+ */
+ private Object container;
+
+ /**
+ * Default constructor.
+ *
+ * @param container
+ * {@link #container}
+ * @param point
+ * {@link #point}
+ */
+ public SelectedPoint(Object container, Point2D point) {
+ if (!(container instanceof Element) && !(container instanceof Reaction)) {
+ throw new InvalidArgumentException("Unknown container class: " + container);
+ }
+ this.container = container;
+ this.point = point;
+ }
+
+ /**
+ * @return the point
+ * @see #point
+ */
+ public Point2D getPoint() {
+ return point;
+ }
+
+ /**
+ * @return the container
+ * @see #container
+ */
+ public Object getContainer() {
+ return container;
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/ElementModifiedEvent.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/ElementModifiedEvent.java
index 43d05e0ef7..785a833d63 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/ElementModifiedEvent.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/ElementModifiedEvent.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.editor.gui;
-
-import java.awt.event.ActionEvent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-
-/**
- * {@link ActionEvent} represeint event when
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias} or
- * {@link lcsb.mapviewer.model.map.reaction.Reaction} changed.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- *
- */
-public class ElementModifiedEvent<T> extends ActionEvent {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Object that changed.
- */
- private T element;
-
- /**
- * {@link ModelCommand} used to change the {@link #element}.
- */
- private ModelCommand command;
-
- /**
- * Default constructor.
- *
- * @param source
- * object that caused the event
- * @param element
- * {@link #element}
- * @param command
- * {@link #command}
- */
- public ElementModifiedEvent(Object source, T element, ModelCommand command) {
- super(source, 0, "Element modified");
- this.element = element;
- this.command = command;
- }
-
- /**
- * @return the project
- * @see #project
- */
- public T getElement() {
- return element;
- }
-
- /**
- * @return the command
- * @see #command
- */
- public ModelCommand getCommand() {
- return command;
- }
-}
+package lcsb.mapviewer.editor.gui;
+
+import java.awt.event.ActionEvent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+
+/**
+ * {@link ActionEvent} represeint event when
+ * {@link lcsb.mapviewer.model.map.species.Element} or
+ * {@link lcsb.mapviewer.model.map.reaction.Reaction} changed.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ *
+ */
+public class ElementModifiedEvent<T> extends ActionEvent {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Object that changed.
+ */
+ private T element;
+
+ /**
+ * {@link ModelCommand} used to change the {@link #element}.
+ */
+ private ModelCommand command;
+
+ /**
+ * Default constructor.
+ *
+ * @param source
+ * object that caused the event
+ * @param element
+ * {@link #element}
+ * @param command
+ * {@link #command}
+ */
+ public ElementModifiedEvent(Object source, T element, ModelCommand command) {
+ super(source, 0, "Element modified");
+ this.element = element;
+ this.command = command;
+ }
+
+ /**
+ * @return the project
+ * @see #project
+ */
+ public T getElement() {
+ return element;
+ }
+
+ /**
+ * @return the command
+ * @see #command
+ */
+ public ModelCommand getCommand() {
+ return command;
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/WindowContent.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/WindowContent.java
index 8218721e8d..6706e8e7b0 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/WindowContent.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/WindowContent.java
@@ -1,136 +1,136 @@
-package lcsb.mapviewer.editor.gui;
-
-import java.awt.BorderLayout;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.util.List;
-
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTabbedPane;
-
-import lcsb.mapviewer.editor.OpenProjectEvent;
-import lcsb.mapviewer.editor.OpenProjectListener;
-import lcsb.mapviewer.editor.OpenedProject;
-import lcsb.mapviewer.editor.Workspace;
-import lcsb.mapviewer.editor.gui.canvas.MinervaCanvas;
-import lcsb.mapviewer.editor.gui.detailstab.ElementDetailsPanel;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.log4j.Logger;
-
-/**
- * Panel representing content of the gui window.
- *
- * @author Piotr Gawron
- *
- */
-public class WindowContent extends JPanel {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(WindowContent.class);
-
- /**
- * Tabs with projects content.
- */
- private JTabbedPane projectsTab;
-
- /**
- * {@link JPanel} with detail information about selected element.
- */
- private ElementDetailsPanel elementDetailsPanel;
-
- /**
- * Currently selected tab on {@link #projectsTab}.
- */
- private ProjectTab selectedTab;
-
- /**
- * Workspace with all opened projects.
- */
- private Workspace workspace;
-
- /**
- * Default constructor.
- *
- * @param workspace
- * {@link #workspace}
- */
- public WindowContent(Workspace workspace) {
- this.workspace = workspace;
- this.setLayout(new BorderLayout(GuiStyle.GAP_BETWEEN_COMPONENTS, GuiStyle.GAP_BETWEEN_COMPONENTS));
-
- projectsTab = new JTabbedPane();
-
- this.add(projectsTab, BorderLayout.CENTER);
-
- elementDetailsPanel = new ElementDetailsPanel();
-
- this.add(new JScrollPane(elementDetailsPanel), BorderLayout.EAST);
-
- projectsTab.addPropertyChangeListener(MinervaCanvas.SELECTED_ELEMENTS, new PropertyChangeListener() {
- @Override
- public void propertyChange(PropertyChangeEvent evt) {
- selectedTab = (ProjectTab) (evt.getSource());
- List<?> selectedElements = (List<?>) evt.getNewValue();
- if (selectedElements.size() == 1) {
- elementDetailsPanel.setElement(selectedElements.get(0));
- } else {
- elementDetailsPanel.setElement(null);
- }
- }
- });
-
- elementDetailsPanel.addAliasModifiedEventListener(new ElementModifiedEventListener<Alias>() {
- @Override
- public void actionPerformed(ElementModifiedEvent<Alias> e) {
- if (e.getCommand().getAffectedRegion() != null) {
- selectedTab.addInvalidRegion(e.getCommand().getAffectedRegion());
- selectedTab.repaint();
- }
- }
- });
-
- elementDetailsPanel.addReactionModifiedEventListener(new ElementModifiedEventListener<Reaction>() {
- @Override
- public void actionPerformed(ElementModifiedEvent<Reaction> e) {
- if (e.getCommand().getAffectedRegion() != null) {
- selectedTab.addInvalidRegion(e.getCommand().getAffectedRegion());
- selectedTab.repaint();
- }
- }
- });
-
- this.workspace.addProjectAddedListener(new OpenTabListener());
- }
-
- /**
- * Listener used to open new tab.
- *
- * @author Piotr Gawron
- *
- */
- private class OpenTabListener implements OpenProjectListener {
-
- @Override
- public void actionPerformed(OpenProjectEvent e) {
- OpenedProject project = e.getProject();
- ProjectTab tab = new ProjectTab(project);
- projectsTab.addTab(FilenameUtils.getName(project.getFileName()), tab);
- for (PropertyChangeListener listener : projectsTab.getPropertyChangeListeners(MinervaCanvas.SELECTED_ELEMENTS)) {
- tab.addPropertyChangeListener(MinervaCanvas.SELECTED_ELEMENTS, listener);
- }
- }
-
- }
-}
+package lcsb.mapviewer.editor.gui;
+
+import java.awt.BorderLayout;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+
+import lcsb.mapviewer.editor.OpenProjectEvent;
+import lcsb.mapviewer.editor.OpenProjectListener;
+import lcsb.mapviewer.editor.OpenedProject;
+import lcsb.mapviewer.editor.Workspace;
+import lcsb.mapviewer.editor.gui.canvas.MinervaCanvas;
+import lcsb.mapviewer.editor.gui.detailstab.ElementDetailsPanel;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
+
+/**
+ * Panel representing content of the gui window.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class WindowContent extends JPanel {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(WindowContent.class);
+
+ /**
+ * Tabs with projects content.
+ */
+ private JTabbedPane projectsTab;
+
+ /**
+ * {@link JPanel} with detail information about selected element.
+ */
+ private ElementDetailsPanel elementDetailsPanel;
+
+ /**
+ * Currently selected tab on {@link #projectsTab}.
+ */
+ private ProjectTab selectedTab;
+
+ /**
+ * Workspace with all opened projects.
+ */
+ private Workspace workspace;
+
+ /**
+ * Default constructor.
+ *
+ * @param workspace
+ * {@link #workspace}
+ */
+ public WindowContent(Workspace workspace) {
+ this.workspace = workspace;
+ this.setLayout(new BorderLayout(GuiStyle.GAP_BETWEEN_COMPONENTS, GuiStyle.GAP_BETWEEN_COMPONENTS));
+
+ projectsTab = new JTabbedPane();
+
+ this.add(projectsTab, BorderLayout.CENTER);
+
+ elementDetailsPanel = new ElementDetailsPanel();
+
+ this.add(new JScrollPane(elementDetailsPanel), BorderLayout.EAST);
+
+ projectsTab.addPropertyChangeListener(MinervaCanvas.SELECTED_ELEMENTS, new PropertyChangeListener() {
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ selectedTab = (ProjectTab) (evt.getSource());
+ List<?> selectedElements = (List<?>) evt.getNewValue();
+ if (selectedElements.size() == 1) {
+ elementDetailsPanel.setElement(selectedElements.get(0));
+ } else {
+ elementDetailsPanel.setElement(null);
+ }
+ }
+ });
+
+ elementDetailsPanel.addAliasModifiedEventListener(new ElementModifiedEventListener<Element>() {
+ @Override
+ public void actionPerformed(ElementModifiedEvent<Element> e) {
+ if (e.getCommand().getAffectedRegion() != null) {
+ selectedTab.addInvalidRegion(e.getCommand().getAffectedRegion());
+ selectedTab.repaint();
+ }
+ }
+ });
+
+ elementDetailsPanel.addReactionModifiedEventListener(new ElementModifiedEventListener<Reaction>() {
+ @Override
+ public void actionPerformed(ElementModifiedEvent<Reaction> e) {
+ if (e.getCommand().getAffectedRegion() != null) {
+ selectedTab.addInvalidRegion(e.getCommand().getAffectedRegion());
+ selectedTab.repaint();
+ }
+ }
+ });
+
+ this.workspace.addProjectAddedListener(new OpenTabListener());
+ }
+
+ /**
+ * Listener used to open new tab.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private class OpenTabListener implements OpenProjectListener {
+
+ @Override
+ public void actionPerformed(OpenProjectEvent e) {
+ OpenedProject project = e.getProject();
+ ProjectTab tab = new ProjectTab(project);
+ projectsTab.addTab(FilenameUtils.getName(project.getFileName()), tab);
+ for (PropertyChangeListener listener : projectsTab.getPropertyChangeListeners(MinervaCanvas.SELECTED_ELEMENTS)) {
+ tab.addPropertyChangeListener(MinervaCanvas.SELECTED_ELEMENTS, listener);
+ }
+ }
+
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java
index 369191c372..6df8bb3626 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/canvas/CanvasSelectMouseListener.java
@@ -1,125 +1,125 @@
-package lcsb.mapviewer.editor.gui.canvas;
-
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link MouseListener} used when canvas is in select mode (allows to select
- * element on the map).
- *
- * @author Piotr Gawron
- *
- */
-public class CanvasSelectMouseListener implements MouseListener {
-
- /**
- * When clicking on the map and the click is not perfectly on the line this
- * distance describe how far from the line click is still considered as
- * clicking on the line.
- */
- private static final double MAX_DISTANCE_TO_SELECTED_ELEMENT = 5;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CanvasSelectMouseListener.class);
-
- /**
- * Canvas where drawing is performed.
- */
- private MinervaCanvas canvas;
-
- /**
- * Default constructor.
- *
- * @param canvas
- * {@link #canvas}
- */
- public CanvasSelectMouseListener(MinervaCanvas canvas) {
- this.canvas = canvas;
- }
-
- @Override
- public void mouseClicked(MouseEvent e) {
- Point2D point = canvas.mouseCoordinatesToPoint2D(e.getPoint());
-
- List<Object> result = new ArrayList<Object>();
-
- Set<Alias> aliases = canvas.getModel().getAliases();
- for (Alias alias : aliases) {
- if (alias instanceof SpeciesAlias) {
- if (alias.contains(point)) {
- result.add(alias);
- }
- }
- }
- double dist = MAX_DISTANCE_TO_SELECTED_ELEMENT;
- if (result.size() == 0) {
- Reaction r = null;
- Set<Reaction> reactions = canvas.getModel().getReactions();
- for (Reaction reaction : reactions) {
- double newDist = reaction.getDistanceFromPoint(point);
- if (newDist < dist) {
- r = reaction;
- dist = reaction.getDistanceFromPoint(point);
- }
- }
- if (r != null) {
- canvas.setSelectedElement(r);
- return;
- }
- }
-
- if (result.size() > 1) {
- Alias alias = (Alias) result.get(0);
- for (Object obj : result) {
- if (((Alias) (obj)).getSize() < alias.getSize()) {
- alias = (Alias) obj;
- }
- }
- result.clear();
- result.add(alias);
- }
- if (result.size() == 0) {
- canvas.setSelectedElement(null);
- } else {
- canvas.setSelectedElement(result.get(0));
- }
- }
-
- @Override
- public void mousePressed(MouseEvent e) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mouseReleased(MouseEvent e) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mouseEntered(MouseEvent e) {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mouseExited(MouseEvent e) {
- // TODO Auto-generated method stub
-
- }
-
-}
+package lcsb.mapviewer.editor.gui.canvas;
+
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link MouseListener} used when canvas is in select mode (allows to select
+ * element on the map).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CanvasSelectMouseListener implements MouseListener {
+
+ /**
+ * When clicking on the map and the click is not perfectly on the line this
+ * distance describe how far from the line click is still considered as
+ * clicking on the line.
+ */
+ private static final double MAX_DISTANCE_TO_SELECTED_ELEMENT = 5;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(CanvasSelectMouseListener.class);
+
+ /**
+ * Canvas where drawing is performed.
+ */
+ private MinervaCanvas canvas;
+
+ /**
+ * Default constructor.
+ *
+ * @param canvas
+ * {@link #canvas}
+ */
+ public CanvasSelectMouseListener(MinervaCanvas canvas) {
+ this.canvas = canvas;
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e) {
+ Point2D point = canvas.mouseCoordinatesToPoint2D(e.getPoint());
+
+ List<Object> result = new ArrayList<Object>();
+
+ Set<Element> aliases = canvas.getModel().getAliases();
+ for (Element alias : aliases) {
+ if (alias instanceof Species) {
+ if (alias.contains(point)) {
+ result.add(alias);
+ }
+ }
+ }
+ double dist = MAX_DISTANCE_TO_SELECTED_ELEMENT;
+ if (result.size() == 0) {
+ Reaction r = null;
+ Set<Reaction> reactions = canvas.getModel().getReactions();
+ for (Reaction reaction : reactions) {
+ double newDist = reaction.getDistanceFromPoint(point);
+ if (newDist < dist) {
+ r = reaction;
+ dist = reaction.getDistanceFromPoint(point);
+ }
+ }
+ if (r != null) {
+ canvas.setSelectedElement(r);
+ return;
+ }
+ }
+
+ if (result.size() > 1) {
+ Element alias = (Element) result.get(0);
+ for (Object obj : result) {
+ if (((Element) (obj)).getSize() < alias.getSize()) {
+ alias = (Element) obj;
+ }
+ }
+ result.clear();
+ result.add(alias);
+ }
+ if (result.size() == 0) {
+ canvas.setSelectedElement(null);
+ } else {
+ canvas.setSelectedElement(result.get(0));
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e) {
+ // TODO Auto-generated method stub
+
+ }
+
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeAbbreviationCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeAbbreviationCommand.java
index 3646c99919..291935c122 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeAbbreviationCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeAbbreviationCommand.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.JTextField;
-import javax.swing.text.JTextComponent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementAbbreviationCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class that creates {@link ChangeElementAbbreviationCommand} object from gui input
- * for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeAbbreviationCommand extends CreatePropertyChangeCommand {
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeAbbreviationCommand(JTextField field) {
- super(field);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- return new ChangeElementAbbreviationCommand(model, alias, ((JTextComponent) getField()).getText());
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.JTextField;
+import javax.swing.text.JTextComponent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementAbbreviationCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class that creates {@link ChangeElementAbbreviationCommand} object from gui input
+ * for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeAbbreviationCommand extends CreatePropertyChangeCommand {
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeAbbreviationCommand(JTextField field) {
+ super(field);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Element alias) {
+ return new ChangeElementAbbreviationCommand(model, alias, ((JTextComponent) getField()).getText());
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeColorCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeColorCommand.java
index fd8c7e61c1..6a12d1680d 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeColorCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeColorCommand.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.JButton;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementColorCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class that creates {@link ChangeElementColorCommand} object from gui input
- * for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeColorCommand extends CreatePropertyChangeCommand {
- /**
- * Default constructor.
- *
- * @param button
- * GUI buton where new color value will be defined
- */
- CreateChangeColorCommand(JButton button) {
- super(button);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- return new ChangeElementColorCommand(model, alias, getField().getBackground());
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.JButton;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementColorCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class that creates {@link ChangeElementColorCommand} object from gui input
+ * for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeColorCommand extends CreatePropertyChangeCommand {
+ /**
+ * Default constructor.
+ *
+ * @param button
+ * GUI buton where new color value will be defined
+ */
+ CreateChangeColorCommand(JButton button) {
+ super(button);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Element alias) {
+ return new ChangeElementColorCommand(model, alias, getField().getBackground());
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFontSizeCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFontSizeCommand.java
index 7d0fb71785..2d1b649cc4 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFontSizeCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFontSizeCommand.java
@@ -1,41 +1,41 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.JTextField;
-import javax.swing.text.JTextComponent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementFontSizeCommand;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.apache.commons.lang3.math.NumberUtils;
-
-/**
- * Class that creates {@link ChangeElementFontSizeCommand} object from gui input
- * for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeFontSizeCommand extends CreatePropertyChangeCommand {
-
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- protected CreateChangeFontSizeCommand(JTextField field) {
- super(field);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- if (NumberUtils.isNumber(((JTextComponent) getField()).getText())) {
- return new ChangeElementFontSizeCommand(model, alias, Double.valueOf(((JTextComponent) getField()).getText()));
- } else {
- throw new InvalidStateException("Input text is not a double value:" + ((JTextComponent) getField()).getText());
- }
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.JTextField;
+import javax.swing.text.JTextComponent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementFontSizeCommand;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.commons.lang3.math.NumberUtils;
+
+/**
+ * Class that creates {@link ChangeElementFontSizeCommand} object from gui input
+ * for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeFontSizeCommand extends CreatePropertyChangeCommand {
+
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ protected CreateChangeFontSizeCommand(JTextField field) {
+ super(field);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Element alias) {
+ if (NumberUtils.isNumber(((JTextComponent) getField()).getText())) {
+ return new ChangeElementFontSizeCommand(model, alias, Double.valueOf(((JTextComponent) getField()).getText()));
+ } else {
+ throw new InvalidStateException("Input text is not a double value:" + ((JTextComponent) getField()).getText());
+ }
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormerSymbolCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormerSymbolCommand.java
index e5782b2e5a..ab410ec8c4 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormerSymbolCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormerSymbolCommand.java
@@ -8,12 +8,12 @@ import lcsb.mapviewer.commands.ModelCommand;
import lcsb.mapviewer.commands.properties.AddElementFormerSymbolsCommand;
import lcsb.mapviewer.commands.properties.ChangeElementFormerSymbolCommand;
import lcsb.mapviewer.commands.properties.RemoveElementFormerSymbolsCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
- * Class that creates commands that modifies {@link Alias#formerSymbols} from
- * gui input for given {@link Model} and {@link Alias}.
+ * Class that creates commands that modifies {@link Element#formerSymbols} from
+ * gui input for given {@link Model} and {@link Element}.
*
* @author Piotr Gawron
*
@@ -31,17 +31,17 @@ public class CreateChangeFormerSymbolCommand extends CreateListPropertyChangeCom
}
@Override
- protected ModelCommand createRemoveCommand(Model model, Alias alias, List<String> values) {
+ protected ModelCommand createRemoveCommand(Model model, Element alias, List<String> values) {
return new RemoveElementFormerSymbolsCommand(model, alias, values);
}
@Override
- protected ModelCommand createChangeCommand(Model model, Alias alias, String newValue, String oldValue) {
+ protected ModelCommand createChangeCommand(Model model, Element alias, String newValue, String oldValue) {
return new ChangeElementFormerSymbolCommand(model, alias, newValue, oldValue);
}
@Override
- protected ModelCommand createAddCommand(Model model, Alias alias, List<String> newValues) {
+ protected ModelCommand createAddCommand(Model model, Element alias, List<String> newValues) {
return new AddElementFormerSymbolsCommand(model, alias, newValues);
}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormulaCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormulaCommand.java
index 2e5236d45c..170886fd88 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormulaCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFormulaCommand.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.JTextField;
-import javax.swing.text.JTextComponent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementFormulaCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class that creates {@link ChangeElementFormulaCommand} object from gui input
- * for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeFormulaCommand extends CreatePropertyChangeCommand {
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeFormulaCommand(JTextField field) {
- super(field);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- return new ChangeElementFormulaCommand(model, alias, ((JTextComponent) getField()).getText());
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.JTextField;
+import javax.swing.text.JTextComponent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementFormulaCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class that creates {@link ChangeElementFormulaCommand} object from gui input
+ * for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeFormulaCommand extends CreatePropertyChangeCommand {
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeFormulaCommand(JTextField field) {
+ super(field);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Element alias) {
+ return new ChangeElementFormulaCommand(model, alias, ((JTextComponent) getField()).getText());
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFullNameCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFullNameCommand.java
index e77102ad6d..7001d5f093 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFullNameCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeFullNameCommand.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.JTextField;
-import javax.swing.text.JTextComponent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementFullNameCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class that creates {@link ChangeElementFullNameCommand} object from gui input
- * for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeFullNameCommand extends CreatePropertyChangeCommand {
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeFullNameCommand(JTextField field) {
- super(field);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- return new ChangeElementFullNameCommand(model, alias, ((JTextComponent) getField()).getText());
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.JTextField;
+import javax.swing.text.JTextComponent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementFullNameCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class that creates {@link ChangeElementFullNameCommand} object from gui input
+ * for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeFullNameCommand extends CreatePropertyChangeCommand {
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeFullNameCommand(JTextField field) {
+ super(field);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Element alias) {
+ return new ChangeElementFullNameCommand(model, alias, ((JTextComponent) getField()).getText());
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeMiriamDataCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeMiriamDataCommand.java
index 0aed10ffb5..8d6f4450eb 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeMiriamDataCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeMiriamDataCommand.java
@@ -1,49 +1,49 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import java.util.List;
-
-import javax.swing.JList;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.AddElementMiriamDataCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementMiriamDataCommand;
-import lcsb.mapviewer.commands.properties.RemoveElementMiriamDataCommand;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class that creates commands that modifies {@link MiriamData miriam
- * annotationd} from gui input for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeMiriamDataCommand extends CreateListPropertyChangeCommand<MiriamData> {
-
- /**
- * Default constructor.
- *
- * @param list
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeMiriamDataCommand(JList<MiriamData> list) {
- super(list);
- }
-
- @Override
- protected ModelCommand createRemoveCommand(Model model, Alias alias, List<MiriamData> values) {
- return new RemoveElementMiriamDataCommand(model, alias, values);
- }
-
- @Override
- protected ModelCommand createChangeCommand(Model model, Alias alias, MiriamData newValue, MiriamData oldValue) {
- return new ChangeElementMiriamDataCommand(model, alias, newValue, oldValue);
- }
-
- @Override
- protected ModelCommand createAddCommand(Model model, Alias alias, List<MiriamData> newValues) {
- return new AddElementMiriamDataCommand(model, alias, newValues);
- }
-
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import java.util.List;
+
+import javax.swing.JList;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.AddElementMiriamDataCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementMiriamDataCommand;
+import lcsb.mapviewer.commands.properties.RemoveElementMiriamDataCommand;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class that creates commands that modifies {@link MiriamData miriam
+ * annotationd} from gui input for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeMiriamDataCommand extends CreateListPropertyChangeCommand<MiriamData> {
+
+ /**
+ * Default constructor.
+ *
+ * @param list
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeMiriamDataCommand(JList<MiriamData> list) {
+ super(list);
+ }
+
+ @Override
+ protected ModelCommand createRemoveCommand(Model model, Element alias, List<MiriamData> values) {
+ return new RemoveElementMiriamDataCommand(model, alias, values);
+ }
+
+ @Override
+ protected ModelCommand createChangeCommand(Model model, Element alias, MiriamData newValue, MiriamData oldValue) {
+ return new ChangeElementMiriamDataCommand(model, alias, newValue, oldValue);
+ }
+
+ @Override
+ protected ModelCommand createAddCommand(Model model, Element alias, List<MiriamData> newValues) {
+ return new AddElementMiriamDataCommand(model, alias, newValues);
+ }
+
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNameCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNameCommand.java
index 01be4fdd69..e9cfe5f198 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNameCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNameCommand.java
@@ -5,11 +5,11 @@ import javax.swing.text.JTextComponent;
import lcsb.mapviewer.commands.ModelCommand;
import lcsb.mapviewer.commands.properties.ChangeElementNameCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
- * Class with method executed when text property of {@link Alias} is changed.
+ * Class with method executed when text property of {@link Element} is changed.
*
*/
public class CreateChangeNameCommand extends CreatePropertyChangeCommand {
@@ -24,7 +24,7 @@ public class CreateChangeNameCommand extends CreatePropertyChangeCommand {
}
@Override
- public ModelCommand createCommand(Model model, Alias alias) {
+ public ModelCommand createCommand(Model model, Element alias) {
return new ChangeElementNameCommand(model, alias, ((JTextComponent) getField()).getText());
}
}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNotesCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNotesCommand.java
index 7e9856d6b8..ee860545fd 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNotesCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeNotesCommand.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.text.JTextComponent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementNotesCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class that creates {@link ChangeElementNotesCommand} object from gui input
- * for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeNotesCommand extends CreatePropertyChangeCommand {
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeNotesCommand(JTextComponent field) {
- super(field);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- return new ChangeElementNotesCommand(model, alias, ((JTextComponent) getField()).getText());
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.text.JTextComponent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementNotesCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class that creates {@link ChangeElementNotesCommand} object from gui input
+ * for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeNotesCommand extends CreatePropertyChangeCommand {
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeNotesCommand(JTextComponent field) {
+ super(field);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Element alias) {
+ return new ChangeElementNotesCommand(model, alias, ((JTextComponent) getField()).getText());
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSymbolCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSymbolCommand.java
index 67c3ea52b1..7976a9e3ee 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSymbolCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSymbolCommand.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.JTextField;
-import javax.swing.text.JTextComponent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.properties.ChangeElementSymbolCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class that creates {@link ChangeElementSymbolCommand} object from gui input
- * for given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeSymbolCommand extends CreatePropertyChangeCommand {
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeSymbolCommand(JTextField field) {
- super(field);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- return new ChangeElementSymbolCommand(model, alias, ((JTextComponent) getField()).getText());
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.JTextField;
+import javax.swing.text.JTextComponent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.properties.ChangeElementSymbolCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Class that creates {@link ChangeElementSymbolCommand} object from gui input
+ * for given {@link Model} and {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeSymbolCommand extends CreatePropertyChangeCommand {
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeSymbolCommand(JTextField field) {
+ super(field);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Element alias) {
+ return new ChangeElementSymbolCommand(model, alias, ((JTextComponent) getField()).getText());
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSynonymCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSynonymCommand.java
index c3cdeb8b8b..0055be2f32 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSynonymCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateChangeSynonymCommand.java
@@ -8,12 +8,12 @@ import lcsb.mapviewer.commands.ModelCommand;
import lcsb.mapviewer.commands.properties.AddElementSynonymsCommand;
import lcsb.mapviewer.commands.properties.ChangeElementSynonymCommand;
import lcsb.mapviewer.commands.properties.RemoveElementSynonymsCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
- * Class that creates commands that modifies {@link Alias#synonyms} from gui
- * input for given {@link Model} and {@link Alias}.
+ * Class that creates commands that modifies {@link Element#synonyms} from gui
+ * input for given {@link Model} and {@link Element}.
*
* @author Piotr Gawron
*
@@ -31,17 +31,17 @@ public class CreateChangeSynonymCommand extends CreateListPropertyChangeCommand<
}
@Override
- protected ModelCommand createRemoveCommand(Model model, Alias alias, List<String> values) {
+ protected ModelCommand createRemoveCommand(Model model, Element alias, List<String> values) {
return new RemoveElementSynonymsCommand(model, alias, values);
}
@Override
- protected ModelCommand createChangeCommand(Model model, Alias alias, String newValue, String oldValue) {
+ protected ModelCommand createChangeCommand(Model model, Element alias, String newValue, String oldValue) {
return new ChangeElementSynonymCommand(model, alias, newValue, oldValue);
}
@Override
- protected ModelCommand createAddCommand(Model model, Alias alias, List<String> newValues) {
+ protected ModelCommand createAddCommand(Model model, Element alias, List<String> newValues) {
return new AddElementSynonymsCommand(model, alias, newValues);
}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateListPropertyChangeCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateListPropertyChangeCommand.java
index 1a51039ea3..817a54d8a6 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateListPropertyChangeCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreateListPropertyChangeCommand.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import java.util.List;
-
-import javax.swing.JList;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Abstract class that creates {@link ModelCommand commands} to
- * add/remove/modify positions on {@link Alias} property that is a list.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * type of the property element
- */
-public abstract class CreateListPropertyChangeCommand<T> {
-
- /**
- * List where elements are stored.
- */
- private JList<T> field;
-
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateListPropertyChangeCommand(JList<T> field) {
- this.field = field;
- }
-
- /**
- * Creates command that should add element to the property list.
- *
- * @param model
- * model where element is located
- * @param alias
- * {@link Alias} that should be modified
- * @param newValues
- * new values that should be added
- * @return {@link ModelCommand} that will add new values
- */
- protected abstract ModelCommand createAddCommand(Model model, Alias alias, List<T> newValues);
-
- /**
- * Creates command that should remove elements from the property list.
- *
- * @param model
- * model where element is located
- * @param alias
- * {@link Alias} that should be modified
- * @param values
- * values that should be removed
- * @return {@link ModelCommand} that will add new values
- */
- protected abstract ModelCommand createRemoveCommand(Model model, Alias alias, List<T> values);
-
- /**
- * Creates command that should modify position on property list.
- *
- * @param model
- * model where element is located
- * @param alias
- * {@link Alias} that should be modified
- * @param newValue
- * new value of the property element
- * @param oldValue
- * old value of the property element
- * @return {@link ModelCommand} that will add new values
- */
- protected abstract ModelCommand createChangeCommand(Model model, Alias alias, T newValue, T oldValue);
-
- /**
- * @return the field
- * @see #field
- */
- protected JList<T> getField() {
- return field;
- }
-
- /**
- * @param field
- * the field to set
- * @see #field
- */
- protected void setField(JList<T> field) {
- this.field = field;
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import java.util.List;
+
+import javax.swing.JList;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Abstract class that creates {@link ModelCommand commands} to
+ * add/remove/modify positions on {@link Element} property that is a list.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * type of the property element
+ */
+public abstract class CreateListPropertyChangeCommand<T> {
+
+ /**
+ * List where elements are stored.
+ */
+ private JList<T> field;
+
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateListPropertyChangeCommand(JList<T> field) {
+ this.field = field;
+ }
+
+ /**
+ * Creates command that should add element to the property list.
+ *
+ * @param model
+ * model where element is located
+ * @param alias
+ * {@link Element} that should be modified
+ * @param newValues
+ * new values that should be added
+ * @return {@link ModelCommand} that will add new values
+ */
+ protected abstract ModelCommand createAddCommand(Model model, Element alias, List<T> newValues);
+
+ /**
+ * Creates command that should remove elements from the property list.
+ *
+ * @param model
+ * model where element is located
+ * @param alias
+ * {@link Element} that should be modified
+ * @param values
+ * values that should be removed
+ * @return {@link ModelCommand} that will add new values
+ */
+ protected abstract ModelCommand createRemoveCommand(Model model, Element alias, List<T> values);
+
+ /**
+ * Creates command that should modify position on property list.
+ *
+ * @param model
+ * model where element is located
+ * @param alias
+ * {@link Element} that should be modified
+ * @param newValue
+ * new value of the property element
+ * @param oldValue
+ * old value of the property element
+ * @return {@link ModelCommand} that will add new values
+ */
+ protected abstract ModelCommand createChangeCommand(Model model, Element alias, T newValue, T oldValue);
+
+ /**
+ * @return the field
+ * @see #field
+ */
+ protected JList<T> getField() {
+ return field;
+ }
+
+ /**
+ * @param field
+ * the field to set
+ * @see #field
+ */
+ protected void setField(JList<T> field) {
+ this.field = field;
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreatePropertyChangeCommand.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreatePropertyChangeCommand.java
index b5f18d58ad..7f866fe951 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreatePropertyChangeCommand.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/CreatePropertyChangeCommand.java
@@ -1,60 +1,60 @@
-package lcsb.mapviewer.editor.gui.detailstab;
-
-import javax.swing.JComponent;
-
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Abstract class that creates {@link ModelCommand commands} to remove property
- * of {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class CreatePropertyChangeCommand {
-
- /**
- * GUI component that stores the data.
- */
- private JComponent field;
-
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreatePropertyChangeCommand(JComponent field) {
- this.field = field;
- }
-
- /**
- * Method that creates a command to modify {@link Alias} property.
- *
- * @param model
- * {@link Model} where alias is stored
- * @param alias
- * {@link Alias} to modify
- * @return {@link ModelCommand} that will modify alias
- */
- protected abstract ModelCommand createCommand(Model model, Alias alias);
-
- /**
- * @return the field
- * @see #field
- */
- protected JComponent getField() {
- return field;
- }
-
- /**
- * @param field
- * the field to set
- * @see #field
- */
- protected void setField(JComponent field) {
- this.field = field;
- }
-}
+package lcsb.mapviewer.editor.gui.detailstab;
+
+import javax.swing.JComponent;
+
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Abstract class that creates {@link ModelCommand commands} to remove property
+ * of {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class CreatePropertyChangeCommand {
+
+ /**
+ * GUI component that stores the data.
+ */
+ private JComponent field;
+
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreatePropertyChangeCommand(JComponent field) {
+ this.field = field;
+ }
+
+ /**
+ * Method that creates a command to modify {@link Element} property.
+ *
+ * @param model
+ * {@link Model} where alias is stored
+ * @param alias
+ * {@link Element} to modify
+ * @return {@link ModelCommand} that will modify alias
+ */
+ protected abstract ModelCommand createCommand(Model model, Element alias);
+
+ /**
+ * @return the field
+ * @see #field
+ */
+ protected JComponent getField() {
+ return field;
+ }
+
+ /**
+ * @param field
+ * the field to set
+ * @see #field
+ */
+ protected void setField(JComponent field) {
+ this.field = field;
+ }
+}
diff --git a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java
index a54e06996c..0cf93582a1 100644
--- a/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java
+++ b/editor/src/main/java/lcsb/mapviewer/editor/gui/detailstab/ElementDetailsPanel.java
@@ -42,14 +42,14 @@ import lcsb.mapviewer.editor.gui.objectedit.MiriamDataDialog;
import lcsb.mapviewer.editor.gui.objectedit.ObjectEditDialog;
import lcsb.mapviewer.editor.gui.objectedit.StringEditDialog;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
/**
- * {@link JPanel} with detail information about selected {@link Alias} or
+ * {@link JPanel} with detail information about selected {@link Element} or
* {@link Reaction}.
*
* @author Piotr Gawron
@@ -74,12 +74,12 @@ public class ElementDetailsPanel extends JPanel {
private final Logger logger = Logger.getLogger(ElementDetailsPanel.class);
/**
- * Label for {@link Alias#name} parameter.
+ * Label for {@link Element#name} parameter.
*/
private JLabel nameLabel;
/**
- * Label for {@link Alias#getElementId()} parameter.
+ * Label for {@link Element#getElementId()} parameter.
*/
private JLabel idLabel;
@@ -89,67 +89,67 @@ public class ElementDetailsPanel extends JPanel {
private JLabel complexLabel;
/**
- * Label for {@link Alias#compartmentAlias} parameter.
+ * Label for {@link Element#compartmentAlias} parameter.
*/
private JLabel compartmentLabel;
/**
- * Label for {@link Alias#fontSize} parameter.
+ * Label for {@link Element#fontSize} parameter.
*/
private JLabel fontSizeLabel;
/**
- * Label for {@link Alias#color} parameter.
+ * Label for {@link Element#color} parameter.
*/
private JLabel colorLabel;
/**
- * Label for {@link Alias#notes} parameter.
+ * Label for {@link Element#notes} parameter.
*/
private JLabel notesLabel;
/**
- * Label for {@link Alias#symbol} parameter.
+ * Label for {@link Element#symbol} parameter.
*/
private JLabel symbolLabel;
/**
- * Label for {@link Alias#fullName} parameter.
+ * Label for {@link Element#fullName} parameter.
*/
private JLabel fullNameLabel;
/**
- * Label for {@link Alias#abbreviation} parameter.
+ * Label for {@link Element#abbreviation} parameter.
*/
private JLabel abbreviationLabel;
/**
- * Label for {@link Alias#formula} parameter.
+ * Label for {@link Element#formula} parameter.
*/
private JLabel formulaLabel;
/**
- * Label for {@link Alias#synonyms} parameter.
+ * Label for {@link Element#synonyms} parameter.
*/
private JLabel synonymsLabel;
/**
- * Label for {@link Alias#formerSymbols} parameter.
+ * Label for {@link Element#formerSymbols} parameter.
*/
private JLabel formerSymbolsLabel;
/**
- * Label for {@link Alias#symbol} parameter.
+ * Label for {@link Element#symbol} parameter.
*/
private JLabel miriamDataLabel;
/**
- * {@link JTextField} for {@link Alias#name} parameter.
+ * {@link JTextField} for {@link Element#name} parameter.
*/
private JTextField nameText;
/**
- * {@link JTextField} for {@link Alias#name} parameter.
+ * {@link JTextField} for {@link Element#name} parameter.
*/
private JTextField idText;
@@ -159,91 +159,91 @@ public class ElementDetailsPanel extends JPanel {
private JTextField complexText;
/**
- * {@link JTextField} for {@link Alias#compartmentAlias} parameter.
+ * {@link JTextField} for {@link Element#compartmentAlias} parameter.
*/
private JTextField compartmentText;
/**
- * {@link JTextField} for {@link Alias#fontSize} parameter.
+ * {@link JTextField} for {@link Element#fontSize} parameter.
*/
private JTextField fontSizeText;
/**
- * {@link JTextField} for {@link Alias#color} parameter.
+ * {@link JTextField} for {@link Element#color} parameter.
*/
private JButton colorButton;
/**
- * {@link JTextField} for {@link Alias#notes} parameter.
+ * {@link JTextField} for {@link Element#notes} parameter.
*/
private JTextArea notesText;
/**
- * {@link JTextField} for {@link Alias#symbol} parameter.
+ * {@link JTextField} for {@link Element#symbol} parameter.
*/
private JTextField symbolText;
/**
- * {@link JTextField} for {@link Alias#fullName} parameter.
+ * {@link JTextField} for {@link Element#fullName} parameter.
*/
private JTextField fullNameText;
/**
- * {@link JTextField} for {@link Alias#abbreviation} parameter.
+ * {@link JTextField} for {@link Element#abbreviation} parameter.
*/
private JTextField abbreviationText;
/**
- * {@link JTextField} for {@link Alias#formula} parameter.
+ * {@link JTextField} for {@link Element#formula} parameter.
*/
private JTextField formulaText;
/**
- * {@link JList} for {@link Alias#synonyms} parameter.
+ * {@link JList} for {@link Element#synonyms} parameter.
*/
private JList<String> synonymsList;
/**
- * {@link JList} for {@link Alias#formerSymbols} parameter.
+ * {@link JList} for {@link Element#formerSymbols} parameter.
*/
private JList<String> formerSymbolsList;
/**
- * {@link JList} for {@link Alias#miriamData} parameter.
+ * {@link JList} for {@link Element#miriamData} parameter.
*/
private JList<MiriamData> miriamDataList;
/**
- * List of synonyms in {@link Alias#synonyms}.
+ * List of synonyms in {@link Element#synonyms}.
*
* @see {@link #synonymsList}
*/
private DefaultListModel<String> synonymsListModel = new DefaultListModel<>();
/**
- * List of synonyms in {@link Alias#formerSymbols}.
+ * List of synonyms in {@link Element#formerSymbols}.
*
* @see {@link #formerSymbolsList}
*/
private DefaultListModel<String> formerSymbolsListModel = new DefaultListModel<>();
/**
- * List of synonyms in {@link Alias#miriamData}.
+ * List of synonyms in {@link Element#miriamData}.
*
* @see {@link #miriamDataList}
*/
private DefaultListModel<MiriamData> miriamDataListModel = new DefaultListModel<>();
/**
- * {@link Alias} or {@link Reaction} that is currently selected.
+ * {@link Element} or {@link Reaction} that is currently selected.
*/
private Object element;
/**
* List of listeners that should be thrown when some properties of selected
- * {@link Alias} is changed.
+ * {@link Element} is changed.
*/
- private List<ElementModifiedEventListener<Alias>> aliasListeners = new ArrayList<>();
+ private List<ElementModifiedEventListener<Element>> aliasListeners = new ArrayList<>();
/**
* List of listeners that should be thrown when some properties of selected
@@ -365,7 +365,7 @@ public class ElementDetailsPanel extends JPanel {
T s = e.getElement();
List<T> values = new ArrayList<>();
values.add(s);
- ModelCommand modelCommand = createCommandObject.createAddCommand(getModel(), (Alias) element, values);
+ ModelCommand modelCommand = createCommandObject.createAddCommand(getModel(), (Element) element, values);
processCommand(modelCommand);
((DefaultListModel<T>) list.getModel()).addElement(s);
}
@@ -385,7 +385,7 @@ public class ElementDetailsPanel extends JPanel {
@Override
public void actionPerformed(ElementModifiedEvent<T> e) throws CommandExecutionException {
T s = e.getElement();
- ModelCommand modelCommand = createCommandObject.createChangeCommand(getModel(), (Alias) element, s, list.getSelectedValue());
+ ModelCommand modelCommand = createCommandObject.createChangeCommand(getModel(), (Element) element, s, list.getSelectedValue());
processCommand(modelCommand);
((DefaultListModel<T>) list.getModel()).set(list.getSelectedIndices()[0], s);
}
@@ -404,7 +404,7 @@ public class ElementDetailsPanel extends JPanel {
for (T string : list.getSelectedValuesList()) {
elements.add(string);
}
- ModelCommand modelCommand = createCommandObject.createRemoveCommand(getModel(), (Alias) element, elements);
+ ModelCommand modelCommand = createCommandObject.createRemoveCommand(getModel(), (Element) element, elements);
try {
processCommand(modelCommand);
for (T string : elements) {
@@ -439,7 +439,7 @@ public class ElementDetailsPanel extends JPanel {
Color newColor = JColorChooser.showDialog(ElementDetailsPanel.this, "Choose Color", colorButton.getBackground());
if (newColor != null) {
colorButton.setBackground(newColor);
- ModelCommand modelCommand = createCommandObject.createCommand(getModel(), (Alias) element);
+ ModelCommand modelCommand = createCommandObject.createCommand(getModel(), (Element) element);
try {
processCommand(modelCommand);
} catch (CommandExecutionException exception) {
@@ -464,9 +464,9 @@ public class ElementDetailsPanel extends JPanel {
public void processCommand(ModelCommand modelCommand) throws CommandExecutionException {
modelCommand.execute();
if (modelCommand != null) {
- if (element instanceof Alias) {
- ElementModifiedEvent<Alias> event = new ElementModifiedEvent<Alias>(this, (Alias) element, modelCommand);
- for (ElementModifiedEventListener<Alias> listener : aliasListeners) {
+ if (element instanceof Element) {
+ ElementModifiedEvent<Element> event = new ElementModifiedEvent<Element>(this, (Element) element, modelCommand);
+ for (ElementModifiedEventListener<Element> listener : aliasListeners) {
listener.actionPerformed(event);
}
} else if (element instanceof Reaction) {
@@ -498,7 +498,7 @@ public class ElementDetailsPanel extends JPanel {
public void focusLost(FocusEvent e) {
if (!updatingData && element != null) {
- ModelCommand modelCommand = createCommandObject.createCommand(getModel(), (Alias) element);
+ ModelCommand modelCommand = createCommandObject.createCommand(getModel(), (Element) element);
try {
processCommand(modelCommand);
} catch (CommandExecutionException exception) {
@@ -512,7 +512,7 @@ public class ElementDetailsPanel extends JPanel {
@Override
public void actionPerformed(ActionEvent e) {
if (!updatingData && element != null) {
- ModelCommand modelCommand = createCommandObject.createCommand(getModel(), (Alias) element);
+ ModelCommand modelCommand = createCommandObject.createCommand(getModel(), (Element) element);
try {
processCommand(modelCommand);
} catch (CommandExecutionException exception) {
@@ -547,8 +547,8 @@ public class ElementDetailsPanel extends JPanel {
updatingData = true;
removeAll();
try {
- if (object instanceof Alias) {
- createAliasPanel((Alias) object);
+ if (object instanceof Element) {
+ createAliasPanel((Element) object);
} else if (object instanceof Reaction) {
createReactionPanel((Reaction) object);
} else if (object != null) {
@@ -577,9 +577,9 @@ public class ElementDetailsPanel extends JPanel {
* Creates property details panel for alias.
*
* @param alias
- * {@link Alias} for which panel will be created
+ * {@link Element} for which panel will be created
*/
- private void createAliasPanel(Alias alias) {
+ private void createAliasPanel(Element alias) {
int row = 0;
add(nameLabel, createLayoutConstraints(0, row));
add(nameText, createLayoutConstraints(1, row));
@@ -593,7 +593,7 @@ public class ElementDetailsPanel extends JPanel {
add(complexLabel, createLayoutConstraints(0, row));
add(complexText, createLayoutConstraints(1, row));
- if (alias.getParent() instanceof ComplexAlias) {
+ if (alias.getParent() instanceof Complex) {
complexText.setText(alias.getParent().getAliasId());
} else {
complexText.setText("N/A");
@@ -602,7 +602,7 @@ public class ElementDetailsPanel extends JPanel {
add(compartmentLabel, createLayoutConstraints(0, row));
add(compartmentText, createLayoutConstraints(1, row));
- if (alias.getCompartmentAlias() instanceof CompartmentAlias) {
+ if (alias.getCompartmentAlias() instanceof Compartment) {
compartmentText.setText(alias.getCompartmentAlias().getAliasId());
} else {
compartmentText.setText("N/A");
@@ -728,7 +728,7 @@ public class ElementDetailsPanel extends JPanel {
* @param e
* {@link ElementModifiedEventListener listener} to add
*/
- public void addAliasModifiedEventListener(ElementModifiedEventListener<Alias> e) {
+ public void addAliasModifiedEventListener(ElementModifiedEventListener<Element> e) {
aliasListeners.add(e);
}
@@ -749,8 +749,8 @@ public class ElementDetailsPanel extends JPanel {
* @return {@link Model} where edited element is located
*/
private Model getModel() {
- if (element instanceof Alias) {
- return ((Alias) element).getModel();
+ if (element instanceof Element) {
+ return ((Element) element).getModel();
} else if (element instanceof Reaction) {
return ((Reaction) element).getModel();
} else if (element != null) {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index 30dd8b7d2d..bdc922d6a7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -15,17 +15,17 @@ import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This {@link ModelCommand} colors a model (nodes and reactions) according to
@@ -142,8 +142,8 @@ public class ColorModelCommand extends ModelCommand {
* @throws InvalidColorSchemaException
* thrown when alias was already colored by other schema
*/
- private void applyColor(Alias alias, ColorSchema schema) throws InvalidColorSchemaException {
- if (alias instanceof SpeciesAlias) {
+ private void applyColor(Element alias, ColorSchema schema) throws InvalidColorSchemaException {
+ if (alias instanceof Species) {
if (!alias.getColor().equals(Color.WHITE)) {
throw new InvalidColorSchemaException("At least two rows try to set color to element: " + alias.getName());
}
@@ -163,8 +163,8 @@ public class ColorModelCommand extends ModelCommand {
* @return <code>true</code> if coloring schema should be used for alias,
* <code>false</code> otherwise
*/
- protected boolean match(Alias alias, ColorSchema schema) {
- if (alias instanceof SpeciesAlias) {
+ protected boolean match(Element alias, ColorSchema schema) {
+ if (alias instanceof Species) {
if (schema.getName() != null) {
if (!alias.getName().equalsIgnoreCase(schema.getName())) {
return false;
@@ -193,7 +193,7 @@ public class ColorModelCommand extends ModelCommand {
if (schema.getCompartments().size() > 0) {
boolean found = false;
- for (CompartmentAlias cAlias : alias.getModelData().getModel().getCompartmentsAliases()) {
+ for (Compartment cAlias : alias.getModelData().getModel().getCompartmentsAliases()) {
for (String compartmentName : schema.getCompartments()) {
if (cAlias.getName().equalsIgnoreCase(compartmentName)) {
if (cAlias.cross(alias)) {
@@ -226,7 +226,7 @@ public class ColorModelCommand extends ModelCommand {
List<ColorSchema> result = new ArrayList<ColorSchema>();
for (ColorSchema schema : schemas) {
boolean found = false;
- for (Alias alias : getModel().getAliases()) {
+ for (Element alias : getModel().getAliases()) {
if (match(alias, schema)) {
found = true;
}
@@ -244,11 +244,11 @@ public class ColorModelCommand extends ModelCommand {
}
/**
- * Returns list of elements ({@link Reaction reactions} and {@link Alias
+ * Returns list of elements ({@link Reaction reactions} and {@link Element
* aliases}) that are modified by the coloring command.
*
* @return {@link Map}, where key corresponds to modified {@link Reaction} or
- * {@link Alias} and value is a {@link ColorSchema} that should be
+ * {@link Element} and value is a {@link ColorSchema} that should be
* used for coloring
* @throws InvalidColorSchemaException
* thrown when more than one {@link ColorSchema} match an element
@@ -261,7 +261,7 @@ public class ColorModelCommand extends ModelCommand {
models.addAll(getModel().getSubmodels());
for (Model model2 : models) {
for (ColorSchema schema : schemas) {
- for (Alias alias : model2.getAliases()) {
+ for (Element alias : model2.getAliases()) {
if (match(alias, schema)) {
if (result.get(alias) != null && !result.get(alias).getNormalizedColor().equals(Color.WHITE)) {
throw new InvalidColorSchemaException("Alias " + alias.getAliasId() + " is colored by more than one rule.");
@@ -306,7 +306,7 @@ public class ColorModelCommand extends ModelCommand {
*/
private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
- for (Alias alias : result.getAliases()) {
+ for (Element alias : result.getAliases()) {
alias.setColor(Color.WHITE);
}
for (Reaction reaction : result.getReactions()) {
@@ -316,7 +316,7 @@ public class ColorModelCommand extends ModelCommand {
}
for (ColorSchema schema : schemas) {
- for (Alias alias : result.getAliases()) {
+ for (Element alias : result.getAliases()) {
if (match(alias, schema)) {
schema.setMatches(schema.getMatches() + 1);
applyColor(alias, schema);
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index e45e2262bb..f9613dda3f 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -10,12 +10,9 @@ import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -26,6 +23,9 @@ import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Command that creates a new instance of the model with the same data.
@@ -137,7 +137,7 @@ public class CopyCommand extends NewModelCommand {
}
}
}
- for (Alias alias : modelCopy.getAliases()) {
+ for (Element alias : modelCopy.getAliases()) {
// if alias has connection to submodel
if (alias.getSubmodel() != null) {
AliasSubmodelConnection connection = alias.getSubmodel();
@@ -174,20 +174,20 @@ public class CopyCommand extends NewModelCommand {
result.setSbgnFormat(model.isSbgnFormat());
- for (Alias alias : model.getAliases()) {
- if (alias instanceof CompartmentAlias) {
- CompartmentAlias copy = ((CompartmentAlias) alias).copy();
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Compartment) {
+ Compartment copy = ((Compartment) alias).copy();
copy.getAliases().clear();
result.addAlias(copy);
}
}
- for (Alias alias : model.getAliases()) {
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias copy = ((SpeciesAlias) alias).copy();
- CompartmentAlias ca = copy.getCompartmentAlias();
- Alias parent = copy.getParent();
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Species) {
+ Species copy = ((Species) alias).copy();
+ Compartment ca = copy.getCompartmentAlias();
+ Element parent = copy.getParent();
copy.setCompartmentAlias(null);
copy.setParent(null);
@@ -200,12 +200,12 @@ public class CopyCommand extends NewModelCommand {
ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
copy.setCompartmentAlias(ca);
}
- if (parent instanceof CompartmentAlias) {
- ca = (CompartmentAlias) parent;
+ if (parent instanceof Compartment) {
+ ca = (Compartment) parent;
ca = result.getCompartmentAliasByCompartmentAliasId(ca.getAliasId());
copy.setParent(ca);
}
- } else if (alias instanceof CompartmentAlias) {
+ } else if (alias instanceof Compartment) {
// we already added compartment alias
continue;
} else {
@@ -227,7 +227,7 @@ public class CopyCommand extends NewModelCommand {
}
result.setProject(model.getProject());
- for (Alias alias : result.getAliases()) {
+ for (Element alias : result.getAliases()) {
updateAliasReferences(alias, result, model);
}
for (Reaction reaction : result.getReactions()) {
@@ -364,32 +364,32 @@ public class CopyCommand extends NewModelCommand {
* @param originalModel
* original model from which alias copy was created
*/
- private void updateAliasReferences(Alias alias, Model model, Model originalModel) {
- if (alias instanceof CompartmentAlias) {
- CompartmentAlias compartmentAlias = (CompartmentAlias) alias;
- CompartmentAlias original = originalModel.getCompartmentAliasByCompartmentAliasId(alias.getAliasId());
- for (Alias a : original.getAliases()) {
+ private void updateAliasReferences(Element alias, Model model, Model originalModel) {
+ if (alias instanceof Compartment) {
+ Compartment compartmentAlias = (Compartment) alias;
+ Compartment original = originalModel.getCompartmentAliasByCompartmentAliasId(alias.getAliasId());
+ for (Element a : original.getAliases()) {
compartmentAlias.addAlias(model.getAliasByAliasId(a.getAliasId()));
}
}
- if (alias instanceof ComplexAlias) {
- ComplexAlias ca = (ComplexAlias) alias;
+ if (alias instanceof Complex) {
+ Complex ca = (Complex) alias;
for (int i = 0; i < ca.getAliases().size(); i++) {
- SpeciesAlias newAlias = (SpeciesAlias) model.getAliasByAliasId(ca.getAliases().get(i).getAliasId());
+ Species newAlias = (Species) model.getAliasByAliasId(ca.getAliases().get(i).getAliasId());
ca.getAliases().set(i, newAlias);
}
}
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias originalAlias = (SpeciesAlias) originalModel.getAliasByAliasId(alias.getAliasId());
- SpeciesAlias sa = (SpeciesAlias) alias;
+ if (alias instanceof Species) {
+ Species originalAlias = (Species) originalModel.getAliasByAliasId(alias.getAliasId());
+ Species sa = (Species) alias;
if (sa.getComplexAlias() != null) {
- sa.setComplexAlias((ComplexAlias) model.getAliasByAliasId(sa.getComplexAlias().getAliasId()));
+ sa.setComplexAlias((Complex) model.getAliasByAliasId(sa.getComplexAlias().getAliasId()));
}
if (originalAlias.getParent() != null) {
- Alias parent = null;
+ Element parent = null;
parent = model.getAliasByAliasId(originalAlias.getParent().getAliasId());
sa.setParent(parent);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index b81b40470e..897797cda6 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -11,15 +11,15 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This {@link ModelCommand command} class allows to transform model into
@@ -85,12 +85,12 @@ public class CreateHierarchyCommand extends ModelCommand {
throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
}
Model model = getModel();
- List<SpeciesAlias> compacts = new ArrayList<>();
- for (Alias alias : model.getAliases()) {
- if (alias instanceof ComplexAlias) {
- if (((ComplexAlias) alias).getState().contains("brief")) {
- compacts.add((SpeciesAlias) alias);
- compacts.addAll(((ComplexAlias) alias).getAliases());
+ List<Species> compacts = new ArrayList<>();
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Complex) {
+ if (((Complex) alias).getState().contains("brief")) {
+ compacts.add((Species) alias);
+ compacts.addAll(((Complex) alias).getAliases());
}
}
}
@@ -101,7 +101,7 @@ public class CreateHierarchyCommand extends ModelCommand {
orderConcludingComplex();
orderConcludingCompartments();
- List<Alias> sortedAliases = model.getAliasesSortedBySize();
+ List<Element> sortedAliases = model.getAliasesSortedBySize();
setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
model.getAliases().addAll(compacts);
sortedAliases = model.getAliasesSortedBySize();
@@ -120,21 +120,21 @@ public class CreateHierarchyCommand extends ModelCommand {
* Cleans hierarchical information from the model.
*/
protected void clean() {
- for (Alias alias : getModel().getAliases()) {
+ for (Element alias : getModel().getAliases()) {
alias.setParent(null);
- if (alias instanceof ComplexAlias) {
- ((ComplexAlias) alias).getAliases().clear();
+ if (alias instanceof Complex) {
+ ((Complex) alias).getAliases().clear();
}
}
- Set<ArtifitialCompartmentAlias> toRemove = new HashSet<>();
- for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
+ Set<PathwayCompartment> toRemove = new HashSet<>();
+ for (Compartment alias : getModel().getCompartmentsAliases()) {
alias.setParent(null);
alias.getAliases().clear();
- if (alias instanceof ArtifitialCompartmentAlias) {
- toRemove.add((ArtifitialCompartmentAlias) alias);
+ if (alias instanceof PathwayCompartment) {
+ toRemove.add((PathwayCompartment) alias);
}
}
- for (ArtifitialCompartmentAlias alias : toRemove) {
+ for (PathwayCompartment alias : toRemove) {
getModel().removeAlias(alias);
}
}
@@ -148,7 +148,7 @@ public class CreateHierarchyCommand extends ModelCommand {
int id = 0;
for (Layer layer : model.getLayers()) {
for (LayerRect rect : layer.getRectangles()) {
- ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias("art" + (id++));
+ PathwayCompartment alias = new PathwayCompartment("art" + (id++));
alias.setX(rect.getX());
alias.setY(rect.getY());
alias.setWidth(rect.getWidth());
@@ -160,7 +160,7 @@ public class CreateHierarchyCommand extends ModelCommand {
model.addAlias(alias);
}
for (LayerText text : layer.getTexts()) {
- ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias("art" + (id++));
+ PathwayCompartment alias = new PathwayCompartment("art" + (id++));
alias.setX(text.getX());
alias.setY(text.getY());
alias.setWidth(text.getWidth());
@@ -190,16 +190,16 @@ public class CreateHierarchyCommand extends ModelCommand {
private void orderConcludingComplex() {
orderingComplexesInCompartments();
orderingComplexesInComplexes();
- List<Alias> list = new ArrayList<Alias>();
- for (Alias alias : getModel().getAliases()) {
- if (alias instanceof ComplexAlias) {
- for (SpeciesAlias specAlias : ((ComplexAlias) alias).getAliases()) {
+ List<Element> list = new ArrayList<Element>();
+ for (Element alias : getModel().getAliases()) {
+ if (alias instanceof Complex) {
+ for (Species specAlias : ((Complex) alias).getAliases()) {
if (list.contains(specAlias)) {
throw new InvalidStateException("Some aliases are in few Complexes");
}
}
- if (alias instanceof CompartmentAlias) {
- for (Alias specAlias : ((CompartmentAlias) alias).getAliases()) {
+ if (alias instanceof Compartment) {
+ for (Element specAlias : ((Compartment) alias).getAliases()) {
if (list.contains(specAlias)) {
throw new InvalidStateException("Some aliases are in few Structures");
}
@@ -207,7 +207,7 @@ public class CreateHierarchyCommand extends ModelCommand {
}
}
}
- for (Alias alias : getModel().getAliases()) {
+ for (Element alias : getModel().getAliases()) {
if (alias.getParent() != null) {
throw new InvalidStateException("WTF");
}
@@ -219,11 +219,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* Checks if hierarchical structure of compartments is valid.
*/
private void orderConcludingCompartments() {
- for (CompartmentAlias compartment1 : getModel().getCompartmentsAliases()) {
- for (CompartmentAlias compartment2 : getModel().getCompartmentsAliases()) {
+ for (Compartment compartment1 : getModel().getCompartmentsAliases()) {
+ for (Compartment compartment2 : getModel().getCompartmentsAliases()) {
if (!compartment1.equals(compartment2)) {
if (compartment1.contains(compartment2)) {
- Set<Alias> duplicates = compartment2.getAliases();
+ Set<Element> duplicates = compartment2.getAliases();
compartment1.getAliases().removeAll(duplicates);
}
}
@@ -239,15 +239,15 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param maxZoomFactor
* max scale used on the map
*/
- private void preSettingOfVisibilityLevel(List<Alias> sortedAliases, double maxZoomFactor) {
- for (Alias alias : sortedAliases) {
+ private void preSettingOfVisibilityLevel(List<Element> sortedAliases, double maxZoomFactor) {
+ for (Element alias : sortedAliases) {
double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
if (alias.getParent() == null) {
logValue = 0;
}
if (logValue >= zoomLevels) {
- if (alias.getParent() instanceof ComplexAlias) {
+ if (alias.getParent() instanceof Complex) {
logValue = zoomLevels - 1;
} else {
logValue = zoomLevels;
@@ -263,11 +263,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param compartment
* comaprtment alias
*/
- private void settingTransparencyLevelForCompartment(CompartmentAlias compartment) {
+ private void settingTransparencyLevelForCompartment(Compartment compartment) {
int maxVisibilityLevel = Integer.MAX_VALUE;
double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Alias child : compartment.getAliases()) {
+ for (Element child : compartment.getAliases()) {
maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
}
if (maxVisibilityLevel >= zoomLevels) {
@@ -277,7 +277,7 @@ public class CreateHierarchyCommand extends ModelCommand {
maxVisibilityLevel = 1;
}
compartment.setTransparencyLevel(maxVisibilityLevel);
- for (Alias child : compartment.getAliases()) {
+ for (Element child : compartment.getAliases()) {
child.setVisibilityLevel(compartment.getTransparencyLevel());
}
}
@@ -288,11 +288,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param complex
* complex alias
*/
- private void settingTransparencyLevelForComplex(ComplexAlias complex) {
+ private void settingTransparencyLevelForComplex(Complex complex) {
int maxVisibilityLevel = Integer.MAX_VALUE;
double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Alias child : complex.getAliases()) {
+ for (Element child : complex.getAliases()) {
maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
}
if (maxVisibilityLevel >= zoomLevels) {
@@ -302,7 +302,7 @@ public class CreateHierarchyCommand extends ModelCommand {
maxVisibilityLevel = 1;
}
complex.setTransparencyLevel(maxVisibilityLevel);
- for (Alias child : complex.getAliases()) {
+ for (Element child : complex.getAliases()) {
child.setVisibilityLevel(complex.getTransparencyLevel());
}
}
@@ -313,12 +313,12 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param sortedAliases
* list of aliases
*/
- private void settingOfTransparencyLevel(List<Alias> sortedAliases) {
- for (Alias alias : sortedAliases) {
- if (alias instanceof CompartmentAlias) {
- settingTransparencyLevelForCompartment((CompartmentAlias) alias);
- } else if (alias instanceof ComplexAlias) {
- settingTransparencyLevelForComplex((ComplexAlias) alias);
+ private void settingOfTransparencyLevel(List<Element> sortedAliases) {
+ for (Element alias : sortedAliases) {
+ if (alias instanceof Compartment) {
+ settingTransparencyLevelForCompartment((Compartment) alias);
+ } else if (alias instanceof Complex) {
+ settingTransparencyLevelForComplex((Complex) alias);
} else {
alias.setTransparencyLevel(0);
}
@@ -331,16 +331,16 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param sortedAliases
* list of aliases
*/
- private void setChildrening(List<Alias> sortedAliases) {
- for (Alias compartment : sortedAliases) {
- if (compartment instanceof CompartmentAlias) {
- Set<Alias> removable = new HashSet<Alias>();
- for (Alias alias : ((CompartmentAlias) compartment).getAliases()) {
+ private void setChildrening(List<Element> sortedAliases) {
+ for (Element compartment : sortedAliases) {
+ if (compartment instanceof Compartment) {
+ Set<Element> removable = new HashSet<Element>();
+ for (Element alias : ((Compartment) compartment).getAliases()) {
if (alias.getParent() != compartment) {
removable.add(alias);
}
}
- ((CompartmentAlias) compartment).getAliases().removeAll(removable);
+ ((Compartment) compartment).getAliases().removeAll(removable);
}
}
}
@@ -351,20 +351,20 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param sortedAliases
* list of aliases
*/
- private void setParentingOfNonComplexChildrens(List<Alias> sortedAliases) {
- for (Alias alias : getModel().getAliases()) {
+ private void setParentingOfNonComplexChildrens(List<Element> sortedAliases) {
+ for (Element alias : getModel().getAliases()) {
if (alias.getParent() == null) {
- for (Alias complex : sortedAliases) {
- if (complex instanceof ComplexAlias) {
- if (((ComplexAlias) complex).getAliases().contains(alias)) {
+ for (Element complex : sortedAliases) {
+ if (complex instanceof Complex) {
+ if (((Complex) complex).getAliases().contains(alias)) {
alias.setParent(complex);
}
}
}
if (alias.getParent() == null) {
- for (Alias compartment : sortedAliases) {
- if (compartment instanceof CompartmentAlias) {
- if (((CompartmentAlias) compartment).getAliases().contains(alias)) {
+ for (Element compartment : sortedAliases) {
+ if (compartment instanceof Compartment) {
+ if (((Compartment) compartment).getAliases().contains(alias)) {
alias.setParent(compartment);
}
}
@@ -380,7 +380,7 @@ public class CreateHierarchyCommand extends ModelCommand {
* @param sortedAliases
* list of aliases
*/
- private void setParentingAndChildreningOfNonComplexChildrens(List<Alias> sortedAliases) {
+ private void setParentingAndChildreningOfNonComplexChildrens(List<Element> sortedAliases) {
setParentingOfNonComplexChildrens(sortedAliases);
setChildrening(sortedAliases);
}
@@ -389,14 +389,14 @@ public class CreateHierarchyCommand extends ModelCommand {
* Assign aliases to compartments.
*/
private void assignToCompartments() {
- for (CompartmentAlias alias : getModel().getCompartmentsAliases()) {
- for (CompartmentAlias alias2 : getModel().getCompartmentsAliases()) {
+ for (Compartment alias : getModel().getCompartmentsAliases()) {
+ for (Compartment alias2 : getModel().getCompartmentsAliases()) {
if (alias.contains(alias2)) {
alias.addAlias(alias2);
}
}
- for (Alias alias2 : getModel().getAliases()) {
- if (!(alias2 instanceof CompartmentAlias)) {
+ for (Element alias2 : getModel().getAliases()) {
+ if (!(alias2 instanceof Compartment)) {
if (alias.contains(alias2)) {
alias.addAlias(alias2);
}
@@ -409,11 +409,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* Assign aliases to complexes.
*/
private void assignToComplexes() {
- for (Alias alias : getModel().getAliases()) {
- if (alias instanceof ComplexAlias) {
- for (Alias alias2 : getModel().getAliases()) {
+ for (Element alias : getModel().getAliases()) {
+ if (alias instanceof Complex) {
+ for (Element alias2 : getModel().getAliases()) {
if (alias.contains(alias2) && !alias.equals(alias2)) {
- ((ComplexAlias) alias).getAliases().add((SpeciesAlias) alias2);
+ ((Complex) alias).getAliases().add((Species) alias2);
}
}
}
@@ -424,14 +424,14 @@ public class CreateHierarchyCommand extends ModelCommand {
* Remove subchildren from complexes.
*/
private void orderingComplexesInComplexes() {
- for (Alias complex1 : getModel().getAliases()) {
- if (complex1 instanceof ComplexAlias) {
- for (Alias complex2 : getModel().getAliases()) {
- if (complex2 instanceof ComplexAlias) {
+ for (Element complex1 : getModel().getAliases()) {
+ if (complex1 instanceof Complex) {
+ for (Element complex2 : getModel().getAliases()) {
+ if (complex2 instanceof Complex) {
if (!complex1.equals(complex2)) {
if (complex1.contains(complex2)) {
- List<SpeciesAlias> duplicates = ((ComplexAlias) complex2).getAliases();
- ((ComplexAlias) complex1).getAliases().removeAll(duplicates);
+ List<Species> duplicates = ((Complex) complex2).getAliases();
+ ((Complex) complex1).getAliases().removeAll(duplicates);
}
}
}
@@ -444,10 +444,10 @@ public class CreateHierarchyCommand extends ModelCommand {
* Remove subchildren from compartments by complexes.
*/
private void orderingComplexesInCompartments() {
- for (CompartmentAlias compartment : getModel().getCompartmentsAliases()) {
- for (Alias complex : getModel().getAliases()) {
- if (complex instanceof ComplexAlias) {
- List<SpeciesAlias> duplicates = ((ComplexAlias) complex).getAliases();
+ for (Compartment compartment : getModel().getCompartmentsAliases()) {
+ for (Element complex : getModel().getAliases()) {
+ if (complex instanceof Complex) {
+ List<Species> duplicates = ((Complex) complex).getAliases();
compartment.getAliases().removeAll(duplicates);
}
}
@@ -458,11 +458,11 @@ public class CreateHierarchyCommand extends ModelCommand {
* Sets proper parents after creating hierarchical structure.
*/
private void parentingInComplexes() {
- for (Alias complex : getModel().getAliases()) {
- if (complex instanceof ComplexAlias) {
- for (Alias child : ((ComplexAlias) complex).getAliases()) {
- if (child instanceof ComplexAlias) {
- if (((ComplexAlias) child).getAliases().contains(complex)) {
+ for (Element complex : getModel().getAliases()) {
+ if (complex instanceof Complex) {
+ for (Element child : ((Complex) complex).getAliases()) {
+ if (child instanceof Complex) {
+ if (((Complex) child).getAliases().contains(complex)) {
if (complex.getParent() != null) {
throw new InvalidStateException(
child.getName() + " has parent " + child.getParent().getName() + " and now again try to add new parent " + complex.getName());
@@ -486,7 +486,7 @@ public class CreateHierarchyCommand extends ModelCommand {
* @return ratio between the minimal object that should be visible, and alias
* visible on the top level
*/
- private double computeRate(Alias alias, double limit) {
+ private double computeRate(Element alias, double limit) {
double length = alias.getWidth() / maxZoomFactor;
double height = alias.getHeight() / maxZoomFactor;
double size = length * height;
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
index d6f392dea1..aefcf90fff 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
@@ -5,10 +5,10 @@ import java.awt.geom.Rectangle2D;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Abstract class representing operation on the model. There are following steps
@@ -201,7 +201,7 @@ public abstract class ModelCommand {
* @param alias
* alias to be included in affected region
*/
- protected void includeInAffectedRegion(Alias alias) {
+ protected void includeInAffectedRegion(Element alias) {
if (affectedRegion == null) {
affectedRegion = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
} else {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
index 36fef91e25..41c480ae8d 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Command which moves model by dx, dy coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class MoveCommand extends ModelCommand {
-
- /**
- * Delta x.
- */
- private double dx;
- /**
- * Delta y.
- */
- private double dy;
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- * @param dx
- * delta x
- * @param dy
- * delat y
- */
- public MoveCommand(Model model, double dx, double dy) {
- super(model);
- this.dx = dx;
- this.dy = dy;
- }
-
- @Override
- protected void undoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void executeImplementation() {
-
- Model model = getModel();
-
- for (Alias alias : model.getAliases()) {
- alias.setX(alias.getX() + dx);
- alias.setY(alias.getY() + dy);
- if (alias instanceof CompartmentAlias) {
- ((CompartmentAlias) alias).setNamePoint(((CompartmentAlias) alias).getNamePoint().getX() + dx, ((CompartmentAlias) alias).getNamePoint().getY() + dy);
- }
- }
- for (Reaction reaction : model.getReactions()) {
- for (AbstractNode node : reaction.getNodes()) {
- for (Point2D point : node.getLine().getPoints()) {
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Command which moves model by dx, dy coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MoveCommand extends ModelCommand {
+
+ /**
+ * Delta x.
+ */
+ private double dx;
+ /**
+ * Delta y.
+ */
+ private double dy;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ * @param dx
+ * delta x
+ * @param dy
+ * delat y
+ */
+ public MoveCommand(Model model, double dx, double dy) {
+ super(model);
+ this.dx = dx;
+ this.dy = dy;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ Model model = getModel();
+
+ for (Element alias : model.getAliases()) {
+ alias.setX(alias.getX() + dx);
+ alias.setY(alias.getY() + dy);
+ if (alias instanceof Compartment) {
+ ((Compartment) alias).setNamePoint(((Compartment) alias).getNamePoint().getX() + dx, ((Compartment) alias).getNamePoint().getY() + dy);
+ }
+ }
+ for (Reaction reaction : model.getReactions()) {
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Point2D point : node.getLine().getPoints()) {
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ }
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
index 059e1ad47f..aade207264 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
@@ -1,181 +1,181 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-
-import org.apache.log4j.Logger;
-
-/**
- * Command which moves elements in model by dx, dy coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class MoveElementsCommand extends ModelCommand {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(MoveElementsCommand.class);
-
- /**
- * Delta x.
- */
- private double dx;
-
- /**
- * Delta y.
- */
- private double dy;
-
- /**
- * List of objects to move.
- */
- private List<Object> objectsToMove = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- * @param elements
- * elements that should be moved
- * @param dx
- * delta x
- * @param dy
- * delat y
- */
- public MoveElementsCommand(Model model, List<Object> elements, double dx, double dy) {
- super(model);
- this.dx = dx;
- this.dy = dy;
- for (Object object : elements) {
- if (object instanceof Alias) {
- if (((Alias) object).getModel() != model) {
- throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
- }
- } else if (object instanceof Reaction) {
- if (((Reaction) object).getModel() != model) {
- throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
- }
- } else {
- throw new InvalidArgumentException("Cannot move element: " + object);
- }
- }
- objectsToMove = elements;
- }
-
- @Override
- protected void undoImplementation() {
- dx = -dx;
- dy = -dy;
- executeImplementation();
- dx = -dx;
- dy = -dy;
- setStatus(ModelCommandStatus.UNDONE);
- }
-
- @Override
- protected void redoImplementation() {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- @Override
- protected void executeImplementation() {
- Set<Alias> aliases = new HashSet<>();
-
- for (Object object : objectsToMove) {
- if (object instanceof Alias) {
- Alias alias = (Alias) object;
-
- includeInAffectedRegion(alias);
-
- alias.setX(alias.getX() + dx);
- alias.setY(alias.getY() + dy);
- if (alias instanceof CompartmentAlias) {
- ((CompartmentAlias) alias)
- .setNamePoint(((CompartmentAlias) alias).getNamePoint().getX() + dx, ((CompartmentAlias) alias).getNamePoint().getY() + dy);
- }
-
- includeInAffectedRegion(alias);
-
- aliases.add(alias);
- } else if (object instanceof Reaction) {
- Reaction reaction = (Reaction) object;
- for (Reactant node : reaction.getReactants()) {
- for (int i = 1; i < node.getLine().getPoints().size(); i++) {
- Point2D point = node.getLine().getPoints().get(i);
- logger.debug("Moving point: " + point);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- for (Product node : reaction.getProducts()) {
- for (int i = 0; i < node.getLine().getPoints().size() - 1; i++) {
- Point2D point = node.getLine().getPoints().get(i);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- for (Modifier node : reaction.getModifiers()) {
- for (int i = 1; i < node.getLine().getPoints().size(); i++) {
- Point2D point = node.getLine().getPoints().get(i);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- for (NodeOperator node : reaction.getOperators()) {
- for (int i = 0; i < node.getLine().getPoints().size(); i++) {
- Point2D point = node.getLine().getPoints().get(i);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- includeInAffectedRegion(reaction);
- } else {
- throw new InvalidStateException("Unknown class type: " + object);
- }
- }
- if (aliases.size() > 0) {
- // TODO this must be improved, we cannot do full search on every move
- for (Reaction reaction : getModel().getReactions()) {
- for (ReactionNode node : reaction.getReactionNodes()) {
- if (aliases.contains(node.getAlias())) {
- if (node instanceof Reactant) {
- Point2D point = node.getLine().getBeginPoint();
- point.setLocation(point.getX() + dx, point.getY() + dy);
-
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getPoints().get(1));
- } else if (node instanceof Modifier) {
- Point2D point = node.getLine().getBeginPoint();
- point.setLocation(point.getX() + dx, point.getY() + dy);
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getPoints().get(1));
- } else if (node instanceof Product) {
- Point2D point = node.getLine().getEndPoint();
- point.setLocation(point.getX() + dx, point.getY() + dy);
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getPoints().get(node.getLine().getPoints().size() - 1));
- }
- }
- }
- }
- }
- }
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Command which moves elements in model by dx, dy coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MoveElementsCommand extends ModelCommand {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(MoveElementsCommand.class);
+
+ /**
+ * Delta x.
+ */
+ private double dx;
+
+ /**
+ * Delta y.
+ */
+ private double dy;
+
+ /**
+ * List of objects to move.
+ */
+ private List<Object> objectsToMove = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ * @param elements
+ * elements that should be moved
+ * @param dx
+ * delta x
+ * @param dy
+ * delat y
+ */
+ public MoveElementsCommand(Model model, List<Object> elements, double dx, double dy) {
+ super(model);
+ this.dx = dx;
+ this.dy = dy;
+ for (Object object : elements) {
+ if (object instanceof Element) {
+ if (((Element) object).getModel() != model) {
+ throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
+ }
+ } else if (object instanceof Reaction) {
+ if (((Reaction) object).getModel() != model) {
+ throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
+ }
+ } else {
+ throw new InvalidArgumentException("Cannot move element: " + object);
+ }
+ }
+ objectsToMove = elements;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ dx = -dx;
+ dy = -dy;
+ executeImplementation();
+ dx = -dx;
+ dy = -dy;
+ setStatus(ModelCommandStatus.UNDONE);
+ }
+
+ @Override
+ protected void redoImplementation() {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ @Override
+ protected void executeImplementation() {
+ Set<Element> aliases = new HashSet<>();
+
+ for (Object object : objectsToMove) {
+ if (object instanceof Element) {
+ Element alias = (Element) object;
+
+ includeInAffectedRegion(alias);
+
+ alias.setX(alias.getX() + dx);
+ alias.setY(alias.getY() + dy);
+ if (alias instanceof Compartment) {
+ ((Compartment) alias)
+ .setNamePoint(((Compartment) alias).getNamePoint().getX() + dx, ((Compartment) alias).getNamePoint().getY() + dy);
+ }
+
+ includeInAffectedRegion(alias);
+
+ aliases.add(alias);
+ } else if (object instanceof Reaction) {
+ Reaction reaction = (Reaction) object;
+ for (Reactant node : reaction.getReactants()) {
+ for (int i = 1; i < node.getLine().getPoints().size(); i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ logger.debug("Moving point: " + point);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ for (Product node : reaction.getProducts()) {
+ for (int i = 0; i < node.getLine().getPoints().size() - 1; i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ for (Modifier node : reaction.getModifiers()) {
+ for (int i = 1; i < node.getLine().getPoints().size(); i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ for (NodeOperator node : reaction.getOperators()) {
+ for (int i = 0; i < node.getLine().getPoints().size(); i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ includeInAffectedRegion(reaction);
+ } else {
+ throw new InvalidStateException("Unknown class type: " + object);
+ }
+ }
+ if (aliases.size() > 0) {
+ // TODO this must be improved, we cannot do full search on every move
+ for (Reaction reaction : getModel().getReactions()) {
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ if (aliases.contains(node.getAlias())) {
+ if (node instanceof Reactant) {
+ Point2D point = node.getLine().getBeginPoint();
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+
+ // we don't have to include point that we change as it's already
+ // on the border of the element
+ includeInAffectedRegion(node.getLine().getPoints().get(1));
+ } else if (node instanceof Modifier) {
+ Point2D point = node.getLine().getBeginPoint();
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ // we don't have to include point that we change as it's already
+ // on the border of the element
+ includeInAffectedRegion(node.getLine().getPoints().get(1));
+ } else if (node instanceof Product) {
+ Point2D point = node.getLine().getEndPoint();
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ // we don't have to include point that we change as it's already
+ // on the border of the element
+ includeInAffectedRegion(node.getLine().getPoints().get(node.getLine().getPoints().size() - 1));
+ }
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
index d77b2eb551..64302e7f96 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
@@ -6,15 +6,15 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Creates a new instance of the model with data limited to region described by
@@ -49,25 +49,25 @@ public class SubModelCommand extends NewModelCommand {
CopyCommand copy = new CopyCommand(getModel());
Model result = copy.execute();
- Set<Alias> aliasNotToRemove = new HashSet<Alias>();
+ Set<Element> aliasNotToRemove = new HashSet<Element>();
- for (Alias alias : result.getAliases()) {
+ for (Element alias : result.getAliases()) {
if (polygon.intersects(alias.getBorder())) {
aliasNotToRemove.add(alias);
}
}
boolean added = false;
do {
- Set<Alias> iterativeAliasNotToRemove = new HashSet<>();
- for (Alias alias : aliasNotToRemove) {
- Alias parent = alias.getParent();
+ Set<Element> iterativeAliasNotToRemove = new HashSet<>();
+ for (Element alias : aliasNotToRemove) {
+ Element parent = alias.getParent();
if (parent != null) {
if (!aliasNotToRemove.contains(parent)) {
iterativeAliasNotToRemove.add(parent);
}
}
- if (alias instanceof SpeciesAlias) {
- parent = ((SpeciesAlias) alias).getComplexAlias();
+ if (alias instanceof Species) {
+ parent = ((Species) alias).getComplexAlias();
if (parent != null) {
if (!aliasNotToRemove.contains(parent)) {
iterativeAliasNotToRemove.add(parent);
@@ -80,27 +80,27 @@ public class SubModelCommand extends NewModelCommand {
aliasNotToRemove.addAll(iterativeAliasNotToRemove);
} while (added);
- List<Alias> aliasToRemove = new ArrayList<Alias>();
- for (Alias alias : result.getAliases()) {
+ List<Element> aliasToRemove = new ArrayList<Element>();
+ for (Element alias : result.getAliases()) {
if (!(polygon.intersects(alias.getBorder()))) {
boolean remove = true;
- if (alias instanceof SpeciesAlias) {
- remove = ((SpeciesAlias) alias).getComplexAlias() == null;
+ if (alias instanceof Species) {
+ remove = ((Species) alias).getComplexAlias() == null;
}
if (aliasNotToRemove.contains(alias)) {
remove = false;
}
if (remove) {
aliasToRemove.add(alias);
- if (alias instanceof ComplexAlias) {
- List<SpeciesAlias> aliases = ((ComplexAlias) alias).getAllChildrenAliases();
+ if (alias instanceof Complex) {
+ List<Species> aliases = ((Complex) alias).getAllChildrenAliases();
aliasToRemove.addAll(aliases);
}
}
}
}
- for (Alias alias : aliasToRemove) {
+ for (Element alias : aliasToRemove) {
result.removeAlias(alias);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java
index c993a480be..f4bb75b0a1 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java
@@ -5,12 +5,12 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes former
- * sybmols of the {@link Alias element}.
+ * sybmols of the {@link Element element}.
*
* @author Piotr Gawron
*
@@ -31,9 +31,9 @@ public class AddElementFormerSymbolsCommand extends AddElementPropertyListEntryC
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * new {@link Alias#synonym} values to be added
+ * new {@link Element#synonym} values to be added
*/
- public AddElementFormerSymbolsCommand(Model model, Alias alias, List<String> values) {
+ public AddElementFormerSymbolsCommand(Model model, Element alias, List<String> values) {
super(model, alias, values);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java
index e1127df55b..d2ab757f64 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java
@@ -6,12 +6,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * {@link MiriamData annotations} of the {@link Alias Element} .
+ * {@link MiriamData annotations} of the {@link Element Element} .
*
* @author Piotr Gawron
*
@@ -34,7 +34,7 @@ public class AddElementMiriamDataCommand extends AddElementPropertyListEntryComm
* @param values
* new annotation values to be added
*/
- public AddElementMiriamDataCommand(Model model, Alias alias, List<MiriamData> values) {
+ public AddElementMiriamDataCommand(Model model, Element alias, List<MiriamData> values) {
super(model, alias, values);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java
index e43cf8d236..2a390f6e6b 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java
@@ -5,12 +5,12 @@ import java.util.List;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.ModelCommand;
import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that add entries
- * into a property of the {@link Alias Element} that is list.
+ * into a property of the {@link Element Element} that is list.
*
* @param <T>
* class of property to edit
@@ -26,9 +26,9 @@ public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand
private List<T> newValues;
/**
- * {@link Alias} for which we will change the property.
+ * {@link Element} for which we will change the property.
*/
- private Alias alias;
+ private Element alias;
/**
* Default constructor.
@@ -43,7 +43,7 @@ public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand
* new values of the element property that will be added
*
*/
- public AddElementPropertyListEntryCommand(Model model, Alias alias, List<T> newValues) {
+ public AddElementPropertyListEntryCommand(Model model, Element alias, List<T> newValues) {
super(model);
this.alias = alias;
this.newValues = newValues;
@@ -59,7 +59,7 @@ public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand
* @return the alias
* @see #alias
*/
- protected Alias getAlias() {
+ protected Element getAlias() {
return alias;
}
@@ -68,7 +68,7 @@ public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand
* the alias to set
* @see #alias
*/
- protected void setAlias(Alias alias) {
+ protected void setAlias(Element alias) {
this.alias = alias;
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java
index 34cc030dd9..6c4587b949 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java
@@ -5,12 +5,12 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * synonyms of the {@link Alias Element}.
+ * synonyms of the {@link Element Element}.
*
* @author Piotr Gawron
*
@@ -31,9 +31,9 @@ public class AddElementSynonymsCommand extends AddElementPropertyListEntryComman
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * new {@link Alias#synonym} values to be added
+ * new {@link Element#synonym} values to be added
*/
- public AddElementSynonymsCommand(Model model, Alias alias, List<String> values) {
+ public AddElementSynonymsCommand(Model model, Element alias, List<String> values) {
super(model, alias, values);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java
index f244eaf7fa..f0db3c5b9d 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java
@@ -1,13 +1,13 @@
package lcsb.mapviewer.commands.properties;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
- * of the element connected to {@link Alias}.
+ * of the element connected to {@link Element}.
*
* @author Piotr Gawron
*
@@ -30,7 +30,7 @@ public class ChangeElementAbbreviationCommand extends ChangeElementPropertyComma
* @param newName
* new name of the elemnt
*/
- public ChangeElementAbbreviationCommand(Model model, Alias alias, String newName) {
+ public ChangeElementAbbreviationCommand(Model model, Element alias, String newName) {
super(model, alias, newName);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
index 49cd2f981e..334ddb8961 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
@@ -1,49 +1,49 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.awt.Color;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that
- * {@link Alias#color}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementColorCommand extends ChangeElementPropertyCommand<Color> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementColorCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Alias#color} value
- */
- public ChangeElementColorCommand(Model model, Alias alias, Color newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getColor());
- getAlias().setColor((Color) getNewValue());
-
- includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that
+ * {@link Element#color}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementColorCommand extends ChangeElementPropertyCommand<Color> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementColorCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#color} value
+ */
+ public ChangeElementColorCommand(Model model, Element alias, Color newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getColor());
+ getAlias().setColor((Color) getNewValue());
+
+ includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java
index cd99b1914c..bd8a4fbcc7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * {@link Alias#fontSize}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementFontSizeCommand extends ChangeElementPropertyCommand<Double> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementFontSizeCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Alias#fontSize} value
- */
- public ChangeElementFontSizeCommand(Model model, Alias alias, Double newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- // abbreviation is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getFontSize());
- getAlias().setFontSize((Double) getNewValue());
-
- // abbreviation is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
+ * {@link Element#fontSize}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementFontSizeCommand extends ChangeElementPropertyCommand<Double> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementFontSizeCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#fontSize} value
+ */
+ public ChangeElementFontSizeCommand(Model model, Element alias, Double newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ // abbreviation is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getFontSize());
+ getAlias().setFontSize((Double) getNewValue());
+
+ // abbreviation is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java
index c4a7bdc963..fc5adb281f 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java
@@ -3,12 +3,12 @@ package lcsb.mapviewer.commands.properties;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes former
- * symbol of the {@link Alias Element}.
+ * symbol of the {@link Element Element}.
*
* @author Piotr Gawron
*
@@ -29,11 +29,11 @@ public class ChangeElementFormerSymbolCommand extends ChangeElementPropertyListE
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newValue
- * new {@link Alias#synonym} value
+ * new {@link Element#synonym} value
* @param oldValue
- * old {@link Alias#synonym} value
+ * old {@link Element#synonym} value
*/
- public ChangeElementFormerSymbolCommand(Model model, Alias alias, String newValue, String oldValue) {
+ public ChangeElementFormerSymbolCommand(Model model, Element alias, String newValue, String oldValue) {
super(model, alias, newValue, oldValue);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java
index 59331221d2..5f3dc88d6f 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java
@@ -2,12 +2,12 @@ package lcsb.mapviewer.commands.properties;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * formula of the element connected to {@link Alias}.
+ * formula of the element connected to {@link Element}.
*
* @author Piotr Gawron
*
@@ -28,9 +28,9 @@ public class ChangeElementFormulaCommand extends ChangeElementPropertyCommand<St
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link Alias#formula} value
+ * new {@link Element#formula} value
*/
- public ChangeElementFormulaCommand(Model model, Alias alias, String newName) {
+ public ChangeElementFormulaCommand(Model model, Element alias, String newName) {
super(model, alias, newName);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java
index 3acb3950d6..db9f6841c0 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java
@@ -1,13 +1,13 @@
package lcsb.mapviewer.commands.properties;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes full
- * name of the element connected to {@link Alias}.
+ * name of the element connected to {@link Element}.
*
* @author Piotr Gawron
*
@@ -28,9 +28,9 @@ public class ChangeElementFullNameCommand extends ChangeElementPropertyCommand<S
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link Alias#fullName} value
+ * new {@link Element#fullName} value
*/
- public ChangeElementFullNameCommand(Model model, Alias alias, String newName) {
+ public ChangeElementFullNameCommand(Model model, Element alias, String newName) {
super(model, alias, newName);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java
index 3fba13b864..34db575c45 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java
@@ -4,12 +4,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * annotations of the {@link Alias Element}.
+ * annotations of the {@link Element Element}.
*
* @author Piotr Gawron
*
@@ -34,7 +34,7 @@ public class ChangeElementMiriamDataCommand extends ChangeElementPropertyListEnt
* @param oldValue
* old annotation value
*/
- public ChangeElementMiriamDataCommand(Model model, Alias alias, MiriamData newValue, MiriamData oldValue) {
+ public ChangeElementMiriamDataCommand(Model model, Element alias, MiriamData newValue, MiriamData oldValue) {
super(model, alias, newValue, oldValue);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java
index 425540c44c..82bfff0c28 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java
@@ -1,13 +1,13 @@
package lcsb.mapviewer.commands.properties;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
- * of the element connected to {@link Alias}.
+ * of the element connected to {@link Element}.
*
* @author Piotr Gawron
*
@@ -30,7 +30,7 @@ public class ChangeElementNameCommand extends ChangeElementPropertyCommand<Strin
* @param newName
* new name of the elemnt
*/
- public ChangeElementNameCommand(Model model, Alias alias, String newName) {
+ public ChangeElementNameCommand(Model model, Element alias, String newName) {
super(model, alias, newName);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java
index 9fb347d855..8e4be7669b 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java
@@ -1,13 +1,13 @@
package lcsb.mapviewer.commands.properties;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes notes
- * of the element connected to {@link Alias}.
+ * of the element connected to {@link Element}.
*
* @author Piotr Gawron
*
@@ -28,9 +28,9 @@ public class ChangeElementNotesCommand extends ChangeElementPropertyCommand<Stri
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link Alias#notes} value
+ * new {@link Element#notes} value
*/
- public ChangeElementNotesCommand(Model model, Alias alias, String newName) {
+ public ChangeElementNotesCommand(Model model, Element alias, String newName) {
super(model, alias, newName);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java
index 27377a08c2..fa157fb75e 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java
@@ -1,120 +1,120 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
- * property of the element connected to {@link Alias}.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ChangeElementPropertyCommand<T> extends ModelCommand {
-
- /**
- * New element property value.
- */
- private T newValue;
-
- /**
- * Old element property value.
- */
- private T oldValue;
-
- /**
- * {@link Alias} for which we will change the property.
- */
- private Alias alias;
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- *
- * @param alias
- * alias to be changed
- *
- * @param newValue
- * new value of the element property
- */
- public ChangeElementPropertyCommand(Model model, Alias alias, T newValue) {
- super(model);
- this.alias = alias;
- this.newValue = newValue;
- }
-
- @Override
- protected void undoImplementation() throws CommandExecutionException {
- T tmp = newValue;
- newValue = oldValue;
- executeImplementation();
- newValue = tmp;
- oldValue = null;
- setStatus(ModelCommandStatus.UNDONE);
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- /**
- * @return the alias
- * @see #alias
- */
- protected Alias getAlias() {
- return alias;
- }
-
- /**
- * @param alias
- * the alias to set
- * @see #alias
- */
- protected void setAlias(Alias alias) {
- this.alias = alias;
- }
-
- /**
- * @return the oldValue
- * @see #oldValue
- */
- protected Object getOldValue() {
- return oldValue;
- }
-
- /**
- * @param oldValue
- * the oldValue to set
- * @see #oldValue
- */
- protected void setOldValue(T oldValue) {
- this.oldValue = oldValue;
- }
-
- /**
- * @return the newValue
- * @see #newValue
- */
- protected Object getNewValue() {
- return newValue;
- }
-
- /**
- * @param newValue
- * the newValue to set
- * @see #newValue
- */
- protected void setNewValue(T newValue) {
- this.newValue = newValue;
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.ModelCommandStatus;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
+ * property of the element connected to {@link Element}.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ChangeElementPropertyCommand<T> extends ModelCommand {
+
+ /**
+ * New element property value.
+ */
+ private T newValue;
+
+ /**
+ * Old element property value.
+ */
+ private T oldValue;
+
+ /**
+ * {@link Element} for which we will change the property.
+ */
+ private Element alias;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ *
+ * @param alias
+ * alias to be changed
+ *
+ * @param newValue
+ * new value of the element property
+ */
+ public ChangeElementPropertyCommand(Model model, Element alias, T newValue) {
+ super(model);
+ this.alias = alias;
+ this.newValue = newValue;
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ T tmp = newValue;
+ newValue = oldValue;
+ executeImplementation();
+ newValue = tmp;
+ oldValue = null;
+ setStatus(ModelCommandStatus.UNDONE);
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ /**
+ * @return the alias
+ * @see #alias
+ */
+ protected Element getAlias() {
+ return alias;
+ }
+
+ /**
+ * @param alias
+ * the alias to set
+ * @see #alias
+ */
+ protected void setAlias(Element alias) {
+ this.alias = alias;
+ }
+
+ /**
+ * @return the oldValue
+ * @see #oldValue
+ */
+ protected Object getOldValue() {
+ return oldValue;
+ }
+
+ /**
+ * @param oldValue
+ * the oldValue to set
+ * @see #oldValue
+ */
+ protected void setOldValue(T oldValue) {
+ this.oldValue = oldValue;
+ }
+
+ /**
+ * @return the newValue
+ * @see #newValue
+ */
+ protected Object getNewValue() {
+ return newValue;
+ }
+
+ /**
+ * @param newValue
+ * the newValue to set
+ * @see #newValue
+ */
+ protected void setNewValue(T newValue) {
+ this.newValue = newValue;
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java
index 4e37d44700..00218400a4 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java
@@ -3,12 +3,12 @@ package lcsb.mapviewer.commands.properties;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.ModelCommand;
import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
- * entry in a property of the {@link Alias Element}
+ * entry in a property of the {@link Element Element}
* that is list.
*
* @param <T>
@@ -30,9 +30,9 @@ public abstract class ChangeElementPropertyListEntryCommand<T> extends ModelComm
private T oldValue;
/**
- * {@link Alias} for which we will change the property.
+ * {@link Element} for which we will change the property.
*/
- private Alias alias;
+ private Element alias;
/**
* Default constructor.
@@ -49,7 +49,7 @@ public abstract class ChangeElementPropertyListEntryCommand<T> extends ModelComm
* @param oldValue
* old value of the element property
*/
- public ChangeElementPropertyListEntryCommand(Model model, Alias alias, T newValue, T oldValue) {
+ public ChangeElementPropertyListEntryCommand(Model model, Element alias, T newValue, T oldValue) {
super(model);
this.alias = alias;
this.oldValue = oldValue;
@@ -78,7 +78,7 @@ public abstract class ChangeElementPropertyListEntryCommand<T> extends ModelComm
* @return the alias
* @see #alias
*/
- protected Alias getAlias() {
+ protected Element getAlias() {
return alias;
}
@@ -87,7 +87,7 @@ public abstract class ChangeElementPropertyListEntryCommand<T> extends ModelComm
* the alias to set
* @see #alias
*/
- protected void setAlias(Alias alias) {
+ protected void setAlias(Element alias) {
this.alias = alias;
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java
index be89028cf0..20fb9cc8df 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java
@@ -1,13 +1,13 @@
package lcsb.mapviewer.commands.properties;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes symbol
- * of the element connected to {@link Alias}.
+ * of the element connected to {@link Element}.
*
* @author Piotr Gawron
*
@@ -28,9 +28,9 @@ public class ChangeElementSymbolCommand extends ChangeElementPropertyCommand<Str
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link Alias#symbol} value
+ * new {@link Element#symbol} value
*/
- public ChangeElementSymbolCommand(Model model, Alias alias, String newName) {
+ public ChangeElementSymbolCommand(Model model, Element alias, String newName) {
super(model, alias, newName);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java
index 4e6d78706b..9f669ca8c4 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java
@@ -3,12 +3,12 @@ package lcsb.mapviewer.commands.properties;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * synonym of the {@link Alias Element}.
+ * synonym of the {@link Element Element}.
*
* @author Piotr Gawron
*
@@ -29,11 +29,11 @@ public class ChangeElementSynonymCommand extends ChangeElementPropertyListEntryC
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newValue
- * new {@link Alias#synonym} value
+ * new {@link Element#synonym} value
* @param oldValue
- * old {@link Alias#synonym} value
+ * old {@link Element#synonym} value
*/
- public ChangeElementSynonymCommand(Model model, Alias alias, String newValue, String oldValue) {
+ public ChangeElementSynonymCommand(Model model, Element alias, String newValue, String oldValue) {
super(model, alias, newValue, oldValue);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java
index ec6fbcd069..9f21a2c821 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java
@@ -5,12 +5,12 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes former
- * symbols from {@link Alias Element}.
+ * symbols from {@link Element Element}.
*
* @author Piotr Gawron
*
@@ -31,9 +31,9 @@ public class RemoveElementFormerSymbolsCommand extends RemoveElementPropertyList
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * {@link Alias#synonym} values to be removed
+ * {@link Element#synonym} values to be removed
*/
- public RemoveElementFormerSymbolsCommand(Model model, Alias alias, List<String> values) {
+ public RemoveElementFormerSymbolsCommand(Model model, Element alias, List<String> values) {
super(model, alias, values);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java
index 6a6a0538f2..d7d6f7f9e7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java
@@ -6,12 +6,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * annotations from {@link Alias Element}.
+ * annotations from {@link Element Element}.
*
* @author Piotr Gawron
*
@@ -32,9 +32,9 @@ public class RemoveElementMiriamDataCommand extends RemoveElementPropertyListEnt
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * {@link Alias#synonym} values to be removed
+ * {@link Element#synonym} values to be removed
*/
- public RemoveElementMiriamDataCommand(Model model, Alias alias, List<MiriamData> values) {
+ public RemoveElementMiriamDataCommand(Model model, Element alias, List<MiriamData> values) {
super(model, alias, values);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java
index 760a01bfd7..9e883c7777 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java
@@ -5,12 +5,12 @@ import java.util.List;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.ModelCommand;
import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * entries from a property of the {@link Alias
+ * entries from a property of the {@link Element
* Element} that is list.
*
* @param <T>
@@ -27,9 +27,9 @@ public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelComm
private List<T> values;
/**
- * {@link Alias} for which we will change the property.
+ * {@link Element} for which we will change the property.
*/
- private Alias alias;
+ private Element alias;
/**
* Default constructor.
@@ -43,7 +43,7 @@ public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelComm
* @param values
* values of the element property to remove
*/
- public RemoveElementPropertyListEntryCommand(Model model, Alias alias, List<T> values) {
+ public RemoveElementPropertyListEntryCommand(Model model, Element alias, List<T> values) {
super(model);
this.alias = alias;
this.values = values;
@@ -59,7 +59,7 @@ public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelComm
* @return the alias
* @see #alias
*/
- protected Alias getAlias() {
+ protected Element getAlias() {
return alias;
}
@@ -68,7 +68,7 @@ public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelComm
* the alias to set
* @see #alias
*/
- protected void setAlias(Alias alias) {
+ protected void setAlias(Element alias) {
this.alias = alias;
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java
index 6849ce3646..fe8a7bbe3d 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java
@@ -5,12 +5,12 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * synonym from {@link Alias Element}.
+ * synonym from {@link Element Element}.
*
* @author Piotr Gawron
*
@@ -31,9 +31,9 @@ public class RemoveElementSynonymsCommand extends RemoveElementPropertyListEntry
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * {@link Alias#synonym} values to be removed
+ * {@link Element#synonym} values to be removed
*/
- public RemoveElementSynonymsCommand(Model model, Alias alias, List<String> values) {
+ public RemoveElementSynonymsCommand(Model model, Element alias, List<String> values) {
super(model, alias, values);
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java
index 3ab919c1fd..4d500fc4a0 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java
@@ -1,8 +1,8 @@
-/**
- * This package contains {@link lcsb.mapviewer.commands.ModelCommand commands}
- * that change properies of {@link java.lang.reflect.AnnotatedElement elements }
- * or {@link lcsb.mapviewer.model.map.layout.alias.Alias aliases}.
- *
- */
-package lcsb.mapviewer.commands.properties;
-
+/**
+ * This package contains {@link lcsb.mapviewer.commands.ModelCommand commands}
+ * that change properies of {@link java.lang.reflect.AnnotatedElement elements }
+ * or {@link lcsb.mapviewer.model.map.species.Element aliases}.
+ *
+ */
+package lcsb.mapviewer.commands.properties;
+
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index 9e42751289..b56126bae3 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -19,14 +19,14 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class ColorModelCommandTest extends CommandTestFunctions {
Logger logger = Logger.getLogger(ColorModelCommandTest.class);
@@ -248,7 +248,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Map<Object, ColorSchema> map = factory.getModifiedElements();
assertEquals(2, map.size());
for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
- assertTrue(entry.getKey() instanceof Alias);
+ assertTrue(entry.getKey() instanceof Element);
}
} catch (Exception e) {
e.printStackTrace();
@@ -313,7 +313,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
colorSchema.setName(null);
colorSchema.setReactionIdentifier("1");
- GenericProteinAlias alias = new GenericProteinAlias("id");
+ GenericProtein alias = new GenericProtein("id");
alias.setName("test");
List<ColorSchema> schemas = new ArrayList<>();
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
index 41c2a99100..685dc44f7c 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -9,10 +9,10 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public abstract class CommandTestFunctions {
public double EPSILON = 1e-6;
@@ -43,7 +43,7 @@ public abstract class CommandTestFunctions {
protected Model createSimpleModel() {
Model model = new ModelFullIndexed(null);
- GenericProteinAlias alias = new GenericProteinAlias("alias_id");
+ GenericProtein alias = new GenericProtein("alias_id");
alias.setNotes(null);
List<String> list = new ArrayList<>();
list.add("synonym");
@@ -52,7 +52,7 @@ public abstract class CommandTestFunctions {
list2.add("f_symbol");
alias.setFormerSymbols(list2);
- ComplexAlias complexAlias = new ComplexAlias("complex_alias_id");
+ Complex complexAlias = new Complex("complex_alias_id");
model.addAlias(complexAlias);
complexAlias.addAlias(alias);
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 5ef2240545..0789519d9c 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -16,9 +16,6 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -27,6 +24,9 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class CopyCommandTest extends CommandTestFunctions {
@@ -58,7 +58,7 @@ public class CopyCommandTest extends CommandTestFunctions {
try {
Model model = new ModelFullIndexed(null);
- GenericProteinAlias protein = new GenericProteinAlias("A");
+ GenericProtein protein = new GenericProtein("A");
protein.setNotes(null);
model.addAlias(protein);
@@ -79,14 +79,14 @@ public class CopyCommandTest extends CommandTestFunctions {
try {
Model model = new ModelFullIndexed(null);
- ComplexAlias complexAlias = new ComplexAlias("id2");
- GenericProteinAlias protein = new GenericProteinAlias("A");
+ Complex complexAlias = new Complex("id2");
+ GenericProtein protein = new GenericProtein("A");
protein.setNotes(null);
complexAlias.addAlias(protein);
model.addAlias(protein);
model.addAlias(complexAlias);
- GenericProteinAlias alias = new GenericProteinAlias("B");
+ GenericProtein alias = new GenericProtein("B");
alias.setNotes(null);
complexAlias.addAlias(alias);
@@ -206,7 +206,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model model3 = getModel();
model3.setNotes("ASDSA");
model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
- Alias alias = model2.getAliasByAliasId("a_id");
+ Element alias = model2.getAliasByAliasId("a_id");
alias.setSubmodel(new AliasSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
Model copy = new CopyCommand(model2).execute();
@@ -279,7 +279,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model model = new ModelFullIndexed(null);
model.setNotes("Some description");
- GenericProteinAlias alias = new GenericProteinAlias("a_id");
+ GenericProtein alias = new GenericProtein("a_id");
alias.setName("ad");
model.addAlias(alias);
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index a1d503c6ec..f6f07bd0f3 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -20,11 +20,11 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
public class CreateHierarchyCommandTest extends CommandTestFunctions {
Logger logger = Logger.getLogger(CreateHierarchyCommandTest.class);
@@ -44,17 +44,17 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, 8, 80).execute();
- Alias alias = model.getAliasByAliasId("sa5033");
+ Element alias = model.getAliasByAliasId("sa5033");
- Set<Alias> parents = new HashSet<Alias>();
- while (alias.getParent() instanceof ComplexAlias) {
+ Set<Element> parents = new HashSet<Element>();
+ while (alias.getParent() instanceof Complex) {
assertFalse("Cyclic nesting", parents.contains(alias.getParent()));
alias = alias.getParent();
parents.add(alias);
}
Set<Integer> levels = new HashSet<Integer>();
- for (Alias a : model.getAliases()) {
+ for (Element a : model.getAliases()) {
levels.add(a.getVisibilityLevel());
}
assertTrue(levels.size() > 2);
@@ -88,8 +88,8 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, 2, 2).execute();
boolean artifitial = false;
- for (CompartmentAlias a : model.getCompartmentsAliases()) {
- if (a instanceof ArtifitialCompartmentAlias) {
+ for (Compartment a : model.getCompartmentsAliases()) {
+ if (a instanceof PathwayCompartment) {
artifitial = true;
}
}
@@ -134,7 +134,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, levels, zoomFactor).execute();
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
if (alias.getParent() == null) {
assertTrue("Alias " + alias.getAliasId() + " is not visible at levels highers than " + alias.getVisibilityLevel(), alias.getVisibilityLevel() <= 1);
}
@@ -156,7 +156,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, levels, zoomFactor).execute();
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
assertTrue(
"Alias " + alias.getAliasId() + " is not visible even at the bottom level (visibility: " + alias.getVisibilityLevel() + ") ",
alias.getVisibilityLevel() <= levels);
@@ -173,7 +173,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
Model model;
try {
model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
- Alias alias = model.getAliasByAliasId("sa1");
+ Element alias = model.getAliasByAliasId("sa1");
Object parent1 = alias.getParent();
new CreateHierarchyCommand(model, 3, 16).execute();
Object parent2 = alias.getParent();
@@ -210,13 +210,13 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
command.clean();
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
assertNull(alias.getParent());
- if (alias instanceof ComplexAlias) {
- assertTrue(((ComplexAlias) alias).getAliases().isEmpty());
+ if (alias instanceof Complex) {
+ assertTrue(((Complex) alias).getAliases().isEmpty());
}
}
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
assertNull(alias.getParent());
assertTrue(alias.getAliases().isEmpty());
}
@@ -239,8 +239,8 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
command.execute();
- for (Alias alias : model.getAliases()) {
- Alias parentAlias = alias.getParent();
+ for (Element alias : model.getAliases()) {
+ Element parentAlias = alias.getParent();
if (parentAlias != null) {
assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
index 6f3ff0ec3e..51eeefd2e5 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
@@ -16,10 +16,10 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
public class MoveElementsCommandTest extends CommandTestFunctions {
@@ -38,8 +38,8 @@ public class MoveElementsCommandTest extends CommandTestFunctions {
try {
Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Alias alias = model.getAliasByAliasId("sa2");
- Alias alias2 = model.getAliasByAliasId("sa1");
+ Element alias = model.getAliasByAliasId("sa2");
+ Element alias2 = model.getAliasByAliasId("sa1");
double anotherAliasX = alias2.getX();
double anotherAliasY = alias2.getY();
@@ -106,8 +106,8 @@ public class MoveElementsCommandTest extends CommandTestFunctions {
try {
Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Alias alias = model.getAliasByAliasId("sa1");
- Alias alias2 = model.getAliasByAliasId("sa2");
+ Element alias = model.getAliasByAliasId("sa1");
+ Element alias2 = model.getAliasByAliasId("sa2");
double anotherAliasX = alias2.getX();
double anotherAliasY = alias2.getY();
Reaction reaction = model.getReactionByReactionId("re1");
@@ -155,7 +155,7 @@ public class MoveElementsCommandTest extends CommandTestFunctions {
public void testMoveReaction() throws Exception {
try {
Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Alias alias2 = model.getAliasByAliasId("sa1");
+ Element alias2 = model.getAliasByAliasId("sa1");
double anotherAliasX = alias2.getX();
double anotherAliasY = alias2.getY();
Reaction reaction = model.getReactionByReactionId("re1");
@@ -196,7 +196,7 @@ public class MoveElementsCommandTest extends CommandTestFunctions {
try {
Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Alias alias = model.getAliasByAliasId("sa2");
+ Element alias = model.getAliasByAliasId("sa2");
List<Object> list = new ArrayList<>();
list.add(alias);
@@ -234,7 +234,7 @@ public class MoveElementsCommandTest extends CommandTestFunctions {
public void testGetAffectedRegion() throws Exception {
try {
Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Alias alias = model.getAliasByAliasId("sa2");
+ Element alias = model.getAliasByAliasId("sa2");
List<Object> list = new ArrayList<>();
list.add(alias);
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java
index 45b4cea777..e5c9676f36 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java
@@ -2,9 +2,9 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -28,7 +28,7 @@ public class ChangeElementAbbreviationCommandTest extends CommandTestFunctions{
@Test
public void testChangeAliasAbbreviation() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementAbbreviationCommand command = new ChangeElementAbbreviationCommand(model, alias, "test");
assertFalse("test".equalsIgnoreCase(alias.getAbbreviation()));
command.execute();
@@ -44,7 +44,7 @@ public class ChangeElementAbbreviationCommandTest extends CommandTestFunctions{
public void testUndo() throws Exception {
try {
Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
// models should be equal before move
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
index a11bc6a187..421f6c5964 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
@@ -1,78 +1,78 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-
-import java.awt.Color;
-
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementColorCommandTest extends CommandTestFunctions {
-
- Model model;
-
- ModelComparator modelComparator = new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasColor() throws Exception {
- try {
- Alias alias = model.getAliasByAliasId("alias_id");
- ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
- assertFalse(alias.getColor().equals(Color.PINK));
- command.execute();
- assertTrue(alias.getColor().equals(Color.PINK));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementColorCommandTest extends CommandTestFunctions {
+
+ Model model;
+
+ ModelComparator modelComparator = new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasColor() throws Exception {
+ try {
+ Element alias = model.getAliasByAliasId("alias_id");
+ ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
+ assertFalse(alias.getColor().equals(Color.PINK));
+ command.execute();
+ assertTrue(alias.getColor().equals(Color.PINK));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getAliasByAliasId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java
index 1f62417e3a..df14ff8a59 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementFontSizeCommandTest extends CommandTestFunctions{
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasFontSize() throws Exception {
- try {
- Alias alias = model.getAliasByAliasId("alias_id");
- ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
- assertFalse(alias.getFontSize().equals(15.0));
- command.execute();
- assertTrue(alias.getFontSize().equals(15.0));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementFontSizeCommandTest extends CommandTestFunctions{
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasFontSize() throws Exception {
+ try {
+ Element alias = model.getAliasByAliasId("alias_id");
+ ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
+ assertFalse(alias.getFontSize().equals(15.0));
+ command.execute();
+ assertTrue(alias.getFontSize().equals(15.0));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getAliasByAliasId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java
index 56f698e93c..73272e8c96 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java
@@ -2,9 +2,9 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -29,7 +29,7 @@ public class ChangeElementFormerSymbolCommandTest extends CommandTestFunctions {
@Test
public void testChangeToTheSame() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementFormerSymbolCommand command = new ChangeElementFormerSymbolCommand(model, alias, "f_symbol","f_symbol");
assertTrue(alias.getFormerSymbols().contains("f_symbol"));
command.execute();
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java
index 7051cdfe96..165351ea16 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java
@@ -2,9 +2,9 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -28,7 +28,7 @@ public class ChangeElementFormulaCommandTest extends CommandTestFunctions{
@Test
public void testChangeAliasFormula() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementFormulaCommand command = new ChangeElementFormulaCommand(model, alias, "test");
assertFalse("test".equals(alias.getFormula()));
command.execute();
@@ -44,7 +44,7 @@ public class ChangeElementFormulaCommandTest extends CommandTestFunctions{
public void testUndo() throws Exception {
try {
Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
// models should be equal before move
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java
index 1108ebd2b1..1f87e26d86 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java
@@ -2,9 +2,9 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -28,7 +28,7 @@ public class ChangeElementFullNameCommandTest extends CommandTestFunctions{
@Test
public void testChangeAliasFullName() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementFullNameCommand command = new ChangeElementFullNameCommand(model, alias, "test");
assertFalse("test".equals(alias.getFullName()));
command.execute();
@@ -44,7 +44,7 @@ public class ChangeElementFullNameCommandTest extends CommandTestFunctions{
public void testUndo() throws Exception {
try {
Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
// models should be equal before move
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java
index b9586e8418..89a69905b9 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java
@@ -5,8 +5,8 @@ import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.CommandTestFunctions;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -28,7 +28,7 @@ public class ChangeElementMiriamDataCommandTest extends CommandTestFunctions {
@Test
public void testWithoutChange() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
alias.addMiriamData(md);
@@ -46,7 +46,7 @@ public class ChangeElementMiriamDataCommandTest extends CommandTestFunctions {
@Test
public void testInvalidChange() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA2");
alias.addMiriamData(md);
@@ -69,7 +69,7 @@ public class ChangeElementMiriamDataCommandTest extends CommandTestFunctions {
@Test
public void testChange() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA2");
MiriamData md3 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java
index 53e28c6ba8..4f1512b344 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java
@@ -4,9 +4,9 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -30,7 +30,7 @@ public class ChangeElementNameCommandTest extends CommandTestFunctions {
@Test
public void testChangeAliasName() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementNameCommand command = new ChangeElementNameCommand(model, alias, "test");
assertFalse(alias.getName().equalsIgnoreCase("test"));
command.execute();
@@ -46,7 +46,7 @@ public class ChangeElementNameCommandTest extends CommandTestFunctions {
public void testUndo() throws Exception {
try {
Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
// models should be equal before move
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java
index d4e8a3005d..1dc3eb230d 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java
@@ -2,9 +2,9 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -28,7 +28,7 @@ public class ChangeElementNotesCommandTest extends CommandTestFunctions{
@Test
public void testChangeAliasNotes() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementNotesCommand command = new ChangeElementNotesCommand(model, alias, "test");
assertFalse("test".equals(alias.getNotes()));
command.execute();
@@ -44,7 +44,7 @@ public class ChangeElementNotesCommandTest extends CommandTestFunctions{
public void testUndo() throws Exception {
try {
Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
// models should be equal before move
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java
index 369eed4129..cae8426700 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java
@@ -2,9 +2,9 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -28,7 +28,7 @@ public class ChangeElementSymbolCommandTest extends CommandTestFunctions{
@Test
public void testChangeAliasSymbol() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementSymbolCommand command = new ChangeElementSymbolCommand(model, alias, "test");
assertFalse("test".equals(alias.getSymbol()));
command.execute();
@@ -44,7 +44,7 @@ public class ChangeElementSymbolCommandTest extends CommandTestFunctions{
public void testUndo() throws Exception {
try {
Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
// models should be equal before move
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java
index 679fe1dc47..90c858494a 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java
@@ -2,9 +2,9 @@ package lcsb.mapviewer.commands.properties;
import static org.junit.Assert.*;
import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
import org.junit.After;
import org.junit.Before;
@@ -28,7 +28,7 @@ public class ChangeElementSynonymCommandTest extends CommandTestFunctions {
@Test
public void testChangeAliasSynonym() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "test","synonym");
assertFalse(alias.getSynonyms().contains("test"));
command.execute();
@@ -43,7 +43,7 @@ public class ChangeElementSynonymCommandTest extends CommandTestFunctions {
@Test
public void testChangeToTheSame() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "synonym","synonym");
assertTrue(alias.getSynonyms().contains("synonym"));
command.execute();
@@ -59,7 +59,7 @@ public class ChangeElementSynonymCommandTest extends CommandTestFunctions {
public void testUndo() throws Exception {
try {
Model model2 = createSimpleModel();
- Alias alias = model.getAliasByAliasId("alias_id");
+ Element alias = model.getAliasByAliasId("alias_id");
// models should be equal before move
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 875ba57f53..7b65e7e495 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -4,15 +4,15 @@ import java.util.ArrayList;
import java.util.List;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
/**
* Type of known miriam annotation.
@@ -44,8 +44,8 @@ public enum MiriamType {
CHEBI("Chebi", //
"http://www.ebi.ac.uk/chebi/", //
new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
- new Class<?>[] { ChemicalAlias.class, DrugAlias.class, }, "MIR:00000002", //
- new Class<?>[] { ChemicalAlias.class }), //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
+ new Class<?>[] { Chemical.class }), //
/**
* ChemSpider database:
@@ -62,7 +62,7 @@ public enum MiriamType {
CHEMBL_COMPOUND("ChEMBL", //
"https://www.ebi.ac.uk/chembldb/", //
new String[] { "urn:miriam:chembl.compound" }, //
- new Class<?>[] { DrugAlias.class }, "MIR:00000084"), //
+ new Class<?>[] { Drug.class }, "MIR:00000084"), //
/**
* Target in chembl database: https://www.ebi.ac.uk/chembldb/.
@@ -70,7 +70,7 @@ public enum MiriamType {
CHEMBL_TARGET("ChEMBL target", //
"https://www.ebi.ac.uk/chembldb/", //
new String[] { "urn:miriam:chembl.target" }, //
- new Class<?>[] { ProteinAlias.class, ComplexAlias.class }, "MIR:00000085"), //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
/**
* Drugbank database: http://www.drugbank.ca/.
@@ -78,7 +78,7 @@ public enum MiriamType {
DRUGBANK("DrugBank", //
"http://www.drugbank.ca/", //
new String[] { "urn:miriam:drugbank" }, //
- new Class<?>[] { DrugAlias.class }, "MIR:00000102"), //
+ new Class<?>[] { Drug.class }, "MIR:00000102"), //
/**
* Drugbank tagrets: http://www.drugbank.ca/targets.
*/
@@ -93,7 +93,7 @@ public enum MiriamType {
EC("Enzyme Nomenclature", //
"http://www.enzyme-database.org/", //
new String[] { "urn:miriam:ec-code" }, //
- new Class<?>[] { ProteinAlias.class, ComplexAlias.class }, "MIR:00000004"), //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
/**
* Ensembl: www.ensembl.org.
@@ -101,7 +101,7 @@ public enum MiriamType {
ENSEMBL("Ensembl", //
"www.ensembl.org", //
new String[] { "urn:miriam:ensembl" }, //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000003"), //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
/**
* Ensembl Plants: http://plants.ensembl.org/.
@@ -117,7 +117,7 @@ public enum MiriamType {
ENTREZ("Entrez Gene", //
"http://www.ncbi.nlm.nih.gov/gene", //
new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" }, //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000069"), //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"), //
/**
* Gene Ontology: http://amigo.geneontology.org/amigo.
@@ -125,7 +125,7 @@ public enum MiriamType {
GO("Gene Ontology", //
"http://amigo.geneontology.org/amigo", //
new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
- new Class<?>[] { PhenotypeAlias.class, CompartmentAlias.class, ComplexAlias.class }, "MIR:00000022"), //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
/**
* HGNC: http://www.genenames.org.
@@ -133,8 +133,8 @@ public enum MiriamType {
HGNC("HGNC", //
"http://www.genenames.org", //
new String[] { "urn:miriam:hgnc" }, //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000080", //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }), //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
/**
* HGNC symbol: http://www.genenames.org.
@@ -142,8 +142,8 @@ public enum MiriamType {
HGNC_SYMBOL("HGNC Symbol", //
"http://www.genenames.org", //
new String[] { "urn:miriam:hgnc.symbol" }, //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000362", //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }), //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
/**
* HMDB: http://www.hmdb.ca/.
@@ -151,7 +151,7 @@ public enum MiriamType {
HMDB("HMDB", //
"http://www.hmdb.ca/", //
"urn:miriam:hmdb", //
- new Class<?>[] { ChemicalAlias.class, DrugAlias.class, }, "MIR:00000051"), //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
/**
* InterPro: http://www.ebi.ac.uk/interpro/.
@@ -159,7 +159,7 @@ public enum MiriamType {
INTERPRO("InterPro", //
"http://www.ebi.ac.uk/interpro/", //
new String[] { "urn:miriam:interpro" }, //
- new Class<?>[] { ProteinAlias.class, ComplexAlias.class }, "MIR:00000011"), //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
/**
* KEGG Compound: http://www.genome.jp/kegg/ligand.html.
@@ -167,7 +167,7 @@ public enum MiriamType {
KEGG_COMPOUND("Kegg Compound", //
"http://www.genome.jp/kegg/ligand.html", //
"urn:miriam:kegg.compound", //
- new Class<?>[] { ChemicalAlias.class }, "MIR:00000013"), //
+ new Class<?>[] { Chemical.class }, "MIR:00000013"), //
/**
* KEGG Genes: http://www.genome.jp/kegg/genes.html.
@@ -175,7 +175,7 @@ public enum MiriamType {
KEGG_GENES("Kegg Genes", //
"http://www.genome.jp/kegg/genes.html", //
new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" }, //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000070"), //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
/**
* KEGG Orthology: http://www.genome.jp/kegg/ko.html.
@@ -207,7 +207,7 @@ public enum MiriamType {
MESH_2012("MeSH 2012", //
"http://www.nlm.nih.gov/mesh/", //
new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
- new Class<?>[] { PhenotypeAlias.class, CompartmentAlias.class, ComplexAlias.class }, "MIR:00000270"), //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
/**
* miRBase Sequence: http://www.mirbase.org/.
@@ -239,7 +239,7 @@ public enum MiriamType {
MGD("Mouse Genome Database", //
"http://www.informatics.jax.org/", //
new String[] { "urn:miriam:mgd" }, //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000037"), //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
/**
* Online Mendelian Inheritance in Man: http://omim.org/.
@@ -247,7 +247,7 @@ public enum MiriamType {
OMIM("Online Mendelian Inheritance in Man", //
"http://omim.org/", //
new String[] { "urn:miriam:omim" }, //
- new Class<?>[] { PhenotypeAlias.class }, "MIR:00000016"), //
+ new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
/**
* PANTHER Family: http://www.pantherdb.org/.
@@ -255,7 +255,7 @@ public enum MiriamType {
PANTHER("PANTHER Family", //
"http://www.pantherdb.org/", //
new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000060"), //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
/**
* Protein Family Database: http://pfam.xfam.org/.
@@ -279,8 +279,8 @@ public enum MiriamType {
PUBCHEM("PubChem-compound", //
"http://pubchem.ncbi.nlm.nih.gov/", //
new String[] { "urn:miriam:pubchem.compound" }, //
- new Class<?>[] { ChemicalAlias.class }, "MIR:00000034", //
- new Class<?>[] { ChemicalAlias.class }), //
+ new Class<?>[] { Chemical.class }, "MIR:00000034", //
+ new Class<?>[] { Chemical.class }), //
/**
* PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
@@ -288,8 +288,8 @@ public enum MiriamType {
PUBCHEM_SUBSTANCE("PubChem-substance", //
"http://pubchem.ncbi.nlm.nih.gov/", //
new String[] { "urn:miriam:pubchem.substance" }, //
- new Class<?>[] { ChemicalAlias.class }, "MIR:00000033", //
- new Class<?>[] { ChemicalAlias.class }), //
+ new Class<?>[] { Chemical.class }, "MIR:00000033", //
+ new Class<?>[] { Chemical.class }), //
/**
* PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
@@ -314,7 +314,7 @@ public enum MiriamType {
REFSEQ("RefSeq", //
"http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
"urn:miriam:refseq", //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000039"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
/**
* SGD: http://www.yeastgenome.org/.
@@ -365,7 +365,7 @@ public enum MiriamType {
UNIPROT("Uniprot", //
"http://www.uniprot.org/", //
"urn:miriam:uniprot", //
- new Class<?>[] { ProteinAlias.class, GeneAlias.class, RnaAlias.class }, "MIR:00000005"),
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
/**
* UniProt Isoform: http://www.uniprot.org/.
@@ -373,7 +373,7 @@ public enum MiriamType {
UNIPROT_ISOFORM("UniProt Isoform", //
"http://www.uniprot.org/", //
"urn:miriam:uniprot.isoform", //
- new Class<?>[] { ProteinAlias.class }, "MIR:00000388"),
+ new Class<?>[] { Protein.class }, "MIR:00000388"),
/**
* Unknown reference type...
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SearchIndex.java b/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
similarity index 88%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SearchIndex.java
rename to model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
index be0bb52b10..584885c4f3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SearchIndex.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map;
import java.io.Serializable;
@@ -13,6 +13,7 @@ import javax.persistence.Table;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This class defines single search index for the element. Every element can
@@ -35,7 +36,7 @@ public class SearchIndex implements Serializable {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Alias.class);
+ private static Logger logger = Logger.getLogger(Element.class);
/**
* Database identifier.
@@ -49,7 +50,7 @@ public class SearchIndex implements Serializable {
* Element to which index is assigned.
*/
@ManyToOne
- private Alias source;
+ private Element source;
/**
* Data of the index.
@@ -137,7 +138,7 @@ public class SearchIndex implements Serializable {
* @return the source
* @see #source
*/
- public Alias getSource() {
+ public Element getSource() {
return source;
}
@@ -146,7 +147,7 @@ public class SearchIndex implements Serializable {
* the source to set
* @see #source
*/
- public void setSource(Alias source) {
+ public void setSource(Element source) {
this.source = source;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/BottomSquareCompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/BottomSquareCompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
index 1632028116..581dc4f308 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/BottomSquareCompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -15,7 +15,7 @@ import lcsb.mapviewer.model.map.model.Model;
*/
@Entity
@DiscriminatorValue("Bottom square Compartment Alias")
-public class BottomSquareCompartmentAlias extends CompartmentAlias {
+public class BottomSquareCompartment extends Compartment {
/**
*
@@ -31,7 +31,7 @@ public class BottomSquareCompartmentAlias extends CompartmentAlias {
* @param model
* model object to which the alias will be assigned
*/
- public BottomSquareCompartmentAlias(CompartmentAlias originalAlias, Model model) {
+ public BottomSquareCompartment(Compartment originalAlias, Model model) {
super(originalAlias);
setX(0.0);
setWidth(model.getWidth() * 2);
@@ -46,21 +46,21 @@ public class BottomSquareCompartmentAlias extends CompartmentAlias {
* @param originalAlias
* orignal alias where the data was kept
*/
- public BottomSquareCompartmentAlias(CompartmentAlias originalAlias) {
+ public BottomSquareCompartment(Compartment originalAlias) {
super(originalAlias);
}
/**
* Default constructor.
*/
- public BottomSquareCompartmentAlias() {
+ public BottomSquareCompartment() {
super();
}
@Override
- public BottomSquareCompartmentAlias copy() {
- if (this.getClass() == BottomSquareCompartmentAlias.class) {
- return new BottomSquareCompartmentAlias(this);
+ public BottomSquareCompartment copy() {
+ if (this.getClass() == BottomSquareCompartment.class) {
+ return new BottomSquareCompartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
similarity index 83%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
index 209ed260ac..019d17705b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import java.awt.Color;
import java.awt.geom.Point2D;
@@ -18,6 +18,9 @@ import org.hibernate.annotations.Type;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines alias for compartment in the model.
@@ -27,7 +30,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*/
@Entity
@DiscriminatorValue("Compartment Alias")
-public class CompartmentAlias extends Alias {
+public class Compartment extends Element {
/**
*
*/
@@ -56,7 +59,7 @@ public class CompartmentAlias extends Alias {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(CompartmentAlias.class.getName());
+ private static Logger logger = Logger.getLogger(Compartment.class.getName());
/**
* Thickness of the compartment border.
@@ -83,7 +86,7 @@ public class CompartmentAlias extends Alias {
*/
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.EAGER, mappedBy = "compartmentAlias")
- private Set<Alias> aliases = new HashSet<>();
+ private Set<Element> aliases = new HashSet<>();
/**
* Constructor that creates an alias which is initialized by the data from the
@@ -92,13 +95,13 @@ public class CompartmentAlias extends Alias {
* @param original
* object from which this object is initialized
*/
- public CompartmentAlias(CompartmentAlias original) {
+ public Compartment(Compartment original) {
super(original);
namePoint.setLocation(original.getNamePoint());
thickness = original.thickness;
outerWidth = original.outerWidth;
innerWidth = original.innerWidth;
- for (Alias alias : original.aliases) {
+ for (Element alias : original.aliases) {
addAlias(alias.copy());
}
}
@@ -106,7 +109,7 @@ public class CompartmentAlias extends Alias {
/**
* Default constructor.
*/
- CompartmentAlias() {
+ Compartment() {
super();
namePoint = new Point2D.Double(0, 0);
thickness = DEFAULT_COMPARTMENT_THICKNESS;
@@ -115,7 +118,7 @@ public class CompartmentAlias extends Alias {
setColor(DEFAULT_COLOR);
}
- public CompartmentAlias(String aliasId) {
+ public Compartment(String aliasId) {
setAliasId(aliasId);
}
@@ -165,8 +168,8 @@ public class CompartmentAlias extends Alias {
* @param aliasToAdd
* alias that should be added
*/
- public void addAlias(Alias aliasToAdd) {
- for (Alias alias : aliases) {
+ public void addAlias(Element aliasToAdd) {
+ for (Element alias : aliases) {
if (alias.getAliasId().equals(aliasToAdd.getAliasId())) {
if (alias.equals(aliasToAdd)) {
return;
@@ -185,12 +188,12 @@ public class CompartmentAlias extends Alias {
*
* @return list of all aliases in the compartment alias
*/
- public Set<Alias> getAllSubAliases() {
- Set<Alias> result = new HashSet<Alias>();
+ public Set<Element> getAllSubAliases() {
+ Set<Element> result = new HashSet<Element>();
result.addAll(getAliases());
- for (Alias abstractAlias : getAliases()) {
- if (abstractAlias instanceof CompartmentAlias) {
- result.addAll(((CompartmentAlias) abstractAlias).getAllSubAliases());
+ for (Element abstractAlias : getAliases()) {
+ if (abstractAlias instanceof Compartment) {
+ result.addAll(((Compartment) abstractAlias).getAllSubAliases());
}
}
@@ -207,11 +210,11 @@ public class CompartmentAlias extends Alias {
* @return true if the alias2 cross this compartment alias, <code>false</code>
* otherwise
*/
- public boolean cross(Alias alias2) {
- Set<Alias> parents = new HashSet<Alias>();
+ public boolean cross(Element alias2) {
+ Set<Element> parents = new HashSet<Element>();
// in case of elements in complexes we have to check if the top level
// complex cross alias
- while (alias2.getParent() != null && alias2.getParent() instanceof ComplexAlias) {
+ while (alias2.getParent() != null && alias2.getParent() instanceof Complex) {
alias2 = alias2.getParent();
if (parents.contains(alias2)) {
throw new InvalidStateException("Cycled nesting in complex parents: " + alias2.getName());
@@ -239,8 +242,8 @@ public class CompartmentAlias extends Alias {
* compartment, <code>false</code> otherwise
*/
public boolean containsIdenticalSpecies() {
- for (Alias innerAlias : aliases) {
- if (innerAlias instanceof SpeciesAlias) {
+ for (Element innerAlias : aliases) {
+ if (innerAlias instanceof Species) {
String name = innerAlias.getName();
if (name.equalsIgnoreCase(getName())) {
return true;
@@ -255,9 +258,9 @@ public class CompartmentAlias extends Alias {
*
* @return copy of the object
*/
- public CompartmentAlias copy() {
- if (this.getClass() == CompartmentAlias.class) {
- return new CompartmentAlias(this);
+ public Compartment copy() {
+ if (this.getClass() == Compartment.class) {
+ return new Compartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -269,7 +272,7 @@ public class CompartmentAlias extends Alias {
* @param alias
* object to be removed
*/
- public void removeAlias(Alias alias) {
+ public void removeAlias(Element alias) {
aliases.remove(alias);
if (alias.getCompartmentAlias() != null) {
if (alias.getCompartmentAlias() == this) {
@@ -296,7 +299,7 @@ public class CompartmentAlias extends Alias {
* @param aliases
* the aliases to set
*/
- public void setAliases(Set<Alias> aliases) {
+ public void setAliases(Set<Element> aliases) {
this.aliases = aliases;
}
@@ -372,7 +375,7 @@ public class CompartmentAlias extends Alias {
* @return the aliases
* @see #aliases
*/
- public Set<Alias> getAliases() {
+ public Set<Element> getAliases() {
return aliases;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
similarity index 78%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
index fc7b054678..2a1769a671 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import java.util.Comparator;
import java.util.HashMap;
@@ -11,20 +11,22 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.PointComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
/**
* This class implements comparator interface for CompartmentAlias.
*
* @author Piotr Gawron
*
- * @see CompartmentAlias
+ * @see Compartment
*
*/
-public class CompartmentAliasComparator implements Comparator<CompartmentAlias> {
+public class CompartmentComparator implements Comparator<Compartment> {
/**
* Default class logger.
*/
- private Logger logger = Logger.getLogger(CompartmentAliasComparator.class);
+ private Logger logger = Logger.getLogger(CompartmentComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -37,19 +39,19 @@ public class CompartmentAliasComparator implements Comparator<CompartmentAlias>
* @param epsilon
* {@link #epsilon}
*/
- public CompartmentAliasComparator(double epsilon) {
+ public CompartmentComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public CompartmentAliasComparator() {
+ public CompartmentComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(CompartmentAlias arg0, CompartmentAlias arg1) {
+ public int compare(Compartment arg0, Compartment arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -78,8 +80,8 @@ public class CompartmentAliasComparator implements Comparator<CompartmentAlias>
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(CompartmentAlias arg0, CompartmentAlias arg1) {
- AliasComparator aliasComparator = new AliasComparator(epsilon);
+ private int internalCompare(Compartment arg0, Compartment arg1) {
+ ElementComparator aliasComparator = new ElementComparator(epsilon);
int result = aliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
@@ -114,25 +116,25 @@ public class CompartmentAliasComparator implements Comparator<CompartmentAlias>
return integerComparator.compare(arg0.getAliases().size(), arg1.getAliases().size());
}
- Map<String, Alias> map1 = new HashMap<>();
- Map<String, Alias> map2 = new HashMap<>();
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
- for (Alias alias : arg0.getAliases()) {
+ for (Element alias : arg0.getAliases()) {
if (map1.get(alias.getAliasId()) != null) {
throw new InvalidArgumentException("Few aliases with the same id: " + alias.getAliasId());
}
map1.put(alias.getAliasId(), alias);
}
- for (Alias alias : arg1.getAliases()) {
+ for (Element alias : arg1.getAliases()) {
if (map2.get(alias.getAliasId()) != null) {
throw new InvalidArgumentException("Few aliases with the same id: " + alias.getAliasId());
}
map2.put(alias.getAliasId(), alias);
}
- for (Alias alias : arg0.getAliases()) {
- Alias alias2 = map2.get(alias.getAliasId());
+ for (Element alias : arg0.getAliases()) {
+ Element alias2 = map2.get(alias.getAliasId());
int status = aliasComparator.compare(alias, alias2);
if (status != 0) {
logger.debug("Couldn't match alias: " + alias.getAliasId() + ", " + alias2);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/LeftSquareCompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/LeftSquareCompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
index 9a912253a3..8df301320b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/LeftSquareCompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -16,7 +16,7 @@ import lcsb.mapviewer.model.map.model.Model;
*/
@Entity
@DiscriminatorValue("Left square Compartment Alias")
-public class LeftSquareCompartmentAlias extends CompartmentAlias {
+public class LeftSquareCompartment extends Compartment {
/**
*
@@ -26,7 +26,7 @@ public class LeftSquareCompartmentAlias extends CompartmentAlias {
/**
* Default constructor.
*/
- public LeftSquareCompartmentAlias() {
+ public LeftSquareCompartment() {
super();
}
@@ -40,7 +40,7 @@ public class LeftSquareCompartmentAlias extends CompartmentAlias {
* model object to which the alias will be assigned
*/
- public LeftSquareCompartmentAlias(CompartmentAlias originalAlias, Model model) {
+ public LeftSquareCompartment(Compartment originalAlias, Model model) {
super(originalAlias);
setX(0.0);
setWidth(model.getWidth() * 2);
@@ -55,14 +55,14 @@ public class LeftSquareCompartmentAlias extends CompartmentAlias {
* @param originalAlias
* orignal alias where the data was kept
*/
- public LeftSquareCompartmentAlias(LeftSquareCompartmentAlias originalAlias) {
+ public LeftSquareCompartment(LeftSquareCompartment originalAlias) {
super(originalAlias);
}
@Override
- public LeftSquareCompartmentAlias copy() {
- if (this.getClass() == LeftSquareCompartmentAlias.class) {
- return new LeftSquareCompartmentAlias(this);
+ public LeftSquareCompartment copy() {
+ if (this.getClass() == LeftSquareCompartment.class) {
+ return new LeftSquareCompartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/OvalCompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
similarity index 67%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/OvalCompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
index 4325ceb5fe..23194155a7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/OvalCompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -13,7 +13,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*/
@Entity
@DiscriminatorValue("Oval Compartment Alias")
-public class OvalCompartmentAlias extends CompartmentAlias {
+public class OvalCompartment extends Compartment {
/**
*
@@ -23,7 +23,7 @@ public class OvalCompartmentAlias extends CompartmentAlias {
/**
* Default constructor.
*/
- public OvalCompartmentAlias() {
+ public OvalCompartment() {
super();
}
@@ -34,14 +34,14 @@ public class OvalCompartmentAlias extends CompartmentAlias {
* @param originalAlias
* orignal alias where the data was kept
*/
- public OvalCompartmentAlias(CompartmentAlias originalAlias) {
+ public OvalCompartment(Compartment originalAlias) {
super(originalAlias);
}
@Override
- public OvalCompartmentAlias copy() {
- if (this.getClass() == OvalCompartmentAlias.class) {
- return new OvalCompartmentAlias(this);
+ public OvalCompartment copy() {
+ if (this.getClass() == OvalCompartment.class) {
+ return new OvalCompartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ArtifitialCompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
similarity index 61%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ArtifitialCompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
index 35860cf34a..eec7511320 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ArtifitialCompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -13,7 +13,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*/
@Entity
@DiscriminatorValue("Artifitial Compartment Alias")
-public class ArtifitialCompartmentAlias extends CompartmentAlias {
+public class PathwayCompartment extends Compartment {
/**
*
@@ -23,11 +23,11 @@ public class ArtifitialCompartmentAlias extends CompartmentAlias {
/**
* Default constructor.
*/
- public ArtifitialCompartmentAlias() {
+ public PathwayCompartment() {
super();
}
- public ArtifitialCompartmentAlias(String aliasId) {
+ public PathwayCompartment(String aliasId) {
super();
setAliasId(aliasId);
}
@@ -38,14 +38,14 @@ public class ArtifitialCompartmentAlias extends CompartmentAlias {
* @param original
* data for initialization
*/
- public ArtifitialCompartmentAlias(ArtifitialCompartmentAlias original) {
+ public PathwayCompartment(PathwayCompartment original) {
super(original);
}
@Override
- public ArtifitialCompartmentAlias copy() {
- if (this.getClass() == ArtifitialCompartmentAlias.class) {
- return new ArtifitialCompartmentAlias(this);
+ public PathwayCompartment copy() {
+ if (this.getClass() == PathwayCompartment.class) {
+ return new PathwayCompartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RightSquareCompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
similarity index 75%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RightSquareCompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
index 5a8fb6b29f..8dd6a3f653 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RightSquareCompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -17,7 +17,7 @@ import lcsb.mapviewer.model.map.model.Model;
*/
@Entity
@DiscriminatorValue("Right square Compartment Alias")
-public class RightSquareCompartmentAlias extends CompartmentAlias {
+public class RightSquareCompartment extends Compartment {
/**
*
*/
@@ -27,12 +27,12 @@ public class RightSquareCompartmentAlias extends CompartmentAlias {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RightSquareCompartmentAlias.class);
+ private static Logger logger = Logger.getLogger(RightSquareCompartment.class);
/**
* Default constructor.
*/
- public RightSquareCompartmentAlias() {
+ public RightSquareCompartment() {
super();
}
@@ -45,7 +45,7 @@ public class RightSquareCompartmentAlias extends CompartmentAlias {
* @param model
* model object to which the alias will be assigned
*/
- public RightSquareCompartmentAlias(CompartmentAlias originalAlias, Model model) {
+ public RightSquareCompartment(Compartment originalAlias, Model model) {
super(originalAlias);
setX(0.0);
setWidth(model.getWidth() * 2);
@@ -76,14 +76,14 @@ public class RightSquareCompartmentAlias extends CompartmentAlias {
* @param originalAlias
* orignal alias where the data was kept
*/
- public RightSquareCompartmentAlias(RightSquareCompartmentAlias originalAlias) {
+ public RightSquareCompartment(RightSquareCompartment originalAlias) {
super(originalAlias);
}
@Override
- public RightSquareCompartmentAlias copy() {
- if (this.getClass() == RightSquareCompartmentAlias.class) {
- return new RightSquareCompartmentAlias(this);
+ public RightSquareCompartment copy() {
+ if (this.getClass() == RightSquareCompartment.class) {
+ return new RightSquareCompartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SquareCompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/SquareCompartment.java
similarity index 64%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SquareCompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/SquareCompartment.java
index 6746edf321..d87ba0c760 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SquareCompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/SquareCompartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -13,7 +13,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*/
@Entity
@DiscriminatorValue("Square Compartment Alias")
-public class SquareCompartmentAlias extends CompartmentAlias {
+public class SquareCompartment extends Compartment {
/**
*
@@ -23,7 +23,7 @@ public class SquareCompartmentAlias extends CompartmentAlias {
/**
* Default constructor.
*/
- public SquareCompartmentAlias() {
+ public SquareCompartment() {
super();
}
@@ -34,19 +34,19 @@ public class SquareCompartmentAlias extends CompartmentAlias {
* @param originalAlias
* orignal alias where the data was kept
*/
- public SquareCompartmentAlias(CompartmentAlias originalAlias) {
+ public SquareCompartment(Compartment originalAlias) {
super(originalAlias);
}
- public SquareCompartmentAlias(String aliasId) {
+ public SquareCompartment(String aliasId) {
super();
setAliasId(aliasId);
}
@Override
- public SquareCompartmentAlias copy() {
- if (this.getClass() == SquareCompartmentAlias.class) {
- return new SquareCompartmentAlias(this);
+ public SquareCompartment copy() {
+ if (this.getClass() == SquareCompartment.class) {
+ return new SquareCompartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TopSquareCompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
similarity index 71%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TopSquareCompartmentAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
index e73ed77efb..f45c36766a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TopSquareCompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -16,7 +16,7 @@ import lcsb.mapviewer.model.map.model.Model;
@Entity
@DiscriminatorValue("Top square Compartment Alias")
-public class TopSquareCompartmentAlias extends CompartmentAlias {
+public class TopSquareCompartment extends Compartment {
/**
*
@@ -26,7 +26,7 @@ public class TopSquareCompartmentAlias extends CompartmentAlias {
/**
* Default constructor.
*/
- public TopSquareCompartmentAlias() {
+ public TopSquareCompartment() {
super();
}
@@ -39,7 +39,7 @@ public class TopSquareCompartmentAlias extends CompartmentAlias {
* @param model
* model object to which the alias will be assigned
*/
- public TopSquareCompartmentAlias(CompartmentAlias originalAlias, Model model) {
+ public TopSquareCompartment(Compartment originalAlias, Model model) {
super(originalAlias);
setX(0.0);
setWidth(model.getWidth() * 2);
@@ -54,14 +54,14 @@ public class TopSquareCompartmentAlias extends CompartmentAlias {
* @param originalAlias
* orignal alias where the data was kept
*/
- public TopSquareCompartmentAlias(TopSquareCompartmentAlias originalAlias) {
+ public TopSquareCompartment(TopSquareCompartment originalAlias) {
super(originalAlias);
}
@Override
- public TopSquareCompartmentAlias copy() {
- if (this.getClass() == TopSquareCompartmentAlias.class) {
- return new TopSquareCompartmentAlias(this);
+ public TopSquareCompartment copy() {
+ if (this.getClass() == TopSquareCompartment.class) {
+ return new TopSquareCompartment(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMining.java b/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMining.java
index 752fab4ae5..e3d988837b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMining.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/graph/DataMining.java
@@ -20,7 +20,7 @@ import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.IndexColumn;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Entity representing data mining entry.
@@ -49,7 +49,7 @@ public class DataMining implements Serializable {
* For which element this entry was created.
*/
@ManyToOne(optional = false)
- private Alias element;
+ private Element element;
/**
* List of the suggested connection.
@@ -163,7 +163,7 @@ public class DataMining implements Serializable {
* @return the element
* @see #element
*/
- public Alias getElement() {
+ public Element getElement() {
return element;
}
@@ -172,7 +172,7 @@ public class DataMining implements Serializable {
* the element to set
* @see #element
*/
- public void setElement(Alias element) {
+ public void setElement(Element element) {
this.element = element;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/BlockDiagram.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/BlockDiagram.java
similarity index 82%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/BlockDiagram.java
rename to model/src/main/java/lcsb/mapviewer/model/map/layout/BlockDiagram.java
index aea48af67b..c2190b9333 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/BlockDiagram.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/BlockDiagram.java
@@ -1,19 +1,19 @@
-package lcsb.mapviewer.model.map.layout.alias;
-
-import java.io.Serializable;
-
-
-/**
- * This model element is used by cell designer but don't know how... We ignore it
- *
- * @author Piotr Gawron
- *
- */
-public abstract class BlockDiagram implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.io.Serializable;
+
+
+/**
+ * This model element is used by cell designer but don't know how... We ignore it
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class BlockDiagram implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
index 0493975e9a..89840fce67 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
@@ -8,7 +8,7 @@ import java.util.List;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Entry of coloring schema used for changing colors in the map. It allows to
@@ -58,7 +58,7 @@ public abstract class ColorSchema implements Serializable {
private static final int MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT = 255;
/**
- * Name of the {@link lcsb.mapviewer.db.model.map.Element Element}. If null
+ * Name of the {@link Element Element}. If null
* then this field will be skiped.
*/
private String name = null;
@@ -86,7 +86,7 @@ public abstract class ColorSchema implements Serializable {
/**
* What types of element should be identified by this entry.
*/
- private List<Class<? extends Alias>> types = new ArrayList<>();
+ private List<Class<? extends Element>> types = new ArrayList<>();
/**
* Value (-1..1 range) that is assigned to filtered elements (it will be
@@ -167,8 +167,8 @@ public abstract class ColorSchema implements Serializable {
* @param types2
* list of classes to add
*/
- public void addTypes(List<Class<? extends Alias>> types2) {
- for (Class<? extends Alias> clazz : types2) {
+ public void addTypes(List<Class<? extends Element>> types2) {
+ for (Class<? extends Element> clazz : types2) {
addType(clazz);
}
}
@@ -303,7 +303,7 @@ public abstract class ColorSchema implements Serializable {
* @return the types
* @see #types
*/
- public List<Class<? extends Alias>> getTypes() {
+ public List<Class<? extends Element>> getTypes() {
return types;
}
@@ -312,7 +312,7 @@ public abstract class ColorSchema implements Serializable {
* the types to set
* @see #types
*/
- public void setTypes(List<Class<? extends Alias>> types) {
+ public void setTypes(List<Class<? extends Element>> types) {
this.types = types;
}
@@ -479,7 +479,7 @@ public abstract class ColorSchema implements Serializable {
* @param clazz
* class to add
*/
- public void addType(Class<? extends Alias> clazz) {
+ public void addType(Class<? extends Element> clazz) {
this.types.add(clazz);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AliasGroup.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AliasGroup.java
rename to model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
index 6adc865c07..9a010c87e6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AliasGroup.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
@@ -1,75 +1,77 @@
-package lcsb.mapviewer.model.map.layout.alias;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * This model element is used by cell designer but we ignore it. Maybe it will
- * be usefull in the future.
- *
- * @author Piotr Gawron
- *
- */
-public class AliasGroup implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * String identifier of the group.
- */
- private String idGroup;
-
- /**
- * List of aliases in the group.
- */
- private List<Alias> aliases = new ArrayList<Alias>();
-
- /**
- * @return the idGroup
- * @see #idGroup
- */
- public String getIdGroup() {
- return idGroup;
- }
-
- /**
- * @param idGroup
- * the idGroup to set
- * @see #idGroup
- */
- public void setIdGroup(String idGroup) {
- this.idGroup = idGroup;
- }
-
- /**
- * @return the aliases
- * @see #aliases
- */
- public List<Alias> getAliases() {
- return aliases;
- }
-
- /**
- * @param aliases
- * the aliases to set
- * @see #aliases
- */
- public void setAliases(List<Alias> aliases) {
- this.aliases = aliases;
- }
-
- /**
- * Add alias to the group.
- *
- * @param alias
- * object to add to the group
- */
- public void addAlias(Alias alias) {
- aliases.add(alias);
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This model element is used by cell designer but we ignore it. Maybe it will
+ * be usefull in the future.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementGroup implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * String identifier of the group.
+ */
+ private String idGroup;
+
+ /**
+ * List of aliases in the group.
+ */
+ private List<Element> aliases = new ArrayList<Element>();
+
+ /**
+ * @return the idGroup
+ * @see #idGroup
+ */
+ public String getIdGroup() {
+ return idGroup;
+ }
+
+ /**
+ * @param idGroup
+ * the idGroup to set
+ * @see #idGroup
+ */
+ public void setIdGroup(String idGroup) {
+ this.idGroup = idGroup;
+ }
+
+ /**
+ * @return the aliases
+ * @see #aliases
+ */
+ public List<Element> getAliases() {
+ return aliases;
+ }
+
+ /**
+ * @param aliases
+ * the aliases to set
+ * @see #aliases
+ */
+ public void setAliases(List<Element> aliases) {
+ this.aliases = aliases;
+ }
+
+ /**
+ * Add alias to the group.
+ *
+ * @param alias
+ * object to add to the group
+ */
+ public void addAlias(Element alias) {
+ aliases.add(alias);
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAliasComparator.java
deleted file mode 100644
index a13c4e4340..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAliasComparator.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package lcsb.mapviewer.model.map.layout.alias;
-
-import java.util.Comparator;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class DegradedAliasComparator implements Comparator<DegradedAlias> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DegradedAliasComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public DegradedAliasComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public DegradedAliasComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(DegradedAlias arg0, DegradedAlias arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(DegradedAlias.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in DegradedAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(DegradedAlias arg0, DegradedAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAliasComparator.java
deleted file mode 100644
index 0372ac214f..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAliasComparator.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package lcsb.mapviewer.model.map.layout.alias;
-
-import java.util.Comparator;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class IonAliasComparator implements Comparator<IonAlias> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(IonAliasComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public IonAliasComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public IonAliasComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(IonAlias arg0, IonAlias arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(IonAlias.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in {@link IonAlias}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper {@link ChemicalAlias} class.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(IonAlias arg0, IonAlias arg1) {
- ChemicalAliasComparator speciesAliasComparator = new ChemicalAliasComparator(epsilon);
- int result = speciesAliasComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- return 0;
- }
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java
index d328f9153f..bad3304df1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnection.java
@@ -7,7 +7,7 @@ import javax.persistence.Entity;
import javax.persistence.ManyToOne;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This class defines connection between alias and submap (submodel). This means
@@ -29,14 +29,14 @@ public class AliasSubmodelConnection extends SubmodelConnection implements Seria
* From which alias this connection start.
*/
@ManyToOne
- private Alias fromAlias;
+ private Element fromAlias;
/**
* This object defines reference element in submodel that represents central
* (or identical) object in reference submodel.
*/
@ManyToOne
- private Alias toAlias;
+ private Element toAlias;
/**
* Default constructor that initialize some fields.
@@ -99,7 +99,7 @@ public class AliasSubmodelConnection extends SubmodelConnection implements Seria
* @return the fromAlias
* @see #fromAlias
*/
- public Alias getFromAlias() {
+ public Element getFromAlias() {
return fromAlias;
}
@@ -108,7 +108,7 @@ public class AliasSubmodelConnection extends SubmodelConnection implements Seria
* the fromAlias to set
* @see #fromAlias
*/
- public void setFromAlias(Alias fromAlias) {
+ public void setFromAlias(Element fromAlias) {
this.fromAlias = fromAlias;
}
@@ -116,7 +116,7 @@ public class AliasSubmodelConnection extends SubmodelConnection implements Seria
* @return the toAlias
* @see #toAlias
*/
- public Alias getToAlias() {
+ public Element getToAlias() {
return toAlias;
}
@@ -125,7 +125,7 @@ public class AliasSubmodelConnection extends SubmodelConnection implements Seria
* the toAlias to set
* @see #toAlias
*/
- public void setToAlias(Alias toAlias) {
+ public void setToAlias(Element toAlias) {
this.toAlias = toAlias;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparator.java
index dd0ac692bf..5db1a1da5b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparator.java
@@ -1,112 +1,112 @@
-package lcsb.mapviewer.model.map.model;
-
-import java.util.Comparator;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasComparator;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class implements comparator interface for {@link AliasSubmodelConnection}.
- *
- * @author Piotr Gawron
- *
- */
-public class AliasSubmodelConnectionComparator implements Comparator<AliasSubmodelConnection> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(AliasSubmodelConnectionComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public AliasSubmodelConnectionComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public AliasSubmodelConnectionComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(AliasSubmodelConnection arg0, AliasSubmodelConnection arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- return internalCompare(arg0, arg1);
- } else {
- logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link AliasSubmodelConnection} class in inheritence tree. It also calls
- * the {@link SubmodelConnectionComparator} for the super class (
- * {@link SubmodelConnection}).
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- public int internalCompare(AliasSubmodelConnection arg0, AliasSubmodelConnection arg1) {
- SubmodelConnectionComparator superComparator = new SubmodelConnectionComparator(epsilon);
-
- int result = superComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
- AliasComparator aliasComparator = new AliasComparator(epsilon);
- Alias alias1 = arg0.getFromAlias();
- Alias alias2 = arg1.getFromAlias();
- arg0.setFromAlias(null);
- arg1.setFromAlias(null);
- int status = aliasComparator.compare(alias1, alias2);
- arg0.setFromAlias(alias1);
- arg1.setFromAlias(alias2);
- if (status != 0) {
- logger.debug("from alias different: " + arg0.getFromAlias() + ", " + arg1.getFromAlias());
- return status;
- }
- alias1 = arg0.getToAlias();
- alias2 = arg1.getToAlias();
- arg0.setToAlias(null);
- arg1.setToAlias(null);
- status = aliasComparator.compare(alias1, alias2);
- arg0.setToAlias(alias1);
- arg1.setToAlias(alias2);
- if (status != 0) {
- logger.debug("to alias different: " + arg0.getToAlias() + ", " + arg1.getToAlias());
- return status;
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import java.util.Comparator;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class implements comparator interface for {@link AliasSubmodelConnection}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AliasSubmodelConnectionComparator implements Comparator<AliasSubmodelConnection> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(AliasSubmodelConnectionComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public AliasSubmodelConnectionComparator(double epsilon) {
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public AliasSubmodelConnectionComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public int compare(AliasSubmodelConnection arg0, AliasSubmodelConnection arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (arg0.getClass().equals(arg1.getClass())) {
+ return internalCompare(arg0, arg1);
+ } else {
+ logger.debug("class different: " + arg0.getClass() + ", " + arg1.getClass());
+ return -1;
+ }
+ }
+
+ /**
+ * This method compares only the fields that are defined in
+ * {@link AliasSubmodelConnection} class in inheritence tree. It also calls
+ * the {@link SubmodelConnectionComparator} for the super class (
+ * {@link SubmodelConnection}).
+ *
+ * @param arg0
+ * first object to compare
+ * @param arg1
+ * second object to compare
+ * @return if all fields are qual then returns 0. If they are different then
+ * -1/1 is returned.
+ */
+ public int internalCompare(AliasSubmodelConnection arg0, AliasSubmodelConnection arg1) {
+ SubmodelConnectionComparator superComparator = new SubmodelConnectionComparator(epsilon);
+
+ int result = superComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+ ElementComparator aliasComparator = new ElementComparator(epsilon);
+ Element alias1 = arg0.getFromAlias();
+ Element alias2 = arg1.getFromAlias();
+ arg0.setFromAlias(null);
+ arg1.setFromAlias(null);
+ int status = aliasComparator.compare(alias1, alias2);
+ arg0.setFromAlias(alias1);
+ arg1.setFromAlias(alias2);
+ if (status != 0) {
+ logger.debug("from alias different: " + arg0.getFromAlias() + ", " + arg1.getFromAlias());
+ return status;
+ }
+ alias1 = arg0.getToAlias();
+ alias2 = arg1.getToAlias();
+ arg0.setToAlias(null);
+ arg1.setToAlias(null);
+ status = aliasComparator.compare(alias1, alias2);
+ arg0.setToAlias(alias1);
+ arg1.setToAlias(alias2);
+ if (status != 0) {
+ logger.debug("to alias different: " + arg0.getToAlias() + ", " + arg1.getToAlias());
+ return status;
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index f26bed4f32..25d9a36416 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -12,16 +12,16 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This interface defines functionality that the model container class should
@@ -52,7 +52,7 @@ public interface Model {
* @param alias
* alias to add
*/
- void addAlias(Alias alias);
+ void addAlias(Element alias);
/**
* Returns map model version.
@@ -118,16 +118,16 @@ public interface Model {
*
* @return set of all alisaes
*/
- Set<Alias> getAliases();
+ Set<Element> getAliases();
/**
- * Returns alias with the given alias identfier ({@link Alias#aliasId}).
+ * Returns alias with the given alias identfier ({@link Element#aliasId}).
*
* @param idAlias
* alias identifier
* @return alias with the given id
*/
- <T extends Alias> T getAliasByAliasId(String idAlias);
+ <T extends Element> T getAliasByAliasId(String idAlias);
/**
* Adds reaction to the model.
@@ -148,16 +148,16 @@ public interface Model {
* Returns compartment alias with the given alias id.
*
* @param id
- * compartment alias identifier ({@link Alias#aliasId})
+ * compartment alias identifier ({@link Element#aliasId})
* @return compartment alias with the given compartment alias id
*/
- CompartmentAlias getCompartmentAliasByCompartmentAliasId(String id);
+ Compartment getCompartmentAliasByCompartmentAliasId(String id);
/**
* @return list of compartment aliases
*/
- List<CompartmentAlias> getCompartmentsAliases();
+ List<Compartment> getCompartmentsAliases();
/**
* Adds layer to the model.
@@ -179,7 +179,7 @@ public interface Model {
* @param aliases
* list of aliases
*/
- void addAliases(List<? extends Alias> aliases);
+ void addAliases(List<? extends Element> aliases);
/**
* Sets new short description of the model.
@@ -213,12 +213,12 @@ public interface Model {
void addLayers(Collection<Layer> layers);
/**
- * Adds {@link AliasGroup} to the model.
+ * Adds {@link ElementGroup} to the model.
*
* @param aliasGroup
* object to add
*/
- void addAliasGroup(AliasGroup aliasGroup);
+ void addAliasGroup(ElementGroup aliasGroup);
/**
* Adds {@link BlockDiagram} to the model.
@@ -317,7 +317,7 @@ public interface Model {
* @param alias
* alias to remove
*/
- void removeAlias(Alias alias);
+ void removeAlias(Element alias);
/**
* Returns list of reactions sorted by reaction id.
@@ -331,23 +331,23 @@ public interface Model {
*
* @return list of aliases sorted by the size
*/
- List<Alias> getSortedAliases();
+ List<Element> getSortedAliases();
/**
* Returns collection of species aliases (excluding complexes).
*
* @return collection of species aliases
*/
- Collection<SpeciesAlias> getNotComplexSpeciesAliases();
+ Collection<Species> getNotComplexSpeciesAliases();
- List<SpeciesAlias> getSpeciesAliases();
+ List<Species> getSpeciesAliases();
/**
* Returns collection of complex aliases.
*
* @return collection of complex aliases
*/
- Collection<ComplexAlias> getComplexAliases();
+ Collection<Complex> getComplexAliases();
/**
* Adds reactions to model.
@@ -366,7 +366,7 @@ public interface Model {
*/
Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData);
- List<Alias> getAliasByName(String name);
+ List<Element> getAliasByName(String name);
/**
*
@@ -420,10 +420,10 @@ public interface Model {
* Returns alias for given database identifier.
*
* @param dbId
- * alias database identifier ({@link Alias#id})
+ * alias database identifier ({@link Element#id})
* @return alias for a given id
*/
- Alias getAliasByDbId(Integer dbId);
+ Element getAliasByDbId(Integer dbId);
/**
* Returns reaction for given database identifier.
@@ -439,14 +439,14 @@ public interface Model {
*
* @return list of aliases sorted by size
*/
- List<CompartmentAlias> getSortedCompartmentsAliases();
+ List<Compartment> getSortedCompartmentsAliases();
/**
* Returns list of aliases sorted by the size.
*
* @return list of aliases sorted by the size
*/
- List<Alias> getAliasesSortedBySize();
+ List<Element> getAliasesSortedBySize();
/**
*
@@ -466,7 +466,7 @@ public interface Model {
* @param aliases
* new {@link ModelData#aliases} collection
*/
- void setAliases(Set<Alias> aliases);
+ void setAliases(Set<Element> aliases);
/**
* @return the modelData
@@ -657,7 +657,7 @@ public interface Model {
/**
* Return list od all {@link AnnotatedObject} in the map. This includes all
- * {@link Reaction reactions} and {@link Alias elements}.
+ * {@link Reaction reactions} and {@link Element elements}.
*
* @return list od all {@link AnnotatedObject} in the map
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
index 7eba1e40b5..eea5155dd2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
@@ -19,12 +19,12 @@ import lcsb.mapviewer.model.map.OverviewImageComparator;
import lcsb.mapviewer.model.map.graph.DataMiningSetComparator;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.LayoutComparator;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasComparator;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerComparator;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionComparator;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
/**
* Comparator for {@link Model} class.
@@ -344,26 +344,26 @@ public class ModelComparator implements Comparator<Model> {
* @return if sets are equal then returns 0. If they are different then -1/1
* is returned.
*/
- private int compareAliases(Set<Alias> aliases, Set<Alias> aliases2) {
- AliasComparator aliasComparator = new AliasComparator(epsilon);
+ private int compareAliases(Set<Element> aliases, Set<Element> aliases2) {
+ ElementComparator aliasComparator = new ElementComparator(epsilon);
- Map<String, Alias> map1 = new HashMap<String, Alias>();
- Map<String, Alias> map2 = new HashMap<String, Alias>();
+ Map<String, Element> map1 = new HashMap<String, Element>();
+ Map<String, Element> map2 = new HashMap<String, Element>();
if (aliases.size() != aliases2.size()) {
logger.debug("Number of aliases different: " + aliases.size() + ", " + aliases2.size());
return ((Integer) aliases.size()).compareTo(aliases2.size());
}
- for (Alias alias : aliases) {
+ for (Element alias : aliases) {
map1.put(alias.getAliasId(), alias);
}
- for (Alias alias : aliases2) {
+ for (Element alias : aliases2) {
map2.put(alias.getAliasId(), alias);
}
- for (Alias alias : aliases) {
+ for (Element alias : aliases) {
int status = aliasComparator.compare(alias, map2.get(alias.getAliasId()));
if (status != 0) {
logger.debug("Alias doesn't have a match: " + alias.getAliasId() + ", " + map2.get(alias.getAliasId()));
@@ -371,7 +371,7 @@ public class ModelComparator implements Comparator<Model> {
}
}
- for (Alias alias : aliases2) {
+ for (Element alias : aliases2) {
int status = aliasComparator.compare(alias, map1.get(alias.getAliasId()));
if (status != 0) {
logger.debug("Alias doesn't have a match: " + alias.getAliasId() + ", " + map2.get(alias.getAliasId()));
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index 6041b05312..b6b0124492 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -29,12 +29,12 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Representation of the model data. It contains all information about single
@@ -69,11 +69,11 @@ public class ModelData implements Serializable {
/**
* Set of all aliases in the map.
*
- * @see Alias
+ * @see Element
*/
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "model", orphanRemoval = true)
- private Set<Alias> aliases = new HashSet<Alias>();
+ private Set<Element> aliases = new HashSet<Element>();
/**
* Set of all layers in the map.
@@ -235,7 +235,7 @@ public class ModelData implements Serializable {
* @param al
* alias to add
*/
- public void addAlias(Alias al) {
+ public void addAlias(Element al) {
al.setModelData(this);
aliases.add(al);
}
@@ -263,13 +263,13 @@ public class ModelData implements Serializable {
}
/**
- * Adds collection of {@link Alias aliases} to model data.
+ * Adds collection of {@link Element aliases} to model data.
*
* @param aliases
* aliases to add
*/
- public void addAliases(List<? extends Alias> aliases) {
- for (Alias alias : aliases) {
+ public void addAliases(List<? extends Element> aliases) {
+ for (Element alias : aliases) {
addAlias(alias);
}
}
@@ -296,7 +296,7 @@ public class ModelData implements Serializable {
* @param aliases
* new {@link #aliases} collection
*/
- public void setAliases(Set<Alias> aliases) {
+ public void setAliases(Set<Element> aliases) {
this.aliases = aliases;
}
@@ -426,12 +426,12 @@ public class ModelData implements Serializable {
}
/**
- * Adds {@link AliasGroup} to the model data.
+ * Adds {@link ElementGroup} to the model data.
*
* @param aliasGroup
* object to add
*/
- public void addAliasGroup(AliasGroup aliasGroup) {
+ public void addAliasGroup(ElementGroup aliasGroup) {
// for now we ignore this information
}
@@ -451,7 +451,7 @@ public class ModelData implements Serializable {
* @param alias
* alias to remove
*/
- public void removeAlias(Alias alias) {
+ public void removeAlias(Element alias) {
if (alias == null) {
throw new InvalidArgumentException("Cannot remove null");
}
@@ -637,7 +637,7 @@ public class ModelData implements Serializable {
* @return the aliases
* @see #aliases
*/
- public Set<Alias> getAliases() {
+ public Set<Element> getAliases() {
return aliases;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index f94a26e612..fbace68fe2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -21,16 +21,16 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewImageLink;
import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class implemets {@link Model} interface. It's is very simple
@@ -48,15 +48,15 @@ public class ModelFullIndexed implements Model {
private static Logger logger = Logger.getLogger(ModelFullIndexed.class);
/**
- * Object that map {@link Alias#aliasId alias identifier} into {@link Alias}.
+ * Object that map {@link Element#aliasId alias identifier} into {@link Element}.
*/
- private Map<String, Alias> aliasByAliasId = new HashMap<String, Alias>();
+ private Map<String, Element> aliasByAliasId = new HashMap<String, Element>();
/**
- * Object that map {@link Alias#id alias database identifier} into
- * {@link Alias}.
+ * Object that map {@link Element#id alias database identifier} into
+ * {@link Element}.
*/
- private Map<Integer, Alias> aliasByDbId = new HashMap<Integer, Alias>();
+ private Map<Integer, Element> aliasByDbId = new HashMap<Integer, Element>();
/**
* Object that map {@link Reaction#idReaction reaction identifier} into
@@ -86,7 +86,7 @@ public class ModelFullIndexed implements Model {
this.modelData = new ModelData();
} else {
this.modelData = model;
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
aliasByAliasId.put(alias.getAliasId(), alias);
aliasByDbId.put(alias.getId(), alias);
}
@@ -114,29 +114,29 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addAlias(Alias alias) {
- if (alias instanceof SpeciesAlias) {
- addSpeciesAlias((SpeciesAlias) alias);
- } else if (alias instanceof CompartmentAlias) {
- addCompartmentAlias((CompartmentAlias) alias);
+ public void addAlias(Element alias) {
+ if (alias instanceof Species) {
+ addSpeciesAlias((Species) alias);
+ } else if (alias instanceof Compartment) {
+ addCompartmentAlias((Compartment) alias);
} else {
throw new InvalidArgumentException("Unknown type of alias: " + alias);
}
}
/**
- * Adds {@link SpeciesAlias} to the model.
+ * Adds {@link Species} to the model.
*
* @param al
* alias to add
*/
- private void addSpeciesAlias(SpeciesAlias al) {
+ private void addSpeciesAlias(Species al) {
if (al.getAliasId() == null || al.getAliasId().isEmpty()) {
throw new InvalidArgumentException("Alias identifier cannot be empty");
}
modelData.addAlias(al);
- Alias alias2 = aliasByAliasId.get(al.getAliasId());
+ Element alias2 = aliasByAliasId.get(al.getAliasId());
if (alias2 == null) {
aliasByAliasId.put(al.getAliasId(), al);
aliasByDbId.put(al.getId(), al);
@@ -186,13 +186,14 @@ public class ModelFullIndexed implements Model {
}
@Override
- public Set<Alias> getAliases() {
+ public Set<Element> getAliases() {
return modelData.getAliases();
}
+ @SuppressWarnings("unchecked")
@Override
- public Alias getAliasByAliasId(String idAlias) {
- return aliasByAliasId.get(idAlias);
+ public <T extends Element> T getAliasByAliasId(String idAlias) {
+ return (T) aliasByAliasId.get(idAlias);
}
@Override
@@ -213,9 +214,9 @@ public class ModelFullIndexed implements Model {
* @param al
* alias to add
*/
- private void addCompartmentAlias(CompartmentAlias al) {
+ private void addCompartmentAlias(Compartment al) {
modelData.addAlias(al);
- Alias alias2 = aliasByAliasId.get(al.getAliasId());
+ Element alias2 = aliasByAliasId.get(al.getAliasId());
if (alias2 == null) {
aliasByAliasId.put(al.getAliasId(), al);
aliasByDbId.put(al.getId(), al);
@@ -225,16 +226,16 @@ public class ModelFullIndexed implements Model {
}
@Override
- public CompartmentAlias getCompartmentAliasByCompartmentAliasId(String id) {
- return (CompartmentAlias) aliasByAliasId.get(id);
+ public Compartment getCompartmentAliasByCompartmentAliasId(String id) {
+ return (Compartment) aliasByAliasId.get(id);
}
@Override
- public List<CompartmentAlias> getCompartmentsAliases() {
- List<CompartmentAlias> result = new ArrayList<CompartmentAlias>();
- for (Alias alias : modelData.getAliases()) {
- if (alias instanceof CompartmentAlias) {
- result.add((CompartmentAlias) alias);
+ public List<Compartment> getCompartmentsAliases() {
+ List<Compartment> result = new ArrayList<Compartment>();
+ for (Element alias : modelData.getAliases()) {
+ if (alias instanceof Compartment) {
+ result.add((Compartment) alias);
}
}
return result;
@@ -251,8 +252,8 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addAliases(List<? extends Alias> aliases) {
- for (Alias alias : aliases) {
+ public void addAliases(List<? extends Element> aliases) {
+ for (Element alias : aliases) {
addAlias(alias);
}
}
@@ -271,7 +272,7 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void setAliases(Set<Alias> aliases) {
+ public void setAliases(Set<Element> aliases) {
this.modelData.setAliases(aliases);
}
@@ -291,17 +292,17 @@ public class ModelFullIndexed implements Model {
}
@Override
- public List<Alias> getAliasesSortedBySize() {
- List<Alias> sortedAliases = new ArrayList<Alias>();
+ public List<Element> getAliasesSortedBySize() {
+ List<Element> sortedAliases = new ArrayList<Element>();
sortedAliases.addAll(getAliases());
- Collections.sort(sortedAliases, Alias.SIZE_COMPARATOR);
+ Collections.sort(sortedAliases, Element.SIZE_COMPARATOR);
return sortedAliases;
}
@Override
- public List<CompartmentAlias> getSortedCompartmentsAliases() {
- List<CompartmentAlias> result = getCompartmentsAliases();
- Collections.sort(result, Alias.SIZE_COMPARATOR);
+ public List<Compartment> getSortedCompartmentsAliases() {
+ List<Compartment> result = getCompartmentsAliases();
+ Collections.sort(result, Element.SIZE_COMPARATOR);
return result;
}
@@ -311,7 +312,7 @@ public class ModelFullIndexed implements Model {
}
@Override
- public Alias getAliasByDbId(Integer dbId) {
+ public Element getAliasByDbId(Integer dbId) {
return aliasByDbId.get(dbId);
}
@@ -353,7 +354,7 @@ public class ModelFullIndexed implements Model {
@Override
public Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData) {
Set<AnnotatedObject> result = new HashSet<AnnotatedObject>();
- for (Alias alias : getAliases()) {
+ for (Element alias : getAliases()) {
for (MiriamData md : alias.getMiriamData()) {
if (md.equals(miriamData)) {
result.add(alias);
@@ -380,22 +381,22 @@ public class ModelFullIndexed implements Model {
}
@Override
- public Collection<ComplexAlias> getComplexAliases() {
- List<ComplexAlias> result = new ArrayList<ComplexAlias>();
- for (Alias alias : modelData.getAliases()) {
- if (alias instanceof ComplexAlias) {
- result.add((ComplexAlias) alias);
+ public Collection<Complex> getComplexAliases() {
+ List<Complex> result = new ArrayList<Complex>();
+ for (Element alias : modelData.getAliases()) {
+ if (alias instanceof Complex) {
+ result.add((Complex) alias);
}
}
return result;
}
@Override
- public Collection<SpeciesAlias> getNotComplexSpeciesAliases() {
- List<SpeciesAlias> result = new ArrayList<SpeciesAlias>();
- for (Alias alias : modelData.getAliases()) {
- if (alias instanceof SpeciesAlias && !(alias instanceof ComplexAlias)) {
- result.add((SpeciesAlias) alias);
+ public Collection<Species> getNotComplexSpeciesAliases() {
+ List<Species> result = new ArrayList<Species>();
+ for (Element alias : modelData.getAliases()) {
+ if (alias instanceof Species && !(alias instanceof Complex)) {
+ result.add((Species) alias);
}
}
return result;
@@ -409,10 +410,10 @@ public class ModelFullIndexed implements Model {
}
@Override
- public List<Alias> getSortedAliases() {
- List<Alias> result = new ArrayList<Alias>();
+ public List<Element> getSortedAliases() {
+ List<Element> result = new ArrayList<Element>();
result.addAll(getAliases());
- Collections.sort(result, Alias.SIZE_COMPARATOR);
+ Collections.sort(result, Element.SIZE_COMPARATOR);
return result;
}
@@ -435,7 +436,7 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addAliasGroup(AliasGroup aliasGroup) {
+ public void addAliasGroup(ElementGroup aliasGroup) {
modelData.addAliasGroup(aliasGroup);
}
@@ -445,32 +446,32 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void removeAlias(Alias alias) {
+ public void removeAlias(Element alias) {
modelData.removeAlias(alias);
aliasByAliasId.remove(alias.getAliasId());
aliasByDbId.remove(alias.getId());
if (alias.getParent() != null) {
- if (alias.getParent() instanceof CompartmentAlias) {
- CompartmentAlias ca = (CompartmentAlias) alias.getParent();
+ if (alias.getParent() instanceof Compartment) {
+ Compartment ca = (Compartment) alias.getParent();
ca.removeAlias(alias);
- } else if (alias.getParent() instanceof ComplexAlias) {
- ComplexAlias ca = (ComplexAlias) alias.getParent();
- ca.removeAlias((SpeciesAlias) alias);
+ } else if (alias.getParent() instanceof Complex) {
+ Complex ca = (Complex) alias.getParent();
+ ca.removeAlias((Species) alias);
} else {
throw new InvalidArgumentException("Unknown type of alias parent: " + alias.getParent().getClass().getName());
}
}
if (alias.getCompartmentAlias() != null) {
- CompartmentAlias ca = alias.getCompartmentAlias();
+ Compartment ca = alias.getCompartmentAlias();
ca.removeAlias(alias);
}
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias al = (SpeciesAlias) alias;
+ if (alias instanceof Species) {
+ Species al = (Species) alias;
if (al.getComplexAlias() != null) {
- ComplexAlias ca = ((SpeciesAlias) alias).getComplexAlias();
+ Complex ca = ((Species) alias).getComplexAlias();
ca.removeAlias(al);
}
}
@@ -757,9 +758,9 @@ public class ModelFullIndexed implements Model {
}
@Override
- public List<Alias> getAliasByName(String name) {
- List<Alias> result = new ArrayList<>();
- for (Alias element : getAliases()) {
+ public List<Element> getAliasByName(String name) {
+ List<Element> result = new ArrayList<>();
+ for (Element element : getAliases()) {
if (element.getName().equalsIgnoreCase(name)) {
result.add(element);
}
@@ -768,11 +769,11 @@ public class ModelFullIndexed implements Model {
}
@Override
- public List<SpeciesAlias> getSpeciesAliases() {
- List<SpeciesAlias> result = new ArrayList<SpeciesAlias>();
- for (Alias alias : modelData.getAliases()) {
- if (alias instanceof SpeciesAlias) {
- result.add((SpeciesAlias) alias);
+ public List<Species> getSpeciesAliases() {
+ List<Species> result = new ArrayList<Species>();
+ for (Element alias : modelData.getAliases()) {
+ if (alias instanceof Species) {
+ result.add((Species) alias);
}
}
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
index 616e6fa843..5d7b8bd08c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
@@ -4,8 +4,8 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines catalysis modifier in the reaction.
@@ -35,7 +35,7 @@ public class Catalysis extends Modifier {
* @param alias
* alias object to which this modifiar is assigned
*/
- public Catalysis(SpeciesAlias alias) {
+ public Catalysis(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
index d6e36305cc..e38d9682b1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
@@ -4,8 +4,8 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines inhibition modifier in the reaction.
@@ -35,7 +35,7 @@ public class Inhibition extends Modifier {
* @param alias
* alias object to which this modifiar is assigned
*/
- public Inhibition(SpeciesAlias alias) {
+ public Inhibition(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
index 7a5d19d33a..5c9c4001eb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
@@ -4,8 +4,8 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines modulation modifier in the reaction.
@@ -35,7 +35,7 @@ public class Modulation extends Modifier {
* @param alias
* alias object to which this modifiar is assigned
*/
- public Modulation(SpeciesAlias alias) {
+ public Modulation(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
index 187bc27cb0..24458c841f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
@@ -4,8 +4,8 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines physical stimulation modifier in the reaction.
@@ -36,7 +36,7 @@ public class PhysicalStimulation extends Modifier {
* @param alias
* alias object to which this modifiar is assigned
*/
- public PhysicalStimulation(SpeciesAlias alias) {
+ public PhysicalStimulation(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
index 877a6d7147..f90175e634 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
@@ -4,8 +4,8 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines trigger modifier in the reaction.
@@ -35,7 +35,7 @@ public class Trigger extends Modifier {
* @param alias
* alias object to which this modifiar is assigned
*/
- public Trigger(SpeciesAlias alias) {
+ public Trigger(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
index 3e2b0d8fb4..cf6f506ea3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
@@ -4,8 +4,8 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines unknown catalysis modifier in the reaction.
@@ -36,7 +36,7 @@ public class UnknownCatalysis extends Modifier {
* @param alias
* alias object to which this modifiar is assigned
*/
- public UnknownCatalysis(SpeciesAlias alias) {
+ public UnknownCatalysis(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
index 511ebf6877..7bfde19c0c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
@@ -4,8 +4,8 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class defines unknown inhibition modifier in the reaction.
@@ -36,7 +36,7 @@ public class UnknownInhibition extends Modifier {
* @param alias
* alias object to which this modifiar is assigned
*/
- public UnknownInhibition(SpeciesAlias alias) {
+ public UnknownInhibition(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
index f61570b290..cda54b65e2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
@@ -4,7 +4,7 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Represents modifier (ie. catalyst) in the {@link Reaction}. It is an
@@ -30,7 +30,7 @@ public class Modifier extends ReactionNode {
}
/**
- * Constructor that creates modifier for given {@link SpeciesAlias}. These
+ * Constructor that creates modifier for given {@link Species}. These
* elements reference to the objects in the
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this modifier.
@@ -38,7 +38,7 @@ public class Modifier extends ReactionNode {
* @param alias
* alias that represent this modifier
*/
- public Modifier(SpeciesAlias alias) {
+ public Modifier(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
index 2e7c9dbbd1..9fa4bd9850 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
@@ -4,7 +4,7 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Represents product of the reaction (in the reaction).
@@ -29,7 +29,7 @@ public class Product extends ReactionNode {
}
/**
- * Constructor that creates product for given {@link SpeciesAlias}. These
+ * Constructor that creates product for given {@link Species}. These
* elements reference to the objects in the
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this product.
@@ -37,7 +37,7 @@ public class Product extends ReactionNode {
* @param alias
* alias that represent this product
*/
- public Product(SpeciesAlias alias) {
+ public Product(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
index f553d769f5..1fbd827ef7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
@@ -4,7 +4,7 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Represents reactant of the reaction.
@@ -29,7 +29,7 @@ public class Reactant extends ReactionNode {
}
/**
- * Constructor that creates reactant for a given {@link SpeciesAlias}. These
+ * Constructor that creates reactant for a given {@link Species}. These
* elements reference to the objects in the
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this reactant.
@@ -37,7 +37,7 @@ public class Reactant extends ReactionNode {
* @param alias
* alias that represent this reactant
*/
- public Reactant(SpeciesAlias alias) {
+ public Reactant(Species alias) {
super(alias);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 16fa2d5e4c..8b89218bf3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -40,12 +40,12 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This class describes reaction in the {@link Model}. Every reaction consists
@@ -521,7 +521,7 @@ public class Reaction implements AnnotatedObject {
* @return <code>true</code> if element is part of the reaction,
* <code>false</code> otherwise
*/
- public boolean containsElement(Alias alias) {
+ public boolean containsElement(Element alias) {
for (ReactionNode node : getReactionNodes()) {
if (node.getAlias().equals(alias)) {
return true;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
index 23643d2030..6ed59c1df0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
@@ -4,7 +4,7 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import javax.persistence.ManyToOne;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* One of two known types of nodes in the {@link Reaction}. It defines input or
@@ -34,7 +34,7 @@ public abstract class ReactionNode extends AbstractNode {
* {@link SpecisAlias} that represents this node in the model.
*/
@ManyToOne
- private Alias alias;
+ private Element alias;
/**
* Default constructor.
@@ -59,9 +59,9 @@ public abstract class ReactionNode extends AbstractNode {
* .
*
* @param alias
- * {@link Alias} to which this node refer to
+ * {@link Element} to which this node refer to
*/
- public ReactionNode(Alias alias) {
+ public ReactionNode(Element alias) {
this.alias = alias;
}
@@ -69,7 +69,7 @@ public abstract class ReactionNode extends AbstractNode {
* @return the alias
* @see #alias
*/
- public Alias getAlias() {
+ public Element getAlias() {
return alias;
}
@@ -78,7 +78,7 @@ public abstract class ReactionNode extends AbstractNode {
* the alias to set
* @see #alias
*/
- public void setAlias(Alias alias) {
+ public void setAlias(Element alias) {
this.alias = alias;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
index 1efc5fba81..0e2d008e73 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
@@ -5,7 +5,7 @@ import java.util.Comparator;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.layout.alias.AliasComparator;
+import lcsb.mapviewer.model.map.species.ElementComparator;
/**
* This class implements comparator interface for {@link ReactionNode}. It also
@@ -77,7 +77,7 @@ public class ReactionNodeComparator implements Comparator<ReactionNode> {
*/
private int internalCompare(ReactionNode arg0, ReactionNode arg1) {
AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
- AliasComparator aliasComparator = new AliasComparator(epsilon);
+ ElementComparator aliasComparator = new ElementComparator(epsilon);
int result = anComparator.internalCompare(arg0, arg1);
if (result != 0) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
similarity index 59%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
index 3f918eac7b..6910928f81 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
@@ -13,10 +13,11 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
@Entity
@DiscriminatorValue("ANTISENSE_RNA_ALIAS")
-public class AntisenseRnaAlias extends SpeciesAlias {
+public class AntisenseRna extends Species {
/**
*
@@ -26,31 +27,31 @@ public class AntisenseRnaAlias extends SpeciesAlias {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "species")
@LazyCollection(LazyCollectionOption.FALSE)
- private List<AntisenseRnaRegionAlias> regions = new ArrayList<>();
+ private List<AntisenseRnaRegion> regions = new ArrayList<>();
- AntisenseRnaAlias() {
+ AntisenseRna() {
}
- public AntisenseRnaAlias(AntisenseRnaAlias original) {
+ public AntisenseRna(AntisenseRna original) {
super(original);
- for (AntisenseRnaRegionAlias region : original.getRegions()) {
- addRegion(new AntisenseRnaRegionAlias(region));
+ for (AntisenseRnaRegion region : original.getRegions()) {
+ addRegion(new AntisenseRnaRegion(region));
}
}
- public void addRegion(AntisenseRnaRegionAlias antisenseRnaRegionAlias) {
+ public void addRegion(AntisenseRnaRegion antisenseRnaRegionAlias) {
regions.add(antisenseRnaRegionAlias);
antisenseRnaRegionAlias.setSpecies(this);
}
- public AntisenseRnaAlias(String aliasId) {
+ public AntisenseRna(String aliasId) {
setAliasId(aliasId);
}
@Override
- public AntisenseRnaAlias copy() {
- if (this.getClass() == AntisenseRnaAlias.class) {
- return new AntisenseRnaAlias(this);
+ public AntisenseRna copy() {
+ if (this.getClass() == AntisenseRna.class) {
+ return new AntisenseRna(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -60,7 +61,7 @@ public class AntisenseRnaAlias extends SpeciesAlias {
* @return the regions
* @see #regions
*/
- public List<AntisenseRnaRegionAlias> getRegions() {
+ public List<AntisenseRnaRegion> getRegions() {
return regions;
}
@@ -69,7 +70,7 @@ public class AntisenseRnaAlias extends SpeciesAlias {
* the regions to set
* @see #regions
*/
- public void setRegions(List<AntisenseRnaRegionAlias> regions) {
+ public void setRegions(List<AntisenseRnaRegion> regions) {
this.regions = regions;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
similarity index 68%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
index 5cdf02b8f7..3929ee6149 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class AntisenseRnaAliasComparator implements Comparator<AntisenseRnaAlias> {
+public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaAliasComparator.class);
+ private static Logger logger = Logger.getLogger(AntisenseRnaComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class AntisenseRnaAliasComparator implements Comparator<AntisenseRnaAlias
* @param epsilon
* {@link #epsilon}
*/
- public AntisenseRnaAliasComparator(double epsilon) {
+ public AntisenseRnaComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public AntisenseRnaAliasComparator() {
+ public AntisenseRnaComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(AntisenseRnaAlias arg0, AntisenseRnaAlias arg1) {
+ public int compare(AntisenseRna arg0, AntisenseRna arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class AntisenseRnaAliasComparator implements Comparator<AntisenseRnaAlias
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(AntisenseRnaAlias.class)) {
+ if (arg0.getClass().equals(AntisenseRna.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class AntisenseRnaAliasComparator implements Comparator<AntisenseRnaAlias
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(AntisenseRnaAlias arg0, AntisenseRnaAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
similarity index 86%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
index b9a0c730c2..72703817ac 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.Column;
import javax.persistence.DiscriminatorValue;
@@ -6,7 +6,7 @@ import javax.persistence.Entity;
@Entity
@DiscriminatorValue("CHEMICAL_ALIAS")
-public abstract class ChemicalAlias extends SpeciesAlias {
+public abstract class Chemical extends Species {
/**
*
@@ -37,10 +37,10 @@ public abstract class ChemicalAlias extends SpeciesAlias {
private String inChIKey;
- ChemicalAlias() {
+ Chemical() {
}
- public ChemicalAlias(ChemicalAlias original) {
+ public Chemical(Chemical original) {
super(original);
smiles = original.getSmiles();
inChI = original.getInChI();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
similarity index 59%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
index 469e355951..4b9cba9976 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,21 +7,21 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class ChemicalAliasComparator implements Comparator<ChemicalAlias> {
+public class ChemicalComparator implements Comparator<Chemical> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ChemicalAliasComparator.class);
+ private static Logger logger = Logger.getLogger(ChemicalComparator.class);
/**
* Epsilon value used for comparison of doubles.
*/
private double epsilon;
- private IonAliasComparator ionAliasComparator;
- private SimpleMoleculeAliasComparator simpleMoleculeAliasComparator;
+ private IonComparator ionAliasComparator;
+ private SimpleMoleculeComparator simpleMoleculeAliasComparator;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -29,21 +29,21 @@ public class ChemicalAliasComparator implements Comparator<ChemicalAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public ChemicalAliasComparator(double epsilon) {
+ public ChemicalComparator(double epsilon) {
this.epsilon = epsilon;
- ionAliasComparator = new IonAliasComparator(epsilon);
- simpleMoleculeAliasComparator = new SimpleMoleculeAliasComparator(epsilon);
+ ionAliasComparator = new IonComparator(epsilon);
+ simpleMoleculeAliasComparator = new SimpleMoleculeComparator(epsilon);
}
/**
* Default constructor.
*/
- public ChemicalAliasComparator() {
+ public ChemicalComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(ChemicalAlias arg0, ChemicalAlias arg1) {
+ public int compare(Chemical arg0, Chemical arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -55,12 +55,12 @@ public class ChemicalAliasComparator implements Comparator<ChemicalAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(ChemicalAlias.class)) {
+ if (arg0.getClass().equals(Chemical.class)) {
return internalCompare(arg0, arg1);
- } else if (arg0.getClass().equals(IonAlias.class)) {
- return ionAliasComparator.compare((IonAlias) arg0, (IonAlias) arg1);
- } else if (arg0.getClass().equals(SimpleMoleculeAlias.class)) {
- return simpleMoleculeAliasComparator.compare((SimpleMoleculeAlias) arg0, (SimpleMoleculeAlias) arg1);
+ } else if (arg0.getClass().equals(Ion.class)) {
+ return ionAliasComparator.compare((Ion) arg0, (Ion) arg1);
+ } else if (arg0.getClass().equals(SimpleMolecule.class)) {
+ return simpleMoleculeAliasComparator.compare((SimpleMolecule) arg0, (SimpleMolecule) arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
}
@@ -81,8 +81,8 @@ public class ChemicalAliasComparator implements Comparator<ChemicalAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- int internalCompare(ChemicalAlias arg0, ChemicalAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ int internalCompare(Chemical arg0, Chemical arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
index 74437c1dfd..0a1fffc9bd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.HashSet;
@@ -24,7 +24,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*/
@Entity
@DiscriminatorValue("Complex Species Alias")
-public class ComplexAlias extends SpeciesAlias {
+public class Complex extends Species {
/**
*
@@ -34,7 +34,7 @@ public class ComplexAlias extends SpeciesAlias {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ComplexAlias.class);
+ private static Logger logger = Logger.getLogger(Complex.class);
/**
* List of aliases that are in this complex alias (only aliases that lies
@@ -42,7 +42,7 @@ public class ComplexAlias extends SpeciesAlias {
*/
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.EAGER, mappedBy = "complexAlias")
- private List<SpeciesAlias> aliases = new ArrayList<>();
+ private List<Species> aliases = new ArrayList<>();
/**
* State of the complex species.
@@ -52,7 +52,7 @@ public class ComplexAlias extends SpeciesAlias {
/**
* Default constructor.
*/
- ComplexAlias() {
+ Complex() {
super();
}
@@ -63,10 +63,10 @@ public class ComplexAlias extends SpeciesAlias {
* @param original
* original alias used for initialization
*/
- public ComplexAlias(ComplexAlias original) {
+ public Complex(Complex original) {
super(original);
- for (SpeciesAlias alias : original.getAliases()) {
+ for (Species alias : original.getAliases()) {
addAlias(alias.copy());
}
this.structuralState = original.getStructuralState();
@@ -78,7 +78,7 @@ public class ComplexAlias extends SpeciesAlias {
* @param aliasId
* identifier of the alias
*/
- public ComplexAlias(String aliasId) {
+ public Complex(String aliasId) {
super(aliasId);
}
@@ -88,9 +88,9 @@ public class ComplexAlias extends SpeciesAlias {
* @param alias
* object to add
*/
- public void addAlias(SpeciesAlias alias) {
+ public void addAlias(Species alias) {
boolean contains = false;
- for (SpeciesAlias alias2 : aliases) {
+ for (Species alias2 : aliases) {
if (alias.getAliasId().equals(alias2.getAliasId())) {
contains = true;
}
@@ -107,7 +107,7 @@ public class ComplexAlias extends SpeciesAlias {
*
* @return list of aliases insied complexAlias.
*/
- public List<SpeciesAlias> getAliases() {
+ public List<Species> getAliases() {
return aliases;
}
@@ -117,21 +117,21 @@ public class ComplexAlias extends SpeciesAlias {
*
* @return list of all aliases insied complex alias.
*/
- public List<SpeciesAlias> getAllChildrenAliases() {
- List<SpeciesAlias> result = new ArrayList<SpeciesAlias>();
+ public List<Species> getAllChildrenAliases() {
+ List<Species> result = new ArrayList<Species>();
result.addAll(aliases);
- for (SpeciesAlias speciesAlias : aliases) {
- if (speciesAlias instanceof ComplexAlias) {
- result.addAll(((ComplexAlias) speciesAlias).getAllChildrenAliases());
+ for (Species speciesAlias : aliases) {
+ if (speciesAlias instanceof Complex) {
+ result.addAll(((Complex) speciesAlias).getAllChildrenAliases());
}
}
return result;
}
@Override
- public ComplexAlias copy() {
- if (this.getClass() == ComplexAlias.class) {
- return new ComplexAlias(this);
+ public Complex copy() {
+ if (this.getClass() == Complex.class) {
+ return new Complex(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -144,7 +144,7 @@ public class ComplexAlias extends SpeciesAlias {
* @param alias
* object to remove
*/
- public void removeAlias(SpeciesAlias alias) {
+ public void removeAlias(Species alias) {
aliases.remove(alias);
if (alias.getComplexAlias() != null) {
if (alias.getComplexAlias() == this) {
@@ -172,11 +172,11 @@ public class ComplexAlias extends SpeciesAlias {
this.structuralState = structuralState;
}
- public Set<SpeciesAlias> getAllSimpleChildren() {
- Set<SpeciesAlias> result = new HashSet<>();
- for (SpeciesAlias element : getAliases()) {
- if (element instanceof ComplexAlias) {
- result.addAll(((ComplexAlias) element).getAllSimpleChildren());
+ public Set<Species> getAllSimpleChildren() {
+ Set<Species> result = new HashSet<>();
+ for (Species element : getAliases()) {
+ if (element instanceof Complex) {
+ result.addAll(((Complex) element).getAllSimpleChildren());
} else {
result.add(element);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
similarity index 71%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
index b34faa1276..844f08650a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
import java.util.HashMap;
@@ -17,11 +17,11 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class ComplexAliasComparator implements Comparator<ComplexAlias> {
+public class ComplexComparator implements Comparator<Complex> {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ComplexAliasComparator.class);
+ private static Logger logger = Logger.getLogger(ComplexComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -34,19 +34,19 @@ public class ComplexAliasComparator implements Comparator<ComplexAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public ComplexAliasComparator(double epsilon) {
+ public ComplexComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public ComplexAliasComparator() {
+ public ComplexComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(ComplexAlias arg0, ComplexAlias arg1) {
+ public int compare(Complex arg0, Complex arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -58,7 +58,7 @@ public class ComplexAliasComparator implements Comparator<ComplexAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(ComplexAlias.class)) {
+ if (arg0.getClass().equals(Complex.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -80,9 +80,9 @@ public class ComplexAliasComparator implements Comparator<ComplexAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(ComplexAlias arg0, ComplexAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
- AliasComparator aliasComparator = new AliasComparator(epsilon);
+ private int internalCompare(Complex arg0, Complex arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
+ ElementComparator aliasComparator = new ElementComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
@@ -95,12 +95,12 @@ public class ComplexAliasComparator implements Comparator<ComplexAlias> {
return integerComparator.compare(arg0.getAliases().size(), arg1.getAliases().size());
}
- Map<String, Alias> map1 = new HashMap<>();
- Map<String, Alias> map2 = new HashMap<>();
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
- for (Alias alias : arg0.getAliases()) {
+ for (Element alias : arg0.getAliases()) {
if (map1.get(alias.getAliasId()) != null) {
- for (Alias alias2 : arg0.getAliases()) {
+ for (Element alias2 : arg0.getAliases()) {
logger.debug(alias2.getAliasId());
}
throw new InvalidArgumentException("Few aliases with the same id: " + alias.getAliasId());
@@ -108,15 +108,15 @@ public class ComplexAliasComparator implements Comparator<ComplexAlias> {
map1.put(alias.getAliasId(), alias);
}
- for (Alias alias : arg1.getAliases()) {
+ for (Element alias : arg1.getAliases()) {
if (map2.get(alias.getAliasId()) != null) {
throw new InvalidArgumentException("Few aliases with the same id: " + alias.getAliasId());
}
map2.put(alias.getAliasId(), alias);
}
- for (Alias alias : arg0.getAliases()) {
- Alias alias2 = map2.get(alias.getAliasId());
+ for (Element alias : arg0.getAliases()) {
+ Element alias2 = map2.get(alias.getAliasId());
int status = aliasComparator.compare(alias, alias2);
if (status != 0) {
logger.debug("child doesn't have a match: " + alias.getAliasId());
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
similarity index 59%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
index d3dd2cc51a..790b82fe0e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("DEGRADED_ALIAS")
-public class DegradedAlias extends SpeciesAlias {
+public class Degraded extends Species {
/**
*
*/
private static final long serialVersionUID = 1L;
- DegradedAlias() {
+ Degraded() {
}
- public DegradedAlias(DegradedAlias original) {
+ public Degraded(Degraded original) {
super(original);
}
- public DegradedAlias(String aliasId) {
+ public Degraded(String aliasId) {
super.setAliasId(aliasId);
}
@Override
- public DegradedAlias copy() {
- if (this.getClass() == DegradedAlias.class) {
- return new DegradedAlias(this);
+ public Degraded copy() {
+ if (this.getClass() == Degraded.class) {
+ return new Degraded(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
similarity index 71%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
index c59ba6e2b4..7f16484bd8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
@@ -1,23 +1,24 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-/**
- * This class implements comparator interface for Degraded.
- *
- * @author Piotr Gawron
- *
- * @see Degraded
- */
public class DegradedComparator implements Comparator<Degraded> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DegradedComparator.class);
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -60,8 +61,9 @@ public class DegradedComparator implements Comparator<Degraded> {
}
/**
- * This method compares only the fields that are defined in Degraded class in
- * inheritence tree. It also calls the comparator for super class (Species).
+ * This method compares only the fields that are defined in DegradedAlias
+ * class in inheritence tree. By the design it calls also comparator of the
+ * upper (SpeciesAlias) class.
*
* @param arg0
* first object to compare
@@ -71,12 +73,11 @@ public class DegradedComparator implements Comparator<Degraded> {
* -1/1 is returned.
*/
private int internalCompare(Degraded arg0, Degraded arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
+ int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
-
return 0;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
similarity index 60%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
index 094acaecf4..1cfa4f2d2d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("DRUG_ALIAS")
-public class DrugAlias extends SpeciesAlias {
+public class Drug extends Species {
/**
*
*/
private static final long serialVersionUID = 1L;
- DrugAlias() {
+ Drug() {
}
- public DrugAlias(DrugAlias original) {
+ public Drug(Drug original) {
super(original);
}
- public DrugAlias(String aliasId) {
+ public Drug(String aliasId) {
setAliasId(aliasId);
}
@Override
- public DrugAlias copy() {
- if (this.getClass() == DrugAlias.class) {
- return new DrugAlias(this);
+ public Drug copy() {
+ if (this.getClass() == Drug.class) {
+ return new Drug(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
index bd512689ee..cc33157ba8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class DrugAliasComparator implements Comparator<DrugAlias> {
+public class DrugComparator implements Comparator<Drug> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DrugAliasComparator.class);
+ private static Logger logger = Logger.getLogger(DrugComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class DrugAliasComparator implements Comparator<DrugAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public DrugAliasComparator(double epsilon) {
+ public DrugComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public DrugAliasComparator() {
+ public DrugComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(DrugAlias arg0, DrugAlias arg1) {
+ public int compare(Drug arg0, Drug arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class DrugAliasComparator implements Comparator<DrugAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(DrugAlias.class)) {
+ if (arg0.getClass().equals(Drug.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class DrugAliasComparator implements Comparator<DrugAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(DrugAlias arg0, DrugAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(Drug arg0, Drug arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/Alias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
similarity index 96%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/Alias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index b2addc67b6..949081c1b2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/Alias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.awt.Color;
import java.awt.geom.Point2D;
@@ -40,6 +40,8 @@ import org.hibernate.annotations.IndexColumn;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -60,7 +62,7 @@ import lcsb.mapviewer.model.map.model.ModelData;
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@DiscriminatorColumn(name = "alias_type_db", discriminatorType = DiscriminatorType.STRING)
@DiscriminatorValue("GENERIC_ALIAS")
-public abstract class Alias implements AnnotatedObject, Serializable {
+public abstract class Element implements AnnotatedObject, Serializable {
/**
*
@@ -81,9 +83,9 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* Comparator of aliases that takes into consideration size (width*height) of
* aliases.
*/
- public static final Comparator<Alias> SIZE_COMPARATOR = new Comparator<Alias>() {
+ public static final Comparator<Element> SIZE_COMPARATOR = new Comparator<Element>() {
@Override
- public int compare(Alias alias1, Alias alias2) {
+ public int compare(Element alias1, Element alias2) {
double size = alias1.getWidth() * alias1.getHeight();
double size2 = alias2.getWidth() * alias2.getHeight();
@@ -100,7 +102,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(Alias.class);
+ private static Logger logger = Logger.getLogger(Element.class);
/**
* Database identifier.
@@ -119,7 +121,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
*/
@Cascade({ CascadeType.ALL })
@ManyToOne
- private Alias parent;
+ private Element parent;
/**
* Map model object to which alias belongs to.
@@ -138,7 +140,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* compartment then null value is assigned.
*/
@ManyToOne
- private CompartmentAlias compartmentAlias;
+ private Compartment compartmentAlias;
/**
* Unique string alias identifier within one model object (usually importet
@@ -272,7 +274,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* @param param
* source alias
*/
- protected Alias(Alias param) {
+ protected Element(Element param) {
aliasId = param.getAliasId();
x = param.getX();
y = param.getY();
@@ -308,7 +310,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
/**
* Default constructor.
*/
- protected Alias() {
+ protected Element() {
super();
aliasId = "";
x = 0.0;
@@ -510,8 +512,8 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* object to be checked
* @return true if alias2 lies in this object, false otherwise
*/
- public boolean contains(Alias alias2) {
- if (alias2 instanceof SpeciesAlias) {
+ public boolean contains(Element alias2) {
+ if (alias2 instanceof Species) {
Point2D p1 = new Point2D.Double(alias2.getX(), alias2.getY());
Point2D p2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight());
Point2D p3 = new Point2D.Double(alias2.getX() + alias2.getWidth(), alias2.getY());
@@ -529,7 +531,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
*
* @return copy of the alias
*/
- public abstract Alias copy();
+ public abstract Element copy();
/**
*
@@ -640,7 +642,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* @return the parent
* @see #parent
*/
- public Alias getParent() {
+ public Element getParent() {
return parent;
}
@@ -649,7 +651,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* the parent to set
* @see #parent
*/
- public void setParent(Alias parent) {
+ public void setParent(Element parent) {
this.parent = parent;
}
@@ -708,7 +710,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* @return the compartmentAlias
* @see #compartmentAlias
*/
- public CompartmentAlias getCompartmentAlias() {
+ public Compartment getCompartmentAlias() {
return compartmentAlias;
}
@@ -717,7 +719,7 @@ public abstract class Alias implements AnnotatedObject, Serializable {
* the compartmentAlias to set
* @see #compartmentAlias
*/
- public void setCompartmentAlias(CompartmentAlias compartmentAlias) {
+ public void setCompartmentAlias(Compartment compartmentAlias) {
this.compartmentAlias = compartmentAlias;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
similarity index 86%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index 6f479bbe47..382f342c6c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
import java.util.HashSet;
@@ -14,6 +14,8 @@ import lcsb.mapviewer.common.comparator.StringListComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnectionComparator;
/**
@@ -23,11 +25,11 @@ import lcsb.mapviewer.model.map.model.AliasSubmodelConnectionComparator;
* @author Piotr Gawron
*
*/
-public class AliasComparator implements Comparator<Alias> {
+public class ElementComparator implements Comparator<Element> {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(AliasComparator.class);
+ private static Logger logger = Logger.getLogger(ElementComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -40,19 +42,19 @@ public class AliasComparator implements Comparator<Alias> {
* @param epsilon
* {@link #epsilon}
*/
- public AliasComparator(double epsilon) {
+ public ElementComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public AliasComparator() {
+ public ElementComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(Alias arg0, Alias arg1) {
+ public int compare(Element arg0, Element arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -64,15 +66,15 @@ public class AliasComparator implements Comparator<Alias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0 instanceof ComplexAlias) {
- ComplexAliasComparator caComparator = new ComplexAliasComparator(epsilon);
- return caComparator.compare((ComplexAlias) arg0, (ComplexAlias) arg1);
- } else if (arg0 instanceof CompartmentAlias) {
- CompartmentAliasComparator caComparator = new CompartmentAliasComparator(epsilon);
- return caComparator.compare((CompartmentAlias) arg0, (CompartmentAlias) arg1);
- } else if (arg0 instanceof SpeciesAlias) {
- SpeciesAliasComparator caComparator = new SpeciesAliasComparator(epsilon);
- return caComparator.compare((SpeciesAlias) arg0, (SpeciesAlias) arg1);
+ if (arg0 instanceof Complex) {
+ ComplexComparator caComparator = new ComplexComparator(epsilon);
+ return caComparator.compare((Complex) arg0, (Complex) arg1);
+ } else if (arg0 instanceof Compartment) {
+ CompartmentComparator caComparator = new CompartmentComparator(epsilon);
+ return caComparator.compare((Compartment) arg0, (Compartment) arg1);
+ } else if (arg0 instanceof Species) {
+ SpeciesComparator caComparator = new SpeciesComparator(epsilon);
+ return caComparator.compare((Species) arg0, (Species) arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
}
@@ -93,7 +95,7 @@ public class AliasComparator implements Comparator<Alias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- public int internalCompare(Alias arg0, Alias arg1) {
+ public int internalCompare(Element arg0, Element arg1) {
StringComparator stringComparator = new StringComparator();
IntegerComparator integerComparator = new IntegerComparator();
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
similarity index 62%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
index fc4f77e53e..12b015a77b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
@@ -13,10 +13,11 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@Entity
@DiscriminatorValue("GENE_ALIAS")
-public class GeneAlias extends SpeciesAlias {
+public class Gene extends Species {
/**
*
@@ -29,32 +30,32 @@ public class GeneAlias extends SpeciesAlias {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "species", orphanRemoval = true)
@LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidueAlias> modificationResidues = new ArrayList<>();
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
- GeneAlias() {
+ Gene() {
}
- public GeneAlias(GeneAlias original) {
+ public Gene(Gene original) {
super(original);
- for (ModificationResidueAlias mr : original.getModificationResidues()) {
- addModificationResidue(new ModificationResidueAlias(mr));
+ for (ModificationResidue mr : original.getModificationResidues()) {
+ addModificationResidue(new ModificationResidue(mr));
}
}
- public void addModificationResidue(ModificationResidueAlias modificationResidue) {
+ public void addModificationResidue(ModificationResidue modificationResidue) {
modificationResidues.add(modificationResidue);
modificationResidue.setSpecies(this);
}
- public GeneAlias(String aliasId) {
+ public Gene(String aliasId) {
setAliasId(aliasId);
}
@Override
- public GeneAlias copy() {
- if (this.getClass() == GeneAlias.class) {
- return new GeneAlias(this);
+ public Gene copy() {
+ if (this.getClass() == Gene.class) {
+ return new Gene(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -64,7 +65,7 @@ public class GeneAlias extends SpeciesAlias {
* @return the modificationResidues
* @see #modificationResidues
*/
- public List<ModificationResidueAlias> getModificationResidues() {
+ public List<ModificationResidue> getModificationResidues() {
return modificationResidues;
}
@@ -73,7 +74,7 @@ public class GeneAlias extends SpeciesAlias {
* the modificationResidues to set
* @see #modificationResidues
*/
- public void setModificationResidues(List<ModificationResidueAlias> modificationResidues) {
+ public void setModificationResidues(List<ModificationResidue> modificationResidues) {
this.modificationResidues = modificationResidues;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
index 111f52eee1..0481515dbf 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class GeneAliasComparator implements Comparator<GeneAlias> {
+public class GeneComparator implements Comparator<Gene> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GeneAliasComparator.class);
+ private static Logger logger = Logger.getLogger(GeneComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class GeneAliasComparator implements Comparator<GeneAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public GeneAliasComparator(double epsilon) {
+ public GeneComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public GeneAliasComparator() {
+ public GeneComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(GeneAlias arg0, GeneAlias arg1) {
+ public int compare(Gene arg0, Gene arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class GeneAliasComparator implements Comparator<GeneAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(GeneAlias.class)) {
+ if (arg0.getClass().equals(Gene.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class GeneAliasComparator implements Comparator<GeneAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(GeneAlias arg0, GeneAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(Gene arg0, Gene arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
similarity index 52%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
index c8a4556809..aa919053ca 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("GENERIC_PROTEIN_ALIAS")
-public class GenericProteinAlias extends ProteinAlias {
+public class GenericProtein extends Protein {
/**
*
*/
private static final long serialVersionUID = 1L;
- GenericProteinAlias() {
+ GenericProtein() {
}
- public GenericProteinAlias(String aliasId) {
+ public GenericProtein(String aliasId) {
super(aliasId);
}
- public GenericProteinAlias(GenericProteinAlias original) {
+ public GenericProtein(GenericProtein original) {
super(original);
}
@Override
- public GenericProteinAlias copy() {
- if (this.getClass() == GenericProteinAlias.class) {
- return new GenericProteinAlias(this);
+ public GenericProtein copy() {
+ if (this.getClass() == GenericProtein.class) {
+ return new GenericProtein(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
similarity index 64%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
index 0b7f83b6e6..6b11bf5ef2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class GenericProteinAliasComparator implements Comparator<GenericProteinAlias> {
+public class GenericProteinComparator implements Comparator<GenericProtein> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GenericProteinAliasComparator.class);
+ private static Logger logger = Logger.getLogger(GenericProteinComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -27,19 +27,19 @@ public class GenericProteinAliasComparator implements Comparator<GenericProteinA
* @param epsilon
* {@link #epsilon}
*/
- public GenericProteinAliasComparator(double epsilon) {
+ public GenericProteinComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public GenericProteinAliasComparator() {
+ public GenericProteinComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(GenericProteinAlias arg0, GenericProteinAlias arg1) {
+ public int compare(GenericProtein arg0, GenericProtein arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -51,7 +51,7 @@ public class GenericProteinAliasComparator implements Comparator<GenericProteinA
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(GenericProteinAlias.class)) {
+ if (arg0.getClass().equals(GenericProtein.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -63,8 +63,8 @@ public class GenericProteinAliasComparator implements Comparator<GenericProteinA
/**
* This method compares only the fields that are defined in
- * {@link GenericProteinAlias} class in inheritence tree. By the design it
- * calls also comparator of the upper ({@link ProteinAlias}) class.
+ * {@link GenericProtein} class in inheritence tree. By the design it
+ * calls also comparator of the upper ({@link Protein}) class.
*
* @param arg0
* first object to compare
@@ -73,8 +73,8 @@ public class GenericProteinAliasComparator implements Comparator<GenericProteinA
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(GenericProteinAlias arg0, GenericProteinAlias arg1) {
- ProteinAliasComparator proteinAliasComparator = new ProteinAliasComparator(epsilon);
+ private int internalCompare(GenericProtein arg0, GenericProtein arg1) {
+ ProteinComparator proteinAliasComparator = new ProteinComparator(epsilon);
int result = proteinAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
similarity index 61%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
index 874434612a..88bcd9956d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("ION_ALIAS")
-public class IonAlias extends ChemicalAlias {
+public class Ion extends Chemical {
/**
*
*/
private static final long serialVersionUID = 1L;
- IonAlias() {
+ Ion() {
}
- public IonAlias(IonAlias original) {
+ public Ion(Ion original) {
super(original);
}
- public IonAlias(String aliasId) {
+ public Ion(String aliasId) {
setAliasId(aliasId);
}
@Override
- public IonAlias copy() {
- if (this.getClass() == IonAlias.class) {
- return new IonAlias(this);
+ public Ion copy() {
+ if (this.getClass() == Ion.class) {
+ return new Ion(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
similarity index 51%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
index a30b28d3b0..56463dfcb0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("ION_CHANNEL_PROTEIN_ALIAS")
-public class IonChannelProteinAlias extends ProteinAlias {
+public class IonChannelProtein extends Protein {
/**
*
*/
private static final long serialVersionUID = 1L;
- IonChannelProteinAlias() {
+ IonChannelProtein() {
}
- public IonChannelProteinAlias(IonChannelProteinAlias original) {
+ public IonChannelProtein(IonChannelProtein original) {
super(original);
}
- public IonChannelProteinAlias(String aliasId) {
+ public IonChannelProtein(String aliasId) {
setAliasId(aliasId);
}
@Override
- public IonChannelProteinAlias copy() {
- if (this.getClass() == IonChannelProteinAlias.class) {
- return new IonChannelProteinAlias(this);
+ public IonChannelProtein copy() {
+ if (this.getClass() == IonChannelProtein.class) {
+ return new IonChannelProtein(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
similarity index 69%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
index 2a8c9de3e2..276547baee 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class IonChannelProteinAliasComparator implements Comparator<IonChannelProteinAlias> {
+public class IonChannelProteinComparator implements Comparator<IonChannelProtein> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(IonChannelProteinAliasComparator.class);
+ private static Logger logger = Logger.getLogger(IonChannelProteinComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class IonChannelProteinAliasComparator implements Comparator<IonChannelPr
* @param epsilon
* {@link #epsilon}
*/
- public IonChannelProteinAliasComparator(double epsilon) {
+ public IonChannelProteinComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public IonChannelProteinAliasComparator() {
+ public IonChannelProteinComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(IonChannelProteinAlias arg0, IonChannelProteinAlias arg1) {
+ public int compare(IonChannelProtein arg0, IonChannelProtein arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class IonChannelProteinAliasComparator implements Comparator<IonChannelPr
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(IonChannelProteinAlias.class)) {
+ if (arg0.getClass().equals(IonChannelProtein.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class IonChannelProteinAliasComparator implements Comparator<IonChannelPr
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(IonChannelProteinAlias arg0, IonChannelProteinAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(IonChannelProtein arg0, IonChannelProtein arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
similarity index 70%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
index 352ad337ba..e17cad0f42 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
@@ -1,23 +1,24 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-/**
- * This class implements comparator interface for Ion.
- *
- * @author Piotr Gawron
- *
- * @see Ion
- */
public class IonComparator implements Comparator<Ion> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(IonComparator.class);
+
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -60,9 +61,9 @@ public class IonComparator implements Comparator<Ion> {
}
/**
- * This method compares only the fields that are defined in {@link Ion} class
- * in inheritence tree. It also calls the {@link SpeciesComparator} for the
- * super class ( {@link Species}).
+ * This method compares only the fields that are defined in {@link Ion}
+ * class in inheritence tree. By the design it calls also comparator of the
+ * upper {@link Chemical} class.
*
* @param arg0
* first object to compare
@@ -72,12 +73,11 @@ public class IonComparator implements Comparator<Ion> {
* -1/1 is returned.
*/
private int internalCompare(Ion arg0, Ion arg1) {
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
- int result = speciesComparator.internalCompare(arg0, arg1);
+ ChemicalComparator speciesAliasComparator = new ChemicalComparator(epsilon);
+ int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
}
return 0;
}
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
similarity index 58%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
index 527a2a3284..c360b50a3f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,28 +7,28 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("PHENTOYPE_ALIAS")
-public class PhenotypeAlias extends SpeciesAlias {
+public class Phenotype extends Species {
/**
*
*/
private static final long serialVersionUID = 1L;
- PhenotypeAlias() {
+ Phenotype() {
}
- public PhenotypeAlias(PhenotypeAlias original) {
+ public Phenotype(Phenotype original) {
super(original);
}
- public PhenotypeAlias(String aliasId) {
+ public Phenotype(String aliasId) {
setAliasId(aliasId);
}
@Override
- public PhenotypeAlias copy() {
- if (this.getClass() == PhenotypeAlias.class) {
- return new PhenotypeAlias(this);
+ public Phenotype copy() {
+ if (this.getClass() == Phenotype.class) {
+ return new Phenotype(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
similarity index 69%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
index f4891b9942..ad63c97a93 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class PhenotypeAliasComparator implements Comparator<PhenotypeAlias> {
+public class PhenotypeComparator implements Comparator<Phenotype> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PhenotypeAliasComparator.class);
+ private static Logger logger = Logger.getLogger(PhenotypeComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class PhenotypeAliasComparator implements Comparator<PhenotypeAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public PhenotypeAliasComparator(double epsilon) {
+ public PhenotypeComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public PhenotypeAliasComparator() {
+ public PhenotypeComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(PhenotypeAlias arg0, PhenotypeAlias arg1) {
+ public int compare(Phenotype arg0, Phenotype arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class PhenotypeAliasComparator implements Comparator<PhenotypeAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(PhenotypeAlias.class)) {
+ if (arg0.getClass().equals(Phenotype.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class PhenotypeAliasComparator implements Comparator<PhenotypeAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(PhenotypeAlias arg0, PhenotypeAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(Phenotype arg0, Phenotype arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
similarity index 69%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
index 95d79fd264..7149cffe9d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
@@ -12,9 +12,11 @@ import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
@Entity
@DiscriminatorValue("PROTEIN_ALIAS")
-public abstract class ProteinAlias extends SpeciesAlias {
+public abstract class Protein extends Species {
/**
*
@@ -32,20 +34,20 @@ public abstract class ProteinAlias extends SpeciesAlias {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "species", orphanRemoval = true)
@LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidueAlias> modificationResidues = new ArrayList<>();
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
- ProteinAlias() {
+ Protein() {
}
- public ProteinAlias(ProteinAlias original) {
+ public Protein(Protein original) {
super(original);
this.structuralState = original.getStructuralState();
- for (ModificationResidueAlias mr : original.getModificationResidues()) {
- addModificationResidue(new ModificationResidueAlias(mr));
+ for (ModificationResidue mr : original.getModificationResidues()) {
+ addModificationResidue(new ModificationResidue(mr));
}
}
- public ProteinAlias(String aliasId) {
+ public Protein(String aliasId) {
super(aliasId);
}
@@ -55,7 +57,7 @@ public abstract class ProteinAlias extends SpeciesAlias {
* @param modificationResidue
* modification to add
*/
- public void addModificationResidue(ModificationResidueAlias modificationResidue) {
+ public void addModificationResidue(ModificationResidue modificationResidue) {
modificationResidues.add(modificationResidue);
modificationResidue.setSpecies(this);
}
@@ -64,7 +66,7 @@ public abstract class ProteinAlias extends SpeciesAlias {
* @return the modificationResidues
* @see #modificationResidues
*/
- public List<ModificationResidueAlias> getModificationResidues() {
+ public List<ModificationResidue> getModificationResidues() {
return modificationResidues;
}
@@ -72,7 +74,7 @@ public abstract class ProteinAlias extends SpeciesAlias {
* @param modificationResidues the modificationResidues to set
* @see #modificationResidues
*/
- public void setModificationResidues(List<ModificationResidueAlias> modificationResidues) {
+ public void setModificationResidues(List<ModificationResidue> modificationResidues) {
this.modificationResidues = modificationResidues;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
similarity index 51%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
index 2ef10ac313..5b0840457e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,23 +7,23 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class ProteinAliasComparator implements Comparator<ProteinAlias> {
+public class ProteinComparator implements Comparator<Protein> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ProteinAliasComparator.class);
+ private static Logger logger = Logger.getLogger(ProteinComparator.class);
/**
* Epsilon value used for comparison of doubles.
*/
private double epsilon;
- private GenericProteinAliasComparator genericProteinAliasComparator;
- private IonChannelProteinAliasComparator ionChannelProteinAliasComparator;
- private ReceptorProteinAliasComparator receptorProteinAliasComparator;
- private TruncatedProteinAliasComparator truncatedProteinAliasComparator;
+ private GenericProteinComparator genericProteinAliasComparator;
+ private IonChannelProteinComparator ionChannelProteinAliasComparator;
+ private ReceptorProteinComparator receptorProteinAliasComparator;
+ private TruncatedProteinComparator truncatedProteinAliasComparator;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -31,23 +31,23 @@ public class ProteinAliasComparator implements Comparator<ProteinAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public ProteinAliasComparator(double epsilon) {
+ public ProteinComparator(double epsilon) {
this.epsilon = epsilon;
- genericProteinAliasComparator = new GenericProteinAliasComparator(epsilon);
- ionChannelProteinAliasComparator = new IonChannelProteinAliasComparator(epsilon);
- receptorProteinAliasComparator = new ReceptorProteinAliasComparator(epsilon);
- truncatedProteinAliasComparator = new TruncatedProteinAliasComparator(epsilon);
+ genericProteinAliasComparator = new GenericProteinComparator(epsilon);
+ ionChannelProteinAliasComparator = new IonChannelProteinComparator(epsilon);
+ receptorProteinAliasComparator = new ReceptorProteinComparator(epsilon);
+ truncatedProteinAliasComparator = new TruncatedProteinComparator(epsilon);
}
/**
* Default constructor.
*/
- public ProteinAliasComparator() {
+ public ProteinComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(ProteinAlias arg0, ProteinAlias arg1) {
+ public int compare(Protein arg0, Protein arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -59,16 +59,16 @@ public class ProteinAliasComparator implements Comparator<ProteinAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(ProteinAlias.class)) {
+ if (arg0.getClass().equals(Protein.class)) {
return internalCompare(arg0, arg1);
- } else if (arg0.getClass().equals(GenericProteinAlias.class)) {
- return genericProteinAliasComparator.compare((GenericProteinAlias) arg0, (GenericProteinAlias) arg1);
- } else if (arg0.getClass().equals(IonChannelProteinAlias.class)) {
- return ionChannelProteinAliasComparator.compare((IonChannelProteinAlias) arg0, (IonChannelProteinAlias) arg1);
- } else if (arg0.getClass().equals(ReceptorProteinAlias.class)) {
- return receptorProteinAliasComparator.compare((ReceptorProteinAlias) arg0, (ReceptorProteinAlias) arg1);
- } else if (arg0.getClass().equals(TruncatedProteinAlias.class)) {
- return truncatedProteinAliasComparator.compare((TruncatedProteinAlias) arg0, (TruncatedProteinAlias) arg1);
+ } else if (arg0.getClass().equals(GenericProtein.class)) {
+ return genericProteinAliasComparator.compare((GenericProtein) arg0, (GenericProtein) arg1);
+ } else if (arg0.getClass().equals(IonChannelProtein.class)) {
+ return ionChannelProteinAliasComparator.compare((IonChannelProtein) arg0, (IonChannelProtein) arg1);
+ } else if (arg0.getClass().equals(ReceptorProtein.class)) {
+ return receptorProteinAliasComparator.compare((ReceptorProtein) arg0, (ReceptorProtein) arg1);
+ } else if (arg0.getClass().equals(TruncatedProtein.class)) {
+ return truncatedProteinAliasComparator.compare((TruncatedProtein) arg0, (TruncatedProtein) arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
}
@@ -89,8 +89,8 @@ public class ProteinAliasComparator implements Comparator<ProteinAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- int internalCompare(ProteinAlias arg0, ProteinAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ int internalCompare(Protein arg0, Protein arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
similarity index 52%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
index 26d5b88d83..71e5c768c2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("RECEPTOR_PROTEIN_ALIAS")
-public class ReceptorProteinAlias extends ProteinAlias {
+public class ReceptorProtein extends Protein {
/**
*
*/
private static final long serialVersionUID = 1L;
- ReceptorProteinAlias() {
+ ReceptorProtein() {
}
- public ReceptorProteinAlias(ReceptorProteinAlias original) {
+ public ReceptorProtein(ReceptorProtein original) {
super(original);
}
- public ReceptorProteinAlias(String aliasId) {
+ public ReceptorProtein(String aliasId) {
super(aliasId);
}
@Override
- public ReceptorProteinAlias copy() {
- if (this.getClass() == ReceptorProteinAlias.class) {
- return new ReceptorProteinAlias(this);
+ public ReceptorProtein copy() {
+ if (this.getClass() == ReceptorProtein.class) {
+ return new ReceptorProtein(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
index d4e9d1432a..f0bc587d0e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class ReceptorProteinAliasComparator implements Comparator<ReceptorProteinAlias> {
+public class ReceptorProteinComparator implements Comparator<ReceptorProtein> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ReceptorProteinAliasComparator.class);
+ private static Logger logger = Logger.getLogger(ReceptorProteinComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class ReceptorProteinAliasComparator implements Comparator<ReceptorProtei
* @param epsilon
* {@link #epsilon}
*/
- public ReceptorProteinAliasComparator(double epsilon) {
+ public ReceptorProteinComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public ReceptorProteinAliasComparator() {
+ public ReceptorProteinComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(ReceptorProteinAlias arg0, ReceptorProteinAlias arg1) {
+ public int compare(ReceptorProtein arg0, ReceptorProtein arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class ReceptorProteinAliasComparator implements Comparator<ReceptorProtei
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(ReceptorProteinAlias.class)) {
+ if (arg0.getClass().equals(ReceptorProtein.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class ReceptorProteinAliasComparator implements Comparator<ReceptorProtei
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(ReceptorProteinAlias arg0, ReceptorProteinAlias arg1) {
- ProteinAliasComparator proteinAliasComparator = new ProteinAliasComparator(epsilon);
+ private int internalCompare(ReceptorProtein arg0, ReceptorProtein arg1) {
+ ProteinComparator proteinAliasComparator = new ProteinComparator(epsilon);
int result = proteinAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
similarity index 64%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
index 02276dd2cc..a06bcb114b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.ArrayList;
import java.util.List;
@@ -13,10 +13,11 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
@Entity
@DiscriminatorValue("RNA_ALIAS")
-public class RnaAlias extends SpeciesAlias {
+public class Rna extends Species {
/**
*
@@ -29,32 +30,32 @@ public class RnaAlias extends SpeciesAlias {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "species", orphanRemoval = true)
@LazyCollection(LazyCollectionOption.FALSE)
- private List<RnaRegionAlias> regions = new ArrayList<>();
+ private List<RnaRegion> regions = new ArrayList<>();
- RnaAlias() {
+ Rna() {
}
- public RnaAlias(RnaAlias original) {
+ public Rna(Rna original) {
super(original);
- for (RnaRegionAlias region : original.getRegions()) {
- addRegion(new RnaRegionAlias(region));
+ for (RnaRegion region : original.getRegions()) {
+ addRegion(new RnaRegion(region));
}
}
- public RnaAlias(String aliasId) {
+ public Rna(String aliasId) {
super();
setAliasId(aliasId);
}
- public void addRegion(RnaRegionAlias rnaRegionAlias) {
+ public void addRegion(RnaRegion rnaRegionAlias) {
regions.add(rnaRegionAlias);
rnaRegionAlias.setSpecies(this);
}
@Override
- public RnaAlias copy() {
- if (this.getClass() == RnaAlias.class) {
- return new RnaAlias(this);
+ public Rna copy() {
+ if (this.getClass() == Rna.class) {
+ return new Rna(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -64,7 +65,7 @@ public class RnaAlias extends SpeciesAlias {
* @return the regions
* @see #regions
*/
- public List<RnaRegionAlias> getRegions() {
+ public List<RnaRegion> getRegions() {
return regions;
}
@@ -73,7 +74,7 @@ public class RnaAlias extends SpeciesAlias {
* the regions to set
* @see #regions
*/
- public void setRegions(List<RnaRegionAlias> regions) {
+ public void setRegions(List<RnaRegion> regions) {
this.regions = regions;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
similarity index 71%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
index 180425ff2f..d5d3e6086a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class RnaAliasComparator implements Comparator<RnaAlias> {
+public class RnaComparator implements Comparator<Rna> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaAliasComparator.class);
+ private static Logger logger = Logger.getLogger(RnaComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class RnaAliasComparator implements Comparator<RnaAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public RnaAliasComparator(double epsilon) {
+ public RnaComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public RnaAliasComparator() {
+ public RnaComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(RnaAlias arg0, RnaAlias arg1) {
+ public int compare(Rna arg0, Rna arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class RnaAliasComparator implements Comparator<RnaAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(RnaAlias.class)) {
+ if (arg0.getClass().equals(Rna.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class RnaAliasComparator implements Comparator<RnaAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(RnaAlias arg0, RnaAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(Rna arg0, Rna arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
similarity index 56%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
index 3d94966e2b..fbd3920c92 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("SIMPLE_MOLECULE_ALIAS")
-public class SimpleMoleculeAlias extends ChemicalAlias {
+public class SimpleMolecule extends Chemical {
/**
*
*/
private static final long serialVersionUID = 1L;
- SimpleMoleculeAlias() {
+ SimpleMolecule() {
}
- public SimpleMoleculeAlias(SimpleMoleculeAlias original) {
+ public SimpleMolecule(SimpleMolecule original) {
super(original);
}
- public SimpleMoleculeAlias(String aliasId) {
+ public SimpleMolecule(String aliasId) {
setAliasId(aliasId);
}
@Override
- public SimpleMoleculeAlias copy() {
- if (this.getClass() == SimpleMoleculeAlias.class) {
- return new SimpleMoleculeAlias(this);
+ public SimpleMolecule copy() {
+ if (this.getClass() == SimpleMolecule.class) {
+ return new SimpleMolecule(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
similarity index 67%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
index 39ddf57491..46cbd69a10 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class SimpleMoleculeAliasComparator implements Comparator<SimpleMoleculeAlias> {
+public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SimpleMoleculeAliasComparator.class);
+ private static Logger logger = Logger.getLogger(SimpleMoleculeComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class SimpleMoleculeAliasComparator implements Comparator<SimpleMoleculeA
* @param epsilon
* {@link #epsilon}
*/
- public SimpleMoleculeAliasComparator(double epsilon) {
+ public SimpleMoleculeComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public SimpleMoleculeAliasComparator() {
+ public SimpleMoleculeComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(SimpleMoleculeAlias arg0, SimpleMoleculeAlias arg1) {
+ public int compare(SimpleMolecule arg0, SimpleMolecule arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class SimpleMoleculeAliasComparator implements Comparator<SimpleMoleculeA
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(SimpleMoleculeAlias.class)) {
+ if (arg0.getClass().equals(SimpleMolecule.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class SimpleMoleculeAliasComparator implements Comparator<SimpleMoleculeA
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(SimpleMoleculeAlias arg0, SimpleMoleculeAlias arg1) {
- ChemicalAliasComparator chemicalAliasComparator = new ChemicalAliasComparator(epsilon);
+ private int internalCompare(SimpleMolecule arg0, SimpleMolecule arg1) {
+ ChemicalComparator chemicalAliasComparator = new ChemicalComparator(epsilon);
int result = chemicalAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
similarity index 89%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index d5c353c94b..0683317e47 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.HashSet;
import java.util.Set;
@@ -17,16 +17,17 @@ import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
/**
- * {@link Alias} structure used for representing {@link Species}.
+ * Structure used for representing information about single element.
*
* @author Piotr Gawron
*
*/
@Entity
@DiscriminatorValue("Species Alias")
-public abstract class SpeciesAlias extends Alias {
+public abstract class Species extends Element {
/**
*
@@ -37,7 +38,7 @@ public abstract class SpeciesAlias extends Alias {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SpeciesAlias.class);
+ private static Logger logger = Logger.getLogger(Species.class);
/**
* Is the alias active.
@@ -76,7 +77,7 @@ public abstract class SpeciesAlias extends Alias {
@ManyToOne
@Cascade({ CascadeType.ALL })
@JoinColumn(name = "idComplexAliasDb")
- private ComplexAlias complexAlias;
+ private Complex complexAlias;
/**
* List of reaction nodes that point to this alias.
@@ -125,9 +126,9 @@ public abstract class SpeciesAlias extends Alias {
* Cunstructor that set alias identifier.
*
* @param aliasId
- * {@link Alias#aliasId}
+ * {@link Element#aliasId}
*/
- public SpeciesAlias(String aliasId) {
+ public Species(String aliasId) {
this();
setAliasId(aliasId);
}
@@ -135,7 +136,7 @@ public abstract class SpeciesAlias extends Alias {
/**
* Default constructor.
*/
- public SpeciesAlias() {
+ public Species() {
super();
activity = false;
lineWidth = 1.0;
@@ -149,7 +150,7 @@ public abstract class SpeciesAlias extends Alias {
* @param alias
* object from which data will be initialized
*/
- public SpeciesAlias(SpeciesAlias alias) {
+ public Species(Species alias) {
super(alias);
activity = alias.getActivity();
lineWidth = alias.getLineWidth();
@@ -225,7 +226,7 @@ public abstract class SpeciesAlias extends Alias {
* @return the complexAlias
* @see #complexAlias
*/
- public ComplexAlias getComplexAlias() {
+ public Complex getComplexAlias() {
return complexAlias;
}
@@ -234,7 +235,7 @@ public abstract class SpeciesAlias extends Alias {
* the complexAlias to set
* @see #complexAlias
*/
- public void setComplexAlias(ComplexAlias complexAlias) {
+ public void setComplexAlias(Complex complexAlias) {
this.complexAlias = complexAlias;
}
@@ -289,7 +290,7 @@ public abstract class SpeciesAlias extends Alias {
this.aliasStateLabel = aliasStateLabel;
}
- public abstract SpeciesAlias copy();
+ public abstract Species copy();
/**
* @return the initialAmount
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
similarity index 59%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
index d9ebdf31f6..bf38449447 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -18,22 +18,22 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
* @author Piotr Gawron
*
*/
-public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
+public class SpeciesComparator implements Comparator<Species> {
/**
* Default class logger.
*/
- private Logger logger = Logger.getLogger(SpeciesAliasComparator.class);
-
- private AntisenseRnaAliasComparator antisenseRnaAliasComparator;
- private ChemicalAliasComparator chemicalAliasComparator;
- private ComplexAliasComparator complexAliasComparator;
- private DegradedAliasComparator degradedAliasComparator;
- private DrugAliasComparator drugAliasComparator;
- private GeneAliasComparator geneAliasComparator;
- private PhenotypeAliasComparator phenotypeAliasComparator;
- private ProteinAliasComparator proteinAliasComparator;
- private RnaAliasComparator rnaAliasComparator;
- private UnknownAliasComparator unknownAliasComparator;
+ private Logger logger = Logger.getLogger(SpeciesComparator.class);
+
+ private AntisenseRnaComparator antisenseRnaAliasComparator;
+ private ChemicalComparator chemicalAliasComparator;
+ private ComplexComparator complexAliasComparator;
+ private DegradedComparator degradedAliasComparator;
+ private DrugComparator drugAliasComparator;
+ private GeneComparator geneAliasComparator;
+ private PhenotypeComparator phenotypeAliasComparator;
+ private ProteinComparator proteinAliasComparator;
+ private RnaComparator rnaAliasComparator;
+ private UnknownComparator unknownAliasComparator;
/**
* Epsilon value used for comparison of doubles.
@@ -46,29 +46,29 @@ public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public SpeciesAliasComparator(double epsilon) {
+ public SpeciesComparator(double epsilon) {
this.epsilon = epsilon;
- antisenseRnaAliasComparator = new AntisenseRnaAliasComparator(epsilon);
- chemicalAliasComparator = new ChemicalAliasComparator(epsilon);
- complexAliasComparator = new ComplexAliasComparator(epsilon);
- degradedAliasComparator = new DegradedAliasComparator(epsilon);
- drugAliasComparator = new DrugAliasComparator(epsilon);
- geneAliasComparator = new GeneAliasComparator(epsilon);
- phenotypeAliasComparator = new PhenotypeAliasComparator(epsilon);
- proteinAliasComparator = new ProteinAliasComparator(epsilon);
- rnaAliasComparator = new RnaAliasComparator(epsilon);
- unknownAliasComparator = new UnknownAliasComparator(epsilon);
+ antisenseRnaAliasComparator = new AntisenseRnaComparator(epsilon);
+ chemicalAliasComparator = new ChemicalComparator(epsilon);
+ complexAliasComparator = new ComplexComparator(epsilon);
+ degradedAliasComparator = new DegradedComparator(epsilon);
+ drugAliasComparator = new DrugComparator(epsilon);
+ geneAliasComparator = new GeneComparator(epsilon);
+ phenotypeAliasComparator = new PhenotypeComparator(epsilon);
+ proteinAliasComparator = new ProteinComparator(epsilon);
+ rnaAliasComparator = new RnaComparator(epsilon);
+ unknownAliasComparator = new UnknownComparator(epsilon);
}
/**
* Default constructor.
*/
- public SpeciesAliasComparator() {
+ public SpeciesComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(SpeciesAlias arg0, SpeciesAlias arg1) {
+ public int compare(Species arg0, Species arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -80,27 +80,27 @@ public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(AntisenseRnaAlias.class)) {
- return antisenseRnaAliasComparator.compare((AntisenseRnaAlias) arg0, (AntisenseRnaAlias) arg1);
- } else if (arg0 instanceof ChemicalAlias) {
- return chemicalAliasComparator.compare((ChemicalAlias) arg0, (ChemicalAlias) arg1);
- } else if (arg0.getClass().equals(ComplexAlias.class)) {
- return complexAliasComparator.compare((ComplexAlias) arg0, (ComplexAlias) arg1);
- } else if (arg0.getClass().equals(DegradedAlias.class)) {
- return degradedAliasComparator.compare((DegradedAlias) arg0, (DegradedAlias) arg1);
- } else if (arg0.getClass().equals(DrugAlias.class)) {
- return drugAliasComparator.compare((DrugAlias) arg0, (DrugAlias) arg1);
- } else if (arg0.getClass().equals(GeneAlias.class)) {
- return geneAliasComparator.compare((GeneAlias) arg0, (GeneAlias) arg1);
- } else if (arg0.getClass().equals(PhenotypeAlias.class)) {
- return phenotypeAliasComparator.compare((PhenotypeAlias) arg0, (PhenotypeAlias) arg1);
- } else if (arg0 instanceof ProteinAlias) {
- return proteinAliasComparator.compare((ProteinAlias) arg0, (ProteinAlias) arg1);
- } else if (arg0.getClass().equals(RnaAlias.class)) {
- return rnaAliasComparator.compare((RnaAlias) arg0, (RnaAlias) arg1);
- } else if (arg0.getClass().equals(UnknownAlias.class)) {
- return unknownAliasComparator.compare((UnknownAlias) arg0, (UnknownAlias) arg1);
- } else if (arg0.getClass().equals(SpeciesAlias.class)) {
+ if (arg0.getClass().equals(AntisenseRna.class)) {
+ return antisenseRnaAliasComparator.compare((AntisenseRna) arg0, (AntisenseRna) arg1);
+ } else if (arg0 instanceof Chemical) {
+ return chemicalAliasComparator.compare((Chemical) arg0, (Chemical) arg1);
+ } else if (arg0.getClass().equals(Complex.class)) {
+ return complexAliasComparator.compare((Complex) arg0, (Complex) arg1);
+ } else if (arg0.getClass().equals(Degraded.class)) {
+ return degradedAliasComparator.compare((Degraded) arg0, (Degraded) arg1);
+ } else if (arg0.getClass().equals(Drug.class)) {
+ return drugAliasComparator.compare((Drug) arg0, (Drug) arg1);
+ } else if (arg0.getClass().equals(Gene.class)) {
+ return geneAliasComparator.compare((Gene) arg0, (Gene) arg1);
+ } else if (arg0.getClass().equals(Phenotype.class)) {
+ return phenotypeAliasComparator.compare((Phenotype) arg0, (Phenotype) arg1);
+ } else if (arg0 instanceof Protein) {
+ return proteinAliasComparator.compare((Protein) arg0, (Protein) arg1);
+ } else if (arg0.getClass().equals(Rna.class)) {
+ return rnaAliasComparator.compare((Rna) arg0, (Rna) arg1);
+ } else if (arg0.getClass().equals(Unknown.class)) {
+ return unknownAliasComparator.compare((Unknown) arg0, (Unknown) arg1);
+ } else if (arg0.getClass().equals(Species.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -112,8 +112,8 @@ public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
/**
* This method compares only the fields that are defined in
- * {@link SpeciesAlias} class in inheritence tree. By the design it calls also
- * comparator of the upper ({@link Alias}) class.
+ * {@link Species} class in inheritence tree. By the design it calls also
+ * comparator of the upper ({@link Element}) class.
*
* @param arg0
* first object to compare
@@ -122,8 +122,8 @@ public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- int internalCompare(SpeciesAlias arg0, SpeciesAlias arg1) {
- AliasComparator aliasComparator = new AliasComparator(epsilon);
+ int internalCompare(Species arg0, Species arg1) {
+ ElementComparator aliasComparator = new ElementComparator(epsilon);
int result = aliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
similarity index 51%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
index ba0ba2b653..58a3d8c52a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,27 +7,27 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("TRUNCATED_PROTEIN_ALIAS")
-public class TruncatedProteinAlias extends ProteinAlias {
+public class TruncatedProtein extends Protein {
/**
*
*/
private static final long serialVersionUID = 1L;
- TruncatedProteinAlias() {
+ TruncatedProtein() {
}
- public TruncatedProteinAlias(TruncatedProteinAlias original) {
+ public TruncatedProtein(TruncatedProtein original) {
super(original);
}
- public TruncatedProteinAlias(String aliasId) {
+ public TruncatedProtein(String aliasId) {
super(aliasId);
}
@Override
- public TruncatedProteinAlias copy() {
- if (this.getClass() == TruncatedProteinAlias.class) {
- return new TruncatedProteinAlias(this);
+ public TruncatedProtein copy() {
+ if (this.getClass() == TruncatedProtein.class) {
+ return new TruncatedProtein(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
index 224da1286f..a8918abee6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class TruncatedProteinAliasComparator implements Comparator<TruncatedProteinAlias> {
+public class TruncatedProteinComparator implements Comparator<TruncatedProtein> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(TruncatedProteinAliasComparator.class);
+ private static Logger logger = Logger.getLogger(TruncatedProteinComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class TruncatedProteinAliasComparator implements Comparator<TruncatedProt
* @param epsilon
* {@link #epsilon}
*/
- public TruncatedProteinAliasComparator(double epsilon) {
+ public TruncatedProteinComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public TruncatedProteinAliasComparator() {
+ public TruncatedProteinComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(TruncatedProteinAlias arg0, TruncatedProteinAlias arg1) {
+ public int compare(TruncatedProtein arg0, TruncatedProtein arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class TruncatedProteinAliasComparator implements Comparator<TruncatedProt
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(TruncatedProteinAlias.class)) {
+ if (arg0.getClass().equals(TruncatedProtein.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class TruncatedProteinAliasComparator implements Comparator<TruncatedProt
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(TruncatedProteinAlias arg0, TruncatedProteinAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(TruncatedProtein arg0, TruncatedProtein arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
similarity index 59%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
index c3122332c2..39e4ccaae6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -7,28 +7,28 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@DiscriminatorValue("UNKNOWN_ALIAS")
-public class UnknownAlias extends SpeciesAlias {
+public class Unknown extends Species {
/**
*
*/
private static final long serialVersionUID = 1L;
- UnknownAlias() {
+ Unknown() {
}
- public UnknownAlias(UnknownAlias original) {
+ public Unknown(Unknown original) {
super(original);
}
- public UnknownAlias(String aliasId) {
+ public Unknown(String aliasId) {
setAliasId(aliasId);
}
@Override
- public UnknownAlias copy() {
- if (this.getClass() == UnknownAlias.class) {
- return new UnknownAlias(this);
+ public Unknown copy() {
+ if (this.getClass() == Unknown.class) {
+ return new Unknown(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
similarity index 69%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAliasComparator.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
index 0a9583364b..b0654cd439 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import java.util.Comparator;
@@ -7,13 +7,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
-public class UnknownAliasComparator implements Comparator<UnknownAlias> {
+public class UnknownComparator implements Comparator<Unknown> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(UnknownAliasComparator.class);
+ private static Logger logger = Logger.getLogger(UnknownComparator.class);
/**
* Epsilon value used for comparison of doubles.
@@ -26,19 +26,19 @@ public class UnknownAliasComparator implements Comparator<UnknownAlias> {
* @param epsilon
* {@link #epsilon}
*/
- public UnknownAliasComparator(double epsilon) {
+ public UnknownComparator(double epsilon) {
this.epsilon = epsilon;
}
/**
* Default constructor.
*/
- public UnknownAliasComparator() {
+ public UnknownComparator() {
this(Configuration.EPSILON);
}
@Override
- public int compare(UnknownAlias arg0, UnknownAlias arg1) {
+ public int compare(Unknown arg0, Unknown arg1) {
if (arg0 == null) {
if (arg1 == null) {
return 0;
@@ -50,7 +50,7 @@ public class UnknownAliasComparator implements Comparator<UnknownAlias> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(UnknownAlias.class)) {
+ if (arg0.getClass().equals(Unknown.class)) {
return internalCompare(arg0, arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
@@ -72,8 +72,8 @@ public class UnknownAliasComparator implements Comparator<UnknownAlias> {
* @return if all fields are qual then returns 0. If they are different then
* -1/1 is returned.
*/
- private int internalCompare(UnknownAlias arg0, UnknownAlias arg1) {
- SpeciesAliasComparator speciesAliasComparator = new SpeciesAliasComparator(epsilon);
+ private int internalCompare(Unknown arg0, Unknown arg1) {
+ SpeciesComparator speciesAliasComparator = new SpeciesComparator(epsilon);
int result = speciesAliasComparator.internalCompare(arg0, arg1);
if (result != 0) {
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaRegionAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
similarity index 86%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaRegionAlias.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
index b2f96d7a56..1b0dfbac41 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaRegionAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species.field;
import java.io.Serializable;
@@ -18,12 +18,11 @@ import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
/**
* This structure contains information about antisense rna region (rna fragment
- * of interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna
- * AntisenseRna}.
+ * of interest) for a specific {@link AntisenseRna}.
*
* @author Piotr Gawron
*
@@ -31,7 +30,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
@Table(name = "antisense_rna_region_table_new")
@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class AntisenseRnaRegionAlias implements Serializable {
+public class AntisenseRnaRegion implements Serializable {
/**
*
@@ -40,8 +39,7 @@ public class AntisenseRnaRegionAlias implements Serializable {
/**
* Enum that enlists types of available modification regions in
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna
- * AntisenseRna}.
+ * {@link AntisenseRna}.
*
* @author Piotr Gawron
*
@@ -112,7 +110,7 @@ public class AntisenseRnaRegionAlias implements Serializable {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaRegionAlias.class.getName());
+ private static Logger logger = Logger.getLogger(AntisenseRnaRegion.class);
/**
* Unique identifier in the database.
@@ -171,12 +169,12 @@ public class AntisenseRnaRegionAlias implements Serializable {
@Cascade({ CascadeType.ALL })
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "idSpeciesDb")
- private AntisenseRnaAlias species;
+ private AntisenseRna species;
/**
* Default constructor.
*/
- public AntisenseRnaRegionAlias() {
+ public AntisenseRnaRegion() {
}
@@ -186,7 +184,7 @@ public class AntisenseRnaRegionAlias implements Serializable {
* @param original
* object from which we initialize data
*/
- public AntisenseRnaRegionAlias(AntisenseRnaRegionAlias original) {
+ public AntisenseRnaRegion(AntisenseRnaRegion original) {
this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
this.name = original.name;
this.size = original.size;
@@ -199,9 +197,9 @@ public class AntisenseRnaRegionAlias implements Serializable {
*
* @return copy of the object
*/
- public AntisenseRnaRegionAlias copy() {
- if (this.getClass() == AntisenseRnaRegionAlias.class) {
- return new AntisenseRnaRegionAlias(this);
+ public AntisenseRnaRegion copy() {
+ if (this.getClass() == AntisenseRnaRegion.class) {
+ return new AntisenseRnaRegion(this);
} else {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
@@ -245,7 +243,7 @@ public class AntisenseRnaRegionAlias implements Serializable {
* @param mr
* object from which we are updating data
*/
- public void update(AntisenseRnaRegionAlias mr) {
+ public void update(AntisenseRnaRegion mr) {
if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("") && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
throw new InvalidArgumentException("Cannot update from mr with different id");
}
@@ -374,7 +372,7 @@ public class AntisenseRnaRegionAlias implements Serializable {
* @return the species
* @see #species
*/
- public AntisenseRnaAlias getSpecies() {
+ public AntisenseRna getSpecies() {
return species;
}
@@ -383,7 +381,7 @@ public class AntisenseRnaRegionAlias implements Serializable {
* the species to set
* @see #species
*/
- public void setSpecies(AntisenseRnaAlias species) {
+ public void setSpecies(AntisenseRna species) {
this.species = species;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
similarity index 79%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
index 6d78eb82d1..fda2fe6567 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
@@ -1,13 +1,22 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.model.map.species.field;
import java.io.Serializable;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class represent modification residue in protein and gene. However, it is
@@ -17,6 +26,9 @@ import lcsb.mapviewer.model.map.layout.alias.ModificationState;
* @author Piotr Gawron
*
*/
+@Entity
+@Table(name = "modification_residue_table_new")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
public class ModificationResidue implements Serializable {
/**
@@ -30,6 +42,14 @@ public class ModificationResidue implements Serializable {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(ModificationResidue.class.getName());
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "iddb", unique = true, nullable = false)
+ private int id;
+
/**
* Identifier of the modification. Must be unique in single map model.
*/
@@ -64,7 +84,9 @@ public class ModificationResidue implements Serializable {
/**
* Species to which this modification belong to.
*/
- private Species species;
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = "idSpeciesDb", nullable = false)
+ private Species species;
/**
* Default constructor.
@@ -87,15 +109,6 @@ public class ModificationResidue implements Serializable {
this.state = mr.state;
}
- public ModificationResidue(ModificationResidueAlias mr) {
- this.idModificationResidue = mr.getIdModificationResidue();
- this.name = mr.getName();
- this.angle = mr.getAngle();
- this.size = mr.getSize();
- this.side = mr.getSide();
- this.state = mr.getState();
- }
-
/**
* Updates fields in the object with the data given in the parameter
* modification.
@@ -177,6 +190,23 @@ public class ModificationResidue implements Serializable {
}
}
+ /**
+ * @return the idModificationResidue
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the idModificationResidue to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
/**
* @return the id
* @see #idModificationResidue
@@ -296,16 +326,4 @@ public class ModificationResidue implements Serializable {
this.species = species;
}
- public ModificationResidueAlias createModificationResidueAlias() {
- ModificationResidueAlias result = new ModificationResidueAlias();
-
- result.setIdModificationResidue(this.getIdModificationResidue());
- result.setName(this.getName());
- result.setAngle(this.getAngle());
- result.setSize(this.getSize());
- result.setSide(this.getSide());
- result.setState(this.getState());
- return result;
- }
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationState.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationState.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
index 5fa20a125a..da3b3308eb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationState.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species.field;
/**
* Defines a type of modification (in protein or rna). Possible values are:
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/PositionToCompartment.java
similarity index 86%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartment.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/field/PositionToCompartment.java
index cb512ced9c..b9e143acd1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/PositionToCompartment.java
@@ -1,9 +1,9 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species.field;
/**
* Defines possible position of
* {@link lcsb.mapviewer.converter.model.celldesigner.structure.Species} on
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Compartment}.
+ * {@link lcsb.mapviewer.model.map.agregator.converter.model.celldesigner.structure.Compartment}.
*
* @author Piotr Gawron
*
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
similarity index 75%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
index 7846d84e8c..d50f5c7354 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
@@ -1,21 +1,32 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
+package lcsb.mapviewer.model.map.species.field;
import java.io.Serializable;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
+import lcsb.mapviewer.model.map.species.Rna;
/**
* This structure contains information about rna region (rna fragment of
- * interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
+ * interest) for a specific {@link Rna}.
*
* @author Piotr Gawron
*
*/
+@Entity
+@Table(name = "rna_region_table_new")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
public class RnaRegion implements Serializable {
/**
@@ -34,12 +45,20 @@ public class RnaRegion implements Serializable {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(RnaRegion.class.getName());
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "iddb", unique = true, nullable = false)
+ private int id;
+
/**
* Identifier of the region. Unique in the
* {@link lcsb.mapviewer.model.map.model.Model}.
*/
+ @Column(name = "idrnaregion")
private String idRnaRegion = "";
-
/**
* Type of the region in the rna. There are three possible values:
* <ul>
@@ -48,6 +67,8 @@ public class RnaRegion implements Serializable {
* <li>Modification site.</li>
* </ul>
*/
+
+ @Column(name = "type")
private String type = "";
/**
@@ -55,27 +76,33 @@ public class RnaRegion implements Serializable {
*
* @see ModificationState
*/
+ @Column(name = "state")
private ModificationState state = null;
/**
* Name of the region.
*/
+ @Column(name = "name")
private String name = "";
/**
* Size of the region in the graphic representation.
*/
+ @Column(name = "size")
private double size = DEFAULT_SIZE;
/**
* Position on the species in graphic representation.
*/
+ @Column(name = "pos")
private Double pos;
/**
* Defines a species where the region belongs to.
*/
- private Rna species;
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = "idSpeciesDb")
+ private Rna species;
/**
* Default constructor.
@@ -91,6 +118,7 @@ public class RnaRegion implements Serializable {
* original {@link RnaRegion}
*/
public RnaRegion(RnaRegion mr) {
+ this.id = mr.id;
this.idRnaRegion = mr.idRnaRegion;
this.size = mr.size;
setPos(mr.getPos());
@@ -160,6 +188,23 @@ public class RnaRegion implements Serializable {
}
+ /**
+ * @return the idRnaRegion
+ * @see #idRnaRegion
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the idRnaRegion to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
/**
* @return the id
* @see #id
@@ -279,15 +324,4 @@ public class RnaRegion implements Serializable {
this.species = species;
}
- public RnaRegionAlias createRnaRegionAlias() {
- RnaRegionAlias result = new RnaRegionAlias();
- result.setIdRnaRegion(this.idRnaRegion);
- result.setSize(this.size);
- result.setPos(this.getPos());
- result.setType(this.type);
- result.setState(this.state);
- result.setName(this.name);
- return result;
- }
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
similarity index 70%
rename from model/src/main/java/lcsb/mapviewer/model/map/layout/alias/package-info.java
rename to model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
index be05884687..274edba7f6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package provides data structures that stores information about aliases
- * for the map elements.
- */
-package lcsb.mapviewer.model.map.layout.alias;
-
+/**
+ * This package provides data structures that stores information about aliases
+ * for the map elements.
+ */
+package lcsb.mapviewer.model.map.species;
+
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 0ed029d9d2..dfa46de1b5 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -13,8 +13,8 @@ import org.reflections.Reflections;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Class with some util method for {@link AnnotatedObject} objects.
@@ -32,9 +32,9 @@ public final class ElementUtils {
/**
* Map between class names (used as user input) and implementation of
- * {@link Alias} class.
+ * {@link Element} class.
*/
- private static Map<String, Class<? extends Alias>> elementClasses = null;
+ private static Map<String, Class<? extends Element>> elementClasses = null;
/**
* Map between class names (used as user input) and implementation of
@@ -73,8 +73,8 @@ public final class ElementUtils {
*/
public String getElementTag(AnnotatedObject element, Object annotator) {
String id = null;
- if (element instanceof Alias) {
- id = ((Alias) element).getAliasId();
+ if (element instanceof Element) {
+ id = ((Element) element).getAliasId();
} else if (element instanceof Reaction) {
id = ((Reaction) element).getIdReaction();
} else {
@@ -143,14 +143,14 @@ public final class ElementUtils {
}
/**
- * Returns list of classes that extends {@link Alias} class, but don't have
+ * Returns list of classes that extends {@link Element} class, but don't have
* children (leaves in the hierarchy tree).
*
- * @return list of classes that extends {@link Alias} class, but don't have
+ * @return list of classes that extends {@link Element} class, but don't have
* children (leaves in the hierarchy tree)
*/
- public List<Class<? extends Alias>> getAvailableElementSubclasses() {
- List<Class<? extends Alias>> result = new ArrayList<Class<? extends Alias>>();
+ public List<Class<? extends Element>> getAvailableElementSubclasses() {
+ List<Class<? extends Element>> result = new ArrayList<Class<? extends Element>>();
if (elementClasses == null) {
refreshClasses();
}
@@ -160,18 +160,18 @@ public final class ElementUtils {
}
/**
- * Refresh list of known implementation of {@link Alias} class.
+ * Refresh list of known implementation of {@link Element} class.
*/
protected void refreshClasses() {
- List<Class<? extends Alias>> tmp = new ArrayList<>();
+ List<Class<? extends Element>> tmp = new ArrayList<>();
Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
- elementClasses = new HashMap<String, Class<? extends Alias>>();
- Set<Class<? extends Alias>> classes = reflections.getSubTypesOf(Alias.class);
+ elementClasses = new HashMap<String, Class<? extends Element>>();
+ Set<Class<? extends Element>> classes = reflections.getSubTypesOf(Element.class);
Set<Class<?>> toRemove = new HashSet<Class<?>>();
- for (Class<? extends Alias> class1 : classes) {
+ for (Class<? extends Element> class1 : classes) {
if (class1.isAnonymousClass() || class1.isMemberClass() || class1.isLocalClass()) {
continue;
}
@@ -181,7 +181,7 @@ public final class ElementUtils {
for (Class<?> clazz : toRemove) {
tmp.remove(clazz);
}
- for (Class<? extends Alias> class1 : tmp) {
+ for (Class<? extends Element> class1 : tmp) {
elementClasses.put(class1.getSimpleName(), class1);
}
@@ -248,7 +248,7 @@ public final class ElementUtils {
* the elementClasses to set
* @see #elementClasses
*/
- protected static void setElementClasses(Map<String, Class<? extends Alias>> elementClasses) {
+ protected static void setElementClasses(Map<String, Class<? extends Element>> elementClasses) {
ElementUtils.elementClasses = elementClasses;
}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
index 14364ccac3..2a844090f0 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
@@ -1,15 +1,15 @@
package lcsb.mapviewer.modelutils.map;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
/**
* List of {@link AnnotatedObject} that must be annototed with at least one
@@ -28,42 +28,42 @@ public enum RequireAnnotationMap {
/**
* {@link Protein}.
*/
- PROTEIN(ProteinAlias.class),
+ PROTEIN(Protein.class),
/**
* {@link Chemical}.
*/
- CHECMICAL(ChemicalAlias.class),
+ CHECMICAL(Chemical.class),
/**
* {@link Rna}.
*/
- RNA(RnaAlias.class),
+ RNA(Rna.class),
/**
* {@link Gene}.
*/
- GENE(GeneAlias.class),
+ GENE(Gene.class),
/**
* {@link Drug}.
*/
- DRUG(DrugAlias.class),
+ DRUG(Drug.class),
/**
* {@link ComplexSpecies}.
*/
- COMPLEX(ComplexAlias.class),
+ COMPLEX(Complex.class),
/**
* {@link AntisenseRna}.
*/
- ANTISENSE_RNA(AntisenseRnaAlias.class),
+ ANTISENSE_RNA(AntisenseRna.class),
/**
* {@link Phenotype}.
*/
- PHENOTYPE(PhenotypeAlias.class);
+ PHENOTYPE(Phenotype.class);
/**
* Class which should be annotated.
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
index d56d039a13..262bc7b6ac 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
@@ -4,6 +4,7 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
+import lcsb.mapviewer.model.map.compartment.AllCompartmentTests;
import lcsb.mapviewer.model.map.graph.AllGraphTests;
import lcsb.mapviewer.model.map.layout.AllLayoutTests;
import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
@@ -13,7 +14,8 @@ import lcsb.mapviewer.model.map.reaction.AllReactionTests;
import lcsb.mapviewer.model.map.statistics.AllStatisticsTests;
@RunWith(Suite.class)
-@SuiteClasses({ AliasInFewParentsExceptionTest.class, //
+@SuiteClasses({ AllCompartmentTests.class, //
+ AliasInFewParentsExceptionTest.class, //
AllGraphTests.class, //
AllGraphicsTests.class, //
AllLayoutTests.class, //
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
new file mode 100644
index 0000000000..fd6f1897ce
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
@@ -0,0 +1,17 @@
+package lcsb.mapviewer.model.map.compartment;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BottomSquareCompartmentAliasTest.class, //
+ CompartmentAliasComparatorTest.class, //
+ CompartmentAliasTest.class, //
+ LeftSquareCompartmentAliasTest.class, //
+ RightSquareCompartmentAliasTest.class, //
+ TopSquareCompartmentAliasTest.class, //
+})
+public class AllCompartmentTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/BottomSquareCompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentAliasTest.java
similarity index 70%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/BottomSquareCompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentAliasTest.java
index fa17d8e743..2c60d8f85d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/BottomSquareCompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
@@ -9,6 +9,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -25,7 +27,7 @@ public class BottomSquareCompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new BottomSquareCompartmentAlias());
+ SerializationUtils.serialize(new BottomSquareCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -35,7 +37,7 @@ public class BottomSquareCompartmentAliasTest {
@Test
public void testConstructor1() {
try {
- BottomSquareCompartmentAlias alias = new BottomSquareCompartmentAlias(new CompartmentAlias());
+ BottomSquareCompartment alias = new BottomSquareCompartment(new Compartment());
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -49,7 +51,7 @@ public class BottomSquareCompartmentAliasTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- BottomSquareCompartmentAlias alias = new BottomSquareCompartmentAlias(new CompartmentAlias(), model);
+ BottomSquareCompartment alias = new BottomSquareCompartment(new Compartment(), model);
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -60,7 +62,7 @@ public class BottomSquareCompartmentAliasTest {
@Test
public void testCopy() {
try {
- BottomSquareCompartmentAlias alias = new BottomSquareCompartmentAlias().copy();
+ BottomSquareCompartment alias = new BottomSquareCompartment().copy();
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -71,7 +73,7 @@ public class BottomSquareCompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new BottomSquareCompartmentAlias() {
+ new BottomSquareCompartment() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentAliasComparatorTest.java
similarity index 68%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparatorTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentAliasComparatorTest.java
index 1cf0304bcf..023498e219 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentAliasComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -12,10 +12,15 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class CompartmentAliasComparatorTest {
- CompartmentAliasComparator comparator = new CompartmentAliasComparator();
+ CompartmentComparator comparator = new CompartmentComparator();
@Before
public void setUp() throws Exception {
@@ -28,8 +33,8 @@ public class CompartmentAliasComparatorTest {
@Test
public void testEquals() {
try {
- CompartmentAlias alias1 = createCompartmentAlias();
- CompartmentAlias alias2 = createCompartmentAlias();
+ Compartment alias1 = createCompartmentAlias();
+ Compartment alias2 = createCompartmentAlias();
assertEquals(0, comparator.compare(alias1, alias2));
@@ -44,9 +49,9 @@ public class CompartmentAliasComparatorTest {
@Test
public void testDifferent2() {
try {
- CompartmentAlias alias1 = createCompartmentAlias();
+ Compartment alias1 = createCompartmentAlias();
- assertTrue(comparator.compare(alias1, new ArtifitialCompartmentAlias()) != 0);
+ assertTrue(comparator.compare(alias1, new PathwayCompartment()) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -57,16 +62,16 @@ public class CompartmentAliasComparatorTest {
@Test
public void testInvalid() {
try {
- CompartmentAlias alias1 = createCompartmentAlias();
- CompartmentAlias alias2 = createCompartmentAlias();
+ Compartment alias1 = createCompartmentAlias();
+ Compartment alias2 = createCompartmentAlias();
- GenericProteinAlias alias = new GenericProteinAlias("1");
+ GenericProtein alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias = new GenericProteinAlias("1");
+ alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias2.getAliases().add(new GenericProteinAlias("b"));
- alias2.getAliases().add(new GenericProteinAlias("a"));
+ alias2.getAliases().add(new GenericProtein("b"));
+ alias2.getAliases().add(new GenericProtein("a"));
comparator.compare(alias1, alias2);
fail("Exception expected");
@@ -81,16 +86,16 @@ public class CompartmentAliasComparatorTest {
@Test
public void testInvalid2() {
try {
- CompartmentAlias alias1 = createCompartmentAlias();
- CompartmentAlias alias2 = createCompartmentAlias();
+ Compartment alias1 = createCompartmentAlias();
+ Compartment alias2 = createCompartmentAlias();
- SpeciesAlias alias = new GenericProteinAlias("1");
+ Species alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias = new GenericProteinAlias("1");
+ alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias2.getAliases().add(new GenericProteinAlias("A"));
- alias2.getAliases().add(new GenericProteinAlias("B"));
+ alias2.getAliases().add(new GenericProtein("A"));
+ alias2.getAliases().add(new GenericProtein("B"));
comparator.compare(alias2, alias1);
fail("Exception expected");
@@ -102,8 +107,8 @@ public class CompartmentAliasComparatorTest {
}
}
- private CompartmentAlias createCompartmentAlias() {
- CompartmentAlias result = new CompartmentAlias();
+ private Compartment createCompartmentAlias() {
+ Compartment result = new Compartment();
result.setAliasId("asd");
result.setX(12.0);
@@ -118,7 +123,7 @@ public class CompartmentAliasComparatorTest {
result.setInnerWidth(65);
result.setNamePoint(new Point2D.Double(9, 2));
- GenericProteinAlias alias = new GenericProteinAlias("S");
+ GenericProtein alias = new GenericProtein("S");
alias.setName("a");
result.addAlias(alias);
@@ -128,8 +133,8 @@ public class CompartmentAliasComparatorTest {
@Test
public void testDifferent() {
try {
- CompartmentAlias alias1 = createCompartmentAlias();
- CompartmentAlias alias2 = createCompartmentAlias();
+ Compartment alias1 = createCompartmentAlias();
+ Compartment alias2 = createCompartmentAlias();
assertTrue(comparator.compare(alias1, null) != 0);
assertTrue(comparator.compare(null, alias1) != 0);
@@ -161,7 +166,7 @@ public class CompartmentAliasComparatorTest {
alias1 = createCompartmentAlias();
alias2 = createCompartmentAlias();
- alias1.addAlias(new GenericProteinAlias());
+ alias1.addAlias(new GenericProtein("idd"));
assertTrue(comparator.compare(alias1, alias2) != 0);
assertTrue(comparator.compare(alias2, alias1) != 0);
@@ -177,7 +182,7 @@ public class CompartmentAliasComparatorTest {
alias1 = createCompartmentAlias();
alias2 = createCompartmentAlias();
- SpeciesAlias speciesAlias = (SpeciesAlias) alias1.getAliases().iterator().next();
+ Species speciesAlias = (Species) alias1.getAliases().iterator().next();
speciesAlias.setName("new namne");
assertTrue(comparator.compare(alias1, alias2) != 0);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentAliasTest.java
similarity index 68%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentAliasTest.java
index 6600e5b85a..92c7be7d4d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -19,8 +19,14 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
public class CompartmentAliasTest {
Logger logger = Logger.getLogger(CompartmentAliasTest.class);
@@ -39,12 +45,12 @@ public class CompartmentAliasTest {
public void testCross() throws Exception {
try {
Model model = createCrossModel();
- Alias ldhbAlias1 = model.getAliasByAliasId("sa1115");
- Alias ldhbAlias2 = model.getAliasByAliasId("sa1117");
- Alias ldhbAlias3 = model.getAliasByAliasId("sa1119");
- Alias ldhbAlias4 = model.getAliasByAliasId("sa1121");
+ Element ldhbAlias1 = model.getAliasByAliasId("sa1115");
+ Element ldhbAlias2 = model.getAliasByAliasId("sa1117");
+ Element ldhbAlias3 = model.getAliasByAliasId("sa1119");
+ Element ldhbAlias4 = model.getAliasByAliasId("sa1121");
- CompartmentAlias cytosolAlias = (CompartmentAlias) model.getAliasByAliasId("ca1");
+ Compartment cytosolAlias = (Compartment) model.getAliasByAliasId("ca1");
assertTrue(cytosolAlias.cross(ldhbAlias1));
assertTrue(cytosolAlias.cross(ldhbAlias2));
@@ -60,8 +66,8 @@ public class CompartmentAliasTest {
@Test
public void testCrossException() throws Exception {
try {
- CompartmentAlias alias = new CompartmentAlias();
- ComplexAlias alias2 = new ComplexAlias();
+ Compartment alias = new Compartment();
+ Complex alias2 = new Complex("idd");
alias2.setParent(alias2);
alias.cross(alias2);
@@ -76,12 +82,12 @@ public class CompartmentAliasTest {
@Test
public void testCross2() throws Exception {
try {
- CompartmentAlias alias = new CompartmentAlias();
+ Compartment alias = new Compartment();
alias.setX(10.0);
alias.setY(10.0);
alias.setWidth(10.0);
alias.setHeight(10.0);
- ComplexAlias alias2 = new ComplexAlias();
+ Complex alias2 = new Complex("idd");
alias2.setWidth(10.0);
alias2.setHeight(10.0);
alias2.setX(5.0);
@@ -127,13 +133,13 @@ public class CompartmentAliasTest {
@Test
public void testContainsIdenticalSpecies() throws Exception {
try {
- CompartmentAlias alias = new CompartmentAlias();
+ Compartment alias = new Compartment();
alias.setName("AS");
assertFalse(alias.containsIdenticalSpecies());
- SpeciesAlias sAlias = new GenericProteinAlias();
+ Species sAlias = new GenericProtein("idd");
sAlias.setName("AS");
alias.addAlias(sAlias);
@@ -148,16 +154,16 @@ public class CompartmentAliasTest {
private Model createCrossModel() {
Model model = new ModelFullIndexed(null);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
model.addAlias(createSpeciesAlias(3264.8333333333335, 7517.75, 86.0, 46.0, "sa1115"));
model.addAlias(createSpeciesAlias(3267.6666666666665, 7438.75, 80.0, 40.0, "sa1117"));
model.addAlias(createSpeciesAlias(3261.6666666666665, 7600.75, 92.0, 52.0, "sa1119"));
model.addAlias(createSpeciesAlias(3203.666666666667, 7687.75, 98.0, 58.0, "sa1121"));
- SpeciesAlias alias = createSpeciesAlias(7817.714285714286, 11287.642857142859, 80.0, 40.0, "sa1422");
- SpeciesAlias alias2 = createSpeciesAlias(8224.964285714286, 11241.392857142859, 80.0, 40.0, "sa1419");
- ComplexAlias alias3 = createComplexAlias(7804.714285714286, 11182.642857142859, 112.0, 172.0, "csa152");
+ Species alias = createSpeciesAlias(7817.714285714286, 11287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(8224.964285714286, 11241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(7804.714285714286, 11182.642857142859, 112.0, 172.0, "csa152");
alias3.addAlias(alias);
alias3.addAlias(alias2);
alias.setParent(alias3);
@@ -171,8 +177,8 @@ public class CompartmentAliasTest {
return model;
}
- private CompartmentAlias createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- CompartmentAlias alias = new CompartmentAlias(aliasId);
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
alias.setAliasId(aliasId);
alias.setX(x);
alias.setY(y);
@@ -181,8 +187,8 @@ public class CompartmentAliasTest {
return alias;
}
- private SpeciesAlias createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- SimpleMoleculeAlias alias = new SimpleMoleculeAlias(aliasId);
+ private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ SimpleMolecule alias = new SimpleMolecule(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -190,8 +196,8 @@ public class CompartmentAliasTest {
return alias;
}
- private ComplexAlias createComplexAlias(double x, double y, double width, double height, String aliasId) {
- ComplexAlias alias = new ComplexAlias(aliasId);
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -203,10 +209,10 @@ public class CompartmentAliasTest {
public void testCrossWithComplexElements() throws Exception {
try {
Model model = createCrossModel();
- Alias ldhbAlias1 = model.getAliasByAliasId("sa1422");
- Alias ldhbAlias2 = model.getAliasByAliasId("sa1419");
+ Element ldhbAlias1 = model.getAliasByAliasId("sa1422");
+ Element ldhbAlias2 = model.getAliasByAliasId("sa1419");
- CompartmentAlias cytosolAlias = (CompartmentAlias) model.getAliasByAliasId("ca1");
+ Compartment cytosolAlias = (Compartment) model.getAliasByAliasId("ca1");
assertTrue(cytosolAlias.cross(ldhbAlias1));
assertTrue(cytosolAlias.cross(ldhbAlias2));
@@ -220,7 +226,7 @@ public class CompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new CompartmentAlias());
+ SerializationUtils.serialize(new Compartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -230,9 +236,9 @@ public class CompartmentAliasTest {
@Test
public void testConstructor() {
try {
- CompartmentAlias alias = new CompartmentAlias();
- alias.addAlias(new GenericProteinAlias());
- CompartmentAlias copy = new CompartmentAlias(alias);
+ Compartment alias = new Compartment();
+ alias.addAlias(new GenericProtein("idd"));
+ Compartment copy = new Compartment(alias);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -243,7 +249,7 @@ public class CompartmentAliasTest {
@Test
public void testSetters() {
try {
- CompartmentAlias alias = new CompartmentAlias();
+ Compartment alias = new Compartment();
String invalidVal = "a1.6";
String val = "1.6";
Double dVal = 1.6;
@@ -275,7 +281,7 @@ public class CompartmentAliasTest {
alias.setNamePoint(2, 3);
assertEquals(0, alias.getNamePoint().distance(2, 3), Configuration.EPSILON);
- Set<Alias> aliases = new HashSet<>();
+ Set<Element> aliases = new HashSet<>();
alias.setAliases(aliases);
assertEquals(aliases, alias.getAliases());
@@ -289,9 +295,9 @@ public class CompartmentAliasTest {
@Test
public void testAddAlias() {
try {
- CompartmentAlias alias = new CompartmentAlias();
+ Compartment alias = new Compartment();
- SpeciesAlias child = new GenericProteinAlias("id");
+ Species child = new GenericProtein("id");
alias.addAlias(child);
alias.addAlias(child);
@@ -307,10 +313,10 @@ public class CompartmentAliasTest {
@Test
public void testAddInvalidAlias() {
try {
- CompartmentAlias alias = new CompartmentAlias();
+ Compartment alias = new Compartment();
- SpeciesAlias child = new GenericProteinAlias("id");
- SpeciesAlias child2 = new GenericProteinAlias("id");
+ Species child = new GenericProtein("id");
+ Species child2 = new GenericProtein("id");
alias.addAlias(child);
alias.addAlias(child2);
@@ -327,10 +333,10 @@ public class CompartmentAliasTest {
@Test
public void testGetAllAlias() {
try {
- CompartmentAlias alias = new CompartmentAlias();
+ Compartment alias = new Compartment();
- SpeciesAlias child = new GenericProteinAlias("id");
- CompartmentAlias child2 = new CompartmentAlias();
+ Species child = new GenericProtein("id");
+ Compartment child2 = new Compartment();
child2.addAlias(child);
alias.addAlias(child2);
@@ -345,7 +351,7 @@ public class CompartmentAliasTest {
@Test
public void testCopy() {
try {
- CompartmentAlias degraded = new CompartmentAlias().copy();
+ Compartment degraded = new Compartment().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
@@ -356,10 +362,10 @@ public class CompartmentAliasTest {
@Test
public void testRemoveAlias() {
try {
- CompartmentAlias comp = new CompartmentAlias();
- SpeciesAlias alias = new GenericProteinAlias();
+ Compartment comp = new Compartment();
+ Species alias = new GenericProtein("idd");
comp.addAlias(alias);
- alias.setCompartmentAlias(new CompartmentAlias());
+ alias.setCompartmentAlias(new Compartment());
comp.removeAlias(alias);
@@ -373,7 +379,7 @@ public class CompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new CompartmentAlias() {
+ new Compartment() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/LeftSquareCompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentAliasTest.java
similarity index 70%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/LeftSquareCompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentAliasTest.java
index af0f63b5e8..84f18497c9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/LeftSquareCompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
@@ -9,6 +9,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -25,7 +27,7 @@ public class LeftSquareCompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new LeftSquareCompartmentAlias());
+ SerializationUtils.serialize(new LeftSquareCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -35,7 +37,7 @@ public class LeftSquareCompartmentAliasTest {
@Test
public void testConstructor1() {
try {
- LeftSquareCompartmentAlias alias = new LeftSquareCompartmentAlias(new LeftSquareCompartmentAlias());
+ LeftSquareCompartment alias = new LeftSquareCompartment(new LeftSquareCompartment());
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -49,7 +51,7 @@ public class LeftSquareCompartmentAliasTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- LeftSquareCompartmentAlias alias = new LeftSquareCompartmentAlias(new CompartmentAlias(), model);
+ LeftSquareCompartment alias = new LeftSquareCompartment(new Compartment(), model);
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -60,7 +62,7 @@ public class LeftSquareCompartmentAliasTest {
@Test
public void testCopy() {
try {
- LeftSquareCompartmentAlias alias = new LeftSquareCompartmentAlias().copy();
+ LeftSquareCompartment alias = new LeftSquareCompartment().copy();
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -71,7 +73,7 @@ public class LeftSquareCompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new LeftSquareCompartmentAlias() {
+ new LeftSquareCompartment() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/RightSquareCompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentAliasTest.java
similarity index 70%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/RightSquareCompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentAliasTest.java
index 95a233c068..c0ab3d3710 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/RightSquareCompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
@@ -10,6 +10,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -26,7 +28,7 @@ public class RightSquareCompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new RightSquareCompartmentAlias());
+ SerializationUtils.serialize(new RightSquareCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -37,7 +39,7 @@ public class RightSquareCompartmentAliasTest {
@Test
public void testConstructor1() {
try {
- RightSquareCompartmentAlias alias = new RightSquareCompartmentAlias(new RightSquareCompartmentAlias());
+ RightSquareCompartment alias = new RightSquareCompartment(new RightSquareCompartment());
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -51,7 +53,7 @@ public class RightSquareCompartmentAliasTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- RightSquareCompartmentAlias alias = new RightSquareCompartmentAlias(new CompartmentAlias(), model);
+ RightSquareCompartment alias = new RightSquareCompartment(new Compartment(), model);
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -62,7 +64,7 @@ public class RightSquareCompartmentAliasTest {
@Test
public void testCopy() {
try {
- RightSquareCompartmentAlias alias = new RightSquareCompartmentAlias().copy();
+ RightSquareCompartment alias = new RightSquareCompartment().copy();
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -73,7 +75,7 @@ public class RightSquareCompartmentAliasTest {
@Test
public void testSetPoint() {
try {
- RightSquareCompartmentAlias alias = new RightSquareCompartmentAlias();
+ RightSquareCompartment alias = new RightSquareCompartment();
alias.setPoint("10", "10");
assertTrue(alias.getWidth()<0);
} catch (Exception e) {
@@ -85,7 +87,7 @@ public class RightSquareCompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new RightSquareCompartmentAlias() {
+ new RightSquareCompartment() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/TopSquareCompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentAliasTest.java
similarity index 71%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/TopSquareCompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentAliasTest.java
index a6306eb181..fc6a019068 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/TopSquareCompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.compartment;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
@@ -9,6 +9,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -25,7 +27,7 @@ public class TopSquareCompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new TopSquareCompartmentAlias());
+ SerializationUtils.serialize(new TopSquareCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -36,7 +38,7 @@ public class TopSquareCompartmentAliasTest {
@Test
public void testConstructor1() {
try {
- TopSquareCompartmentAlias alias = new TopSquareCompartmentAlias(new TopSquareCompartmentAlias());
+ TopSquareCompartment alias = new TopSquareCompartment(new TopSquareCompartment());
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -50,7 +52,7 @@ public class TopSquareCompartmentAliasTest {
Model model = new ModelFullIndexed(null);
model.setWidth(1);
model.setHeight(1);
- TopSquareCompartmentAlias alias = new TopSquareCompartmentAlias(new CompartmentAlias(), model);
+ TopSquareCompartment alias = new TopSquareCompartment(new Compartment(), model);
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -61,7 +63,7 @@ public class TopSquareCompartmentAliasTest {
@Test
public void testCopy() {
try {
- TopSquareCompartmentAlias alias = new TopSquareCompartmentAlias().copy();
+ TopSquareCompartment alias = new TopSquareCompartment().copy();
assertNotNull(alias);
} catch (Exception e) {
e.printStackTrace();
@@ -72,7 +74,7 @@ public class TopSquareCompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new TopSquareCompartmentAlias() {
+ new TopSquareCompartment() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/graph/DataMiningTest.java b/model/src/test/java/lcsb/mapviewer/model/map/graph/DataMiningTest.java
index bd6ed6c44c..9f0dfedcbf 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/graph/DataMiningTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/graph/DataMiningTest.java
@@ -11,8 +11,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class DataMiningTest {
@@ -39,7 +39,7 @@ public class DataMiningTest {
try {
DataMining dm = new DataMining();
String description = "xdg";
- Alias element = new GenericProteinAlias("id");
+ Element element = new GenericProtein("id");
Integer id = 61;
List<MiriamData> references = new ArrayList<>();
List<MiriamData> suggestedConnections = new ArrayList<>();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
index 217cad91d9..8f9daf1179 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
@@ -1,14 +1,14 @@
package lcsb.mapviewer.model.map.layout;
-import lcsb.mapviewer.model.map.layout.alias.AllAliasTests;
import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
+import lcsb.mapviewer.model.map.species.AllSpeciesTests;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ AllAliasTests.class, //
+@SuiteClasses({ AllSpeciesTests.class, //
AllGraphicsTests.class, //
ColorSchemaTest.class, //
GenericColorSchemaTest.class, //
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
index b16bec7df7..181cce38fa 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
@@ -14,9 +14,9 @@ import org.junit.Test;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
public class ColorSchemaTest {
@@ -33,7 +33,7 @@ public class ColorSchemaTest {
try {
ColorSchema cs = new GenericColorSchema();
List<String> compartments = new ArrayList<>();
- List<Class<? extends Alias>> types = new ArrayList<>();
+ List<Class<? extends Element>> types = new ArrayList<>();
String name = "S";
String generalIdentifier = "id";
List<Pair<MiriamType, String>> identifierColumns = new ArrayList<>();
@@ -149,7 +149,7 @@ public class ColorSchemaTest {
assertNotNull(cs.toString());
cs.setName("gene name");
cs.addCompartment("A");
- cs.addType(SpeciesAlias.class);
+ cs.addType(Species.class);
cs.setValue(1.2);
cs.setColor(Color.BLACK);
cs.setGeneralIdentifier("a");
@@ -206,9 +206,9 @@ public class ColorSchemaTest {
public void testAddTypes() throws Exception {
try {
ColorSchema cs = new GenericColorSchema();
- List<Class<? extends Alias>> compartments = new ArrayList<>();
- compartments.add(SpeciesAlias.class);
- compartments.add(ProteinAlias.class);
+ List<Class<? extends Element>> compartments = new ArrayList<>();
+ compartments.add(Species.class);
+ compartments.add(Protein.class);
cs.addTypes(compartments);
assertEquals(2, cs.getTypes().size());
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AllAliasTests.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AllAliasTests.java
deleted file mode 100644
index cc98feb306..0000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AllAliasTests.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package lcsb.mapviewer.model.map.layout.alias;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AliasComparatorTest.class, //
- AliasGroupTest.class, //
- AliasTest.class, //
- ArtifitialCompartmentAliasTest.class, //
- BottomSquareCompartmentAliasTest.class, //
- CompartmentAliasComparatorTest.class, //
- CompartmentAliasTest.class, //
- ComplexAliasComparatorTest.class, //
- ComplexAliasTest.class, //
- LeftSquareCompartmentAliasTest.class, //
- OvalCompartmentAliasTest.class, //
- RightSquareCompartmentAliasTest.class, //
- SearchIndexTest.class, //
- SpeciesAliasComparatorTest.class, //
- SpeciesAliasTest.class, //
- SquareCompartmentAliasTest.class, //
- TopSquareCompartmentAliasTest.class,//
-})
-public class AllAliasTests {
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparatorTest.java
index 3649aed846..6d28272b8a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/AliasSubmodelConnectionComparatorTest.java
@@ -9,11 +9,11 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class AliasSubmodelConnectionComparatorTest {
@@ -94,15 +94,15 @@ public class AliasSubmodelConnectionComparatorTest {
Model model = new ModelFullIndexed(null);
model.setNotes("Some description");
- GenericProteinAlias protein = new GenericProteinAlias("A");
+ GenericProtein protein = new GenericProtein("A");
protein.setName("ad");
model.addAlias(protein);
- GenericProteinAlias alias = new GenericProteinAlias("a_id");
+ GenericProtein alias = new GenericProtein("a_id");
alias.setName("ad");
model.addAlias(alias);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
@@ -120,8 +120,8 @@ public class AliasSubmodelConnectionComparatorTest {
return result;
}
- private Alias createAlias() {
- Alias alias = new GenericProteinAlias("alias_id");
+ private Element createAlias() {
+ Element alias = new GenericProtein("alias_id");
alias.setColor(Color.BLACK);
return alias;
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
index c2076026bb..83c038e0d1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
@@ -16,15 +16,15 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ModelComparatorTest {
Logger logger = Logger.getLogger(ModelComparatorTest.class);
@@ -84,16 +84,16 @@ public class ModelComparatorTest {
Model model1 = getModel();
Model model2 = getModel();
- CompartmentAlias alias = new ArtifitialCompartmentAlias();
+ Compartment alias = new PathwayCompartment();
alias.setAliasId("1");
- CompartmentAlias alias2 = new ArtifitialCompartmentAlias();
+ Compartment alias2 = new PathwayCompartment();
alias2.setAliasId("12");
model1.addAlias(alias);
model1.addAlias(alias2);
- alias = new ArtifitialCompartmentAlias();
+ alias = new PathwayCompartment();
alias.setAliasId("1");
- alias2 = new ArtifitialCompartmentAlias();
+ alias2 = new PathwayCompartment();
alias2.setAliasId("12");
model2.addAlias(alias);
model2.addAlias(alias2);
@@ -145,7 +145,7 @@ public class ModelComparatorTest {
Model model1 = getModel();
Model model2 = getModel();
- SpeciesAlias mockAlias = Mockito.mock(SpeciesAlias.class);
+ Species mockAlias = Mockito.mock(Species.class);
when(mockAlias.getAliasId()).thenReturn("1");
model1.addAlias(mockAlias);
@@ -192,7 +192,7 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- GenericProteinAlias alias = new GenericProteinAlias("SAd");
+ GenericProtein alias = new GenericProtein("SAd");
model1.addAlias(alias);
@@ -210,7 +210,7 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.addAlias(new CompartmentAlias("unk_id"));
+ model1.addAlias(new Compartment("unk_id"));
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -242,7 +242,7 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.addAlias(new GenericProteinAlias("ASdas"));
+ model1.addAlias(new GenericProtein("ASdas"));
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -386,12 +386,12 @@ public class ModelComparatorTest {
private Model getModel() {
Model model = new ModelFullIndexed(null);
model.setNotes("Some description");
- GenericProteinAlias alias = new GenericProteinAlias("a_id");
+ GenericProtein alias = new GenericProtein("a_id");
alias.setName("ad");
model.addAlias(alias);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
index 56c1808e30..e5031f22c3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
@@ -20,12 +20,12 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class ModelDataTest {
@@ -51,8 +51,8 @@ public class ModelDataTest {
public void testAddAliases() {
try {
ModelData md = new ModelData();
- List<Alias> aliases = new ArrayList<>();
- aliases.add(new GenericProteinAlias("unk_id"));
+ List<Element> aliases = new ArrayList<>();
+ aliases.add(new GenericProtein("unk_id"));
md.addAliases(aliases);
assertEquals(1, md.getAliases().size());
} catch (Exception e) {
@@ -157,7 +157,7 @@ public class ModelDataTest {
public void testRemoveAlias2() {
try {
ModelData md = new ModelData();
- md.removeAlias(new GenericProteinAlias("unk_id"));
+ md.removeAlias(new GenericProtein("unk_id"));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -168,7 +168,7 @@ public class ModelDataTest {
public void testRemoveAlias3() {
try {
ModelData md = new ModelData();
- Alias alias = new GenericProteinAlias("unk_id");
+ Element alias = new GenericProtein("unk_id");
md.addAlias(alias);
assertEquals(1, md.getAliases().size());
md.removeAlias(alias);
@@ -323,7 +323,7 @@ public class ModelDataTest {
public void testGetters() {
try {
ModelData md = new ModelData();
- Set<Alias> aliases = new HashSet<>();
+ Set<Element> aliases = new HashSet<>();
List<Layout> layouts = new ArrayList<>();
Set<Layer> layers = new HashSet<>();
Set<Reaction> reactions = new HashSet<>();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index 00f0471eb2..968d063f21 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -29,19 +29,19 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewImageLink;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.User;
public class ModelFullIndexedTest {
@@ -59,13 +59,13 @@ public class ModelFullIndexedTest {
public void testConstructor() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- SpeciesAlias proteinAlias = new GenericProteinAlias("1a");
- SpeciesAlias proteinAlias2 = new GenericProteinAlias("f");
- SpeciesAlias proteinAlias3 = new GenericProteinAlias("fa");
+ Species proteinAlias = new GenericProtein("1a");
+ Species proteinAlias2 = new GenericProtein("f");
+ Species proteinAlias3 = new GenericProtein("fa");
- Alias compartmentAlias = new CompartmentAlias("aaa");
- Alias compartmentAlias3 = new CompartmentAlias("aaa3");
- Alias compartmentAlias2 = new ArtifitialCompartmentAlias();
+ Element compartmentAlias = new Compartment("aaa");
+ Element compartmentAlias3 = new Compartment("aaa3");
+ Element compartmentAlias2 = new PathwayCompartment();
compartmentAlias2.setAliasId("aaa2");
model.addAlias(proteinAlias);
model.addAlias(proteinAlias2);
@@ -117,7 +117,7 @@ public class ModelFullIndexedTest {
@Test
public void testAddInvalidAlias() {
try {
- Alias alias = Mockito.mock(Alias.class);
+ Element alias = Mockito.mock(Element.class);
ModelFullIndexed model = new ModelFullIndexed(null);
model.addAlias(alias);
@@ -137,7 +137,7 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- ComplexAlias alias = new ComplexAlias("1");
+ Complex alias = new Complex("1");
model.addAlias(alias);
try {
@@ -171,11 +171,11 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
- ComplexAlias alias = new ComplexAlias("1");
+ Complex alias = new Complex("1");
- Alias proteinAlias = new GenericProteinAlias("asd");
+ Element proteinAlias = new GenericProtein("asd");
proteinAlias.setAliasId("zz");
proteinAlias.setParent(alias);
@@ -196,13 +196,13 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- CompartmentAlias compAlias = new CompartmentAlias("default");
+ Compartment compAlias = new Compartment("default");
model.addAlias(compAlias);
- ComplexAlias alias = new ComplexAlias("1");
+ Complex alias = new Complex("1");
alias.setParent(compAlias);
- Alias proteinAlias = new GenericProteinAlias("asd");
+ Element proteinAlias = new GenericProtein("asd");
proteinAlias.setAliasId("zz");
proteinAlias.setParent(alias);
@@ -224,7 +224,7 @@ public class ModelFullIndexedTest {
ModelFullIndexed model = new ModelFullIndexed(null);
assertNull(model.getAliasByAliasId("id"));
- SpeciesAlias alias = new GenericProteinAlias("asd");
+ Species alias = new GenericProtein("asd");
alias.setAliasId("id");
model.addAlias(alias);
@@ -242,7 +242,7 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- CompartmentAlias alias = new CompartmentAlias("1");
+ Compartment alias = new Compartment("1");
assertEquals(0, model.getCompartmentsAliases().size());
model.addAlias(alias);
@@ -296,7 +296,7 @@ public class ModelFullIndexedTest {
try {
int aliasId = 12;
ModelFullIndexed model = new ModelFullIndexed(null);
- Alias alias = new GenericProteinAlias("1");
+ Element alias = new GenericProtein("1");
alias.setId(aliasId);
assertNull(model.getAliasByDbId(aliasId));
model.addAlias(alias);
@@ -312,20 +312,20 @@ public class ModelFullIndexedTest {
public void testGetSortedCompartmentAliases() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- CompartmentAlias alias = new CompartmentAlias("a1");
+ Compartment alias = new Compartment("a1");
alias.setWidth(12);
alias.setHeight(12);
model.addAlias(alias);
- alias = new CompartmentAlias("a2");
+ alias = new Compartment("a2");
alias.setWidth(14);
alias.setHeight(14);
model.addAlias(alias);
- alias = new CompartmentAlias("a3");
+ alias = new Compartment("a3");
alias.setWidth(13);
alias.setHeight(13);
model.addAlias(alias);
- List<CompartmentAlias> aliases = model.getSortedCompartmentsAliases();
+ List<Compartment> aliases = model.getSortedCompartmentsAliases();
assertEquals(196.0, aliases.get(0).getSize(), Configuration.EPSILON);
assertEquals(169.0, aliases.get(1).getSize(), Configuration.EPSILON);
assertEquals(144.0, aliases.get(2).getSize(), Configuration.EPSILON);
@@ -340,12 +340,12 @@ public class ModelFullIndexedTest {
public void testRemoveCompartmentAliases() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- CompartmentAlias alias = new CompartmentAlias("a1");
+ Compartment alias = new Compartment("a1");
alias.setWidth(12);
alias.setHeight(12);
model.addAlias(alias);
- alias = new CompartmentAlias("a2");
+ alias = new Compartment("a2");
alias.setWidth(14);
alias.setHeight(14);
model.addAlias(alias);
@@ -365,18 +365,18 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- CompartmentAlias alias = new CompartmentAlias("1");
+ Compartment alias = new Compartment("1");
alias.setWidth(100);
alias.setHeight(100);
- List<Alias> aliases = new ArrayList<>();
+ List<Element> aliases = new ArrayList<>();
aliases.add(alias);
- ComplexAlias cAlias = new ComplexAlias("ca1");
+ Complex cAlias = new Complex("ca1");
aliases.add(cAlias);
cAlias.setWidth(10);
cAlias.setHeight(10);
- SpeciesAlias sAlias = new GenericProteinAlias("a1");
+ Species sAlias = new GenericProtein("a1");
aliases.add(sAlias);
sAlias.setWidth(20);
sAlias.setHeight(20);
@@ -387,7 +387,7 @@ public class ModelFullIndexedTest {
assertEquals(1, model.getComplexAliases().size());
assertEquals(1, model.getNotComplexSpeciesAliases().size());
- List<Alias> sortedAliases = model.getSortedAliases();
+ List<Element> sortedAliases = model.getSortedAliases();
assertEquals(alias, sortedAliases.get(0));
assertEquals(sAlias, sortedAliases.get(1));
@@ -404,9 +404,9 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- CompartmentAlias parentAlias = new CompartmentAlias("parent_id");
+ Compartment parentAlias = new Compartment("parent_id");
- CompartmentAlias alias = new CompartmentAlias("child_id");
+ Compartment alias = new Compartment("child_id");
alias.setParent(parentAlias);
model.addAlias(alias);
@@ -426,22 +426,22 @@ public class ModelFullIndexedTest {
public void testRemoveComplexAlias() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
- ComplexAlias parentAlias = new ComplexAlias("a");
+ Complex parentAlias = new Complex("a");
- ComplexAlias alias = new ComplexAlias("b");
+ Complex alias = new Complex("b");
alias.setParent(parentAlias);
alias.setAliasId("1");
- alias.setCompartmentAlias(new CompartmentAlias("comp_alias"));
- alias.setComplexAlias(new ComplexAlias("d"));
+ alias.setCompartmentAlias(new Compartment("comp_alias"));
+ alias.setComplexAlias(new Complex("d"));
model.addAlias(alias);
assertEquals(2, model.getAliases().size());
- alias.setComplexAlias(new ComplexAlias("xxx"));
+ alias.setComplexAlias(new Complex("xxx"));
model.removeAlias(alias);
assertEquals(1, model.getAliases().size());
@@ -457,8 +457,8 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- Alias alias = new GenericProteinAlias("id");
- alias.setParent(Mockito.mock(Alias.class));
+ Element alias = new GenericProtein("id");
+ alias.setParent(Mockito.mock(Element.class));
model.removeAlias(alias);
@@ -754,7 +754,7 @@ public class ModelFullIndexedTest {
Double height = 13.0;
String heightStr = "13.0";
int heightInt = 13;
- Set<Alias> aliases = new HashSet<>();
+ Set<Element> aliases = new HashSet<>();
List<Layout> layouts = new ArrayList<>();
int zoomLevels = 98;
int tileSize = 1024;
@@ -826,7 +826,7 @@ public class ModelFullIndexedTest {
Reaction reaction = new Reaction();
reaction.setIdReaction(reactionId);
model.addReaction(reaction);
- SpeciesAlias alias = new GenericProteinAlias("2");
+ Species alias = new GenericProtein("2");
model.addAlias(alias);
Collection<AnnotatedObject> obj = model.getAnnotatedObjects();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
index ad3ac46f5e..fe5dcd2ee1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
@@ -7,11 +7,11 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ModelSubmodelConnectionComparatorTest {
@@ -86,11 +86,11 @@ public class ModelSubmodelConnectionComparatorTest {
model.setNotes("Some description");
- SpeciesAlias alias = new GenericProteinAlias("a_id");
+ Species alias = new GenericProtein("a_id");
alias.setName("ad");
model.addAlias(alias);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
index 6d33781d45..7aa22330bb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
@@ -18,32 +18,29 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ModelTest {
Logger logger = Logger.getLogger(ModelTest.class);
- private SpeciesAlias alias;
+ private Species alias;
- private ComplexAlias cAlias;
+ private Complex cAlias;
private Model model;
- private CompartmentAlias compAlias;
@Before
public void setUp() throws Exception {
model = new ModelFullIndexed(null);
- alias = new GenericProteinAlias("sa1");
+ alias = new GenericProtein("sa1");
- cAlias = new ComplexAlias("sa2");
-
- compAlias = new CompartmentAlias("comp_id");
+ cAlias = new Complex("sa2");
}
@@ -55,7 +52,7 @@ public class ModelTest {
public void testAddAlias() {
try {
model.addAlias(alias);
- Alias sAlias = model.getAliasByAliasId(alias.getAliasId());
+ Element sAlias = model.getAliasByAliasId(alias.getAliasId());
assertNotNull(sAlias);
sAlias = model.getAliasByAliasId(alias.getAliasId() + "blbla");
assertNull(sAlias);
@@ -69,12 +66,12 @@ public class ModelTest {
@Test
public void testGetAliasList() {
try {
- Set<Alias> aliases = model.getAliases();
+ Set<Element> aliases = model.getAliases();
assertEquals(0, aliases.size());
model.addAlias(alias);
assertEquals(1, aliases.size());
- Alias sAlias = model.getAliasByAliasId(alias.getAliasId());
+ Element sAlias = model.getAliasByAliasId(alias.getAliasId());
assertNotNull(sAlias);
sAlias = model.getAliasByAliasId(alias.getAliasId() + "blbla");
assertNull(sAlias);
@@ -131,16 +128,16 @@ public class ModelTest {
assertNotNull(elements);
assertEquals(1, elements.size());
AnnotatedObject element = elements.iterator().next();
- assertTrue(element instanceof SpeciesAlias);
- SpeciesAlias species = (SpeciesAlias) element;
+ assertTrue(element instanceof Species);
+ Species species = (Species) element;
assertEquals("s5", species.getName());
elements = model.getElementsByAnnotation(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEBI, "CHEBI:12"));
assertNotNull(elements);
assertEquals(1, elements.size());
element = elements.iterator().next();
- assertTrue(element instanceof CompartmentAlias);
- CompartmentAlias compartment = (CompartmentAlias) element;
+ assertTrue(element instanceof Compartment);
+ Compartment compartment = (Compartment) element;
assertEquals("c1", compartment.getName());
elements = model.getElementsByAnnotation(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEBI, "CHEBI:12234"));
@@ -156,24 +153,24 @@ public class ModelTest {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias proteinAlias = new GenericProteinAlias("sa1");
+ Species proteinAlias = new GenericProtein("sa1");
proteinAlias.setName("s1");
model.addAlias(proteinAlias);
- SpeciesAlias proteinAlias2 = new GenericProteinAlias("sa2");
+ Species proteinAlias2 = new GenericProtein("sa2");
proteinAlias2.setName("s1");
model.addAlias(proteinAlias2);
- SpeciesAlias proteinAlias3 = new GenericProteinAlias("sa3");
+ Species proteinAlias3 = new GenericProtein("sa3");
proteinAlias3.setName("s1");
model.addAlias(proteinAlias3);
- SpeciesAlias proteinAlias4 = new GenericProteinAlias("sa4");
+ Species proteinAlias4 = new GenericProtein("sa4");
proteinAlias4.setName("s5");
proteinAlias4.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEMBL_TARGET, "CHEMBL12345"));
model.addAlias(proteinAlias4);
- CompartmentAlias compartmentAlias = new CompartmentAlias("cca");
+ Compartment compartmentAlias = new Compartment("cca");
compartmentAlias.setName("c1");
compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEBI, "CHEBI:12"));
@@ -187,40 +184,40 @@ public class ModelTest {
try {
Model model = new ModelFullIndexed(null);
- SpeciesAlias alias = new GenericProteinAlias("2");
+ Species alias = new GenericProtein("2");
alias.setWidth(100);
alias.setHeight(100);
model.addAlias(alias);
- alias = new GenericProteinAlias("3");
+ alias = new GenericProtein("3");
alias.setWidth(10);
alias.setHeight(10);
model.addAlias(alias);
- alias = new GenericProteinAlias("4");
+ alias = new GenericProtein("4");
alias.setWidth(200);
alias.setHeight(100);
model.addAlias(alias);
- CompartmentAlias cAlias = new CompartmentAlias("5");
+ Compartment cAlias = new Compartment("5");
cAlias.setWidth(10);
cAlias.setHeight(20);
model.addAlias(cAlias);
- cAlias = new CompartmentAlias("6");
+ cAlias = new Compartment("6");
cAlias.setWidth(100);
cAlias.setHeight(200);
model.addAlias(cAlias);
- cAlias = new CompartmentAlias("7");
+ cAlias = new Compartment("7");
cAlias.setWidth(20);
cAlias.setHeight(30);
model.addAlias(cAlias);
- List<Alias> sortedAliases = model.getAliasesSortedBySize();
+ List<Element> sortedAliases = model.getAliasesSortedBySize();
if (sortedAliases.size() > 0) {
double last = (sortedAliases.get(0)).getHeight() * (sortedAliases.get(0)).getWidth();
- for (Alias a : sortedAliases) {
+ for (Element a : sortedAliases) {
assertTrue(last >= a.getHeight() * a.getWidth());
}
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
index daf95263a3..dbf30972ba 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
@@ -9,11 +9,11 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class SubmodelConnectionComparatorTest {
@@ -165,12 +165,12 @@ public class SubmodelConnectionComparatorTest {
model.setNotes("Some description");
- SpeciesAlias alias = new GenericProteinAlias("a_id");
+ Species alias = new GenericProtein("a_id");
alias.setName("ad");
alias.setAliasId("a_id");
model.addAlias(alias);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java
index 0d8269a0e6..ba1b40daf9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
public class CatalysisTest {
@@ -35,7 +35,7 @@ public class CatalysisTest {
@Test
public void testConstructor() {
try {
- Catalysis modifier = new Catalysis(new AntisenseRnaAlias("unk_id"));
+ Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
assertNotNull(modifier);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +46,7 @@ public class CatalysisTest {
@Test
public void testConstructor2() {
try {
- Catalysis modifier = new Catalysis(new AntisenseRnaAlias("unk_id"));
+ Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
modifier.setLine(new PolylineData());
Catalysis modifier2 = new Catalysis(modifier);
assertNotNull(modifier2);
@@ -59,7 +59,7 @@ public class CatalysisTest {
@Test
public void testCopy() {
try {
- Catalysis modifier = new Catalysis(new AntisenseRnaAlias("unk_id"));
+ Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
modifier.setLine(new PolylineData());
Catalysis modifier2 = modifier.copy();
assertNotNull(modifier2);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java
index c3818fc0da..3f8af64c8d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class InhibitionTest {
@@ -35,7 +35,7 @@ public class InhibitionTest {
@Test
public void testConstructor() {
try {
- Inhibition modifier = new Inhibition(new GenericProteinAlias("unk_id"));
+ Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
assertNotNull(modifier);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +46,7 @@ public class InhibitionTest {
@Test
public void testConstructor2() {
try {
- Inhibition modifier = new Inhibition(new GenericProteinAlias("unk_id"));
+ Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
Inhibition modifier2 = new Inhibition(modifier);
assertNotNull(modifier2);
@@ -59,7 +59,7 @@ public class InhibitionTest {
@Test
public void testCopy() {
try {
- Inhibition modifier = new Inhibition(new GenericProteinAlias("unk_id"));
+ Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
Inhibition modifier2 = modifier.copy();
assertNotNull(modifier2);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java
index 5508d9c5a4..d465085a0e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class ModulationTest {
@@ -35,7 +35,7 @@ public class ModulationTest {
@Test
public void testConstructor() {
try {
- Modulation modifier = new Modulation(new GenericProteinAlias("unk_id"));
+ Modulation modifier = new Modulation(new GenericProtein("unk_id"));
assertNotNull(modifier);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +46,7 @@ public class ModulationTest {
@Test
public void testConstructor2() {
try {
- Modulation modifier = new Modulation(new GenericProteinAlias("unk_id"));
+ Modulation modifier = new Modulation(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
Modulation modifier2 = new Modulation(modifier);
assertNotNull(modifier2);
@@ -77,7 +77,7 @@ public class ModulationTest {
@Test
public void testCopy() {
try {
- Modulation modifier = new Modulation(new GenericProteinAlias("unk_id"));
+ Modulation modifier = new Modulation(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
Modulation modifier2 = modifier.copy();
assertNotNull(modifier2);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java
index b6f2ca0e75..106238c323 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class PhysicalStimulationTest {
@@ -35,7 +35,7 @@ public class PhysicalStimulationTest {
@Test
public void testConstructor() {
try {
- PhysicalStimulation modifier = new PhysicalStimulation(new GenericProteinAlias("unk_id"));
+ PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
assertNotNull(modifier);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +46,7 @@ public class PhysicalStimulationTest {
@Test
public void testConstructor2() {
try {
- PhysicalStimulation modifier = new PhysicalStimulation(new GenericProteinAlias("unk_id"));
+ PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
PhysicalStimulation modifier2 = new PhysicalStimulation(modifier);
assertNotNull(modifier2);
@@ -77,7 +77,7 @@ public class PhysicalStimulationTest {
@Test
public void testCopy() {
try {
- PhysicalStimulation modifier = new PhysicalStimulation(new GenericProteinAlias("unk_id"));
+ PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
PhysicalStimulation modifier2 = modifier.copy();
assertNotNull(modifier2);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java
index f6ea1e96e4..f0d3ebb23b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class TriggerTest {
@@ -35,7 +35,7 @@ public class TriggerTest {
@Test
public void testConstructor() {
try {
- Trigger modifier = new Trigger(new GenericProteinAlias("unk_id"));
+ Trigger modifier = new Trigger(new GenericProtein("unk_id"));
assertNotNull(modifier);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +46,7 @@ public class TriggerTest {
@Test
public void testConstructor2() {
try {
- Trigger modifier = new Trigger(new GenericProteinAlias("unk_id"));
+ Trigger modifier = new Trigger(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
Trigger modifier2 = new Trigger(modifier);
assertNotNull(modifier2);
@@ -59,7 +59,7 @@ public class TriggerTest {
@Test
public void testCopy() {
try {
- Trigger modifier = new Trigger(new GenericProteinAlias("unk_id"));
+ Trigger modifier = new Trigger(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
Trigger modifier2 = modifier.copy();
assertNotNull(modifier2);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java
index 8e2a4eff08..dcf4d289ae 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class UnknownCatalysisTest {
@@ -35,7 +35,7 @@ public class UnknownCatalysisTest {
@Test
public void testConstructor() {
try {
- UnknownCatalysis modifier = new UnknownCatalysis(new GenericProteinAlias("unk_id"));
+ UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
assertNotNull(modifier);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +46,7 @@ public class UnknownCatalysisTest {
@Test
public void testConstructor2() {
try {
- UnknownCatalysis modifier = new UnknownCatalysis(new GenericProteinAlias("unk_id"));
+ UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
UnknownCatalysis modifier2 = new UnknownCatalysis(modifier);
assertNotNull(modifier2);
@@ -59,7 +59,7 @@ public class UnknownCatalysisTest {
@Test
public void testCopy() {
try {
- UnknownCatalysis modifier = new UnknownCatalysis(new GenericProteinAlias("unk_id"));
+ UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
UnknownCatalysis modifier2 = modifier.copy();
assertNotNull(modifier2);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java
index 9d6214a920..c50a4c87e2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java
@@ -10,7 +10,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class UnknownInhibitionTest {
@@ -35,7 +35,7 @@ public class UnknownInhibitionTest {
@Test
public void testConstructor() {
try {
- UnknownInhibition modifier = new UnknownInhibition(new GenericProteinAlias("unk_id"));
+ UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
assertNotNull(modifier);
} catch (Exception e) {
e.printStackTrace();
@@ -46,7 +46,7 @@ public class UnknownInhibitionTest {
@Test
public void testConstructor2() {
try {
- UnknownInhibition modifier = new UnknownInhibition(new GenericProteinAlias("unk_id"));
+ UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
UnknownInhibition modifier2 = new UnknownInhibition(modifier);
assertNotNull(modifier2);
@@ -59,7 +59,7 @@ public class UnknownInhibitionTest {
@Test
public void testCopy() {
try {
- UnknownInhibition modifier = new UnknownInhibition(new GenericProteinAlias("unk_id"));
+ UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
modifier.setLine(new PolylineData());
UnknownInhibition modifier2 = modifier.copy();
assertNotNull(modifier2);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
index 3b161e9152..752671aace 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
@@ -10,9 +10,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class NodeOperatorComparatorTest {
@@ -74,7 +74,7 @@ public class NodeOperatorComparatorTest {
operator2 = createNodeOperator();
Reactant reactant = (Reactant) operator1.getInputs().get(0);
- reactant.setAlias(new GenericProteinAlias("id666"));
+ reactant.setAlias(new GenericProtein("id666"));
assertTrue(comparator.compare(operator1, operator2) != 0);
assertTrue(comparator.compare(operator2, operator1) != 0);
@@ -100,7 +100,7 @@ public class NodeOperatorComparatorTest {
private NodeOperator createNodeOperator() {
AndOperator result = new AndOperator();
- SpeciesAlias alias0 = new GenericProteinAlias("id0");
+ Species alias0 = new GenericProtein("id0");
alias0.setName("protein a");
alias0.setX(12.0);
alias0.setY(1.0);
@@ -111,7 +111,7 @@ public class NodeOperatorComparatorTest {
result.addOutput(product);
- SpeciesAlias alias1 = new GenericProteinAlias("id1");
+ Species alias1 = new GenericProtein("id1");
alias1.setName("protein b");
alias1.setX(120.0);
alias1.setY(10.0);
@@ -122,7 +122,7 @@ public class NodeOperatorComparatorTest {
result.addInput(reactant);
- SpeciesAlias alias2 = new GeneAlias("id2");
+ Species alias2 = new Gene("id2");
alias2.setName("gene b");
alias2.setX(320.0);
alias2.setY(30.0);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
index 1c987b9b18..e6c1ceb06f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
@@ -13,13 +13,13 @@ import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
import lcsb.mapviewer.model.map.modifier.Catalysis;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
public class ReactionComparatorTest {
@@ -248,19 +248,19 @@ public class ReactionComparatorTest {
private Reaction createReaction() {
Reaction reaction = new Reaction();
- SpeciesAlias alias = new GenericProteinAlias("id1");
+ Species alias = new GenericProtein("id1");
alias.setName("ASD");
Reactant reactant = new Reactant(alias);
- SpeciesAlias alias2 = new GenericProteinAlias("id2");
+ Species alias2 = new GenericProtein("id2");
alias2.setName("ASD2");
Reactant reactant2 = new Reactant(alias2);
- SpeciesAlias moelculeAlias = new SimpleMoleculeAlias("id3");
+ Species moelculeAlias = new SimpleMolecule("id3");
moelculeAlias.setName("mol");
Product product = new Product(moelculeAlias);
- SpeciesAlias unknownAlias = new UnknownAlias("id4");
+ Species unknownAlias = new Unknown("id4");
unknownAlias.setName("unk");
Modifier modifier = new Catalysis(unknownAlias);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
index 89c180e1e8..c317a22021 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
@@ -10,9 +10,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ReactionNodeComparatorTest {
@@ -73,7 +73,7 @@ public class ReactionNodeComparatorTest {
operator1 = createNodeOperator();
operator2 = createNodeOperator();
- operator1.setAlias(new GenericProteinAlias("new_id"));
+ operator1.setAlias(new GenericProtein("new_id"));
assertTrue(comparator.compare(operator1, operator2) != 0);
assertTrue(comparator.compare(operator2, operator1) != 0);
@@ -94,7 +94,7 @@ public class ReactionNodeComparatorTest {
private ReactionNode createNodeOperator() {
- SpeciesAlias alias2 = new GeneAlias("id_1");
+ Species alias2 = new Gene("id_1");
alias2.setName("gene b");
alias2.setX(320.0);
alias2.setY(30.0);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index d31a79533a..12a353ab6b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -25,25 +25,25 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Catalysis;
import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ReactionTest extends ModelTestFunctions {
Logger logger = Logger.getLogger(ReactantTest.class);
- private SpeciesAlias alias;
+ private Species alias;
@Before
public void setUp() throws Exception {
- alias = new GenericProteinAlias("sa1");
+ alias = new GenericProtein("sa1");
}
@After
@@ -235,7 +235,7 @@ public class ReactionTest extends ModelTestFunctions {
assertEquals(0, reaction1.getVisibilityLevel());
Reactant reactant = new Reactant();
- Alias alias = new GenericProteinAlias("id_xyz");
+ Element alias = new GenericProtein("id_xyz");
alias.setVisibilityLevel(2);
reactant.setAlias(alias);
reaction1.addReactant(reactant);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AliasComparatorTest.java
similarity index 59%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasComparatorTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/AliasComparatorTest.java
index 802c590322..768b5697b4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AliasComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -12,16 +12,23 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
public class AliasComparatorTest {
- AliasComparator comparator = new AliasComparator();
+ ElementComparator comparator = new ElementComparator();
@Before
public void setUp() throws Exception {
@@ -34,7 +41,7 @@ public class AliasComparatorTest {
@Test
public void testCompareException() throws Exception {
try {
- comparator.compare(Mockito.mock(Alias.class), Mockito.mock(Alias.class));
+ comparator.compare(Mockito.mock(Element.class), Mockito.mock(Element.class));
fail("Exception should occur");
} catch (NotImplementedException e) {
@@ -48,8 +55,8 @@ public class AliasComparatorTest {
@Test
public void testEquals() throws Exception {
try {
- assertEquals(0, comparator.compare(new GenericProteinAlias("id2"), new GenericProteinAlias("id2")));
- assertEquals(0, comparator.compare(new ComplexAlias(), new ComplexAlias()));
+ assertEquals(0, comparator.compare(new GenericProtein("id2"), new GenericProtein("id2")));
+ assertEquals(0, comparator.compare(new Complex(), new Complex()));
assertEquals(0, comparator.compare(null, null));
} catch (Exception e) {
@@ -61,39 +68,39 @@ public class AliasComparatorTest {
@Test
public void testDifferent() throws Exception {
try {
- assertTrue(comparator.compare(new GenericProteinAlias("id2"), new GenericProteinAlias("id1")) != 0);
+ assertTrue(comparator.compare(new GenericProtein("id2"), new GenericProtein("id1")) != 0);
- assertTrue(comparator.compare(null, new GenericProteinAlias()) != 0);
- assertTrue(comparator.compare(new GenericProteinAlias(), null) != 0);
- assertTrue(comparator.compare(new GenericProteinAlias(), new ComplexAlias()) != 0);
+ assertTrue(comparator.compare(null, new GenericProtein()) != 0);
+ assertTrue(comparator.compare(new GenericProtein(), null) != 0);
+ assertTrue(comparator.compare(new GenericProtein(), new Complex()) != 0);
- SpeciesAlias sa1 = new GenericProteinAlias("id2");
- SpeciesAlias sa2 = new GenericProteinAlias("id2");
+ Species sa1 = new GenericProtein("id2");
+ Species sa2 = new GenericProtein("id2");
sa2.setY(2);
assertTrue(comparator.compare(sa1, sa2) != 0);
- sa1 = new GenericProteinAlias("id2");
- sa2 = new GenericProteinAlias("id2");
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
sa2.setY(2);
assertTrue(comparator.compare(sa1, sa2) != 0);
- sa1 = new GenericProteinAlias("id2");
- sa2 = new GenericProteinAlias("id2");
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
sa2.setHeight(2);
assertTrue(comparator.compare(sa1, sa2) != 0);
- sa1 = new GenericProteinAlias("id2");
- sa2 = new GenericProteinAlias("id2");
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
sa2.setFontSize(2);
assertTrue(comparator.compare(sa1, sa2) != 0);
- sa1 = new GenericProteinAlias("id2");
- sa2 = new GenericProteinAlias("id2");
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
sa2.setColor(Color.BLUE);
assertTrue(comparator.compare(sa1, sa2) != 0);
- sa1 = new GenericProteinAlias("id2");
- sa2 = new GenericProteinAlias("id2");
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
sa2.setVisibilityLevel(6);
assertTrue(comparator.compare(sa1, sa2) != 0);
@@ -106,8 +113,8 @@ public class AliasComparatorTest {
@Test
public void testCompareSubmodel() throws Exception {
try {
- Alias alias1 = createAlias();
- Alias alias2 = createAlias();
+ Element alias1 = createAlias();
+ Element alias2 = createAlias();
assertEquals(0, comparator.compare(alias1, alias2));
alias1.setSubmodel(null);
@@ -128,8 +135,8 @@ public class AliasComparatorTest {
}
}
- private Alias createAlias() {
- Alias result = new GenericProteinAlias("id2");
+ private Element createAlias() {
+ Element result = new GenericProtein("id2");
AliasSubmodelConnection submodel = new AliasSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
result.setSubmodel(submodel);
return result;
@@ -139,15 +146,15 @@ public class AliasComparatorTest {
Model model = new ModelFullIndexed(null);
model.setNotes("Some description");
- GenericProteinAlias protein = new GenericProteinAlias("A");
+ GenericProtein protein = new GenericProtein("A");
protein.setName("ad");
model.addAlias(protein);
- ProteinAlias alias = new GenericProteinAlias("a_id");
+ Protein alias = new GenericProtein("a_id");
alias.setName("ad");
model.addAlias(alias);
- model.addAlias(new CompartmentAlias("default"));
+ model.addAlias(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasGroupTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AliasGroupTest.java
similarity index 65%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasGroupTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/AliasGroupTest.java
index d9502c7273..058e4f8f56 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasGroupTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AliasGroupTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
@@ -10,6 +10,10 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
public class AliasGroupTest {
@Before
@@ -23,7 +27,7 @@ public class AliasGroupTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new AliasGroup());
+ SerializationUtils.serialize(new ElementGroup());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -33,9 +37,9 @@ public class AliasGroupTest {
@Test
public void testGetters() {
try {
- AliasGroup group = new AliasGroup();
+ ElementGroup group = new ElementGroup();
String idGroup = "str";
- List<Alias> aliases = new ArrayList<>();
+ List<Element> aliases = new ArrayList<>();
group.setIdGroup(idGroup);
group.setAliases(aliases);
@@ -51,8 +55,8 @@ public class AliasGroupTest {
@Test
public void testAddAlias() {
try {
- AliasGroup group = new AliasGroup();
- group.addAlias(new GenericProteinAlias());
+ ElementGroup group = new ElementGroup();
+ group.addAlias(new GenericProtein());
assertEquals(1, group.getAliases().size());
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AliasTest.java
similarity index 85%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/AliasTest.java
index b62ef6a5e0..02340a265c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -17,11 +17,16 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class AliasTest {
@@ -37,8 +42,8 @@ public class AliasTest {
@Test
public void testDistance1() {
- SpeciesAlias alias;
- alias = new GenericProteinAlias();
+ Species alias;
+ alias = new GenericProtein();
alias.setWidth(10);
alias.setHeight(20);
alias.setX(100.0);
@@ -49,8 +54,8 @@ public class AliasTest {
@Test
public void testDistance2() {
- SpeciesAlias alias;
- alias = new GenericProteinAlias();
+ Species alias;
+ alias = new GenericProtein();
alias.setWidth(10);
alias.setHeight(20);
alias.setX(100.0);
@@ -61,8 +66,8 @@ public class AliasTest {
@Test
public void testDistance6() {
- SpeciesAlias alias;
- alias = new GenericProteinAlias();
+ Species alias;
+ alias = new GenericProtein();
alias.setWidth(10);
alias.setHeight(20);
alias.setX(100.0);
@@ -73,8 +78,8 @@ public class AliasTest {
@Test
public void testDistance3() {
- SpeciesAlias alias;
- alias = new GenericProteinAlias();
+ Species alias;
+ alias = new GenericProtein();
alias.setWidth(10);
alias.setHeight(20);
alias.setX(100.0);
@@ -85,8 +90,8 @@ public class AliasTest {
@Test
public void testDistance4() {
- SpeciesAlias alias;
- alias = new GenericProteinAlias();
+ Species alias;
+ alias = new GenericProtein();
alias.setWidth(10);
alias.setHeight(20);
alias.setX(100.0);
@@ -98,10 +103,10 @@ public class AliasTest {
@Test
public void testConstructor() {
try {
- GenericProteinAlias alias = new GenericProteinAlias();
+ GenericProtein alias = new GenericProtein();
alias.addSearchIndex(new SearchIndex());
alias.setSubmodel(new AliasSubmodelConnection());
- Alias copy = new GenericProteinAlias(alias);
+ Element copy = new GenericProtein(alias);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -112,7 +117,7 @@ public class AliasTest {
@Test
public void testIncreaseBorder() {
try {
- SpeciesAlias alias = new GenericProteinAlias();
+ Species alias = new GenericProtein();
assertEquals(0.0, alias.getSize(), Configuration.EPSILON);
alias.increaseBorder(2);
assertEquals(16.0, alias.getSize(), Configuration.EPSILON);
@@ -125,7 +130,7 @@ public class AliasTest {
@Test
public void testGetters() {
try {
- SpeciesAlias alias = new GenericProteinAlias();
+ Species alias = new GenericProtein();
Double nullDouble = null;
String xStr = "1.2";
Double x = 1.2;
@@ -139,7 +144,7 @@ public class AliasTest {
String heightStr = "4.0";
Double height = 4.0;
ModelData modelData = new ModelData();
- CompartmentAlias compartmentAlias = new CompartmentAlias();
+ Compartment compartmentAlias = new Compartment("idd");
int id = 72;
int transparencyLevel = 2;
Model model = new ModelFullIndexed(modelData);
@@ -218,10 +223,10 @@ public class AliasTest {
@Test
public void testContainsAlias() {
try {
- SpeciesAlias alias = new GenericProteinAlias();
+ Species alias = new GenericProtein();
alias.setWidth(100);
alias.setHeight(100);
- SpeciesAlias alias2 = new GenericProteinAlias();
+ Species alias2 = new GenericProtein();
alias2.setX(-2);
alias2.setY(-2);
alias2.setWidth(100);
@@ -244,7 +249,7 @@ public class AliasTest {
alias2.setHeight(200);
assertFalse(alias.contains(alias2));
- CompartmentAlias alias3 = new CompartmentAlias();
+ Compartment alias3 = new Compartment("idd");
alias3.setX(2);
alias3.setY(2);
alias3.setWidth(10);
@@ -279,7 +284,7 @@ public class AliasTest {
@Test
public void testContainsLayerText() {
try {
- SpeciesAlias alias = new GenericProteinAlias();
+ Species alias = new GenericProtein();
alias.setWidth(100);
alias.setHeight(100);
LayerText alias2 = new LayerText();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
new file mode 100644
index 0000000000..851a16e81f
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
@@ -0,0 +1,27 @@
+package lcsb.mapviewer.model.map.species;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartmentAliasTest;
+import lcsb.mapviewer.model.map.compartment.CompartmentAliasComparatorTest;
+import lcsb.mapviewer.model.map.compartment.CompartmentAliasTest;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartmentAliasTest;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartmentAliasTest;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartmentAliasTest;
+
+@RunWith(Suite.class)
+@SuiteClasses({
+ AliasGroupTest.class, //
+ AliasTest.class, //
+ ArtifitialCompartmentAliasTest.class, //
+ ComplexAliasComparatorTest.class, //
+ ComplexAliasTest.class, //
+ SearchIndexTest.class, //
+ SpeciesAliasComparatorTest.class, //
+ SpeciesAliasTest.class, //
+})
+public class AllSpeciesTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ArtifitialCompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ArtifitialCompartmentAliasTest.java
similarity index 67%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ArtifitialCompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/ArtifitialCompartmentAliasTest.java
index d4d7c28c60..2150eef721 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ArtifitialCompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ArtifitialCompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -10,6 +10,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
public class ArtifitialCompartmentAliasTest {
@@ -24,9 +27,9 @@ public class ArtifitialCompartmentAliasTest {
@Test
public void test() throws Exception {
try {
- CompartmentAliasComparator comparator = new CompartmentAliasComparator();
- CompartmentAlias alias = new ArtifitialCompartmentAlias();
- CompartmentAlias copy = alias.copy();
+ CompartmentComparator comparator = new CompartmentComparator();
+ Compartment alias = new PathwayCompartment();
+ Compartment copy = alias.copy();
assertEquals(0, comparator.compare(alias, copy));
} catch (Exception e) {
@@ -39,7 +42,7 @@ public class ArtifitialCompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new ArtifitialCompartmentAlias());
+ SerializationUtils.serialize(new PathwayCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -49,7 +52,7 @@ public class ArtifitialCompartmentAliasTest {
@Test
public void testGetters() {
try {
- ArtifitialCompartmentAlias alias = new ArtifitialCompartmentAlias();
+ PathwayCompartment alias = new PathwayCompartment();
String title = "tit27";
alias.setName(title);
assertEquals(title, alias.getName());
@@ -63,7 +66,7 @@ public class ArtifitialCompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new ArtifitialCompartmentAlias() {
+ new PathwayCompartment() {
/**
*
@@ -81,7 +84,7 @@ public class ArtifitialCompartmentAliasTest {
@Test
public void testCopy() {
try {
- ArtifitialCompartmentAlias degraded = new ArtifitialCompartmentAlias().copy();
+ PathwayCompartment degraded = new PathwayCompartment().copy();
assertNotNull(degraded);
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexAliasComparatorTest.java
similarity index 68%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparatorTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/ComplexAliasComparatorTest.java
index 2577ab598d..9c63b53a90 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexAliasComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -12,10 +12,14 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.ComplexComparator;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ComplexAliasComparatorTest {
- ComplexAliasComparator comparator = new ComplexAliasComparator();
+ ComplexComparator comparator = new ComplexComparator();
@Before
public void setUp() throws Exception {
@@ -28,8 +32,8 @@ public class ComplexAliasComparatorTest {
@Test
public void testEquals() {
try {
- ComplexAlias alias1 = createComplexAlias();
- ComplexAlias alias2 = createComplexAlias();
+ Complex alias1 = createComplexAlias();
+ Complex alias2 = createComplexAlias();
assertEquals(0, comparator.compare(alias1, alias2));
@@ -41,8 +45,8 @@ public class ComplexAliasComparatorTest {
}
}
- private ComplexAlias createComplexAlias() {
- ComplexAlias result = new ComplexAlias();
+ private Complex createComplexAlias() {
+ Complex result = new Complex();
result.setName("complex");
result.setAliasId("asd");
@@ -54,7 +58,7 @@ public class ComplexAliasComparatorTest {
result.setColor(Color.BLUE);
result.setVisibilityLevel(14);
- SpeciesAlias alias = new GenericProteinAlias("S");
+ Species alias = new GenericProtein("S");
alias.setName("a");
result.addAlias(alias);
@@ -64,8 +68,8 @@ public class ComplexAliasComparatorTest {
@Test
public void testDifferent() {
try {
- ComplexAlias alias1 = createComplexAlias();
- ComplexAlias alias2 = createComplexAlias();
+ Complex alias1 = createComplexAlias();
+ Complex alias2 = createComplexAlias();
assertTrue(comparator.compare(alias1, null) != 0);
assertTrue(comparator.compare(null, alias1) != 0);
@@ -81,7 +85,7 @@ public class ComplexAliasComparatorTest {
alias1 = createComplexAlias();
alias2 = createComplexAlias();
- alias1.addAlias(new GenericProteinAlias("id"));
+ alias1.addAlias(new GenericProtein("id"));
assertTrue(comparator.compare(alias1, alias2) != 0);
assertTrue(comparator.compare(alias2, alias1) != 0);
@@ -97,7 +101,7 @@ public class ComplexAliasComparatorTest {
alias1 = createComplexAlias();
alias2 = createComplexAlias();
- SpeciesAlias speciesAlias = (SpeciesAlias) alias1.getAliases().iterator().next();
+ Species speciesAlias = (Species) alias1.getAliases().iterator().next();
speciesAlias.setName("new namne");
assertTrue(comparator.compare(alias1, alias2) != 0);
@@ -111,7 +115,7 @@ public class ComplexAliasComparatorTest {
assertTrue(comparator.compare(alias1, alias2) != 0);
assertTrue(comparator.compare(alias2, alias1) != 0);
- assertTrue(comparator.compare(alias2, new ComplexAlias() {
+ assertTrue(comparator.compare(alias2, new Complex() {
private static final long serialVersionUID = 1L;
}) != 0);
@@ -124,16 +128,16 @@ public class ComplexAliasComparatorTest {
@Test
public void testInvalid() {
try {
- ComplexAlias alias1 = createComplexAlias();
- ComplexAlias alias2 = createComplexAlias();
+ Complex alias1 = createComplexAlias();
+ Complex alias2 = createComplexAlias();
- GenericProteinAlias alias = new GenericProteinAlias("1");
+ GenericProtein alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias = new GenericProteinAlias("1");
+ alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias2.getAliases().add(new GenericProteinAlias("b"));
- alias2.getAliases().add(new GenericProteinAlias("a"));
+ alias2.getAliases().add(new GenericProtein("b"));
+ alias2.getAliases().add(new GenericProtein("a"));
comparator.compare(alias1, alias2);
fail("Exception expected");
@@ -148,7 +152,7 @@ public class ComplexAliasComparatorTest {
@Test
public void testInvalid3() {
try {
- class Tmp extends ComplexAlias {
+ class Tmp extends Complex {
private static final long serialVersionUID = 1L;
}
;
@@ -168,16 +172,16 @@ public class ComplexAliasComparatorTest {
@Test
public void testInvalid2() {
try {
- ComplexAlias alias1 = createComplexAlias();
- ComplexAlias alias2 = createComplexAlias();
+ Complex alias1 = createComplexAlias();
+ Complex alias2 = createComplexAlias();
- SpeciesAlias alias = new GenericProteinAlias("1");
+ Species alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias = new GenericProteinAlias("1");
+ alias = new GenericProtein("1");
alias1.getAliases().add(alias);
- alias2.getAliases().add(new GenericProteinAlias("A"));
- alias2.getAliases().add(new GenericProteinAlias("B"));
+ alias2.getAliases().add(new GenericProtein("A"));
+ alias2.getAliases().add(new GenericProtein("B"));
comparator.compare(alias2, alias1);
fail("Exception expected");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexAliasTest.java
similarity index 65%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/ComplexAliasTest.java
index 2390121c6d..6019ce77f2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -10,6 +10,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class ComplexAliasTest {
@@ -24,7 +27,7 @@ public class ComplexAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new ComplexAlias());
+ SerializationUtils.serialize(new Complex());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -34,9 +37,9 @@ public class ComplexAliasTest {
@Test
public void testConstructor() {
try {
- ComplexAlias complex = new ComplexAlias();
- complex.addAlias(new GenericProteinAlias());
- ComplexAlias copy = new ComplexAlias(complex);
+ Complex complex = new Complex();
+ complex.addAlias(new GenericProtein());
+ Complex copy = new Complex(complex);
assertNotNull(copy);
} catch (Exception e) {
@@ -48,13 +51,13 @@ public class ComplexAliasTest {
@Test
public void testAddAlias() {
try {
- ComplexAlias complex = new ComplexAlias();
- SpeciesAlias alias = new GenericProteinAlias("id1");
+ Complex complex = new Complex();
+ Species alias = new GenericProtein("id1");
complex.addAlias(alias);
assertEquals(1, complex.getAllChildrenAliases().size());
complex.addAlias(alias);
assertEquals(1, complex.getAllChildrenAliases().size());
- SpeciesAlias alias2 = new GenericProteinAlias("s");
+ Species alias2 = new GenericProtein("s");
complex.addAlias(alias2);
assertEquals(2, complex.getAllChildrenAliases().size());
} catch (Exception e) {
@@ -66,12 +69,12 @@ public class ComplexAliasTest {
@Test
public void testGetAllChildren() {
try {
- ComplexAlias complex = new ComplexAlias();
+ Complex complex = new Complex();
- complex.addAlias(new GenericProteinAlias("1"));
- ComplexAlias complex2 = new ComplexAlias("c3");
- complex2.addAlias(new GenericProteinAlias("2"));
- complex2.addAlias(new GenericProteinAlias("4"));
+ complex.addAlias(new GenericProtein("1"));
+ Complex complex2 = new Complex("c3");
+ complex2.addAlias(new GenericProtein("2"));
+ complex2.addAlias(new GenericProtein("4"));
complex.addAlias(complex2);
@@ -87,12 +90,12 @@ public class ComplexAliasTest {
@Test
public void testRemoveAlias() {
try {
- ComplexAlias complex = new ComplexAlias();
+ Complex complex = new Complex();
- SpeciesAlias alias = new GenericProteinAlias("1");
+ Species alias = new GenericProtein("1");
complex.addAlias(alias);
- complex.addAlias(new GenericProteinAlias("2"));
- complex.addAlias(new GenericProteinAlias("4"));
+ complex.addAlias(new GenericProtein("2"));
+ complex.addAlias(new GenericProtein("4"));
assertEquals(3, complex.getAliases().size());
complex.removeAlias(alias);
@@ -109,8 +112,8 @@ public class ComplexAliasTest {
@Test
public void testCopy() {
try {
- ComplexAlias original = new ComplexAlias();
- ComplexAlias copy = original.copy();
+ Complex original = new Complex();
+ Complex copy = original.copy();
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -121,7 +124,7 @@ public class ComplexAliasTest {
@Test
public void testInvalidCopy() {
try {
- new ComplexAlias() {
+ new Complex() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ModificationStateTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ModificationStateTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ModificationStateTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/ModificationStateTest.java
index 4f2f9a91c8..1a1987dc82 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ModificationStateTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ModificationStateTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
@@ -7,6 +7,8 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
public class ModificationStateTest {
@Before
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/OvalCompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/OvalCompartmentAliasTest.java
similarity index 70%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/OvalCompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/OvalCompartmentAliasTest.java
index 9faf499ccb..728f9f04f8 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/OvalCompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/OvalCompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
@@ -9,6 +9,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
public class OvalCompartmentAliasTest {
@@ -23,7 +24,7 @@ public class OvalCompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new OvalCompartmentAlias());
+ SerializationUtils.serialize(new OvalCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -33,8 +34,8 @@ public class OvalCompartmentAliasTest {
@Test
public void testConstructor() {
try {
- OvalCompartmentAlias original = new OvalCompartmentAlias();
- OvalCompartmentAlias copy = new OvalCompartmentAlias(original);
+ OvalCompartment original = new OvalCompartment();
+ OvalCompartment copy = new OvalCompartment(original);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -45,8 +46,8 @@ public class OvalCompartmentAliasTest {
@Test
public void testCopy() {
try {
- OvalCompartmentAlias original = new OvalCompartmentAlias();
- OvalCompartmentAlias copy = original.copy();
+ OvalCompartment original = new OvalCompartment();
+ OvalCompartment copy = original.copy();
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +58,7 @@ public class OvalCompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new OvalCompartmentAlias() {
+ new OvalCompartment() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/PositionToCompartmentTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartmentTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/PositionToCompartmentTest.java
index 9758966dda..d8ca94fbd5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/PositionToCompartmentTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
@@ -7,6 +7,8 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+
public class PositionToCompartmentTest {
@Before
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SearchIndexTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SearchIndexTest.java
similarity index 87%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SearchIndexTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/SearchIndexTest.java
index 4d61d33148..c32f503d9a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SearchIndexTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SearchIndexTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -10,6 +10,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
public class SearchIndexTest {
@@ -101,7 +104,7 @@ public class SearchIndexTest {
int id = 54;
int weight = 8;
String value = "val5";
- Alias alias = new GeneAlias();
+ Element alias = new Gene();
SearchIndex index = new SearchIndex();
index.setId(id);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesAliasComparatorTest.java
similarity index 75%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparatorTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesAliasComparatorTest.java
index ffbafe9f43..d0fe439e7c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesAliasComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -12,10 +12,14 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.SpeciesComparator;
public class SpeciesAliasComparatorTest {
- SpeciesAliasComparator comparator = new SpeciesAliasComparator();
+ SpeciesComparator comparator = new SpeciesComparator();
@Before
public void setUp() throws Exception {
@@ -28,14 +32,14 @@ public class SpeciesAliasComparatorTest {
@Test
public void testEquals() {
try {
- SpeciesAlias alias1 = createSpeciesAlias();
- SpeciesAlias alias2 = createSpeciesAlias();
+ Species alias1 = createSpeciesAlias();
+ Species alias2 = createSpeciesAlias();
assertEquals(0, comparator.compare(alias1, alias2));
assertEquals(0, comparator.compare(null, null));
- assertEquals(0, comparator.compare(new ComplexAlias(), new ComplexAlias()));
+ assertEquals(0, comparator.compare(new Complex(), new Complex()));
} catch (Exception e) {
e.printStackTrace();
@@ -47,7 +51,7 @@ public class SpeciesAliasComparatorTest {
public void testCompareInvalid() {
try {
- SpeciesAlias alias = Mockito.mock(SpeciesAlias.class);
+ Species alias = Mockito.mock(Species.class);
comparator.compare(alias, alias);
fail("Exception expected");
@@ -58,8 +62,8 @@ public class SpeciesAliasComparatorTest {
}
}
- private SpeciesAlias createSpeciesAlias() {
- GenericProteinAlias result = new GenericProteinAlias();
+ private Species createSpeciesAlias() {
+ GenericProtein result = new GenericProtein();
result.setName("a");
result.setAliasId("asd");
@@ -79,13 +83,13 @@ public class SpeciesAliasComparatorTest {
@Test
public void testDifferent() throws Exception {
try {
- SpeciesAlias alias1 = createSpeciesAlias();
- SpeciesAlias alias2 = createSpeciesAlias();
+ Species alias1 = createSpeciesAlias();
+ Species alias2 = createSpeciesAlias();
assertTrue(comparator.compare(alias1, null) != 0);
assertTrue(comparator.compare(null, alias1) != 0);
- assertTrue(comparator.compare(new ComplexAlias(), alias1) != 0);
+ assertTrue(comparator.compare(new Complex(), alias1) != 0);
alias1 = createSpeciesAlias();
alias2 = createSpeciesAlias();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesAliasTest.java
similarity index 74%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesAliasTest.java
index ee478ed37c..585a6b15d6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertEquals;
@@ -10,6 +10,8 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
public class SpeciesAliasTest {
@@ -24,7 +26,7 @@ public class SpeciesAliasTest {
@Test
public void testGetter() {
try {
- SpeciesAlias alias = new GenericProteinAlias("id");
+ Species alias = new GenericProtein("id");
String state = "as";
Set<ReactionNode> node = new HashSet<>();
alias.setState(state);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SquareCompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SquareCompartmentAliasTest.java
similarity index 69%
rename from model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SquareCompartmentAliasTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/species/SquareCompartmentAliasTest.java
index 88af098c8a..609af84b7b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SquareCompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SquareCompartmentAliasTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.layout.alias;
+package lcsb.mapviewer.model.map.species;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
@@ -9,6 +9,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
public class SquareCompartmentAliasTest {
@@ -23,7 +24,7 @@ public class SquareCompartmentAliasTest {
@Test
public void testSerialization() {
try {
- SerializationUtils.serialize(new SquareCompartmentAlias());
+ SerializationUtils.serialize(new SquareCompartment());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -33,8 +34,8 @@ public class SquareCompartmentAliasTest {
@Test
public void testConstructor() {
try {
- SquareCompartmentAlias original = new SquareCompartmentAlias();
- SquareCompartmentAlias copy = new SquareCompartmentAlias(original);
+ SquareCompartment original = new SquareCompartment();
+ SquareCompartment copy = new SquareCompartment(original);
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -45,8 +46,8 @@ public class SquareCompartmentAliasTest {
@Test
public void testCopy() {
try {
- SquareCompartmentAlias original = new SquareCompartmentAlias();
- SquareCompartmentAlias copy = original.copy();
+ SquareCompartment original = new SquareCompartment();
+ SquareCompartment copy = original.copy();
assertNotNull(copy);
} catch (Exception e) {
e.printStackTrace();
@@ -57,7 +58,7 @@ public class SquareCompartmentAliasTest {
@Test
public void testInvalidCopy() {
try {
- new SquareCompartmentAlias() {
+ new SquareCompartment() {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
index 0bc877fd6c..949c2fb8e5 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
@@ -16,12 +16,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Protein;
public class ElementUtilsTest {
Logger logger = Logger.getLogger(ElementUtilsTest.class);
@@ -93,9 +93,9 @@ public class ElementUtilsTest {
try {
ElementUtils elementUtils = new ElementUtils();
- List<Class<? extends Alias>> list = elementUtils.getAvailableElementSubclasses();
- assertTrue(list.contains(IonChannelProteinAlias.class));
- assertFalse(list.contains(ProteinAlias.class));
+ List<Class<? extends Element>> list = elementUtils.getAvailableElementSubclasses();
+ assertTrue(list.contains(IonChannelProtein.class));
+ assertFalse(list.contains(Protein.class));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -106,8 +106,8 @@ public class ElementUtilsTest {
public void tesClassByName() throws Exception {
try {
ElementUtils elementUtils = new ElementUtils();
- assertEquals(IonAlias.class, elementUtils.getClassByName(IonAlias.class.getSimpleName()));
- assertEquals(IonAlias.class, elementUtils.getClassByName("Ion"));
+ assertEquals(Ion.class, elementUtils.getClassByName(Ion.class.getSimpleName()));
+ assertEquals(Ion.class, elementUtils.getClassByName("Ion"));
assertNull(elementUtils.getClassByName("unknown class name"));
} catch (Exception e) {
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index 3d76640ca2..5403bf1b76 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -26,20 +26,9 @@ import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.OvalCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
@@ -60,6 +49,17 @@ import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
import lcsb.mapviewer.model.map.reaction.type.ReducedNotation;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.wikipathway.model.DataNode;
import lcsb.mapviewer.wikipathway.model.Edge;
@@ -121,7 +121,7 @@ public class ModelContructor {
/**
* List of {@link Shape#shape shapes} that are not supported to be part of a
- * {@link ComplexAlias complex}.
+ * {@link Complex complex}.
*/
private static final Set<String> INALID_COMPLEX_SHAPE_CHILDREN = new HashSet<>();
@@ -221,7 +221,7 @@ public class ModelContructor {
/**
* Map between graphId and aliases created from gpml elements.
*/
- private Map<String, Alias> id2alias;
+ private Map<String, Element> id2alias;
/**
* Default layer.
@@ -232,7 +232,7 @@ public class ModelContructor {
* Default constructor.
*/
private Data() {
- id2alias = new HashMap<String, Alias>();
+ id2alias = new HashMap<String, Element>();
layer = new Layer();
layer.setVisible(true);
layer.setLayerId("1");
@@ -247,32 +247,32 @@ public class ModelContructor {
* object from which species is created
* @param data
* ...
- * @return {@link SpeciesAlias} created from input {@link DataNode}
+ * @return {@link Species} created from input {@link DataNode}
*/
- protected SpeciesAlias createAlias(DataNode dataNode, Data data) {
- SpeciesAlias res = null;
+ protected Species createAlias(DataNode dataNode, Data data) {
+ Species res = null;
String type = dataNode.getType();
if (type == null || type.equals("")) {
type = null;
}
if (type != null && type.equalsIgnoreCase("Metabolite")) {
- res = new SimpleMoleculeAlias(dataNode.getGraphId());
+ res = new SimpleMolecule(dataNode.getGraphId());
} else if (type != null && type.equalsIgnoreCase("GeneProduct")) {
- res = new GeneAlias(dataNode.getGraphId());
+ res = new Gene(dataNode.getGraphId());
} else if (type != null && type.equalsIgnoreCase("Pathway")) {
- res = new PhenotypeAlias(dataNode.getGraphId());
+ res = new Phenotype(dataNode.getGraphId());
} else if (type != null && type.equalsIgnoreCase("Rna")) {
- res = new RnaAlias(dataNode.getGraphId());
+ res = new Rna(dataNode.getGraphId());
} else if (type != null && type.equalsIgnoreCase("Protein")) {
- res = new GenericProteinAlias(dataNode.getGraphId());
+ res = new GenericProtein(dataNode.getGraphId());
} else if (type != null && type.equalsIgnoreCase("Complex")) {
- res = new ComplexAlias(dataNode.getGraphId());
+ res = new Complex(dataNode.getGraphId());
} else if (type != null && type.equalsIgnoreCase("None")) {
- res = new UnknownAlias(dataNode.getGraphId());
+ res = new Unknown(dataNode.getGraphId());
} else {
logger.warn("[" + dataNode.getGraphId() + "]\tUnknown species type: " + type + ". Using Unknown");
- res = new UnknownAlias(dataNode.getGraphId());
+ res = new Unknown(dataNode.getGraphId());
}
res.addMiriamData(dataNode.getReferences());
@@ -293,7 +293,7 @@ public class ModelContructor {
*/
protected void addComplexSpecies(Model model, Graph graph, Data data) {
for (Group group : graph.getGroups()) {
- ComplexAlias alias = new ComplexAlias(group.getGraphId());
+ Complex alias = new Complex(group.getGraphId());
alias.setName(group.getGraphId());
if ("Complex".equalsIgnoreCase(group.getStyle())) {
alias.setHypothetical(false);
@@ -328,20 +328,20 @@ public class ModelContructor {
*/
protected void addElement(Model model, Graph graph, Data data) {
for (DataNode dataNode : graph.getDataNodes()) {
- SpeciesAlias species = createAlias(dataNode, data);
+ Species species = createAlias(dataNode, data);
species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReference()));
- Alias alias = updateAlias(dataNode, species);
+ Element alias = updateAlias(dataNode, species);
data.id2alias.put(dataNode.getGraphId(), alias);
model.addAlias(alias);
}
for (Label label : graph.getLabels()) {
if (label.isTreatAsNode()) {
- SpeciesAlias species = createSpecies(label);
+ Species species = createSpecies(label);
species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), label.getBiopaxReference()));
- Alias alias = updateAlias(label, species);
+ Element alias = updateAlias(label, species);
data.id2alias.put(label.getGraphId(), alias);
model.addAlias(alias);
@@ -352,10 +352,10 @@ public class ModelContructor {
}
for (Shape shape : graph.getShapes()) {
if (shape.isTreatAsNode()) {
- SpeciesAlias species = createSpecies(shape);
+ Species species = createSpecies(shape);
species.addMiriamData(biopaxParser.getMiriamData(graph.getBiopaxData(), shape.getBiopaxReference()));
- Alias alias = updateAlias(shape, species);
+ Element alias = updateAlias(shape, species);
data.id2alias.put(shape.getGraphId(), alias);
model.addAlias(alias);
@@ -370,8 +370,8 @@ public class ModelContructor {
data.layer.addLayerRect(rect);
}
} else {
- CompartmentAlias compartment = new CompartmentAlias(shape.getGraphId());
- Alias cmpAl = updateAlias(shape, compartment);
+ Compartment compartment = new Compartment(shape.getGraphId());
+ Element cmpAl = updateAlias(shape, compartment);
model.addAlias(cmpAl);
}
}
@@ -379,9 +379,9 @@ public class ModelContructor {
for (State state : graph.getStates()) {
// TODO this might not work
- Alias species = data.id2alias.get(state.getGraphRef());
+ Element species = data.id2alias.get(state.getGraphRef());
if (state.getType() != null) {
- ModificationResidueAlias mr = new ModificationResidueAlias();
+ ModificationResidue mr = new ModificationResidue();
mr.setIdModificationResidue(state.getGraphId());
mr.setState(state.getType());
Double angle = null;
@@ -406,16 +406,16 @@ public class ModelContructor {
// CHECKSTYLE:ON
mr.setAngle(angle);
- if (species instanceof ProteinAlias) {
- ((ProteinAlias) species).addModificationResidue(mr);
- } else if (species instanceof GeneAlias) {
- ((GeneAlias) species).addModificationResidue(mr);
+ if (species instanceof Protein) {
+ ((Protein) species).addModificationResidue(mr);
+ } else if (species instanceof Gene) {
+ ((Gene) species).addModificationResidue(mr);
} else {
logger.warn(state.getWarningPrefix() + "state for " + species.getClass().getSimpleName() + " is not supported.");
}
} else if (state.getStructuralState() != null) {
- if (species instanceof ProteinAlias) {
- ProteinAlias protein = ((ProteinAlias) species);
+ if (species instanceof Protein) {
+ Protein protein = ((Protein) species);
if (protein.getStructuralState() == null) {
protein.setStructuralState(state.getStructuralState());
} else {
@@ -489,20 +489,20 @@ public class ModelContructor {
/**
* Creates alias for {@link GraphicalPathwayElement}. Type of the alias is
- * defined by the parameter {@link SpeciesAlias}
+ * defined by the parameter {@link Species}
*
* @param gpmlElement
* object from which alias will be create
* @param alias
* specie for which alias will be created
- * @return {@link SpeciesAlias} created from input {@link Label}
+ * @return {@link Species} created from input {@link Label}
*/
- public Alias updateAlias(GraphicalPathwayElement gpmlElement, Alias alias) {
- if (alias instanceof CompartmentAlias) {
+ public Element updateAlias(GraphicalPathwayElement gpmlElement, Element alias) {
+ if (alias instanceof Compartment) {
if (((Shape) gpmlElement).getShape().equalsIgnoreCase("oval")) {
- alias = new OvalCompartmentAlias((CompartmentAlias) alias);
+ alias = new OvalCompartment((Compartment) alias);
} else {
- alias = new SquareCompartmentAlias((CompartmentAlias) alias);
+ alias = new SquareCompartment((Compartment) alias);
}
}
Rectangle2D rec = gpmlElement.getRectangle();
@@ -515,31 +515,31 @@ public class ModelContructor {
}
/**
- * Creates {@link UnknownAlias species} from {@link Label}.
+ * Creates {@link Unknown species} from {@link Label}.
*
* @param label
* original label from which output should be created
- * @return {@link UnknownAlias} object created from input {@link Label}
+ * @return {@link Unknown} object created from input {@link Label}
*/
- private SpeciesAlias createSpecies(Label label) {
+ private Species createSpecies(Label label) {
logger.warn(label.getWarningPrefix() + " Label cannot be part of reaction. Tranforming to Unknown");
- SpeciesAlias res = new UnknownAlias(label.getGraphId());
+ Species res = new Unknown(label.getGraphId());
res.setName(label.getName());
return res;
}
/**
- * Creates {@link UnknownAlias species} from {@link Shape}.
+ * Creates {@link Unknown species} from {@link Shape}.
*
* @param shape
* original label from which output should be created
- * @return {@link UnknownAlias} object created from input {@link Label}
+ * @return {@link Unknown} object created from input {@link Label}
*/
- private SpeciesAlias createSpecies(Shape shape) {
+ private Species createSpecies(Shape shape) {
logger.warn(shape.getWarningPrefix() + " Shape can not be part of reaction. Tranforming to Unknown");
- SpeciesAlias res = new UnknownAlias(shape.getGraphId());
+ Species res = new Unknown(shape.getGraphId());
res.setName(shape.getName());
return res;
}
@@ -557,13 +557,13 @@ public class ModelContructor {
protected void putSpeciesIntoComplexes(Graph graph, Data data) throws UnknownChildClassException {
for (Group group : graph.getGroups()) {
- ComplexAlias complexSpecies = (ComplexAlias) data.id2alias.get(group.getGraphId());
+ Complex complexSpecies = (Complex) data.id2alias.get(group.getGraphId());
for (PathwayElement pe : group.getNodes()) {
- Alias species = data.id2alias.get(pe.getGraphId());
+ Element species = data.id2alias.get(pe.getGraphId());
if (species != null) {
- if (species instanceof SpeciesAlias) {
+ if (species instanceof Species) {
- SpeciesAlias speciesAlias = (SpeciesAlias) species;
+ Species speciesAlias = (Species) species;
speciesAlias.setComplexAlias(complexSpecies);
complexSpecies.addAlias(speciesAlias);
@@ -836,7 +836,7 @@ public class ModelContructor {
throw new InvalidStateException("This modifier is invalid");
}
- Modifier mod = createModifierByType(modifierType, (SpeciesAlias) data.id2alias.get(id));
+ Modifier mod = createModifierByType(modifierType, (Species) data.id2alias.get(id));
ModifierType mt = mtu.getModifierTypeForClazz(mod.getClass());
@@ -868,12 +868,12 @@ public class ModelContructor {
* @param modifierType
* type of modifier in reaction to create
* @param alias
- * {@link SpeciesAlias alias } to which modifier is attached
+ * {@link Species alias } to which modifier is attached
* @return new instance of the modifierType
*/
- private Modifier createModifierByType(Class<? extends ReactionNode> modifierType, SpeciesAlias alias) {
+ private Modifier createModifierByType(Class<? extends ReactionNode> modifierType, Species alias) {
try {
- Modifier result = (Modifier) modifierType.getConstructor(SpeciesAlias.class).newInstance(alias);
+ Modifier result = (Modifier) modifierType.getConstructor(Species.class).newInstance(alias);
return result;
} catch (Exception e) {
throw new InvalidArgumentException("Cannot create modifier.", e);
@@ -956,18 +956,18 @@ public class ModelContructor {
}
/**
- * Method that put {@link SpeciesAlias aliases} that are not assigned into any
- * {@link CompartmentAlias} into a proper compartment.
+ * Method that put {@link Species aliases} that are not assigned into any
+ * {@link Compartment} into a proper compartment.
*
* @param model
* model where aliases will be modifed
*/
private void putAliasesIntoCompartments(Model model) {
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
if (alias.getParent() == null) {
- if (alias instanceof SpeciesAlias) {
- CompartmentAlias selectedAlias = null;
- for (CompartmentAlias cAlias : model.getCompartmentsAliases()) {
+ if (alias instanceof Species) {
+ Compartment selectedAlias = null;
+ for (Compartment cAlias : model.getCompartmentsAliases()) {
if (cAlias.cross(alias)) {
if (selectedAlias == null) {
selectedAlias = cAlias;
@@ -991,17 +991,17 @@ public class ModelContructor {
* model where operation is performed
*/
private void removeEmptyComplexes(Model model) {
- Set<Alias> aliasesInReaction = new HashSet<>();
+ Set<Element> aliasesInReaction = new HashSet<>();
for (Reaction reaction : model.getReactions()) {
for (ReactionNode node : reaction.getReactionNodes()) {
aliasesInReaction.add(node.getAlias());
}
}
- List<Alias> toRemove = new ArrayList<>();
+ List<Element> toRemove = new ArrayList<>();
ElementUtils eu = new ElementUtils();
- for (Alias alias : model.getAliases()) {
- if (alias instanceof ComplexAlias) {
- ComplexAlias cAlias = (ComplexAlias) alias;
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Complex) {
+ Complex cAlias = (Complex) alias;
if (cAlias.getSize() <= EPSILON && cAlias.getAllChildrenAliases().size() == 0) {
if (aliasesInReaction.contains(alias)) {
logger.warn(eu.getElementTag(alias) + "Empty element is invalid, but it's a part of reaction.");
@@ -1012,7 +1012,7 @@ public class ModelContructor {
}
}
}
- for (Alias alias : toRemove) {
+ for (Element alias : toRemove) {
model.removeAlias(alias);
}
}
@@ -1025,8 +1025,8 @@ public class ModelContructor {
* model where complexes are placed
*/
private void assignNamesToComplexes(Model model) {
- for (Alias alias : model.getAliases()) {
- if (alias instanceof ComplexAlias) {
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Complex) {
if (alias.getName() == null || (alias.getName().isEmpty())) {
for (Layer layer : model.getLayers()) {
LayerText toRemove = null;
@@ -1055,8 +1055,8 @@ public class ModelContructor {
* model where compartments are placed
*/
private void assignNamesToCompartments(Model model) {
- for (Alias alias : model.getAliases()) {
- if (alias instanceof CompartmentAlias) {
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Compartment) {
if (alias.getName() == null || alias.getName().isEmpty()) {
for (Layer layer : model.getLayers()) {
LayerText toRemove = null;
@@ -1100,25 +1100,25 @@ public class ModelContructor {
* model where assignments are fixed.
*/
private void fixCompartmentAliases(Model model) {
- List<CompartmentAlias> aliases = model.getCompartmentsAliases();
+ List<Compartment> aliases = model.getCompartmentsAliases();
// clear all assignments
- for (CompartmentAlias compartmentAlias : aliases) {
+ for (Compartment compartmentAlias : aliases) {
compartmentAlias.getAliases().clear();
}
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
// elements inside complexes shouldn't be considered
- if (alias instanceof SpeciesAlias) {
- if (((SpeciesAlias) alias).getComplexAlias() != null) {
+ if (alias instanceof Species) {
+ if (((Species) alias).getComplexAlias() != null) {
continue;
}
}
// skip compartments
- if (alias instanceof CompartmentAlias) {
+ if (alias instanceof Compartment) {
continue;
}
- CompartmentAlias parentAlias = null;
- for (CompartmentAlias compartmentAlias : aliases) {
+ Compartment parentAlias = null;
+ for (Compartment compartmentAlias : aliases) {
if (compartmentAlias.contains(alias)) {
if (parentAlias == null) {
parentAlias = compartmentAlias;
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index 3d19dc42b2..cdfc86cc56 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -12,21 +12,8 @@ import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.OvalCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
@@ -34,6 +21,19 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.wikipathway.utils.Geo;
/**
@@ -107,27 +107,27 @@ public class ModelToGPML {
* species for which gpml type will be returned
* @return String - type
*/
- private String getType(SpeciesAlias species) {
+ private String getType(Species species) {
String res = "";
- if (species instanceof AntisenseRnaAlias) {
+ if (species instanceof AntisenseRna) {
res = "Rna";
- } else if (species instanceof RnaAlias) {
+ } else if (species instanceof Rna) {
res = "Rna";
- } else if (species instanceof GeneAlias) {
+ } else if (species instanceof Gene) {
res = "GeneProduct";
- } else if (species instanceof ProteinAlias) {
+ } else if (species instanceof Protein) {
res = "Protein";
- } else if (species instanceof SimpleMoleculeAlias) {
+ } else if (species instanceof SimpleMolecule) {
res = "Metabolite";
- } else if (species instanceof IonAlias) {
+ } else if (species instanceof Ion) {
res = "Metabolite";
- } else if (species instanceof DrugAlias) {
+ } else if (species instanceof Drug) {
res = "Metabolite";
- } else if (species instanceof PhenotypeAlias) {
+ } else if (species instanceof Phenotype) {
res = "Pathway";
- } else if (species instanceof UnknownAlias) {
+ } else if (species instanceof Unknown) {
res = "Unknown";
- } else if (species instanceof DegradedAlias) {
+ } else if (species instanceof Degraded) {
res = "Unknown";
} else {
throw new InvalidArgumentException("Unknown class type: " + species.getClass());
@@ -145,23 +145,23 @@ public class ModelToGPML {
* alias for which rectangle border is calculated
* @return rectangle border for alias
*/
- private Rectangle2D getRectangle(Alias alias) {
+ private Rectangle2D getRectangle(Element alias) {
Rectangle2D res = null;
- if (alias instanceof ComplexAlias) {
- ComplexAlias ca = (ComplexAlias) alias;
+ if (alias instanceof Complex) {
+ Complex ca = (Complex) alias;
if (ca.getAliases().size() == 0) {
res = (Rectangle2D) ca.getBorder().clone();
} else {
res = getRectangle(ca.getAliases().get(0));
- for (Alias al : ca.getAliases()) {
+ for (Element al : ca.getAliases()) {
Rectangle2D.union(res, getRectangle(al), res);
}
res = new Rectangle2D.Double(
res.getX() - GROUP_RECTANGLE_BORDER_MARGIN, res.getY() - GROUP_RECTANGLE_BORDER_MARGIN, res.getWidth() + 2 * GROUP_RECTANGLE_BORDER_MARGIN,
res.getHeight() + 2 * GROUP_RECTANGLE_BORDER_MARGIN);
}
- } else if (alias instanceof SpeciesAlias) {
+ } else if (alias instanceof Species) {
res = (Rectangle2D) alias.getBorder().clone();
}
return res;
@@ -273,11 +273,11 @@ public class ModelToGPML {
* compartment alias
* @return string with list of species names in a compartment
*/
- private String getAllNames(CompartmentAlias ca) {
+ private String getAllNames(Compartment ca) {
StringBuilder res = new StringBuilder("");
- for (Alias a : ca.getAllSubAliases()) {
- if (a instanceof SpeciesAlias) {
- SpeciesAlias sp = (SpeciesAlias) a;
+ for (Element a : ca.getAllSubAliases()) {
+ if (a instanceof Species) {
+ Species sp = (Species) a;
res.append(sp.getName() + ";");
}
}
@@ -294,11 +294,11 @@ public class ModelToGPML {
*/
private String getComparments(Model model) {
StringBuilder comparments = new StringBuilder("");
- for (CompartmentAlias ca : model.getCompartmentsAliases()) {
+ for (Compartment ca : model.getCompartmentsAliases()) {
double x = ca.getCenterX(), y = ca.getCenterY(), h = ca.getHeight(), w = ca.getWidth();
String shape;
- if (ca instanceof OvalCompartmentAlias) {
+ if (ca instanceof OvalCompartment) {
shape = "Oval";
} else {
shape = "Rectangle";
@@ -411,8 +411,8 @@ public class ModelToGPML {
protected String getDataNodes(Model model) throws ConverterException {
StringBuilder dataNodes = new StringBuilder("");
- for (SpeciesAlias sa : model.getNotComplexSpeciesAliases()) {
- if (!(sa instanceof ComplexAlias)) {
+ for (Species sa : model.getNotComplexSpeciesAliases()) {
+ if (!(sa instanceof Complex)) {
dataNodes.append(" <DataNode TextLabel=\"" + sa.getName() + "\" GraphId=\"" + sa.getAliasId() + "\" Type=\"" + getType(sa) + "\"");
if (sa.getComplexAlias() != null) {
dataNodes.append(" GroupRef=\"" + sa.getComplexAlias().getAliasId() + "\"");
@@ -447,7 +447,7 @@ public class ModelToGPML {
}
/** Special Case for empty Complexes **/
- for (ComplexAlias ca : model.getComplexAliases()) {
+ for (Complex ca : model.getComplexAliases()) {
if (ca.getAliases().size() == 0) {
dataNodes.append(" <DataNode TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getAliasId() + "\" Type=\"Complex\"");
if (ca.getComplexAlias() != null) {
@@ -480,7 +480,7 @@ public class ModelToGPML {
protected String getGroups(Model model) {
StringBuilder groups = new StringBuilder("");
- for (ComplexAlias ca : model.getComplexAliases()) {
+ for (Complex ca : model.getComplexAliases()) {
if (ca.getAliases().size() > 0) {
groups.append(" <Group GroupId=\"" + ca.getAliasId() + "\" GraphId=\"" + ca.getAliasId() + "\"");
if (ca.getComplexAlias() != null) {
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
index 28c1614bd0..47b8237bf1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.wikipathway.model;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
* This enum represents type of line in GPML format.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
index e0214ab593..244f58f44b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
@@ -6,8 +6,8 @@ import java.util.List;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
* Class used to store data about {@link DataNode} state from .gpml.
@@ -38,7 +38,7 @@ public class State extends GraphicalPathwayElement {
private String graphRef;
/**
- * State correspondig to {@link ProteinAlias#structuralState protein structural state}.
+ * State correspondig to {@link Protein#structuralState protein structural state}.
*/
private String structuralState;
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
index b961c5363e..c2086f350b 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -11,11 +11,11 @@ import java.nio.charset.StandardCharsets;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
import org.apache.log4j.Logger;
@@ -176,8 +176,8 @@ public class ComplexReactionToModelTest {
assertFalse(Color.BLACK.equals(reaction.getReactants().get(0).getLine().getColor()));
- Alias redAlias = model.getAliasByAliasId("d9620");
- Alias blackAlias = model.getAliasByAliasId("d046f");
+ Element redAlias = model.getAliasByAliasId("d9620");
+ Element blackAlias = model.getAliasByAliasId("d046f");
assertFalse(Color.BLACK.equals(redAlias.getColor()));
assertTrue(Color.WHITE.equals(blackAlias.getColor()));
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 1d8c019c63..181a15f9ee 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -20,13 +20,13 @@ import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
public class GPMLToModelTest {
@@ -403,7 +403,7 @@ public class GPMLToModelTest {
try {
String fileName = "testFiles/complex/hypothetical_complex.gpml";
Model model = new GPMLToModel().getModel(fileName);
- for (ComplexAlias species : model.getComplexAliases()) {
+ for (Complex species : model.getComplexAliases()) {
assertTrue("Complex parsed from gpml should be hypothetical", species.isHypothetical());
}
@@ -419,7 +419,7 @@ public class GPMLToModelTest {
try {
String fileName = "testFiles/complex/nonhypothetical_complex.gpml";
Model model = new GPMLToModel().getModel(fileName);
- for (ComplexAlias species : model.getComplexAliases()) {
+ for (Complex species : model.getComplexAliases()) {
assertFalse("Complex parsed from gpml should be hypothetical", species.isHypothetical());
}
assertEquals(0, model.getCreationWarnings().size());
@@ -435,7 +435,7 @@ public class GPMLToModelTest {
String fileName = "testFiles/complex/complex_with_name.gpml";
Model model = new GPMLToModel().getModel(fileName);
boolean nameFound = false;
- for (ComplexAlias species : model.getComplexAliases()) {
+ for (Complex species : model.getComplexAliases()) {
if ("p70 S6 Kinases".equals(species.getName())) {
nameFound = true;
}
@@ -453,7 +453,7 @@ public class GPMLToModelTest {
try {
String fileName = "testFiles/compartment/compartment_name.gpml";
Model model = new GPMLToModel().getModel(fileName);
- for (CompartmentAlias compartment : model.getCompartmentsAliases()) {
+ for (Compartment compartment : model.getCompartmentsAliases()) {
assertEquals("Compartment parsed from gpml should have a valid name", "Label", compartment.getName());
}
assertEquals(0, model.getCreationWarnings().size());
@@ -580,7 +580,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(fileName);
assertEquals(0, model1.getCreationWarnings().size());
- GeneAlias protein = (GeneAlias)model1.getAliasByAliasId("be3de");
+ Gene protein = (Gene)model1.getAliasByAliasId("be3de");
assertNotNull(protein);
assertEquals(2, protein.getModificationResidues().size());
@@ -605,7 +605,7 @@ public class GPMLToModelTest {
Model model1 = new GPMLToModel().getModel(fileName);
assertEquals(0, model1.getCreationWarnings().size());
- GeneAlias protein = (GeneAlias)model1.getAliasByAliasId("be3de");
+ Gene protein = (Gene)model1.getAliasByAliasId("be3de");
assertNotNull(protein);
assertEquals(2, protein.getModificationResidues().size());
@@ -695,7 +695,7 @@ public class GPMLToModelTest {
String fileName = "testFiles/small/protein_with_state.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- ProteinAlias protein = (ProteinAlias) model1.getAliasByName("Protein").get(0);
+ Protein protein = (Protein) model1.getAliasByName("Protein").get(0);
assertEquals(0, protein.getModificationResidues().size());
assertEquals("GTP", protein.getStructuralState());
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
index f4057ac931..0232a42c1d 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
@@ -12,10 +12,10 @@ import org.junit.Test;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
public class BugTest extends WikipathwaysTestFunctions {
@@ -45,8 +45,8 @@ public class BugTest extends WikipathwaysTestFunctions {
assertEquals(7, model1.getCreationWarnings().size());
int complexes = 0;
- for (Alias alias : model1.getAliases()) {
- if (alias instanceof ComplexAlias) {
+ for (Element alias : model1.getAliases()) {
+ if (alias instanceof Complex) {
complexes++;
}
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
index 26f5cfec57..f4696072ab 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
@@ -16,10 +16,10 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
public class ModelToGPMLTest extends WikipathwaysTestFunctions {
@@ -62,7 +62,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
model.setWidth(1000);
model.setHeight(1000);
- GenericProteinAlias alias = new GenericProteinAlias("sa");
+ GenericProtein alias = new GenericProtein("sa");
alias.setName("s2");
alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "123"));
@@ -80,7 +80,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
- Alias p = model2.getAliasByAliasId("sa");
+ Element p = model2.getAliasByAliasId("sa");
assertEquals(alias.getMiriamData().size(), p.getMiriamData().size());
for (MiriamData md : p.getMiriamData()) {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
index e4b453e25b..8cf9a8c01a 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
@@ -8,7 +8,7 @@ import org.junit.Test;
import org.w3c.dom.Element;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
import lcsb.mapviewer.wikipathway.model.State;
diff --git a/persist/src/db/10.0.3/fix_db_20161003.sql b/persist/src/db/10.0.3/fix_db_20161003.sql
index 8e95a724a3..1443be02a5 100644
--- a/persist/src/db/10.0.3/fix_db_20161003.sql
+++ b/persist/src/db/10.0.3/fix_db_20161003.sql
@@ -71,4 +71,14 @@ drop table datamining;
drop table associated_phenotype_element_table;
drop table external_project;
-drop table external_user;
\ No newline at end of file
+drop table external_user;
+
+-- clean info about annotations
+delete from class_annotator_annotators_table ;
+delete from class_annotator_table ;
+delete from class_required_annotation_miriam_type_table ;
+delete from class_required_annotation_table ;
+delete from class_valid_annotation_miriam_type_table ;
+delete from class_valid_annotation_table ;
+update user_table set annotationschema_iddb =null;
+delete from user_annotation_schema_table ;
\ No newline at end of file
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDao.java
index 3e9ff16669..71d0a089b7 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDao.java
@@ -8,7 +8,7 @@ import org.apache.log4j.Logger;
import org.hibernate.Query;
import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.persist.dao.BaseDao;
/**
@@ -40,7 +40,7 @@ public class DataMiningDao extends BaseDao<DataMining> {
* node for which data mining entries should be returned
* @return the data mining elements for unified node
*/
- public Collection<DataMining> getMissingConnectionForElement(Alias node) {
+ public Collection<DataMining> getMissingConnectionForElement(Element node) {
if (node.getId() == 0) {
return new ArrayList<DataMining>();
} else {
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDao.java
index 2ed1749f8a..3f697e5c4e 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDao.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.persist.dao.map.layout.alias;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data Access Object class for Alias class.
- *
- * @author Piotr Gawron
- *
- */
-public class AliasDao extends BaseDao<Alias> {
-
- /**
- * Default constructor.
- */
- public AliasDao() {
- super(Alias.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout.alias;
+
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data Access Object class for Alias class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AliasDao extends BaseDao<Element> {
+
+ /**
+ * Default constructor.
+ */
+ public AliasDao() {
+ super(Element.class);
+ }
+
+}
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 841302ad1f..6ef66e1cfa 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -156,49 +156,44 @@
<value>lcsb.mapviewer.model.map.layout.ReferenceGenome</value>
<value>lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping</value>
- <value>lcsb.mapviewer.model.map.layout.alias.Alias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.BottomSquareCompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.ChemicalAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.CompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.ComplexAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.DegradedAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.DrugAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.GeneAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.IonAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.LeftSquareCompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.OvalCompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.ReceptorProteinAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.RightSquareCompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.RnaAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.SpeciesAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.SearchIndex</value>
- <value>lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.TopSquareCompartmentAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.TruncatedProteinAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.UnknownAlias</value>
-
- <value>lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias</value>
+ <value>lcsb.mapviewer.model.map.compartment.PathwayCompartment</value>
+ <value>lcsb.mapviewer.model.map.compartment.BottomSquareCompartment</value>
+ <value>lcsb.mapviewer.model.map.compartment.Compartment</value>
+ <value>lcsb.mapviewer.model.map.compartment.LeftSquareCompartment</value>
+ <value>lcsb.mapviewer.model.map.compartment.OvalCompartment</value>
+ <value>lcsb.mapviewer.model.map.compartment.RightSquareCompartment</value>
+ <value>lcsb.mapviewer.model.map.compartment.SquareCompartment</value>
+ <value>lcsb.mapviewer.model.map.compartment.TopSquareCompartment</value>
-
+ <value>lcsb.mapviewer.model.map.species.Element</value>
+ <value>lcsb.mapviewer.model.map.species.AntisenseRna</value>
+ <value>lcsb.mapviewer.model.map.species.Chemical</value>
+ <value>lcsb.mapviewer.model.map.species.Complex</value>
+ <value>lcsb.mapviewer.model.map.species.Degraded</value>
+ <value>lcsb.mapviewer.model.map.species.Drug</value>
+ <value>lcsb.mapviewer.model.map.species.Gene</value>
+ <value>lcsb.mapviewer.model.map.species.GenericProtein</value>
+ <value>lcsb.mapviewer.model.map.species.Ion</value>
+ <value>lcsb.mapviewer.model.map.species.IonChannelProtein</value>
+ <value>lcsb.mapviewer.model.map.species.Phenotype</value>
+ <value>lcsb.mapviewer.model.map.species.ReceptorProtein</value>
+ <value>lcsb.mapviewer.model.map.species.Rna</value>
+ <value>lcsb.mapviewer.model.map.species.SimpleMolecule</value>
+ <value>lcsb.mapviewer.model.map.species.Species</value>
+ <value>lcsb.mapviewer.model.map.species.TruncatedProtein</value>
+ <value>lcsb.mapviewer.model.map.species.Unknown</value>
+
+ <value>lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion</value>
+ <value>lcsb.mapviewer.model.map.species.field.ModificationResidue</value>
+ <value>lcsb.mapviewer.model.map.species.field.RnaRegion</value>
<value>lcsb.mapviewer.model.map.layout.graphics.Layer</value>
<value>lcsb.mapviewer.model.map.layout.graphics.LayerText</value>
<value>lcsb.mapviewer.model.map.layout.graphics.LayerRect</value>
<value>lcsb.mapviewer.model.map.layout.graphics.LayerOval</value>
- <value>lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias</value>
- <value>lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias</value>
-
<value>lcsb.mapviewer.model.map.MiriamData</value>
+ <value>lcsb.mapviewer.model.map.SearchIndex</value>
</list>
</property>
<property name="hibernateProperties">
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
index 9d254af509..b7e079d5b2 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -14,13 +14,13 @@ import org.junit.Test;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ProjectDaoTest extends PersistTestFunctions {
@@ -176,9 +176,9 @@ public class ProjectDaoTest extends PersistTestFunctions {
model.addAlias(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
model.addAlias(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
- SpeciesAlias alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- SpeciesAlias alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- ComplexAlias alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
alias3.addAlias(alias);
alias3.addAlias(alias2);
alias.setParent(alias3);
@@ -194,8 +194,8 @@ public class ProjectDaoTest extends PersistTestFunctions {
return model;
}
- private CompartmentAlias createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- CompartmentAlias alias = new CompartmentAlias(aliasId);
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -203,8 +203,8 @@ public class ProjectDaoTest extends PersistTestFunctions {
return alias;
}
- private SpeciesAlias createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- SpeciesAlias alias = new SimpleMoleculeAlias(aliasId);
+ private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ Species alias = new SimpleMolecule(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -212,8 +212,8 @@ public class ProjectDaoTest extends PersistTestFunctions {
return alias;
}
- private ComplexAlias createComplexAlias(double x, double y, double width, double height, String aliasId) {
- ComplexAlias alias = new ComplexAlias(aliasId);
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
index 0544fad958..4b8a46b053 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
@@ -13,11 +13,7 @@ import lcsb.mapviewer.model.map.Comment;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.model.Model;
@@ -26,6 +22,10 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class CommentDaoTest extends PersistTestFunctions {
@@ -102,7 +102,7 @@ public class CommentDaoTest extends PersistTestFunctions {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- GenericProteinAlias alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
model.addAlias(alias);
alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
model.addAlias(alias);
@@ -112,8 +112,8 @@ public class CommentDaoTest extends PersistTestFunctions {
model.addAlias(alias);
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- SpeciesAlias alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- ComplexAlias alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
alias3.addAlias(alias);
alias3.addAlias(alias2);
alias.setParent(alias3);
@@ -123,7 +123,7 @@ public class CommentDaoTest extends PersistTestFunctions {
model.addAlias(alias2);
model.addAlias(alias3);
- CompartmentAlias cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
model.addAlias(cAlias);
model.setWidth(2000);
model.setHeight(2000);
@@ -144,7 +144,7 @@ public class CommentDaoTest extends PersistTestFunctions {
alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
model.addAlias(alias);
- ModificationResidueAlias mr = new ModificationResidueAlias();
+ ModificationResidue mr = new ModificationResidue();
mr.setName("mr");
alias.addModificationResidue(mr);
@@ -152,8 +152,8 @@ public class CommentDaoTest extends PersistTestFunctions {
return model;
}
- private CompartmentAlias createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- CompartmentAlias alias = new CompartmentAlias(aliasId);
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -161,8 +161,8 @@ public class CommentDaoTest extends PersistTestFunctions {
return alias;
}
- private GenericProteinAlias createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProteinAlias alias = new GenericProteinAlias(aliasId);
+ private GenericProtein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein(aliasId);
alias.setName("SNCA");
alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
@@ -173,8 +173,8 @@ public class CommentDaoTest extends PersistTestFunctions {
return alias;
}
- private ComplexAlias createComplexAlias(double x, double y, double width, double height, String aliasId) {
- ComplexAlias alias = new ComplexAlias(aliasId);
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
index 0f3d09e5df..d1e9e9cf83 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
@@ -18,13 +18,8 @@ import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.model.Model;
@@ -33,6 +28,11 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class LayoutDaoTest extends PersistTestFunctions {
@@ -149,7 +149,7 @@ public class LayoutDaoTest extends PersistTestFunctions {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- SpeciesAlias alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ Species alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
model.addAlias(alias);
alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
model.addAlias(alias);
@@ -159,8 +159,8 @@ public class LayoutDaoTest extends PersistTestFunctions {
model.addAlias(alias);
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- SpeciesAlias alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- ComplexAlias alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
alias3.addAlias(alias);
alias3.addAlias(alias2);
alias.setParent(alias3);
@@ -170,7 +170,7 @@ public class LayoutDaoTest extends PersistTestFunctions {
model.addAlias(alias2);
model.addAlias(alias3);
- CompartmentAlias cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
model.addAlias(cAlias);
model.setWidth(2000);
model.setHeight(2000);
@@ -188,10 +188,10 @@ public class LayoutDaoTest extends PersistTestFunctions {
reaction.setIdReaction("re" + identifierCounter++);
model.addReaction(reaction);
- ProteinAlias protein = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ Protein protein = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
model.addAlias(protein);
- ModificationResidueAlias mr = new ModificationResidueAlias();
+ ModificationResidue mr = new ModificationResidue();
mr.setName("mr");
protein.addModificationResidue(mr);
@@ -199,8 +199,8 @@ public class LayoutDaoTest extends PersistTestFunctions {
return model;
}
- private CompartmentAlias createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- CompartmentAlias alias = new CompartmentAlias(aliasId);
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -208,8 +208,8 @@ public class LayoutDaoTest extends PersistTestFunctions {
return alias;
}
- private ProteinAlias createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProteinAlias alias = new GenericProteinAlias("s" + identifierCounter++);
+ private Protein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein("s" + identifierCounter++);
alias.setAliasId(aliasId);
alias.setX(x);
alias.setY(y);
@@ -218,8 +218,8 @@ public class LayoutDaoTest extends PersistTestFunctions {
return alias;
}
- private ComplexAlias createComplexAlias(double x, double y, double width, double height, String aliasId) {
- ComplexAlias alias = new ComplexAlias(aliasId);
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index bb1dd1c877..ed8a97c14c 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -17,15 +17,9 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.model.Model;
@@ -35,6 +29,12 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ModelDaoTest extends PersistTestFunctions {
@@ -106,15 +106,15 @@ public class ModelDaoTest extends PersistTestFunctions {
// check if we really performed a test
boolean test = false;
- for (Alias alias : model.getAliases()) {
+ for (Element alias : model.getAliases()) {
assertNotNull(fullModel.getAliasByAliasId(alias.getAliasId()));
test = true;
}
assertTrue(test);
test = false;
- for (Alias alias : model.getAliases()) {
- if (alias instanceof CompartmentAlias) {
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Compartment) {
assertNotNull(fullModel.getCompartmentAliasByCompartmentAliasId(alias.getAliasId()));
test = true;
}
@@ -216,8 +216,8 @@ public class ModelDaoTest extends PersistTestFunctions {
projectDao.evict(project);
Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
- ProteinAlias originalSpecies = (ProteinAlias) model.getAliasByAliasId("pr1");
- ProteinAlias fromDbSpecies = (ProteinAlias) model2.getAliasByAliasId("pr1");
+ Protein originalSpecies = (Protein) model.getAliasByAliasId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getAliasByAliasId("pr1");
assertFalse(originalSpecies.equals(fromDbSpecies));
assertEquals(originalSpecies.getModificationResidues().size(), fromDbSpecies.getModificationResidues().size());
@@ -278,8 +278,8 @@ public class ModelDaoTest extends PersistTestFunctions {
projectDao.evict(project);
Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
- ProteinAlias originalSpecies = (ProteinAlias) model.getAliasByAliasId("pr1");
- ProteinAlias fromDbSpecies = (ProteinAlias) model2.getAliasByAliasId("pr1");
+ Protein originalSpecies = (Protein) model.getAliasByAliasId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getAliasByAliasId("pr1");
assertFalse(originalSpecies.equals(fromDbSpecies));
assertEquals(originalSpecies.getMiriamData().size(), fromDbSpecies.getMiriamData().size());
@@ -329,7 +329,7 @@ public class ModelDaoTest extends PersistTestFunctions {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- GenericProteinAlias alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
model.addAlias(alias);
alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
model.addAlias(alias);
@@ -339,8 +339,8 @@ public class ModelDaoTest extends PersistTestFunctions {
model.addAlias(alias);
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- SpeciesAlias alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- ComplexAlias alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
alias3.addAlias(alias);
alias3.addAlias(alias2);
alias.setParent(alias3);
@@ -350,7 +350,7 @@ public class ModelDaoTest extends PersistTestFunctions {
model.addAlias(alias2);
model.addAlias(alias3);
- CompartmentAlias cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
model.addAlias(cAlias);
model.setWidth(2000);
model.setHeight(2000);
@@ -371,7 +371,7 @@ public class ModelDaoTest extends PersistTestFunctions {
alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
model.addAlias(alias);
- ModificationResidueAlias mr = new ModificationResidueAlias();
+ ModificationResidue mr = new ModificationResidue();
mr.setName("mr");
alias.addModificationResidue(mr);
@@ -379,8 +379,8 @@ public class ModelDaoTest extends PersistTestFunctions {
return model;
}
- private CompartmentAlias createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- CompartmentAlias alias = new CompartmentAlias(aliasId);
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -388,8 +388,8 @@ public class ModelDaoTest extends PersistTestFunctions {
return alias;
}
- private GenericProteinAlias createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProteinAlias alias = new GenericProteinAlias(aliasId);
+ private GenericProtein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein(aliasId);
alias.setName("SNCA");
alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
@@ -401,8 +401,8 @@ public class ModelDaoTest extends PersistTestFunctions {
return alias;
}
- private ComplexAlias createComplexAlias(double x, double y, double width, double height, String aliasId) {
- ComplexAlias alias = new ComplexAlias(aliasId);
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDaoTest.java
index 3956dea410..352746c1d4 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/graph/DataMiningDaoTest.java
@@ -10,10 +10,10 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class DataMiningDaoTest extends PersistTestFunctions {
@@ -31,7 +31,7 @@ public class DataMiningDaoTest extends PersistTestFunctions {
@Test
public void testGetConnections() {
- assertEquals(0, dataMiningDao.getMissingConnectionForElement(new GenericProteinAlias("id")).size());
+ assertEquals(0, dataMiningDao.getMissingConnectionForElement(new GenericProtein("id")).size());
}
@Test
@@ -41,7 +41,7 @@ public class DataMiningDaoTest extends PersistTestFunctions {
Project project = new Project();
project.setProjectId(projectId);
Model model = new ModelFullIndexed(null);
- Alias alias = new GenericProteinAlias("some_el_id");
+ Element alias = new GenericProtein("some_el_id");
model.addAlias(alias);
project.addModel(model);
projectDao.add(project);
@@ -66,7 +66,7 @@ public class DataMiningDaoTest extends PersistTestFunctions {
@Test
public void testGetConnections2() {
- Alias species = new GenericProteinAlias("id");
+ Element species = new GenericProtein("id");
species.setId(1);
assertEquals(0, dataMiningDao.getMissingConnectionForElement(species).size());
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
index c9222bafd7..1e05e8b055 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest.java
@@ -8,16 +8,16 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.SearchIndex;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class AliasDaoTest extends PersistTestFunctions {
@@ -50,7 +50,7 @@ public class AliasDaoTest extends PersistTestFunctions {
Model model = createModel();
project.addModel(model);
- SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId("sa2");
+ Species alias = (Species) model.getAliasByAliasId("sa2");
alias.getSearchIndexes().add(new SearchIndex("blabla"));
@@ -58,7 +58,7 @@ public class AliasDaoTest extends PersistTestFunctions {
Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
- SpeciesAlias alias2 = (SpeciesAlias) aliasDao.getById(model2.getAliasByAliasId("sa2").getId());
+ Species alias2 = (Species) aliasDao.getById(model2.getAliasByAliasId("sa2").getId());
assertEquals(1, alias2.getSearchIndexes().size());
@@ -76,9 +76,9 @@ public class AliasDaoTest extends PersistTestFunctions {
model.addAlias(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
model.addAlias(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
- SpeciesAlias alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- SpeciesAlias alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- ComplexAlias alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
alias3.addAlias(alias);
alias3.addAlias(alias2);
alias.setParent(alias3);
@@ -94,8 +94,8 @@ public class AliasDaoTest extends PersistTestFunctions {
return model;
}
- private CompartmentAlias createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- CompartmentAlias alias = new CompartmentAlias(aliasId);
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -103,8 +103,8 @@ public class AliasDaoTest extends PersistTestFunctions {
return alias;
}
- private SpeciesAlias createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- SimpleMoleculeAlias alias = new SimpleMoleculeAlias(aliasId);
+ private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ SimpleMolecule alias = new SimpleMolecule(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -112,8 +112,8 @@ public class AliasDaoTest extends PersistTestFunctions {
return alias;
}
- private ComplexAlias createComplexAlias(double x, double y, double width, double height, String aliasId) {
- ComplexAlias alias = new ComplexAlias(aliasId);
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
alias.setX(x);
alias.setY(y);
alias.setWidth(width);
@@ -127,7 +127,7 @@ public class AliasDaoTest extends PersistTestFunctions {
long count = modelDao.getCount();
Model model = createModel();
Model model1 = createModel();
- Alias alias = model.getAliasByAliasId("sa2");
+ Element alias = model.getAliasByAliasId("sa2");
AliasSubmodelConnection submodel = new AliasSubmodelConnection(model1, SubmodelType.UNKNOWN);
alias.setSubmodel(submodel);
project.addModel(model);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
index 4f9125351f..a1a99c857e 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
@@ -12,20 +12,20 @@ import org.junit.Test;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationState;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion.AntisenseRnaRegionType;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class AliasDaoTest2 extends PersistTestFunctions {
@@ -51,7 +51,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
public void testAdd() throws Exception {
try {
- GenericProteinAlias sp = new GenericProteinAlias(testIdAlias);
+ GenericProtein sp = new GenericProtein(testIdAlias);
sp.setCharge(testChargeVal);
sp.setInitialAmount(testInitialAmount);
sp.setInitialConcentration(testInitialConcentration);
@@ -59,7 +59,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
sp.setNotes(testNotes);
sp.setOnlySubstanceUnits(testOnlySubstanceunits);
- CompartmentAlias parent = new CompartmentAlias("comp id");
+ Compartment parent = new Compartment("comp id");
sp.setParent(parent);
MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
@@ -67,7 +67,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
aliasDao.add(sp);
- SpeciesAlias sp2 = (SpeciesAlias) aliasDao.getById(sp.getId());
+ Species sp2 = (Species) aliasDao.getById(sp.getId());
assertNotNull(sp2);
assertEquals(sp.getCharge(), sp2.getCharge());
assertEquals(sp.getAliasId(), sp2.getAliasId());
@@ -77,7 +77,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
assertEquals(sp.getNotes(), sp2.getNotes());
assertEquals(sp.hasOnlySubstanceUnits(), sp2.hasOnlySubstanceUnits());
- CompartmentAlias parent2 = (CompartmentAlias) sp2.getParent();
+ Compartment parent2 = (Compartment) sp2.getParent();
assertNotNull(parent2);
assertEquals("comp id", parent2.getAliasId());
@@ -90,7 +90,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
assertEquals(md.getResource(), md2.getResource());
aliasDao.delete(sp);
- sp2 = (SpeciesAlias) aliasDao.getById(sp.getId());
+ sp2 = (Species) aliasDao.getById(sp.getId());
assertNull(sp2);
} catch (Exception e) {
@@ -103,8 +103,8 @@ public class AliasDaoTest2 extends PersistTestFunctions {
public void testProtein() throws Exception {
try {
- ProteinAlias protein = new GenericProteinAlias(testIdAlias);
- ModificationResidueAlias mr = new ModificationResidueAlias();
+ Protein protein = new GenericProtein(testIdAlias);
+ ModificationResidue mr = new ModificationResidue();
mr.setAngle(2.0);
mr.setName("name");
mr.setSide("side");
@@ -114,7 +114,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
aliasDao.add(protein);
- ProteinAlias sp2 = (ProteinAlias) aliasDao.getById(protein.getId());
+ Protein sp2 = (Protein) aliasDao.getById(protein.getId());
assertNotNull(sp2);
assertEquals(protein.getAliasId(), sp2.getAliasId());
@@ -129,7 +129,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
assertEquals(sp2.getModificationResidues().get(0).getState(), mr.getState());
aliasDao.delete(sp2);
- sp2 = (ProteinAlias) aliasDao.getById(protein.getId());
+ sp2 = (Protein) aliasDao.getById(protein.getId());
assertNull(sp2);
} catch (Exception e) {
@@ -142,8 +142,8 @@ public class AliasDaoTest2 extends PersistTestFunctions {
public void testRna() throws Exception {
try {
- RnaAlias sp = new RnaAlias(testIdAlias);
- RnaRegionAlias mr = new RnaRegionAlias();
+ Rna sp = new Rna(testIdAlias);
+ RnaRegion mr = new RnaRegion();
mr.setName("name");
mr.setSize(3.0);
mr.setState(ModificationState.DONT_CARE);
@@ -152,7 +152,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
aliasDao.add(sp);
aliasDao.evict(sp);
- RnaAlias sp2 = (RnaAlias) aliasDao.getById(sp.getId());
+ Rna sp2 = (Rna) aliasDao.getById(sp.getId());
assertNotNull(sp2);
assertEquals(sp.getAliasId(), sp2.getAliasId());
@@ -165,7 +165,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
assertEquals(sp2.getRegions().get(0).getState(), mr.getState());
aliasDao.delete(sp2);
- sp2 = (RnaAlias) aliasDao.getById(sp.getId());
+ sp2 = (Rna) aliasDao.getById(sp.getId());
assertNull(sp2);
} catch (Exception e) {
@@ -178,8 +178,8 @@ public class AliasDaoTest2 extends PersistTestFunctions {
public void testAntisenseRna() throws Exception {
try {
- AntisenseRnaAlias sp = new AntisenseRnaAlias(testIdAlias);
- AntisenseRnaRegionAlias mr = new AntisenseRnaRegionAlias();
+ AntisenseRna sp = new AntisenseRna(testIdAlias);
+ AntisenseRnaRegion mr = new AntisenseRnaRegion();
mr.setName("name");
mr.setSize(3.0);
mr.setType(AntisenseRnaRegionType.MODIFICATION_SITE);
@@ -189,7 +189,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
aliasDao.add(sp);
aliasDao.evict(sp);
- AntisenseRnaAlias sp2 = (AntisenseRnaAlias) aliasDao.getById(sp.getId());
+ AntisenseRna sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
assertNotNull(sp2);
assertEquals(sp.getAliasId(), sp2.getAliasId());
@@ -203,7 +203,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
assertEquals(sp2.getRegions().get(0).getType(), mr.getType());
aliasDao.delete(sp2);
- sp2 = (AntisenseRnaAlias) aliasDao.getById(sp.getId());
+ sp2 = (AntisenseRna) aliasDao.getById(sp.getId());
assertNull(sp2);
} catch (Exception e) {
@@ -215,7 +215,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
@Test
public void testSynonymsInAlias() throws Exception {
try {
- ProteinAlias protein = new GenericProteinAlias(testIdAlias);
+ Protein protein = new GenericProtein(testIdAlias);
protein.addSynonym("Synonym");
protein.addSynonym("Synonym A");
protein.addSynonym("A");
@@ -228,7 +228,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
aliasDao.flush();
aliasDao.evict(protein);
- ProteinAlias sp2 = (ProteinAlias) aliasDao.getById(protein.getId());
+ Protein sp2 = (Protein) aliasDao.getById(protein.getId());
assertNotNull(sp2.getSynonyms());
assertEquals(protein.getSynonyms().size(), sp2.getSynonyms().size());
@@ -245,7 +245,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
}
aliasDao.delete(sp2);
- sp2 = (ProteinAlias) aliasDao.getById(protein.getId());
+ sp2 = (Protein) aliasDao.getById(protein.getId());
assertNull(sp2);
} catch (Exception e) {
@@ -257,7 +257,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
@Test
public void testChemicals() throws Exception {
try {
- ChemicalAlias ion = new IonAlias(testIdAlias);
+ Chemical ion = new Ion(testIdAlias);
ion.setInChI("come inchi");
ion.setInChIKey("keyyy");
ion.setSmiles("smile");
@@ -266,7 +266,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
aliasDao.flush();
aliasDao.evict(ion);
- IonAlias sp2 = (IonAlias) aliasDao.getById(ion.getId());
+ Ion sp2 = (Ion) aliasDao.getById(ion.getId());
assertNotNull(sp2.getSynonyms());
assertEquals(ion.getSynonyms().size(), sp2.getSynonyms().size());
@@ -276,7 +276,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
assertEquals(ion.getInChI(), sp2.getInChI());
aliasDao.delete(sp2);
- sp2 = (IonAlias) aliasDao.getById(ion.getId());
+ sp2 = (Ion) aliasDao.getById(ion.getId());
assertNull(sp2);
} catch (Exception e) {
@@ -288,19 +288,19 @@ public class AliasDaoTest2 extends PersistTestFunctions {
@Test
public void testPhenotype() throws Exception {
try {
- PhenotypeAlias phenotype = new PhenotypeAlias(testIdAlias);
+ Phenotype phenotype = new Phenotype(testIdAlias);
aliasDao.add(phenotype);
aliasDao.flush();
aliasDao.evict(phenotype);
- PhenotypeAlias sp2 = (PhenotypeAlias) aliasDao.getById(phenotype.getId());
+ Phenotype sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
assertNotNull(sp2.getSynonyms());
assertEquals(phenotype.getSynonyms().size(), phenotype.getSynonyms().size());
aliasDao.delete(sp2);
- sp2 = (PhenotypeAlias) aliasDao.getById(phenotype.getId());
+ sp2 = (Phenotype) aliasDao.getById(phenotype.getId());
assertNull(sp2);
} catch (Exception e) {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
index cd3d7063e7..8f8121b864 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
@@ -11,11 +11,11 @@ import org.junit.Test;
import org.springframework.test.annotation.Rollback;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.persist.PersistTestFunctions;
@Rollback(true)
@@ -56,11 +56,11 @@ public class AntisenseRnaTest extends PersistTestFunctions {
Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
- Alias sp = model.getAliases().iterator().next();
- AntisenseRnaAlias ar = (AntisenseRnaAlias) sp;
+ Element sp = model.getAliases().iterator().next();
+ AntisenseRna ar = (AntisenseRna) sp;
- Alias sp2 = model2.getAliases().iterator().next();
- AntisenseRnaAlias ar2 = (AntisenseRnaAlias) sp2;
+ Element sp2 = model2.getAliases().iterator().next();
+ AntisenseRna ar2 = (AntisenseRna) sp2;
projectDao.delete(project2);
@@ -74,8 +74,8 @@ public class AntisenseRnaTest extends PersistTestFunctions {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- AntisenseRnaAlias alias = new AntisenseRnaAlias("As");
- alias.addRegion(new AntisenseRnaRegionAlias());
+ AntisenseRna alias = new AntisenseRna("As");
+ alias.addRegion(new AntisenseRnaRegion());
alias.setX(1);
alias.setY(2);
alias.setWidth(10);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
index 6da43f4e7f..b275d90736 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
@@ -10,11 +10,11 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class RnaTest extends PersistTestFunctions {
@@ -55,11 +55,11 @@ public class RnaTest extends PersistTestFunctions {
Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
- Alias sp = model.getAliases().iterator().next();
- RnaAlias ar = (RnaAlias) sp;
+ Element sp = model.getAliases().iterator().next();
+ Rna ar = (Rna) sp;
- Alias sp2 = model2.getAliases().iterator().next();
- RnaAlias ar2 = (RnaAlias) sp2;
+ Element sp2 = model2.getAliases().iterator().next();
+ Rna ar2 = (Rna) sp2;
projectDao.delete(project2);
@@ -73,8 +73,8 @@ public class RnaTest extends PersistTestFunctions {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- RnaAlias alias = new RnaAlias("As");
- alias.addRegion(new RnaRegionAlias());
+ Rna alias = new Rna("As");
+ alias.addRegion(new RnaRegion());
alias.setX(1);
alias.setY(2);
alias.setWidth(10);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
index caacbb840d..c36edb9b85 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
@@ -18,8 +18,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.security.crypto.password.PasswordEncoder;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.model.user.UserAnnotationSchema;
import lcsb.mapviewer.model.user.UserClassAnnotators;
@@ -243,7 +243,7 @@ public class UserDaoTest extends PersistTestFunctions {
UserAnnotationSchema uas = new UserAnnotationSchema();
uas.setValidateMiriamTypes(true);
UserClassAnnotators ca = new UserClassAnnotators();
- ca.setClassName(SpeciesAlias.class);
+ ca.setClassName(Species.class);
ca.addAnnotator(String.class);
ca.addAnnotator(Integer.class);
uas.addClassAnnotator(ca);
@@ -264,7 +264,7 @@ public class UserDaoTest extends PersistTestFunctions {
assertNotNull(uas2);
assertEquals(2, uas2.getClassAnnotators().size());
assertEquals(3, uas2.getClassValidAnnotators().size());
- assertEquals(SpeciesAlias.class.getCanonicalName(), uas.getClassAnnotators().get(0).getClassName());
+ assertEquals(Species.class.getCanonicalName(), uas.getClassAnnotators().get(0).getClassName());
assertEquals(String.class.getCanonicalName(), uas.getClassAnnotators().get(0).getAnnotators().get(0));
assertEquals(Integer.class.getCanonicalName(), uas.getClassAnnotators().get(0).getAnnotators().get(1));
assertEquals(Reaction.class.getCanonicalName(), uas.getClassValidAnnotators().get(0).getClassName());
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
index 67c6241e77..6bd52eb98f 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
@@ -11,8 +11,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
@@ -54,16 +54,16 @@ public class DataFormatter {
* @throws IOException
* @throws AnnotatorException
*/
- private String speciesListToString(List<Alias> list) throws IOException, AnnotatorException {
+ private String speciesListToString(List<Element> list) throws IOException, AnnotatorException {
String result = "";
- for (Alias species : list) {
+ for (Element species : list) {
if (!result.equals("")) {
result += ",<hr/>";
}
result += species.getName() + "<br/>";
Set<MiriamData> ids = null;
- if (species instanceof ComplexAlias) {
- ids = rcu.getIdsForComplex((ComplexAlias) species);
+ if (species instanceof Complex) {
+ ids = rcu.getIdsForComplex((Complex) species);
} else {
ids = rcu.getIdsForSpecies(species);
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
index f3d7c1210c..e0d388081f 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
@@ -15,7 +15,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -57,7 +57,7 @@ public class ElementUtil {
* @throws AnnotatorException
* thrown when there is a problem with accessing external resource
*/
- public Set<MiriamData> getMiriamByType(Alias element, MiriamType mt, boolean queryServer) throws AnnotatorException {
+ public Set<MiriamData> getMiriamByType(Element element, MiriamType mt, boolean queryServer) throws AnnotatorException {
Set<MiriamData> result = new HashSet<MiriamData>();
for (MiriamData md : element.getMiriamData()) {
if (mt.equals(md.getDataType())) {
@@ -92,7 +92,7 @@ public class ElementUtil {
* @throws AnnotatorException
* thrown when there is a problem with accessing external server
*/
- private Collection<? extends MiriamData> getUniprot(Alias element) throws AnnotatorException {
+ private Collection<? extends MiriamData> getUniprot(Element element) throws AnnotatorException {
Set<MiriamData> result = new HashSet<MiriamData>();
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType()) || MiriamType.HGNC.equals(md.getDataType())) {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
index 89c33c312e..1ec4d89ac5 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
@@ -7,10 +7,10 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
@@ -63,16 +63,16 @@ public class ReactionComparator {
}
for (ReactionNode node : reaction.getReactionNodes()) {
- if (node.getAlias() instanceof PhenotypeAlias) {
+ if (node.getAlias() instanceof Phenotype) {
result.setStatus(MatchStatus.INVALID_REACTION_WITH_PHEONTYPE);
return result;
}
}
int matchingElements = 0;
- Set<Alias> invalidReactionModifier = new HashSet<>();
- Set<Alias> invalidReactionInput = new HashSet<>();
- Set<Alias> invalidReactionOutput = new HashSet<>();
+ Set<Element> invalidReactionModifier = new HashSet<>();
+ Set<Element> invalidReactionInput = new HashSet<>();
+ Set<Element> invalidReactionOutput = new HashSet<>();
Set<ReactomeDatabaseObject> validReactomeCatalyst = new HashSet<ReactomeDatabaseObject>();
Set<ReactomeDatabaseObject> validReactomeInput = new HashSet<ReactomeDatabaseObject>();
@@ -80,7 +80,7 @@ public class ReactionComparator {
for (ReactionNode node : reaction.getModifiers()) {
boolean verified = false;
- Alias species = node.getAlias();
+ Element species = node.getAlias();
for (ReactomeCatalystActivity catalystActivity : reactomeReaction.getCatalystActivities()) {
if (nc.compareNodes(species, catalystActivity)) {
@@ -95,7 +95,7 @@ public class ReactionComparator {
}
}
for (ReactionNode node : reaction.getReactants()) {
- Alias species = node.getAlias();
+ Element species = node.getAlias();
boolean verified = false;
for (ReactomePhysicalEntity input : reactomeReaction.getInputs()) {
if (nc.compareNodes(species, input)) {
@@ -110,7 +110,7 @@ public class ReactionComparator {
}
}
for (ReactionNode node : reaction.getProducts()) {
- Alias species = node.getAlias();
+ Element species = node.getAlias();
boolean verified = false;
for (ReactomePhysicalEntity input : reactomeReaction.getOutputs()) {
if (nc.compareNodes(species, input)) {
@@ -127,15 +127,15 @@ public class ReactionComparator {
int totalElements = matchingElements;
- for (Alias species : invalidReactionInput) {
+ for (Element species : invalidReactionInput) {
result.addInvalidLocalInput(species);
totalElements++;
}
- for (Alias species : invalidReactionModifier) {
+ for (Element species : invalidReactionModifier) {
result.addInvalidLocalModifier(species);
totalElements++;
}
- for (Alias species : invalidReactionOutput) {
+ for (Element species : invalidReactionOutput) {
result.addInvalidLocalOutput(species);
totalElements++;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
index e14bb5e6bf..36b03907ce 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
@@ -21,15 +21,15 @@ import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
@@ -97,7 +97,7 @@ public class ReactomeQueryUtil {
* @return list of reactome reactions that contais all species given in the
* parameter
*/
- public List<ReactomeReactionlikeEvent> getReactionsBetweenSpecies(List<Alias> speciesList) {
+ public List<ReactomeReactionlikeEvent> getReactionsBetweenSpecies(List<Element> speciesList) {
return getReactionsBetweenSpecies(speciesList, false);
}
@@ -113,7 +113,7 @@ public class ReactomeQueryUtil {
* @return list of reactome reactions that contais all species given in the
* parameter
*/
- public List<ReactomeReactionlikeEvent> getReactionsBetweenSpecies(List<Alias> speciesList, boolean exact) {
+ public List<ReactomeReactionlikeEvent> getReactionsBetweenSpecies(List<Element> speciesList, boolean exact) {
List<ReactomeReactionlikeEvent> result = getReactionsBetweenSpecies(speciesList, exact, false);
if (result.size() == 0) {
result = getReactionsBetweenSpecies(speciesList, exact, true);
@@ -135,7 +135,7 @@ public class ReactomeQueryUtil {
* @return list of reactome reactions that contais all species given in the
* parameter
*/
- public List<ReactomeReactionlikeEvent> getReactionsBetweenSpecies(List<Alias> speciesList, boolean exact, boolean deepSearch) {
+ public List<ReactomeReactionlikeEvent> getReactionsBetweenSpecies(List<Element> speciesList, boolean exact, boolean deepSearch) {
try {
List<ReactomeReactionlikeEvent> result = new ArrayList<ReactomeReactionlikeEvent>();
@@ -146,8 +146,8 @@ public class ReactomeQueryUtil {
List<List<ReactomePhysicalEntity>> entities = new ArrayList<List<ReactomePhysicalEntity>>();
int shortestIndex = -1;
boolean notMolecule = true;
- for (Alias species : speciesList) {
- if (species instanceof ChemicalAlias) {
+ for (Element species : speciesList) {
+ if (species instanceof Chemical) {
Set<MiriamData> chebiIds = new HashSet<MiriamData>();
chebiIds.add(chebiBackend.getChebiForChebiName(species.getName()));
List<ReactomePhysicalEntity> entityList = rc.getEntitiesForChebiId(chebiIds, deepSearch);
@@ -160,7 +160,7 @@ public class ReactomeQueryUtil {
shortestIndex = entities.size() - 1;
}
}
- } else if (species instanceof ProteinAlias) {
+ } else if (species instanceof Protein) {
Set<MiriamData> uniprotId = elementUtil.getMiriamByType(species, MiriamType.UNIPROT, true);
List<ReactomePhysicalEntity> entityList;
if (uniprotId.size() > 0) {
@@ -181,8 +181,8 @@ public class ReactomeQueryUtil {
shortestIndex = entities.size() - 1;
notMolecule = false;
}
- } else if (species instanceof ComplexAlias) {
- Set<MiriamData> identifiers = getIdsForComplex((ComplexAlias) species);
+ } else if (species instanceof Complex) {
+ Set<MiriamData> identifiers = getIdsForComplex((Complex) species);
if (identifiers == null) {
return result;
}
@@ -199,7 +199,7 @@ public class ReactomeQueryUtil {
shortestIndex = entities.size() - 1;
notMolecule = false;
}
- } else if (species instanceof UnknownAlias) {
+ } else if (species instanceof Unknown) {
// try to find by name
List<ReactomePhysicalEntity> entityList = rc.getEntitiesForName(species.getName());
entities.add(entityList);
@@ -214,7 +214,7 @@ public class ReactomeQueryUtil {
shortestIndex = entities.size() - 1;
notMolecule = false;
}
- } else if (species instanceof PhenotypeAlias) {
+ } else if (species instanceof Phenotype) {
// we cannot do anything with phenotype
return result;
} else {
@@ -330,7 +330,7 @@ public class ReactomeQueryUtil {
* species to be checked
* @return reactome stable identifier
*/
- public String getReactomeIdentifierForSpecies(Alias species) {
+ public String getReactomeIdentifierForSpecies(Element species) {
String stableIdentifier = null;
for (MiriamData md : species.getMiriamData()) {
if (md.getDataType().equals(MiriamType.REACTOME)) {
@@ -540,9 +540,9 @@ public class ReactomeQueryUtil {
* service
* @throws AnnotatorException
*/
- public Set<MiriamData> getIdsForComplex(ComplexAlias complex) throws IOException, AnnotatorException {
+ public Set<MiriamData> getIdsForComplex(Complex complex) throws IOException, AnnotatorException {
Set<MiriamData> result = new HashSet<MiriamData>();
- for (SpeciesAlias species : complex.getAllSimpleChildren()) {
+ for (Species species : complex.getAllSimpleChildren()) {
result.addAll(getIdsForSpecies(species));
}
return result;
@@ -559,13 +559,13 @@ public class ReactomeQueryUtil {
* service
* @throws AnnotatorException
*/
- public Set<MiriamData> getIdsForSpecies(Alias species) throws IOException, AnnotatorException {
+ public Set<MiriamData> getIdsForSpecies(Element species) throws IOException, AnnotatorException {
Set<MiriamData> result = new HashSet<>();
- if (species instanceof ProteinAlias) {
+ if (species instanceof Protein) {
result.addAll(elementUtil.getMiriamByType(species, MiriamType.UNIPROT, true));
- } else if (species instanceof PhenotypeAlias) {
+ } else if (species instanceof Phenotype) {
return null;
- } else if (species instanceof ChemicalAlias) {
+ } else if (species instanceof Chemical) {
result.addAll(elementUtil.getMiriamByType(species, MiriamType.CHEBI, true));
} else {
logger.warn("Don't know how to handle " + species.getClass() + " in a complex comparison.");
@@ -626,7 +626,7 @@ public class ReactomeQueryUtil {
* parametr.
*/
public ReactomeReactionlikeEvent getSimilarReaction(Reaction reaction) {
- List<Alias> list = new ArrayList<>();
+ List<Element> list = new ArrayList<>();
for (ReactionNode node : reaction.getReactionNodes()) {
list.add(node.getAlias());
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
index 271a0e1dff..6e86182897 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
@@ -10,7 +10,7 @@ import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.utils.ComparatorException;
@@ -31,7 +31,7 @@ import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
// TODO should implements comparable<T,U>
@Transactional(value = "txManager")
-public abstract class ANodeComparator<T extends Alias, U extends ReactomeDatabaseObject> {
+public abstract class ANodeComparator<T extends Element, U extends ReactomeDatabaseObject> {
/**
* Default class logger.
*/
@@ -65,7 +65,7 @@ public abstract class ANodeComparator<T extends Alias, U extends ReactomeDatabas
/**
* Comparator that allows to compare everything with everything else.
*/
- private ANodeComparator<Alias, ReactomeDatabaseObject> globalComparator;
+ private ANodeComparator<Element, ReactomeDatabaseObject> globalComparator;
/**
* Type of the object in internal representation for which the comparator is
@@ -169,7 +169,7 @@ public abstract class ANodeComparator<T extends Alias, U extends ReactomeDatabas
/**
* @return the globalComparator
*/
- protected ANodeComparator<Alias, ReactomeDatabaseObject> getGlobalComparator() {
+ protected ANodeComparator<Element, ReactomeDatabaseObject> getGlobalComparator() {
return globalComparator;
}
@@ -177,7 +177,7 @@ public abstract class ANodeComparator<T extends Alias, U extends ReactomeDatabas
* @param globalComparator
* the globalComparator to set
*/
- protected void setGlobalComparator(ANodeComparator<Alias, ReactomeDatabaseObject> globalComparator) {
+ protected void setGlobalComparator(ANodeComparator<Element, ReactomeDatabaseObject> globalComparator) {
this.globalComparator = globalComparator;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCandidateSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCandidateSetComparator.java
index 41462001a2..21538e5bf7 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCandidateSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCandidateSetComparator.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import org.apache.poi.ss.formula.functions.Complex;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
/**
@@ -13,7 +12,7 @@ import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
* @author Piotr Gawron
*
*/
-public class ComplexAndCandidateSetComparator extends ANodeComparator<ComplexAlias, ReactomeCandidateSet> {
+public class ComplexAndCandidateSetComparator extends ANodeComparator<Complex, ReactomeCandidateSet> {
/**
* Default class logger.
@@ -24,11 +23,11 @@ public class ComplexAndCandidateSetComparator extends ANodeComparator<ComplexAli
* Default constructor.
*/
public ComplexAndCandidateSetComparator() {
- super(ComplexAlias.class, ReactomeCandidateSet.class);
+ super(Complex.class, ReactomeCandidateSet.class);
}
@Override
- public boolean compareNodes(ComplexAlias species, ReactomeCandidateSet rSpecies) {
+ public boolean compareNodes(Complex species, ReactomeCandidateSet rSpecies) {
logger.warn(getElementTag(species) + " and " + rSpecies.getClass() + ", " + rSpecies.getDbId() + " should be comparable, but how??? Assuming FALSE");
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCatalystComparator.java
index 74723b91a6..246a814ce6 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndCatalystComparator.java
@@ -1,9 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import org.apache.poi.ss.formula.functions.Complex;
-
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
@@ -18,17 +16,17 @@ import lcsb.mapviewer.reactome.utils.ComparatorException;
* @author Piotr Gawron
*
*/
-public class ComplexAndCatalystComparator extends ANodeComparator<ComplexAlias, ReactomeCatalystActivity> {
+public class ComplexAndCatalystComparator extends ANodeComparator<Complex, ReactomeCatalystActivity> {
/**
* Default constructor.
*/
public ComplexAndCatalystComparator() {
- super(ComplexAlias.class, ReactomeCatalystActivity.class);
+ super(Complex.class, ReactomeCatalystActivity.class);
}
@Override
- public boolean compareNodes(ComplexAlias species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
+ public boolean compareNodes(Complex species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
ReactomePhysicalEntity pEntity = cSpecies.getPhysicalEntity();
if (pEntity instanceof ReactomeComplex) {
return getGlobalComparator().compareNodes(species, (ReactomeComplex) pEntity);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndComplexComparator.java
index 80da4bc9ad..7cc7e873bb 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndComplexComparator.java
@@ -3,10 +3,9 @@ package lcsb.mapviewer.reactome.utils.comparators;
import java.util.Set;
import org.apache.log4j.Logger;
-import org.apache.poi.ss.formula.functions.Complex;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.utils.ComparatorException;
@@ -17,22 +16,22 @@ import lcsb.mapviewer.reactome.utils.ComparatorException;
* @author Piotr Gawron
*
*/
-public class ComplexAndComplexComparator extends ANodeComparator<ComplexAlias, ReactomeComplex> {
+public class ComplexAndComplexComparator extends ANodeComparator<Complex, ReactomeComplex> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ComplexAndComplexComparator.class);
+ private static Logger logger = Logger.getLogger(ComplexAndComplexComparator.class);
/**
* Default constructor.
*/
public ComplexAndComplexComparator() {
- super(ComplexAlias.class, ReactomeComplex.class);
+ super(Complex.class, ReactomeComplex.class);
}
@Override
- public boolean compareNodes(ComplexAlias complex, ReactomeComplex reactomeComplex) throws ComparatorException {
+ public boolean compareNodes(Complex complex, ReactomeComplex reactomeComplex) throws ComparatorException {
try {
Set<MiriamData> complex1Ids = getRcu().getIdsForComplex(complex);
if (complex1Ids == null || complex1Ids.size() == 0) {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndDefinedSetComparator.java
index 5970230458..3ce3152549 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndDefinedSetComparator.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import org.apache.poi.ss.formula.functions.Complex;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
/**
@@ -13,7 +12,7 @@ import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
* @author Piotr Gawron
*
*/
-public class ComplexAndDefinedSetComparator extends ANodeComparator<ComplexAlias, ReactomeDefinedSet> {
+public class ComplexAndDefinedSetComparator extends ANodeComparator<Complex, ReactomeDefinedSet> {
/**
* Default class logger.
@@ -24,11 +23,11 @@ public class ComplexAndDefinedSetComparator extends ANodeComparator<ComplexAlias
* Default constructor.
*/
public ComplexAndDefinedSetComparator() {
- super(ComplexAlias.class, ReactomeDefinedSet.class);
+ super(Complex.class, ReactomeDefinedSet.class);
}
@Override
- public boolean compareNodes(ComplexAlias species, ReactomeDefinedSet rSpecies) {
+ public boolean compareNodes(Complex species, ReactomeDefinedSet rSpecies) {
logger.warn(getElementTag(species) + " and " + rSpecies.getClass() + ", " + rSpecies.getDbId() + " should be comparable, but how??? Assuming FALSE");
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndEntityWithAccessionedSequenceComparator.java
index 6fd7bda33f..63c7a06813 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndEntityWithAccessionedSequenceComparator.java
@@ -3,11 +3,9 @@ package lcsb.mapviewer.reactome.utils.comparators;
import java.util.HashSet;
import java.util.Set;
-import org.apache.poi.ss.formula.functions.Complex;
-
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
import lcsb.mapviewer.reactome.model.ReactomeReferenceEntity;
import lcsb.mapviewer.reactome.model.ReactomeReferenceGeneProduct;
@@ -21,17 +19,17 @@ import lcsb.mapviewer.reactome.utils.ComparatorException;
* @author Piotr Gawron
*
*/
-public class ComplexAndEntityWithAccessionedSequenceComparator extends ANodeComparator<ComplexAlias, ReactomeEntityWithAccessionedSequence> {
+public class ComplexAndEntityWithAccessionedSequenceComparator extends ANodeComparator<Complex, ReactomeEntityWithAccessionedSequence> {
/**
* Default constructor.
*/
public ComplexAndEntityWithAccessionedSequenceComparator() {
- super(ComplexAlias.class, ReactomeEntityWithAccessionedSequence.class);
+ super(Complex.class, ReactomeEntityWithAccessionedSequence.class);
}
@Override
- public boolean compareNodes(ComplexAlias complex, ReactomeEntityWithAccessionedSequence entity) throws ComparatorException {
+ public boolean compareNodes(Complex complex, ReactomeEntityWithAccessionedSequence entity) throws ComparatorException {
Set<MiriamData> complex1Ids;
try {
complex1Ids = getRcu().getIdsForComplex(complex);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndOtherEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndOtherEntityComparator.java
index b04274a805..b7f0acd9af 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndOtherEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndOtherEntityComparator.java
@@ -1,9 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import org.apache.poi.ss.formula.functions.Complex;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
/**
@@ -13,7 +12,7 @@ import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
* @author Piotr Gawron
*
*/
-public class ComplexAndOtherEntityComparator extends ANodeComparator<ComplexAlias, ReactomeOtherEntity> {
+public class ComplexAndOtherEntityComparator extends ANodeComparator<Complex, ReactomeOtherEntity> {
/**
* Default class logger.
@@ -24,11 +23,11 @@ public class ComplexAndOtherEntityComparator extends ANodeComparator<ComplexAlia
* Default constructor.
*/
public ComplexAndOtherEntityComparator() {
- super(ComplexAlias.class, ReactomeOtherEntity.class);
+ super(Complex.class, ReactomeOtherEntity.class);
}
@Override
- public boolean compareNodes(ComplexAlias species, ReactomeOtherEntity rSpecies) {
+ public boolean compareNodes(Complex species, ReactomeOtherEntity rSpecies) {
logger.warn(getElementTag(species) + " and " + rSpecies.getClass() + ", " + rSpecies.getDbId() + " should be comparable, but how??? Assuming FALSE");
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java
index fecbce6275..dd7761548c 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ComplexAndSimpleEntityComparator.java
@@ -3,12 +3,10 @@ package lcsb.mapviewer.reactome.utils.comparators;
import java.util.HashSet;
import java.util.Set;
-import org.apache.poi.ss.formula.functions.Complex;
-
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.reactome.model.ReactomeReferenceEntity;
import lcsb.mapviewer.reactome.model.ReactomeReferenceMolecule;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
@@ -21,17 +19,17 @@ import lcsb.mapviewer.reactome.utils.ComparatorException;
* @author Piotr Gawron
*
*/
-public class ComplexAndSimpleEntityComparator extends ANodeComparator<ComplexAlias, ReactomeSimpleEntity> {
+public class ComplexAndSimpleEntityComparator extends ANodeComparator<Complex, ReactomeSimpleEntity> {
/**
* Default constructor.
*/
public ComplexAndSimpleEntityComparator() {
- super(ComplexAlias.class, ReactomeSimpleEntity.class);
+ super(Complex.class, ReactomeSimpleEntity.class);
}
@Override
- public boolean compareNodes(ComplexAlias complex, ReactomeSimpleEntity simpleEntity) throws ComparatorException {
+ public boolean compareNodes(Complex complex, ReactomeSimpleEntity simpleEntity) throws ComparatorException {
Set<MiriamData> complex1Ids;
try {
complex1Ids = getRcu().getIdsForComplex(complex);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DegradedAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DegradedAndEntityWithAccessionedSequenceComparator.java
index c4a944aaf4..cc9e7d414a 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DegradedAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DegradedAndEntityWithAccessionedSequenceComparator.java
@@ -1,22 +1,22 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
+import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
/**
- * This class allows to compare {@link DegradedAlias} element (internal
+ * This class allows to compare {@link Degraded} element (internal
* representation) and {@link ReactomeEntityWithAccessionedSequence} (reactome
* model).
*
* @author Piotr Gawron
*
*/
-public class DegradedAndEntityWithAccessionedSequenceComparator extends ANodeComparator<DegradedAlias, ReactomeEntityWithAccessionedSequence> {
+public class DegradedAndEntityWithAccessionedSequenceComparator extends ANodeComparator<Degraded, ReactomeEntityWithAccessionedSequence> {
/**
* Default constructor.
*/
public DegradedAndEntityWithAccessionedSequenceComparator() {
- super(DegradedAlias.class, ReactomeEntityWithAccessionedSequence.class);
+ super(Degraded.class, ReactomeEntityWithAccessionedSequence.class);
}
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
index b053e372fd..9558a7306c 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/DrugAndCatalystComparator.java
@@ -2,17 +2,17 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
+import lcsb.mapviewer.model.map.species.Drug;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
/**
- * This class allows to compare {@link DrugAlias} element (internal
+ * This class allows to compare {@link Drug} element (internal
* representation) and {@link ReactomeCatalystActivity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class DrugAndCatalystComparator extends ANodeComparator<DrugAlias, ReactomeCatalystActivity> {
+public class DrugAndCatalystComparator extends ANodeComparator<Drug, ReactomeCatalystActivity> {
/**
* Default class logger.
*/
@@ -22,11 +22,11 @@ public class DrugAndCatalystComparator extends ANodeComparator<DrugAlias, Reacto
* Default constructor.
*/
public DrugAndCatalystComparator() {
- super(DrugAlias.class, ReactomeCatalystActivity.class);
+ super(Drug.class, ReactomeCatalystActivity.class);
}
@Override
- public boolean compareNodes(DrugAlias species, ReactomeCatalystActivity cSpecies) {
+ public boolean compareNodes(Drug species, ReactomeCatalystActivity cSpecies) {
logger.warn("Don't know how to compare: " + species.getClass() + " and " + cSpecies.getClass() + ". Assuming false.");
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
index e399fcca7e..f2e0f7d0aa 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndDefinedSetComparator.java
@@ -2,17 +2,17 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
+import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
/**
- * This class allows to compare {@link GeneAlias} element (internal
+ * This class allows to compare {@link Gene} element (internal
* representation) and {@link ReactomeDefinedSet} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class GeneAndDefinedSetComparator extends ANodeComparator<GeneAlias, ReactomeDefinedSet> {
+public class GeneAndDefinedSetComparator extends ANodeComparator<Gene, ReactomeDefinedSet> {
/**
* Default class logger.
@@ -23,11 +23,11 @@ public class GeneAndDefinedSetComparator extends ANodeComparator<GeneAlias, Reac
* Default constructor.
*/
public GeneAndDefinedSetComparator() {
- super(GeneAlias.class, ReactomeDefinedSet.class);
+ super(Gene.class, ReactomeDefinedSet.class);
}
@Override
- public boolean compareNodes(GeneAlias species, ReactomeDefinedSet rSpecies) {
+ public boolean compareNodes(Gene species, ReactomeDefinedSet rSpecies) {
logger.warn(getElementTag(species) + " and " + rSpecies.getClass() + ", " + rSpecies.getDbId() + " should be comparable, but how??? Assuming FALSE");
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
index d43765ed4d..91cd665c34 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/GeneAndOtherEntityComparator.java
@@ -2,17 +2,17 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
+import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
/**
- * This class allows to compare {@link GeneAlias} element (internal
+ * This class allows to compare {@link Gene} element (internal
* representation) and {@link ReactomeOtherEntity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class GeneAndOtherEntityComparator extends ANodeComparator<GeneAlias, ReactomeOtherEntity> {
+public class GeneAndOtherEntityComparator extends ANodeComparator<Gene, ReactomeOtherEntity> {
/**
* Default class logger.
@@ -23,11 +23,11 @@ public class GeneAndOtherEntityComparator extends ANodeComparator<GeneAlias, Rea
* Default constructor.
*/
public GeneAndOtherEntityComparator() {
- super(GeneAlias.class, ReactomeOtherEntity.class);
+ super(Gene.class, ReactomeOtherEntity.class);
}
@Override
- public boolean compareNodes(GeneAlias species, ReactomeOtherEntity rSpecies) {
+ public boolean compareNodes(Gene species, ReactomeOtherEntity rSpecies) {
logger.warn(getElementTag(species) + " and " + rSpecies.getClass() + ", " + rSpecies.getDbId() + " should be comparable, but how??? Assuming FALSE");
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndCatalystComparator.java
index 64b37cd44c..6b0a640249 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndCatalystComparator.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
+import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
@@ -11,23 +11,23 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link IonAlias} element (internal
+ * This class allows to compare {@link Ion} element (internal
* representation) and {@link ReactomeCatalystActivity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class IonAndCatalystComparator extends ANodeComparator<IonAlias, ReactomeCatalystActivity> {
+public class IonAndCatalystComparator extends ANodeComparator<Ion, ReactomeCatalystActivity> {
/**
* Default constructor.
*/
public IonAndCatalystComparator() {
- super(IonAlias.class, ReactomeCatalystActivity.class);
+ super(Ion.class, ReactomeCatalystActivity.class);
}
@Override
- public boolean compareNodes(IonAlias species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
+ public boolean compareNodes(Ion species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
ReactomePhysicalEntity pEntity = cSpecies.getPhysicalEntity();
if (pEntity instanceof ReactomeComplex) {
return getGlobalComparator().compareNodes(species, (ReactomeComplex) pEntity);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
index 061b4ef15b..2c3efb2541 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndComplexComparator.java
@@ -5,7 +5,7 @@ import java.util.List;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
+import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
@@ -16,23 +16,23 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link IonAlias} element (internal
+ * This class allows to compare {@link Ion} element (internal
* representation) and {@link ReactomeComplex} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class IonAndComplexComparator extends ANodeComparator<IonAlias, ReactomeComplex> {
+public class IonAndComplexComparator extends ANodeComparator<Ion, ReactomeComplex> {
/**
* Default constructor.
*/
public IonAndComplexComparator() {
- super(IonAlias.class, ReactomeComplex.class);
+ super(Ion.class, ReactomeComplex.class);
}
@Override
- public boolean compareNodes(IonAlias species, ReactomeComplex entity) throws ComparatorException {
+ public boolean compareNodes(Ion species, ReactomeComplex entity) throws ComparatorException {
try {
List<MiriamData> chebi1 = getChebiBackend().getOntologyChebiIdsForChebiName(species.getName());
String chebi2 = null;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
index 104b0ddffc..0a34a14ccb 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndDefinedSetComparator.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
+import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
@@ -10,23 +10,23 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link IonAlias} element (internal
+ * This class allows to compare {@link Ion} element (internal
* representation) and {@link ReactomeDefinedSet} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class IonAndDefinedSetComparator extends ANodeComparator<IonAlias, ReactomeDefinedSet> {
+public class IonAndDefinedSetComparator extends ANodeComparator<Ion, ReactomeDefinedSet> {
/**
* Default constructor.
*/
public IonAndDefinedSetComparator() {
- super(IonAlias.class, ReactomeDefinedSet.class);
+ super(Ion.class, ReactomeDefinedSet.class);
}
@Override
- public boolean compareNodes(IonAlias species, ReactomeDefinedSet rSpecies) throws ComparatorException {
+ public boolean compareNodes(Ion species, ReactomeDefinedSet rSpecies) throws ComparatorException {
boolean result = false;
for (ReactomePhysicalEntity entity : rSpecies.getHasMembers()) {
if (entity instanceof ReactomeSimpleEntity) {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
index 9c6df33aa6..735254dcc1 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndEntityWithAccessionedSequenceComparator.java
@@ -1,27 +1,27 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
+import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
/**
- * This class allows to compare {@link IonAlias} element (internal
+ * This class allows to compare {@link Ion} element (internal
* representation) and {@link ReactomeEntityWithAccessionedSequence} (reactome
* model).
*
* @author Piotr Gawron
*
*/
-public class IonAndEntityWithAccessionedSequenceComparator extends ANodeComparator<IonAlias, ReactomeEntityWithAccessionedSequence> {
+public class IonAndEntityWithAccessionedSequenceComparator extends ANodeComparator<Ion, ReactomeEntityWithAccessionedSequence> {
/**
* Default constructor.
*/
public IonAndEntityWithAccessionedSequenceComparator() {
- super(IonAlias.class, ReactomeEntityWithAccessionedSequence.class);
+ super(Ion.class, ReactomeEntityWithAccessionedSequence.class);
}
@Override
- public boolean compareNodes(IonAlias species, ReactomeEntityWithAccessionedSequence simpleEntity) {
+ public boolean compareNodes(Ion species, ReactomeEntityWithAccessionedSequence simpleEntity) {
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndSimpleEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndSimpleEntityComparator.java
index 13b9678c85..7d22f28e59 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndSimpleEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/IonAndSimpleEntityComparator.java
@@ -5,28 +5,28 @@ import java.util.Set;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
+import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link IonAlias} element (internal
+ * This class allows to compare {@link Ion} element (internal
* representation) and {@link ReactomeSimpleEntity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class IonAndSimpleEntityComparator extends ANodeComparator<IonAlias, ReactomeSimpleEntity> {
+public class IonAndSimpleEntityComparator extends ANodeComparator<Ion, ReactomeSimpleEntity> {
/**
* Default constructor.
*/
public IonAndSimpleEntityComparator() {
- super(IonAlias.class, ReactomeSimpleEntity.class);
+ super(Ion.class, ReactomeSimpleEntity.class);
}
@Override
- public boolean compareNodes(IonAlias species, ReactomeSimpleEntity simpleEntity) throws ComparatorException {
+ public boolean compareNodes(Ion species, ReactomeSimpleEntity simpleEntity) throws ComparatorException {
try {
List<MiriamData> chebi1 = getChebiBackend().getOntologyChebiIdsForChebiName(species.getName());
if (chebi1.size() == 0) { // if we don't have id then return false (even
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MatchResult.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MatchResult.java
index aa7c6ef1c9..60294e9c1e 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MatchResult.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MatchResult.java
@@ -5,8 +5,8 @@ import java.util.List;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
@@ -46,15 +46,15 @@ public class MatchResult {
/**
* Which local reactants couldn't be matched into reactome nodes.
*/
- private List<Alias> invalidLocalInput = new ArrayList<>();
+ private List<Element> invalidLocalInput = new ArrayList<>();
/**
* Which local products couldn't be matched into reactome nodes.
*/
- private List<Alias> invalidLocalOutput = new ArrayList<>();
+ private List<Element> invalidLocalOutput = new ArrayList<>();
/**
* Which local modifiers couldn't be matched into reactome nodes.
*/
- private List<Alias> invalidLocalModifier = new ArrayList<>();
+ private List<Element> invalidLocalModifier = new ArrayList<>();
/**
* Which reactome reactants couldn't be matched into local reaction nodes.
@@ -105,7 +105,7 @@ public class MatchResult {
* @param invalidLocalInput
* species to be added
*/
- public void addInvalidLocalInput(Alias invalidLocalInput) {
+ public void addInvalidLocalInput(Element invalidLocalInput) {
this.invalidLocalInput.add(invalidLocalInput);
}
@@ -115,7 +115,7 @@ public class MatchResult {
* @param invalidLocalOutput
* species to be added
*/
- public void addInvalidLocalOutput(Alias invalidLocalOutput) {
+ public void addInvalidLocalOutput(Element invalidLocalOutput) {
this.invalidLocalOutput.add(invalidLocalOutput);
}
@@ -125,7 +125,7 @@ public class MatchResult {
* @param invalidLocalModifier
* species to be added
*/
- public void addInvalidLocalModifier(Alias invalidLocalModifier) {
+ public void addInvalidLocalModifier(Element invalidLocalModifier) {
this.invalidLocalModifier.add(invalidLocalModifier);
}
@@ -231,7 +231,7 @@ public class MatchResult {
* @return the invalidLocalInput
* @see #invalidLocalInput
*/
- public List<Alias> getInvalidLocalInput() {
+ public List<Element> getInvalidLocalInput() {
return invalidLocalInput;
}
@@ -240,7 +240,7 @@ public class MatchResult {
* the invalidLocalInput to set
* @see #invalidLocalInput
*/
- public void setInvalidLocalInput(List<Alias> invalidLocalInput) {
+ public void setInvalidLocalInput(List<Element> invalidLocalInput) {
this.invalidLocalInput = invalidLocalInput;
}
@@ -248,7 +248,7 @@ public class MatchResult {
* @return the invalidLocalOutput
* @see #invalidLocalOutput
*/
- public List<Alias> getInvalidLocalOutput() {
+ public List<Element> getInvalidLocalOutput() {
return invalidLocalOutput;
}
@@ -257,7 +257,7 @@ public class MatchResult {
* the invalidLocalOutput to set
* @see #invalidLocalOutput
*/
- public void setInvalidLocalOutput(List<Alias> invalidLocalOutput) {
+ public void setInvalidLocalOutput(List<Element> invalidLocalOutput) {
this.invalidLocalOutput = invalidLocalOutput;
}
@@ -265,7 +265,7 @@ public class MatchResult {
* @return the invalidLocalModifier
* @see #invalidLocalModifier
*/
- public List<Alias> getInvalidLocalModifier() {
+ public List<Element> getInvalidLocalModifier() {
return invalidLocalModifier;
}
@@ -274,7 +274,7 @@ public class MatchResult {
* the invalidLocalModifier to set
* @see #invalidLocalModifier
*/
- public void setInvalidLocalModifier(List<Alias> invalidLocalModifier) {
+ public void setInvalidLocalModifier(List<Element> invalidLocalModifier) {
this.invalidLocalModifier = invalidLocalModifier;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
index dd64991b26..83b4dc5d82 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndCatalystComparator.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
@@ -11,23 +11,23 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link SimpleMoleculeAlias} element (internal
+ * This class allows to compare {@link SimpleMolecule} element (internal
* representation) and {@link ReactomeCatalystActivity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class MoleculeAndCatalystComparator extends ANodeComparator<SimpleMoleculeAlias, ReactomeCatalystActivity> {
+public class MoleculeAndCatalystComparator extends ANodeComparator<SimpleMolecule, ReactomeCatalystActivity> {
/**
* Default constructor.
*/
public MoleculeAndCatalystComparator() {
- super(SimpleMoleculeAlias.class, ReactomeCatalystActivity.class);
+ super(SimpleMolecule.class, ReactomeCatalystActivity.class);
}
@Override
- public boolean compareNodes(SimpleMoleculeAlias species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
+ public boolean compareNodes(SimpleMolecule species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
ReactomePhysicalEntity pEntity = cSpecies.getPhysicalEntity();
if (pEntity instanceof ReactomeComplex) {
return getGlobalComparator().compareNodes(species, (ReactomeComplex) pEntity);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
index 0221ea8f21..0f4c3b37b8 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndComplexComparator.java
@@ -3,7 +3,7 @@ package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
@@ -14,23 +14,23 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link SimpleMoleculeAlias} element (internal
+ * This class allows to compare {@link SimpleMolecule} element (internal
* representation) and {@link ReactomeComplex} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class MoleculeAndComplexComparator extends ANodeComparator<SimpleMoleculeAlias, ReactomeComplex> {
+public class MoleculeAndComplexComparator extends ANodeComparator<SimpleMolecule, ReactomeComplex> {
/**
* Default constructor.
*/
public MoleculeAndComplexComparator() {
- super(SimpleMoleculeAlias.class, ReactomeComplex.class);
+ super(SimpleMolecule.class, ReactomeComplex.class);
}
@Override
- public boolean compareNodes(SimpleMoleculeAlias species, ReactomeComplex entity) throws ComparatorException {
+ public boolean compareNodes(SimpleMolecule species, ReactomeComplex entity) throws ComparatorException {
try {
MiriamData chebi1 = getChebiBackend().getChebiForChebiName(species.getName());
String chebi2 = null;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
index 3cbd349b76..1d5444c50d 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndDefinedSetComparator.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
@@ -10,23 +10,23 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link SimpleMoleculeAlias} element (internal
+ * This class allows to compare {@link SimpleMolecule} element (internal
* representation) and {@link ReactomeDefinedSet} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class MoleculeAndDefinedSetComparator extends ANodeComparator<SimpleMoleculeAlias, ReactomeDefinedSet> {
+public class MoleculeAndDefinedSetComparator extends ANodeComparator<SimpleMolecule, ReactomeDefinedSet> {
/**
* Default constructor.
*/
public MoleculeAndDefinedSetComparator() {
- super(SimpleMoleculeAlias.class, ReactomeDefinedSet.class);
+ super(SimpleMolecule.class, ReactomeDefinedSet.class);
}
@Override
- public boolean compareNodes(SimpleMoleculeAlias species, ReactomeDefinedSet rSpecies) throws ComparatorException {
+ public boolean compareNodes(SimpleMolecule species, ReactomeDefinedSet rSpecies) throws ComparatorException {
boolean result = false;
for (ReactomePhysicalEntity entity : rSpecies.getHasMembers()) {
if (entity instanceof ReactomeSimpleEntity) {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
index 20d37fad35..7532e39b7f 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndEntityWithAccessionedSequenceComparator.java
@@ -1,27 +1,27 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
/**
- * This class allows to compare {@link SimpleMoleculeAlias} element (internal
+ * This class allows to compare {@link SimpleMolecule} element (internal
* representation) and {@link ReactomeEntityWithAccessionedSequence} (reactome
* model).
*
* @author Piotr Gawron
*
*/
-public class MoleculeAndEntityWithAccessionedSequenceComparator extends ANodeComparator<SimpleMoleculeAlias, ReactomeEntityWithAccessionedSequence> {
+public class MoleculeAndEntityWithAccessionedSequenceComparator extends ANodeComparator<SimpleMolecule, ReactomeEntityWithAccessionedSequence> {
/**
* Default constructor.
*/
public MoleculeAndEntityWithAccessionedSequenceComparator() {
- super(SimpleMoleculeAlias.class, ReactomeEntityWithAccessionedSequence.class);
+ super(SimpleMolecule.class, ReactomeEntityWithAccessionedSequence.class);
}
@Override
- public boolean compareNodes(SimpleMoleculeAlias species, ReactomeEntityWithAccessionedSequence simpleEntity) {
+ public boolean compareNodes(SimpleMolecule species, ReactomeEntityWithAccessionedSequence simpleEntity) {
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndSimpleEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndSimpleEntityComparator.java
index 74111693c1..e40a5f9535 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndSimpleEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/MoleculeAndSimpleEntityComparator.java
@@ -5,28 +5,28 @@ import java.util.Set;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link SimpleMoleculeAlias} element (internal
+ * This class allows to compare {@link SimpleMolecule} element (internal
* representation) and {@link ReactomeSimpleEntity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class MoleculeAndSimpleEntityComparator extends ANodeComparator<SimpleMoleculeAlias, ReactomeSimpleEntity> {
+public class MoleculeAndSimpleEntityComparator extends ANodeComparator<SimpleMolecule, ReactomeSimpleEntity> {
/**
* Default constructor.
*/
public MoleculeAndSimpleEntityComparator() {
- super(SimpleMoleculeAlias.class, ReactomeSimpleEntity.class);
+ super(SimpleMolecule.class, ReactomeSimpleEntity.class);
}
@Override
- public boolean compareNodes(SimpleMoleculeAlias species, ReactomeSimpleEntity simpleEntity) throws ComparatorException {
+ public boolean compareNodes(SimpleMolecule species, ReactomeSimpleEntity simpleEntity) throws ComparatorException {
try {
List<MiriamData> chebi1 = getChebiBackend().getOntologyChebiIdsForChebiName(species.getName());
if (chebi1.size() == 0) { // if we don't have id then return false (even
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparator.java
index 032fe85cc8..29a4c8070f 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparator.java
@@ -6,8 +6,8 @@ import java.util.Map;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.persist.SpringApplicationContext;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.utils.ComparatorException;
@@ -19,7 +19,7 @@ import lcsb.mapviewer.reactome.utils.ComparatorException;
* @author Piotr Gawron
*
*/
-public class NodeComparator extends ANodeComparator<Alias, ReactomeDatabaseObject> {
+public class NodeComparator extends ANodeComparator<Element, ReactomeDatabaseObject> {
/**
* Default class logger.
*/
@@ -36,7 +36,7 @@ public class NodeComparator extends ANodeComparator<Alias, ReactomeDatabaseObjec
* implementation of {@link ANodeComparator}.
*/
public NodeComparator() {
- super(Alias.class, ReactomeDatabaseObject.class);
+ super(Element.class, ReactomeDatabaseObject.class);
}
/**
@@ -51,16 +51,16 @@ public class NodeComparator extends ANodeComparator<Alias, ReactomeDatabaseObjec
}
@Override
- public boolean compareNodes(Alias species, ReactomeDatabaseObject reactomeSpecies) throws ComparatorException {
+ @SuppressWarnings({ "rawtypes", "unchecked" })
+ public boolean compareNodes(Element species, ReactomeDatabaseObject reactomeSpecies) throws ComparatorException {
String speciesName = species.getClass().getName();
- if (species instanceof ProteinAlias) {
- speciesName = ProteinAlias.class.getName();
+ if (species instanceof Protein) {
+ speciesName = Protein.class.getName();
}
String serializedClassComparator = speciesName + "," + reactomeSpecies.getClass().getName();
if (serializedClassComparator.indexOf("_$$_javassist_") >= 0) {
serializedClassComparator = serializedClassComparator.substring(0, serializedClassComparator.indexOf("_$$_javassist_"));
}
- @SuppressWarnings("rawtypes")
ANodeComparator comparator = getComparator(serializedClassComparator);
if (comparator != null) {
return comparator.compareNodes(species, reactomeSpecies);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCandidateSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCandidateSetComparator.java
index 0ffe9cec14..0f245bffcd 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCandidateSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCandidateSetComparator.java
@@ -4,7 +4,7 @@ import java.util.HashSet;
import java.util.Set;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
@@ -12,23 +12,23 @@ import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeCandidateSet} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndCandidateSetComparator extends ANodeComparator<ProteinAlias, ReactomeCandidateSet> {
+public class ProteinAndCandidateSetComparator extends ANodeComparator<Protein, ReactomeCandidateSet> {
/**
* Default constructor.
*/
public ProteinAndCandidateSetComparator() {
- super(ProteinAlias.class, ReactomeCandidateSet.class);
+ super(Protein.class, ReactomeCandidateSet.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeCandidateSet rSpecies) throws ComparatorException {
+ public boolean compareNodes(Protein species, ReactomeCandidateSet rSpecies) throws ComparatorException {
boolean result = false;
Set<ReactomePhysicalEntity> objects = new HashSet<ReactomePhysicalEntity>();
objects.addAll(rSpecies.getHasMembers());
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCatalystComparator.java
index 0d5249d6ca..037cc520ef 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndCatalystComparator.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeCandidateSet;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
@@ -12,23 +12,23 @@ import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeCatalystActivity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndCatalystComparator extends ANodeComparator<ProteinAlias, ReactomeCatalystActivity> {
+public class ProteinAndCatalystComparator extends ANodeComparator<Protein, ReactomeCatalystActivity> {
/**
* Default constructor.
*/
public ProteinAndCatalystComparator() {
- super(ProteinAlias.class, ReactomeCatalystActivity.class);
+ super(Protein.class, ReactomeCatalystActivity.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
+ public boolean compareNodes(Protein species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
ReactomePhysicalEntity pEntity = cSpecies.getPhysicalEntity();
if (pEntity instanceof ReactomeComplex) {
return getGlobalComparator().compareNodes(species, (ReactomeComplex) pEntity);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndComplexComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndComplexComparator.java
index 550064e07e..cd50e74ecc 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndComplexComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndComplexComparator.java
@@ -7,18 +7,18 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeComplex} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndComplexComparator extends ANodeComparator<ProteinAlias, ReactomeComplex> {
+public class ProteinAndComplexComparator extends ANodeComparator<Protein, ReactomeComplex> {
/**
* Default class logger.
*/
@@ -29,11 +29,11 @@ public class ProteinAndComplexComparator extends ANodeComparator<ProteinAlias, R
* Default constructor.
*/
public ProteinAndComplexComparator() {
- super(ProteinAlias.class, ReactomeComplex.class);
+ super(Protein.class, ReactomeComplex.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeComplex complex) throws ComparatorException {
+ public boolean compareNodes(Protein species, ReactomeComplex complex) throws ComparatorException {
try {
Set<MiriamData> uniprotIds1 = getElementUtil().getMiriamByType(species, MiriamType.UNIPROT, true);
Set<MiriamData> uniprotIds2 = new HashSet<MiriamData>();
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndDefinedSetComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndDefinedSetComparator.java
index 65de0babef..eca0bb74ac 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndDefinedSetComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndDefinedSetComparator.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
@@ -10,23 +10,23 @@ import lcsb.mapviewer.reactome.model.ReactomePolymer;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeDefinedSet} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndDefinedSetComparator extends ANodeComparator<ProteinAlias, ReactomeDefinedSet> {
+public class ProteinAndDefinedSetComparator extends ANodeComparator<Protein, ReactomeDefinedSet> {
/**
* Default constructor.
*/
public ProteinAndDefinedSetComparator() {
- super(ProteinAlias.class, ReactomeDefinedSet.class);
+ super(Protein.class, ReactomeDefinedSet.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeDefinedSet rSpecies) throws ComparatorException {
+ public boolean compareNodes(Protein species, ReactomeDefinedSet rSpecies) throws ComparatorException {
boolean result = false;
for (ReactomePhysicalEntity entity : rSpecies.getHasMembers()) {
if (entity instanceof ReactomeComplex) {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndEntityWithAccessionedSequenceComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndEntityWithAccessionedSequenceComparator.java
index bb77ec02b0..037924e79c 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndEntityWithAccessionedSequenceComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndEntityWithAccessionedSequenceComparator.java
@@ -7,21 +7,21 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
import lcsb.mapviewer.reactome.model.ReactomeReferenceEntity;
import lcsb.mapviewer.reactome.model.ReactomeReferenceGeneProduct;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeEntityWithAccessionedSequence} (reactome
* model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndEntityWithAccessionedSequenceComparator extends ANodeComparator<ProteinAlias, ReactomeEntityWithAccessionedSequence> {
+public class ProteinAndEntityWithAccessionedSequenceComparator extends ANodeComparator<Protein, ReactomeEntityWithAccessionedSequence> {
/**
* Default class logger.
*/
@@ -32,11 +32,11 @@ public class ProteinAndEntityWithAccessionedSequenceComparator extends ANodeComp
* Default constructor.
*/
public ProteinAndEntityWithAccessionedSequenceComparator() {
- super(ProteinAlias.class, ReactomeEntityWithAccessionedSequence.class);
+ super(Protein.class, ReactomeEntityWithAccessionedSequence.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeEntityWithAccessionedSequence entity) throws ComparatorException {
+ public boolean compareNodes(Protein species, ReactomeEntityWithAccessionedSequence entity) throws ComparatorException {
try {
Set<MiriamData> uniprotId1 = getElementUtil().getMiriamByType(species, MiriamType.UNIPROT, true);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndGenomeEncodedEntity.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndGenomeEncodedEntity.java
index dc85f16b9f..a5b731ef28 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndGenomeEncodedEntity.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndGenomeEncodedEntity.java
@@ -2,17 +2,17 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeGenomeEncodedEntity;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeGenomeEncodedEntity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndGenomeEncodedEntity extends ANodeComparator<ProteinAlias, ReactomeGenomeEncodedEntity> {
+public class ProteinAndGenomeEncodedEntity extends ANodeComparator<Protein, ReactomeGenomeEncodedEntity> {
/**
* Default class logger.
*/
@@ -23,11 +23,11 @@ public class ProteinAndGenomeEncodedEntity extends ANodeComparator<ProteinAlias,
* Default constructor.
*/
public ProteinAndGenomeEncodedEntity() {
- super(ProteinAlias.class, ReactomeGenomeEncodedEntity.class);
+ super(Protein.class, ReactomeGenomeEncodedEntity.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeGenomeEncodedEntity entity) {
+ public boolean compareNodes(Protein species, ReactomeGenomeEncodedEntity entity) {
for (String name : entity.getNames()) {
if (name.trim().equalsIgnoreCase(name.trim())) {
return true;
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndOtherEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndOtherEntityComparator.java
index ae0339ef61..96f121a16c 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndOtherEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndOtherEntityComparator.java
@@ -2,17 +2,17 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeOtherEntity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndOtherEntityComparator extends ANodeComparator<ProteinAlias, ReactomeOtherEntity> {
+public class ProteinAndOtherEntityComparator extends ANodeComparator<Protein, ReactomeOtherEntity> {
/**
* Default class logger.
@@ -23,11 +23,11 @@ public class ProteinAndOtherEntityComparator extends ANodeComparator<ProteinAlia
* Default constructor.
*/
public ProteinAndOtherEntityComparator() {
- super(ProteinAlias.class, ReactomeOtherEntity.class);
+ super(Protein.class, ReactomeOtherEntity.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeOtherEntity rSpecies) {
+ public boolean compareNodes(Protein species, ReactomeOtherEntity rSpecies) {
logger.warn(getElementTag(species) + " and " + rSpecies.getClass() + ", " + rSpecies.getDbId() + " should be comparable, but how??? Assuming FALSE");
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndPolymerComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndPolymerComparator.java
index 2349aad77e..980eb07352 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndPolymerComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndPolymerComparator.java
@@ -9,7 +9,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeComplex;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
@@ -22,13 +22,13 @@ import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomePolymer} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndPolymerComparator extends ANodeComparator<ProteinAlias, ReactomePolymer> {
+public class ProteinAndPolymerComparator extends ANodeComparator<Protein, ReactomePolymer> {
/**
* Default class logger.
*/
@@ -38,11 +38,11 @@ public class ProteinAndPolymerComparator extends ANodeComparator<ProteinAlias, R
* Default constructor.
*/
public ProteinAndPolymerComparator() {
- super(ProteinAlias.class, ReactomePolymer.class);
+ super(Protein.class, ReactomePolymer.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomePolymer polymer) throws ComparatorException {
+ public boolean compareNodes(Protein species, ReactomePolymer polymer) throws ComparatorException {
Set<MiriamData> uniprotIds1 = new HashSet<MiriamData>();
Set<MiriamData> uniprotIds2 = new HashSet<MiriamData>();
for (MiriamData md : species.getMiriamData()) {
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndSimpleEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndSimpleEntityComparator.java
index c47a2e68bd..010d106bc2 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndSimpleEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ProteinAndSimpleEntityComparator.java
@@ -1,26 +1,26 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
/**
- * This class allows to compare {@link ProteinAlias} element (internal
+ * This class allows to compare {@link Protein} element (internal
* representation) and {@link ReactomeSimpleEntity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class ProteinAndSimpleEntityComparator extends ANodeComparator<ProteinAlias, ReactomeSimpleEntity> {
+public class ProteinAndSimpleEntityComparator extends ANodeComparator<Protein, ReactomeSimpleEntity> {
/**
* Default constructor.
*/
public ProteinAndSimpleEntityComparator() {
- super(ProteinAlias.class, ReactomeSimpleEntity.class);
+ super(Protein.class, ReactomeSimpleEntity.class);
}
@Override
- public boolean compareNodes(ProteinAlias species, ReactomeSimpleEntity cSpecies) {
+ public boolean compareNodes(Protein species, ReactomeSimpleEntity cSpecies) {
return false;
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndCatalystComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndCatalystComparator.java
index 79498edcd4..428415f981 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndCatalystComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndCatalystComparator.java
@@ -1,30 +1,30 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeGenomeEncodedEntity;
import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
import lcsb.mapviewer.reactome.utils.ComparatorException;
/**
- * This class allows to compare {@link UnknownAlias} element (internal
+ * This class allows to compare {@link Unknown} element (internal
* representation) and {@link ReactomeCatalystActivity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class UnknownAndCatalystComparator extends ANodeComparator<UnknownAlias, ReactomeCatalystActivity> {
+public class UnknownAndCatalystComparator extends ANodeComparator<Unknown, ReactomeCatalystActivity> {
/**
* Default constructor.
*/
public UnknownAndCatalystComparator() {
- super(UnknownAlias.class, ReactomeCatalystActivity.class);
+ super(Unknown.class, ReactomeCatalystActivity.class);
}
@Override
- public boolean compareNodes(UnknownAlias species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
+ public boolean compareNodes(Unknown species, ReactomeCatalystActivity cSpecies) throws ComparatorException {
ReactomePhysicalEntity pEntity = cSpecies.getPhysicalEntity();
if (pEntity instanceof ReactomeGenomeEncodedEntity) {
return getGlobalComparator().compareNodes(species, (ReactomeGenomeEncodedEntity) pEntity);
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndGenomeEncodedEntityComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndGenomeEncodedEntityComparator.java
index ff73b72d4c..18c6ed871c 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndGenomeEncodedEntityComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/UnknownAndGenomeEncodedEntityComparator.java
@@ -1,26 +1,26 @@
package lcsb.mapviewer.reactome.utils.comparators;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.reactome.model.ReactomeGenomeEncodedEntity;
/**
- * This class allows to compare {@link UnknownAlias} element (internal
+ * This class allows to compare {@link Unknown} element (internal
* representation) and {@link ReactomeGenomeEncodedEntity} (reactome model).
*
* @author Piotr Gawron
*
*/
-public class UnknownAndGenomeEncodedEntityComparator extends ANodeComparator<UnknownAlias, ReactomeGenomeEncodedEntity> {
+public class UnknownAndGenomeEncodedEntityComparator extends ANodeComparator<Unknown, ReactomeGenomeEncodedEntity> {
/**
* Default constructor.
*/
public UnknownAndGenomeEncodedEntityComparator() {
- super(UnknownAlias.class, ReactomeGenomeEncodedEntity.class);
+ super(Unknown.class, ReactomeGenomeEncodedEntity.class);
}
@Override
- public boolean compareNodes(UnknownAlias species, ReactomeGenomeEncodedEntity entity) {
+ public boolean compareNodes(Unknown species, ReactomeGenomeEncodedEntity entity) {
// we can compare the objects only using names...
for (String name : entity.getNames()) {
if (name.trim().equalsIgnoreCase(species.getName().trim())) {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtilTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtilTest.java
index 47c57ede08..16a106f1fb 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtilTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtilTest.java
@@ -18,10 +18,10 @@ import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.ReactomeTestFunctions;
import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
import lcsb.mapviewer.reactome.xml.ReactomeCatalystActivityParser;
@@ -58,11 +58,11 @@ public class ReactomeQueryUtilTest extends ReactomeTestFunctions {
public void testGetReactionsBetweenSpecies() {
try {
// based on reaction re1107 from PD_130712_3.xml
- SimpleMoleculeAlias input = new SimpleMoleculeAlias("id1");
+ SimpleMolecule input = new SimpleMolecule("id1");
input.setName("coenzyme A");
- SimpleMoleculeAlias output = new SimpleMoleculeAlias("id2");
+ SimpleMolecule output = new SimpleMolecule("id2");
output.setName("acetyl-CoA");
- List<Alias> list = new ArrayList<>();
+ List<Element> list = new ArrayList<>();
list.add(input);
list.add(output);
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparatorTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparatorTest.java
index 4cd4facd8a..ae7fe04c5c 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparatorTest.java
+++ b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/comparators/NodeComparatorTest.java
@@ -11,8 +11,8 @@ import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.reactome.ReactomeTestFunctions;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
@@ -55,7 +55,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/reactome/cell_designer_references/reaction.xml", true);
- Alias speciesL_glu = model.getAliasByAliasId("sa6");
+ Element speciesL_glu = model.getAliasByAliasId("sa6");
ReactomePhysicalEntity reactomeL_glu = seParser
.parseObject(getXmlDocumentFromFile("testFiles/reactome/cell_designer_references/reactomeInput1.xml").getChildNodes().item(0));
@@ -76,7 +76,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/reactome/cell_designer_references/reaction.xml", true);
- Alias speciesNADP_PLUS = model.getAliasByAliasId("sa5");
+ Element speciesNADP_PLUS = model.getAliasByAliasId("sa5");
ReactomeDefinedSet reactomeNAD_P_PLUS = dsParser
.parseObject(getXmlDocumentFromFile("testFiles/reactome/cell_designer_references/reactomeInput2.xml").getChildNodes().item(0));
@@ -94,7 +94,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/reactome/cell_designer_references/reaction.xml", true);
- Alias h2o = model.getAliasByAliasId("sa7");
+ Element h2o = model.getAliasByAliasId("sa7");
ReactomePhysicalEntity reactomeH2O = seParser
.parseObject(getXmlDocumentFromFile("testFiles/reactome/cell_designer_references/reactomeInput3.xml").getChildNodes().item(0));
@@ -112,7 +112,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/reactome/cell_designer_references/reaction.xml", true);
- Alias oxoglutarate = model.getAliasByAliasId("sa1");
+ Element oxoglutarate = model.getAliasByAliasId("sa1");
ReactomePhysicalEntity reactomeOxoglutaric = seParser
.parseObject(getXmlDocumentFromFile("testFiles/reactome/cell_designer_references/reactomeOutput1.xml").getChildNodes().item(0));
@@ -130,7 +130,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/reactome/cell_designer_references/reaction.xml", true);
- Alias nadph = model.getAliasByAliasId("sa2");
+ Element nadph = model.getAliasByAliasId("sa2");
ReactomeDefinedSet reactomeNadph = dsParser
.parseObject(getXmlDocumentFromFile("testFiles/reactome/cell_designer_references/reactomeOutput3.xml").getChildNodes().item(0));
@@ -148,7 +148,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/reactome/cell_designer_references/reaction.xml", true);
- Alias hydron = model.getAliasByAliasId("sa3");
+ Element hydron = model.getAliasByAliasId("sa3");
ReactomePhysicalEntity reactomeHydron = seParser
.parseObject(getXmlDocumentFromFile("testFiles/reactome/cell_designer_references/reactomeOutput4.xml").getChildNodes().item(0));
@@ -166,7 +166,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/reactome/cell_designer_references/reaction.xml", true);
- Alias hydron = model.getAliasByAliasId("sa4");
+ Element hydron = model.getAliasByAliasId("sa4");
ReactomeCatalystActivity reactomeHydron = caParser
.parseObject(getXmlDocumentFromFile("testFiles/reactome/cell_designer_references/reactomeCatalyst1.xml").getChildNodes().item(0));
@@ -184,7 +184,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/tbid_bax_complex.xml", true);
- Alias species = model.getAliasByAliasId("csa1");
+ Element species = model.getAliasByAliasId("csa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(168850);
// these nodes match
@@ -201,7 +201,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/bax.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(139907);
// these nodes match
@@ -218,7 +218,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/bid.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(139953);
// these nodes match
@@ -235,7 +235,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/fumarate_hydratase.xml", true);
- Alias species = model.getAliasByAliasId("csa1");
+ Element species = model.getAliasByAliasId("csa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(70981);
// these nodes match
@@ -253,7 +253,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/acadl.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(77258);
// these nodes match
@@ -271,7 +271,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/phosphate_ion.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(113548);
// these nodes match
@@ -289,7 +289,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/dna.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(29428);
// these nodes match
@@ -307,7 +307,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/atp.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(416325);
// these nodes match
@@ -324,7 +324,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/bcl2l11_2.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(140526);
// these nodes match
@@ -341,7 +341,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/diablo_xiap_casp9.xml", true);
- Alias species = model.getAliasByAliasId("csa1");
+ Element species = model.getAliasByAliasId("csa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(114318);
// these nodes match
@@ -358,7 +358,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/unknown.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(500676);
// these nodes don't match after update of reactome
@@ -375,7 +375,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/pcca_pccb_complex.xml", true);
- Alias species = model.getAliasByAliasId("csa1");
+ Element species = model.getAliasByAliasId("csa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(71030);
// these nodes match
@@ -392,7 +392,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/dffb.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(211238);
// these nodes match
@@ -409,7 +409,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/caspase_7.xml", true);
- Alias species = model.getAliasByAliasId("csa1");
+ Element species = model.getAliasByAliasId("csa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(202853);
// these nodes match
@@ -427,7 +427,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/coa.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(548839);
// these nodes match
@@ -444,7 +444,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/pdp1_complex.xml", true);
- Alias species = model.getAliasByAliasId("csa1");
+ Element species = model.getAliasByAliasId("csa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(204160);
// these nodes match
@@ -461,7 +461,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/ca2.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(204160);
// these nodes match
@@ -478,7 +478,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/dna2.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(266214);
// these nodes match
@@ -495,7 +495,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/caspase_3.xml", true);
- Alias species = model.getAliasByAliasId("csa1");
+ Element species = model.getAliasByAliasId("csa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(114327);
// these nodes match
@@ -512,7 +512,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/gpd1.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(1500607);
// these nodes match
@@ -529,7 +529,7 @@ public class NodeComparatorTest extends ReactomeTestFunctions {
try {
Model model = getModelForFile("testFiles/small/prkacb.xml", true);
- Alias species = model.getAliasByAliasId("sa1");
+ Element species = model.getAliasByAliasId("sa1");
ReactomeDatabaseObject reactomeObject = rc.getFullObjectForDbId(443469);
// these nodes match
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
index 6cb02ae5ce..c2961ae1f7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
@@ -21,11 +21,11 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.CommentDao;
import lcsb.mapviewer.services.interfaces.ICommentService;
@@ -172,8 +172,8 @@ public class CommentService implements ICommentService {
if (object != null) {
comment.setTableName(object.getClass());
comment.setTableId(ObjectUtils.getIdOfObject(object));
- if (object instanceof Alias) {
- comment.setSubmodel(((Alias) object).getModel());
+ if (object instanceof Element) {
+ comment.setSubmodel(((Element) object).getModel());
} else if (object instanceof Reaction) {
comment.setSubmodel(((Reaction) object).getModel());
} else {
@@ -294,9 +294,9 @@ public class CommentService implements ICommentService {
logger.warn("Invalid reaction dbID: " + comment.getTableId() + ". Table: " + comment.getTableName().getName());
}
} else {
- Alias alias = model.getAliasByDbId(comment.getTableId());
+ Element alias = model.getAliasByDbId(comment.getTableId());
if (alias != null) {
- identifier = ((SpeciesAlias) alias).getAliasId();
+ identifier = ((Species) alias).getAliasId();
} else {
logger.warn("Invalid alias dbID: " + comment.getTableId());
}
@@ -550,7 +550,7 @@ public class CommentService implements ICommentService {
return result;
} else if (ElementIdentifierType.ALIAS.getJsName().equalsIgnoreCase(element.getType())) {
for (FullCommentView comment : comments) {
- if (Alias.class.equals(comment.getType())) {
+ if (Element.class.equals(comment.getType())) {
if (comment.getIdObject().equals(element.getObjectId()) && comment.getModelId().equals(element.getModelId())) {
for (Pair<String, String> c : comment.getComments()) {
result.add(new CommentDetails(c.getLeft(), c.getRight()));
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java b/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
index 94ec03f711..691a276741 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
@@ -31,11 +31,11 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.graph.DataMiningType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.map.graph.DataMiningDao;
import lcsb.mapviewer.persist.dao.map.graph.DataMiningSetDao;
@@ -119,14 +119,14 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
private BiocompendiumAnnotator annotationRestService;
@Override
- public Collection<DataMining> getMissingConnections(Alias alias) {
+ public Collection<DataMining> getMissingConnections(Element alias) {
return missingConnectionDao.getMissingConnectionForElement(alias);
}
@Override
public void addMissingConnection(DataMining connection) {
missingConnectionDao.add(connection);
- Alias element = connection.getElement();
+ Element element = connection.getElement();
String id = element.getName() + " (" + element.getStringType() + ")";
String toString = "";
for (MiriamData md : connection.getSuggestedConnections()) {
@@ -139,7 +139,7 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
@Override
public void deleteMissingConnection(DataMining connection, String reason) {
missingConnectionDao.delete(connection);
- Alias element = connection.getElement();
+ Element element = connection.getElement();
String id = element.getName() + " (" + element.getStringType() + ")";
String toString = "";
for (MiriamData md : connection.getSuggestedConnections()) {
@@ -157,12 +157,12 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
}
@Override
- public Collection<Alias> getSpeciesWithMissingConnectionsByGeneName(Model model, String geneName) {
- Set<Alias> result = new HashSet<>();
+ public Collection<Element> getSpeciesWithMissingConnectionsByGeneName(Model model, String geneName) {
+ Set<Element> result = new HashSet<>();
if (geneName == null) {
return result;
}
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
Collection<DataMining> set = missingConnectionDao.getMissingConnectionForElement(element);
for (DataMining dataMining : set) {
for (MiriamData md : dataMining.getSuggestedConnections()) {
@@ -243,10 +243,10 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
@Override
public void removeConnectionsForModel(ModelData model) {
- Collection<Alias> nodes = model.getAliases();
+ Collection<Element> nodes = model.getAliases();
dbUtils.setAutoFlush(false);
- for (Alias node : nodes) {
+ for (Element node : nodes) {
Collection<DataMining> mcs = missingConnectionDao.getMissingConnectionForElement(node);
for (DataMining missingConnection : mcs) {
missingConnectionDao.delete(missingConnection);
@@ -261,7 +261,7 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
}
@Override
- public Set<DataMining> parseData(String filename, DataMiningType type, Collection<Alias> nodes, Set<Reaction> reactions, IProgressUpdater updater)
+ public Set<DataMining> parseData(String filename, DataMiningType type, Collection<Element> nodes, Set<Reaction> reactions, IProgressUpdater updater)
throws IOException, InvalidDataMiningInputFile {
InputStream is = new FileInputStream(filename);
String name = new File(filename).getName();
@@ -285,7 +285,7 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
* @throws InvalidDataMiningInputFile
* thrown when the input file is invalid
*/
- protected Set<DataMining> parseData(Collection<Alias> nodes, Set<Reaction> reactions, InputStream is, String warningPrefix)
+ protected Set<DataMining> parseData(Collection<Element> nodes, Set<Reaction> reactions, InputStream is, String warningPrefix)
throws InvalidDataMiningInputFile {
Set<DataMining> result = new HashSet<DataMining>();
String content = null;
@@ -337,10 +337,10 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
if (targetColumnId == null) {
throw new InvalidDataMiningInputFile(warningPrefix + " Column \"" + TARGET_COLUMN_NAME + "\" wasn't found in the input file.");
}
- Map<MiriamData, List<Alias>> map = new HashMap<>();
- for (Alias element : nodes) {
+ Map<MiriamData, List<Element>> map = new HashMap<>();
+ for (Element element : nodes) {
for (MiriamData md : element.getMiriamData()) {
- List<Alias> elList = map.get(md);
+ List<Element> elList = map.get(md);
if (elList == null) {
elList = new ArrayList<>();
map.put(md, elList);
@@ -391,9 +391,9 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
exists = reactionsHash.contains(new Pair<MiriamData, MiriamData>(md2, md1));
}
if (!exists) {
- List<Alias> listEl = map.get(md1);
+ List<Element> listEl = map.get(md1);
if (listEl != null) {
- for (Alias el : listEl) {
+ for (Element el : listEl) {
DataMining dm = new DataMining();
dm.setElement(el);
dm.setDescription(description);
@@ -505,7 +505,7 @@ public class DataMiningService extends XmlParser implements IDataMiningService {
}
@Override
- public Set<DataMining> parseData(DataMiningSet dataMiningSet, Collection<Alias> nodes, Set<Reaction> reactions, IProgressUpdater secondPartUpdater)
+ public Set<DataMining> parseData(DataMiningSet dataMiningSet, Collection<Element> nodes, Set<Reaction> reactions, IProgressUpdater secondPartUpdater)
throws InvalidDataMiningInputFile {
String name = dataMiningSet.getName();
String warningPrefix = "[Data mining, " + name + "] ";
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
index b88827ddf6..ac91c3c6f9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
@@ -19,30 +19,30 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaRegionAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.services.interfaces.IExporterService;
import lcsb.mapviewer.services.utils.data.ExportColumn;
import lcsb.mapviewer.services.utils.data.ExportFileType;
@@ -91,9 +91,9 @@ public class ExporterService implements IExporterService {
}
builder.append("\n");
for (Model model : parameters.getModels()) {
- for (Alias alias : model.getAliases()) {
- if (alias instanceof SpeciesAlias) {
- SpeciesAlias speciesAlias = (SpeciesAlias) alias;
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Species) {
+ Species speciesAlias = (Species) alias;
boolean toBeProcessed = false;
// check type
for (Class<?> type : parameters.getTypes()) {
@@ -108,12 +108,12 @@ public class ExporterService implements IExporterService {
// check where it lays
toBeProcessed = (parameters.getIncludedAliases().size() == 0);
- for (CompartmentAlias ca : parameters.getIncludedAliases()) {
+ for (Compartment ca : parameters.getIncludedAliases()) {
if (ca.cross(alias)) {
toBeProcessed = true;
}
}
- for (CompartmentAlias ca : parameters.getExcludedAliases()) {
+ for (Compartment ca : parameters.getExcludedAliases()) {
if (ca.cross(alias)) {
toBeProcessed = false;
}
@@ -148,24 +148,24 @@ public class ExporterService implements IExporterService {
* export string are generated for this alias
* @return list of strings representing exported data
*/
- protected List<String> getExportStringForOneSpecies(SpeciesAlias species, ExporterParameters parameters) {
+ protected List<String> getExportStringForOneSpecies(Species species, ExporterParameters parameters) {
if (parameters.getFileType() != ExportFileType.TAB_SEPARATED) {
throw new InvalidArgumentException("Unhandled file type: " + parameters.getFileType());
}
- List<CompartmentAlias> aliases = getComponentList(species);
+ List<Compartment> aliases = getComponentList(species);
List<String> result = new ArrayList<String>();
- CompartmentAlias smallestCompartment = getCompartment(species);
+ Compartment smallestCompartment = getCompartment(species);
List<ExportColumn> processedColumns = new ArrayList<ExportColumn>();
for (ExportColumn column : parameters.getColumns()) {
- if (column.getClazz().isAssignableFrom(SpeciesAlias.class)) {
+ if (column.getClazz().isAssignableFrom(Species.class)) {
processedColumns.add(column);
}
}
- for (CompartmentAlias compartment : aliases) {
+ for (Compartment compartment : aliases) {
String separator = "";
StringBuilder line = new StringBuilder();
for (ExportColumn column : processedColumns) {
@@ -182,11 +182,11 @@ public class ExporterService implements IExporterService {
} else if (column == ExportColumn.COMPONENT_NAME) {
line.append(compartment.getName());
} else if (column == ExportColumn.NAME) {
- if (species instanceof ComplexAlias) {
+ if (species instanceof Complex) {
if (!parameters.isComplexElementsName()) {
line.append(species.getName());
} else {
- line.append(getComplexNameWithElements((ComplexAlias) species, parameters));
+ line.append(getComplexNameWithElements((Complex) species, parameters));
}
} else {
line.append(species.getName());
@@ -232,19 +232,19 @@ public class ExporterService implements IExporterService {
}
/**
- * Returns {@link CompartmentAlias} to which element belongs to.
+ * Returns {@link Compartment} to which element belongs to.
*
* @param element
* alias of the element
- * @return {@link CompartmentAlias} to which element belongs to
+ * @return {@link Compartment} to which element belongs to
*/
- private CompartmentAlias getCompartment(SpeciesAlias element) {
- CompartmentAlias smallestAlias = null;
- List<CompartmentAlias> compartmentAliases = new ArrayList<CompartmentAlias>();
+ private Compartment getCompartment(Species element) {
+ Compartment smallestAlias = null;
+ List<Compartment> compartmentAliases = new ArrayList<Compartment>();
- for (CompartmentAlias alias : element.getModel().getCompartmentsAliases()) {
+ for (Compartment alias : element.getModel().getCompartmentsAliases()) {
if (alias.cross(element)) {
- if (!(alias instanceof ArtifitialCompartmentAlias)) {
+ if (!(alias instanceof PathwayCompartment)) {
compartmentAliases.add(alias);
}
}
@@ -253,7 +253,7 @@ public class ExporterService implements IExporterService {
if (compartmentAliases.size() > 0) {
smallestAlias = compartmentAliases.get(0);
}
- for (CompartmentAlias compartmentAlias : compartmentAliases) {
+ for (Compartment compartmentAlias : compartmentAliases) {
if (compartmentAlias.getSize() < smallestAlias.getSize()) {
smallestAlias = compartmentAlias;
}
@@ -266,14 +266,14 @@ public class ExporterService implements IExporterService {
*
* @param element
* alias of the element
- * @return list of {@link CompartmentAlias} representing pathways
+ * @return list of {@link Compartment} representing pathways
*/
- private List<CompartmentAlias> getComponentList(SpeciesAlias element) {
+ private List<Compartment> getComponentList(Species element) {
Model model = element.getModel();
- List<CompartmentAlias> aliases = new ArrayList<CompartmentAlias>();
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
- if (alias instanceof ArtifitialCompartmentAlias) {
+ List<Compartment> aliases = new ArrayList<Compartment>();
+ for (Compartment alias : model.getCompartmentsAliases()) {
+ if (alias instanceof PathwayCompartment) {
if (alias.cross(element)) {
aliases.add(alias);
}
@@ -283,7 +283,7 @@ public class ExporterService implements IExporterService {
// in case the element is outside any component then we have to crate
// artifical null component
if (aliases.size() == 0) {
- ArtifitialCompartmentAlias nullAlias = new ArtifitialCompartmentAlias();
+ PathwayCompartment nullAlias = new PathwayCompartment();
nullAlias.setName("null");
aliases.add(nullAlias);
}
@@ -303,10 +303,10 @@ public class ExporterService implements IExporterService {
* @return name of a complex with the names of all species included in this
* complex
*/
- private String getComplexNameWithElements(ComplexAlias complex, ExporterParameters parameters) {
+ private String getComplexNameWithElements(Complex complex, ExporterParameters parameters) {
StringBuilder result = new StringBuilder();
String separator = "";
- for (Alias species2 : complex.getAllSimpleChildren()) {
+ for (Element species2 : complex.getAllSimpleChildren()) {
boolean add = false;
if (parameters.getTypes().size() == 0) {
add = true;
@@ -368,7 +368,7 @@ public class ExporterService implements IExporterService {
for (Reaction reaction : model.getReactions()) {
int counter = 0;
for (ReactionNode node : reaction.getReactionNodes()) {
- Alias element = node.getAlias();
+ Element element = node.getAlias();
for (Class<?> type : parameters.getTypes()) {
if (type.isAssignableFrom(element.getClass())) {
counter++;
@@ -383,22 +383,22 @@ public class ExporterService implements IExporterService {
}
if (parameters.isMoleculeEdges()) {
for (Model model : parameters.getModels()) {
- for (Alias element : model.getAliases()) {
- if (element instanceof SpeciesAlias) {
- if (element instanceof SimpleMoleculeAlias) {
+ for (Element element : model.getAliases()) {
+ if (element instanceof Species) {
+ if (element instanceof SimpleMolecule) {
boolean ok = false;
- for (CompartmentAlias alias : parameters.getIncludedAliases()) {
+ for (Compartment alias : parameters.getIncludedAliases()) {
if (alias.cross(element)) {
ok = true;
}
}
- for (CompartmentAlias alias : parameters.getExcludedAliases()) {
+ for (Compartment alias : parameters.getExcludedAliases()) {
if (alias.cross(element)) {
ok = false;
}
}
if (ok) {
- String string = getExportSingleInteractionStringFromSpecies((SimpleMoleculeAlias) element, parameters);
+ String string = getExportSingleInteractionStringFromSpecies((SimpleMolecule) element, parameters);
if (parameters.getFileType() == ExportFileType.SIF) {
if (!uniqueLines.contains(string.replace("molecule_type", "reaction_type"))) {
uniqueLines.add(string);
@@ -436,7 +436,7 @@ public class ExporterService implements IExporterService {
* {@link ExporterParameters export parameters}
* @return string representing exported reaction
*/
- protected String getExportSingleInteractionStringFromSpecies(SimpleMoleculeAlias species, ExporterParameters parameters) {
+ protected String getExportSingleInteractionStringFromSpecies(SimpleMolecule species, ExporterParameters parameters) {
if (parameters.getFileType() != ExportFileType.SIF) {
throw new InvalidArgumentException("Unsupported file format: " + parameters.getFileType());
}
@@ -446,8 +446,8 @@ public class ExporterService implements IExporterService {
for (Reaction reaction : model.getReactions()) {
boolean goodReaction = false;
for (ReactionNode node : reaction.getReactionNodes()) {
- if (node.getAlias() instanceof SimpleMoleculeAlias) {
- Alias species2 = node.getAlias();
+ if (node.getAlias() instanceof SimpleMolecule) {
+ Element species2 = node.getAlias();
if (species.getName().equalsIgnoreCase(species2.getName())) {
goodReaction = true;
}
@@ -461,31 +461,31 @@ public class ExporterService implements IExporterService {
if (parameters.getIncludedAliases().size() == 0) {
ok = true;
}
- for (CompartmentAlias alias2 : parameters.getIncludedAliases()) {
+ for (Compartment alias2 : parameters.getIncludedAliases()) {
if (alias2.cross(node.getAlias())) {
ok = true;
break;
}
}
- for (CompartmentAlias alias2 : parameters.getExcludedAliases()) {
+ for (Compartment alias2 : parameters.getExcludedAliases()) {
if (alias2.cross(node.getAlias())) {
ok = false;
break;
}
}
if (ok) {
- Alias element = node.getAlias();
+ Element element = node.getAlias();
for (Class<?> type : parameters.getTypes()) {
if (type.isAssignableFrom(element.getClass())) {
- if (element instanceof ComplexAlias) {
+ if (element instanceof Complex) {
if (!parameters.isComplexElementsName()) {
- elements.add(((SpeciesAlias) element).getName());
+ elements.add(((Species) element).getName());
} else {
- String name = getComplexNameWithElements((ComplexAlias) element, parameters);
+ String name = getComplexNameWithElements((Complex) element, parameters);
elements.add(name);
}
} else {
- elements.add(((SpeciesAlias) element).getName());
+ elements.add(((Species) element).getName());
}
break;
}
@@ -523,26 +523,26 @@ public class ExporterService implements IExporterService {
List<String> result = new ArrayList<String>();
if (parameters.getFileType() == ExportFileType.SIF) {
StringBuilder builder = new StringBuilder();
- Set<Alias> elements = new HashSet<>();
+ Set<Element> elements = new HashSet<>();
for (ReactionNode node : reaction.getReactionNodes()) {
boolean ok = false;
if (parameters.getIncludedAliases().size() == 0) {
ok = true;
}
- for (CompartmentAlias alias2 : parameters.getIncludedAliases()) {
+ for (Compartment alias2 : parameters.getIncludedAliases()) {
if (alias2.cross(node.getAlias())) {
ok = true;
break;
}
}
- for (CompartmentAlias alias2 : parameters.getExcludedAliases()) {
+ for (Compartment alias2 : parameters.getExcludedAliases()) {
if (alias2.cross(node.getAlias())) {
ok = false;
break;
}
}
if (ok) {
- Alias element = node.getAlias();
+ Element element = node.getAlias();
if (parameters.getTypes().size() == 0) {
elements.add(element);
} else {
@@ -556,17 +556,17 @@ public class ExporterService implements IExporterService {
}
}
Set<String> elementsNames = new HashSet<>();
- for (Alias element : elements) {
- if (element instanceof ComplexAlias) {
+ for (Element element : elements) {
+ if (element instanceof Complex) {
if (!parameters.isComplexElementsName()) {
- elementsNames.add(((SpeciesAlias) element).getName());
+ elementsNames.add(((Species) element).getName());
} else {
- String name = getComplexNameWithElements((ComplexAlias) element, parameters);
+ String name = getComplexNameWithElements((Complex) element, parameters);
elementsNames.add(name);
}
} else {
- elementsNames.add(((SpeciesAlias) element).getName());
+ elementsNames.add(((Species) element).getName());
}
}
@@ -628,13 +628,13 @@ public class ExporterService implements IExporterService {
for (Reactant reactant : reaction.getReactants()) {
result.append("REACTANT");
result.append("\t");
- result.append(getExportSingleSpecies((SpeciesAlias) reactant.getAlias(), parameters));
+ result.append(getExportSingleSpecies((Species) reactant.getAlias(), parameters));
result.append("\t");
}
for (Product product : reaction.getProducts()) {
result.append("PRODUCT");
result.append("\t");
- result.append(getExportSingleSpecies((SpeciesAlias) product.getAlias(), parameters));
+ result.append(getExportSingleSpecies((Species) product.getAlias(), parameters));
result.append("\t");
}
for (Modifier modifier : reaction.getModifiers()) {
@@ -642,7 +642,7 @@ public class ExporterService implements IExporterService {
result.append("\t");
result.append("type=" + modifier.getClass().getSimpleName());
result.append("\t");
- result.append(getExportSingleSpecies((SpeciesAlias) modifier.getAlias(), parameters));
+ result.append(getExportSingleSpecies((Species) modifier.getAlias(), parameters));
result.append("\t");
}
return result.toString();
@@ -700,14 +700,14 @@ public class ExporterService implements IExporterService {
if (splitReaction) {
String base = builder.toString();
- Set<Alias> inputs = new HashSet<Alias>();
- Set<Alias> outputs = new HashSet<Alias>();
+ Set<Element> inputs = new HashSet<Element>();
+ Set<Element> outputs = new HashSet<Element>();
for (Reactant reactant : reaction.getReactants()) {
if (!isAssignable(parameters, reactant.getAlias())) {
continue;
}
- if (reactant.getAlias() instanceof ComplexAlias) {
- inputs.addAll(((ComplexAlias) (reactant.getAlias())).getAllChildrenAliases());
+ if (reactant.getAlias() instanceof Complex) {
+ inputs.addAll(((Complex) (reactant.getAlias())).getAllChildrenAliases());
} else {
inputs.add(reactant.getAlias());
}
@@ -716,8 +716,8 @@ public class ExporterService implements IExporterService {
if (!isAssignable(parameters, product.getAlias())) {
continue;
}
- if (product.getAlias() instanceof ComplexAlias) {
- outputs.addAll(((ComplexAlias) (product.getAlias())).getAllChildrenAliases());
+ if (product.getAlias() instanceof Complex) {
+ outputs.addAll(((Complex) (product.getAlias())).getAllChildrenAliases());
} else {
outputs.add(product.getAlias());
}
@@ -726,17 +726,17 @@ public class ExporterService implements IExporterService {
if (!isAssignable(parameters, modifier.getAlias())) {
continue;
}
- if (modifier.getAlias() instanceof ComplexAlias) {
- inputs.addAll(((ComplexAlias) (modifier.getAlias())).getAllChildrenAliases());
+ if (modifier.getAlias() instanceof Complex) {
+ inputs.addAll(((Complex) (modifier.getAlias())).getAllChildrenAliases());
} else {
inputs.add(modifier.getAlias());
}
}
- for (Alias input : inputs) {
+ for (Element input : inputs) {
if (!isAssignable(parameters, input)) {
continue;
}
- for (Alias output : outputs) {
+ for (Element output : outputs) {
if (!isAssignable(parameters, output)) {
continue;
}
@@ -797,7 +797,7 @@ public class ExporterService implements IExporterService {
* @return true if element can exist in export string, <code>false</code>
* otherwise
*/
- private boolean isAssignable(ExporterParameters parameters, Alias element) {
+ private boolean isAssignable(ExporterParameters parameters, Element element) {
boolean ok = false;
for (Class<?> clazz : parameters.getTypes()) {
if (clazz.isAssignableFrom(element.getClass())) {
@@ -816,7 +816,7 @@ public class ExporterService implements IExporterService {
* {@link ExporterParameters export parameters}
* @return export string representation of the element
*/
- private String getExportSingleSpecies(SpeciesAlias alias, ExporterParameters parameters) {
+ private String getExportSingleSpecies(Species alias, ExporterParameters parameters) {
if (parameters.getFileType() != ExportFileType.TAB_SEPARATED) {
throw new InvalidArgumentException("Unsupported file format: " + parameters.getFileType());
}
@@ -829,8 +829,8 @@ public class ExporterService implements IExporterService {
sb.append("initialAmount=" + alias.getInitialAmount() + "\t");
sb.append("initialConcentration=" + alias.getInitialConcentration() + "\t");
String compartment = null;
- if (alias.getParent() instanceof CompartmentAlias) {
- compartment = ((CompartmentAlias) alias.getParent()).getName();
+ if (alias.getParent() instanceof Compartment) {
+ compartment = ((Compartment) alias.getParent()).getName();
}
sb.append("compartment=" + compartment);
sb.append("\t");
@@ -845,15 +845,15 @@ public class ExporterService implements IExporterService {
sb.append("positionToCompartment=" + alias.getPositionToCompartment());
sb.append("\t");
- if (alias instanceof ProteinAlias) {
- ProteinAlias protein = (ProteinAlias) alias;
+ if (alias instanceof Protein) {
+ Protein protein = (Protein) alias;
sb.append("dimer=" + protein.getHomodimer());
sb.append("\t");
sb.append("structuralState=" + protein.getStructuralState());
sb.append("\t");
sb.append("hypothetical=" + protein.isHypothetical());
sb.append("\t");
- for (ModificationResidueAlias mr : protein.getModificationResidues()) {
+ for (ModificationResidue mr : protein.getModificationResidues()) {
sb.append("MODIFICATION RESIDUE");
sb.append("\t");
sb.append("angle=" + mr.getAngle());
@@ -872,9 +872,9 @@ public class ExporterService implements IExporterService {
sb.append("state=" + mr.getState().getFullName() + "\t");
}
}
- } else if (alias instanceof GeneAlias) {
- GeneAlias gene = (GeneAlias) alias;
- for (ModificationResidueAlias mr : gene.getModificationResidues()) {
+ } else if (alias instanceof Gene) {
+ Gene gene = (Gene) alias;
+ for (ModificationResidue mr : gene.getModificationResidues()) {
sb.append("MODIFICATION RESIDUE");
sb.append("\t");
sb.append("angle=" + mr.getAngle());
@@ -892,26 +892,26 @@ public class ExporterService implements IExporterService {
sb.append("state=" + mr.getState().getFullName() + "\t");
}
}
- } else if (alias instanceof ComplexAlias) {
- ComplexAlias complex = (ComplexAlias) alias;
+ } else if (alias instanceof Complex) {
+ Complex complex = (Complex) alias;
sb.append("dimer=" + complex.getHomodimer());
sb.append("\t");
sb.append("hypothetical=" + complex.isHypothetical());
sb.append("\t");
- } else if (alias instanceof SimpleMoleculeAlias) {
- SimpleMoleculeAlias molecule = (SimpleMoleculeAlias) alias;
+ } else if (alias instanceof SimpleMolecule) {
+ SimpleMolecule molecule = (SimpleMolecule) alias;
sb.append("dimer=" + molecule.getHomodimer());
sb.append("\t");
- } else if (alias instanceof IonAlias) {
+ } else if (alias instanceof Ion) {
sb.append("");
- } else if (alias instanceof PhenotypeAlias) {
+ } else if (alias instanceof Phenotype) {
sb.append("");
- } else if (alias instanceof DrugAlias) {
+ } else if (alias instanceof Drug) {
sb.append("");
- } else if (alias instanceof RnaAlias) {
- RnaAlias rna = (RnaAlias) alias;
- for (RnaRegionAlias region : rna.getRegions()) {
+ } else if (alias instanceof Rna) {
+ Rna rna = (Rna) alias;
+ for (RnaRegion region : rna.getRegions()) {
sb.append("RNA_REGION");
sb.append("\t");
sb.append("type=" + region.getType());
@@ -925,9 +925,9 @@ public class ExporterService implements IExporterService {
sb.append("pos=" + region.getPos());
sb.append("\t");
}
- } else if (alias instanceof AntisenseRnaAlias) {
- AntisenseRnaAlias antisenseRna = (AntisenseRnaAlias) alias;
- for (AntisenseRnaRegionAlias region : antisenseRna.getRegions()) {
+ } else if (alias instanceof AntisenseRna) {
+ AntisenseRna antisenseRna = (AntisenseRna) alias;
+ for (AntisenseRnaRegion region : antisenseRna.getRegions()) {
sb.append("RNA_REGION" + "\t");
if (region.getType() != null) {
sb.append("type=" + region.getType().getName() + "\t");
@@ -936,9 +936,9 @@ public class ExporterService implements IExporterService {
sb.append("size=" + region.getSize() + "\t");
sb.append("pos=" + region.getPos() + "\t");
}
- } else if (alias instanceof UnknownAlias) {
+ } else if (alias instanceof Unknown) {
sb.append("");
- } else if (alias instanceof DegradedAlias) {
+ } else if (alias instanceof Degraded) {
sb.append("");
} else {
throw new InvalidArgumentException("Invalid class type: " + alias.getClass());
@@ -975,16 +975,16 @@ public class ExporterService implements IExporterService {
Set<String> uniqeLines = new HashSet<>();
StringBuilder builder = new StringBuilder();
for (Model model : parameters.getModels()) {
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
// check where it lays
boolean toBeProcessed = (parameters.getIncludedAliases().size() == 0);
- for (CompartmentAlias ca : parameters.getIncludedAliases()) {
+ for (Compartment ca : parameters.getIncludedAliases()) {
if (ca.cross(alias)) {
toBeProcessed = true;
}
}
- for (CompartmentAlias ca : parameters.getExcludedAliases()) {
+ for (Compartment ca : parameters.getExcludedAliases()) {
if (ca.cross(alias)) {
toBeProcessed = false;
}
@@ -1016,7 +1016,7 @@ public class ExporterService implements IExporterService {
* parameters used in export
* @return string srepresenting compartment in export format
*/
- private List<String> getExportStringForOneCompartment(CompartmentAlias compartment, ExporterParameters parameters) {
+ private List<String> getExportStringForOneCompartment(Compartment compartment, ExporterParameters parameters) {
List<String> result = new ArrayList<String>();
if (parameters.getFileType() != ExportFileType.TAB_SEPARATED) {
throw new InvalidArgumentException("Unhandled file type: " + parameters.getFileType());
@@ -1048,7 +1048,7 @@ public class ExporterService implements IExporterService {
* alis for which identifier will be returned
* @return identifier that should be used for a given alias
*/
- private String getId(Alias alias) {
+ private String getId(Element alias) {
return alias.getAliasId();
}
@@ -1066,7 +1066,7 @@ public class ExporterService implements IExporterService {
models.addAll(model.getSubmodels());
Set<MiriamData> miriamDatas = new HashSet<>();
for (Model m : models) {
- for (Alias element : m.getAliases()) {
+ for (Element element : m.getAliases()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.PUBMED.equals(md.getDataType())) {
miriamDatas.add(md);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 7727c2cc35..599b71bcf3 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -40,10 +40,10 @@ import lcsb.mapviewer.model.map.layout.GenericColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.LayoutStatus;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
@@ -756,7 +756,7 @@ public class LayoutService implements ILayoutService {
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.TYPE)) {
- for (Class<? extends Alias> str : schema.getTypes()) {
+ for (Class<? extends Element> str : schema.getTypes()) {
sb.append(str.getSimpleName() + ", ");
}
sb.append("\t");
@@ -812,7 +812,7 @@ public class LayoutService implements ILayoutService {
}
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.TYPE)) {
- for (Class<? extends Alias> str : schema.getTypes()) {
+ for (Class<? extends Element> str : schema.getTypes()) {
sb.append(str.getSimpleName() + ", ");
}
sb.append("\t");
@@ -892,8 +892,8 @@ public class LayoutService implements ILayoutService {
LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
List<LightLayoutAliasView> result = new ArrayList<>();
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Alias) {
- result.add(factory.create(new Pair<Alias, ColorSchema>((Alias) entry.getKey(), entry.getValue())));
+ if (entry.getKey() instanceof Element) {
+ result.add(factory.create(new Pair<Element, ColorSchema>((Element) entry.getKey(), entry.getValue())));
}
}
return result;
@@ -958,10 +958,10 @@ public class LayoutService implements ILayoutService {
// TODO poor performance, improve it
for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Alias) {
- Alias alias = (Alias) entry.getKey();
+ if (entry.getKey() instanceof Element) {
+ Element alias = (Element) entry.getKey();
if (ids.contains(alias.getId())) {
- result.add(factory.create(new Pair<Alias, ColorSchema>(alias, entry.getValue())));
+ result.add(factory.create(new Pair<Element, ColorSchema>(alias, entry.getValue())));
}
}
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index e465adb7c5..4752653eec 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -26,11 +26,11 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ILayoutService;
@@ -180,7 +180,7 @@ public class ModelService implements IModelService {
if (model != null) {
Set<Integer> pubmedIds = new HashSet<>();
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.PUBMED.equals(md.getDataType())) {
try {
@@ -344,7 +344,7 @@ public class ModelService implements IModelService {
if (model != null) {
Set<MiriamData> pubmedIds = new HashSet<MiriamData>();
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
pubmedIds.addAll(element.getMiriamData());
}
for (Reaction reaction : model.getReactions()) {
@@ -409,7 +409,7 @@ public class ModelService implements IModelService {
}
/**
- * Returns list of {@link Alias aliases} for given identifiers.
+ * Returns list of {@link Element aliases} for given identifiers.
*
* @param model
* model where aliases are located
@@ -417,11 +417,11 @@ public class ModelService implements IModelService {
* list of alias identifiers in a given submodel. Every {@link Pair}
* contains information about {@link Model#getId() model identifier}
* (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias#getId() alias
+ * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
* identifier} (in {@link Pair#right}).
- * @return list of {@link Alias aliases} for given identifiers
+ * @return list of {@link Element aliases} for given identifiers
*/
- private List<Alias> getAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+ private List<Element> getAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
for (Pair<Integer, Integer> pair : identifiers) {
Set<Integer> set = identifiersForMap.get(pair.getLeft());
@@ -432,14 +432,14 @@ public class ModelService implements IModelService {
set.add(pair.getRight());
}
- List<Alias> result = new ArrayList<>();
+ List<Element> result = new ArrayList<>();
List<Model> models = new ArrayList<>();
models.add(model);
models.addAll(model.getSubmodels());
for (Model model2 : models) {
Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
if (set != null) {
- for (Alias alias : model2.getAliases()) {
+ for (Element alias : model2.getAliases()) {
if (set.contains(alias.getId())) {
result.add(alias);
set.remove(alias.getId());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index f1fe2a0658..2668362530 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -65,11 +65,11 @@ import lcsb.mapviewer.model.map.graph.DataMining;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.LayoutStatus;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
@@ -783,7 +783,7 @@ public class ProjectService implements IProjectService {
EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
try {
Logger.getRootLogger().addAppender(appender);
- Set<Alias> nodes = new HashSet<>();
+ Set<Element> nodes = new HashSet<>();
nodes.addAll(model.getAliases());
for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
nodes.addAll(connection.getSubmodel().getAliases());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index 4a9dc04c4a..e9e5789c5e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -21,24 +21,24 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SearchIndex;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
@@ -111,34 +111,34 @@ public class SearchService implements ISearchService {
/**
* This object maps class of elements on the map into short string prefixes
- * used in the search query. For instance elements of the {@link ComplexAlias}
+ * used in the search query. For instance elements of the {@link Complex}
* class could be searched with the prefix "complex" (example query:
* "complex:alpha subcomplex").
*/
- private Map<Class<? extends Alias>, String> speciesSearchPrefix = new HashMap<>();
+ private Map<Class<? extends Element>, String> speciesSearchPrefix = new HashMap<>();
/**
* This object maps short string prefixes into class of elements on the map
* that will be searched. For instance prefix "complex" might refer to
- * {@link ComplexAlias} class and and example query would look like:
+ * {@link Complex} class and and example query would look like:
* "complex:alpha subcomplex".
*/
- private Map<String, Class<? extends Alias>> speciesSearchReversePrefix = new HashMap<>();
+ private Map<String, Class<? extends Element>> speciesSearchReversePrefix = new HashMap<>();
/**
* Default constructor that set list of prefixes used in the search queries.
*/
public SearchService() {
- addSearchPrefix("complex", ComplexAlias.class);
- addSearchPrefix("degrded", DegradedAlias.class);
- addSearchPrefix("drug", DrugAlias.class);
- addSearchPrefix("gene", GeneAlias.class);
- addSearchPrefix("ion", IonAlias.class);
- addSearchPrefix("phenotype", PhenotypeAlias.class);
- addSearchPrefix("protein", ProteinAlias.class);
- addSearchPrefix("rna", RnaAlias.class);
- addSearchPrefix("molecule", SimpleMoleculeAlias.class);
- addSearchPrefix("unknown", UnknownAlias.class);
+ addSearchPrefix("complex", Complex.class);
+ addSearchPrefix("degrded", Degraded.class);
+ addSearchPrefix("drug", Drug.class);
+ addSearchPrefix("gene", Gene.class);
+ addSearchPrefix("ion", Ion.class);
+ addSearchPrefix("phenotype", Phenotype.class);
+ addSearchPrefix("protein", Protein.class);
+ addSearchPrefix("rna", Rna.class);
+ addSearchPrefix("molecule", SimpleMolecule.class);
+ addSearchPrefix("unknown", Unknown.class);
}
/**
@@ -149,7 +149,7 @@ public class SearchService implements ISearchService {
* @param clazz
* class for which this prefix stands
*/
- private void addSearchPrefix(String prefix, Class<? extends Alias> clazz) {
+ private void addSearchPrefix(String prefix, Class<? extends Element> clazz) {
speciesSearchPrefix.put(clazz, prefix);
speciesSearchReversePrefix.put(prefix, clazz);
}
@@ -231,17 +231,17 @@ public class SearchService implements ISearchService {
* class type of the elements that limits the results
* @return list of object found for the query string sorted by the score value
*/
- protected List<IHeavyView> searchByIndexedQuery(Model model, String query, int limit, Boolean perfectMatch, Class<? extends Alias> type) {
+ protected List<IHeavyView> searchByIndexedQuery(Model model, String query, int limit, Boolean perfectMatch, Class<? extends Element> type) {
List<IHeavyView> result = new ArrayList<>();
if (query.startsWith(REACTION_SEARCH_PREFIX)) {
return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
} else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
result.add(fullAliasViewFactory.create(model.getAliasByAliasId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""))));
} else {
- Set<Alias> aliases = model.getAliases();
+ Set<Element> aliases = model.getAliases();
List<SearchResult> sortedResults = new ArrayList<SearchService.SearchResult>();
- for (Alias alias : aliases) {
+ for (Element alias : aliases) {
if (type.isAssignableFrom(alias.getClass())) {
List<SearchIndex> indexes = alias.getSearchIndexes();
if (indexes.size() == 0) {
@@ -258,7 +258,7 @@ public class SearchService implements ISearchService {
sortedResults.add(sResult);
break;
}
- } else if (score > 0 || (query.equals("") && type != Alias.class)) {
+ } else if (score > 0 || (query.equals("") && type != Element.class)) {
SearchResult sResult = new SearchResult();
sResult.setObj(alias);
sResult.setScore(score);
@@ -279,8 +279,8 @@ public class SearchService implements ISearchService {
for (SearchResult searchResult : sortedResults) {
if (searchResult.getObj() instanceof Reaction) {
result.add(fullReactionViewFactory.create((Reaction) searchResult.getObj()));
- } else if (searchResult.getObj() instanceof Alias) {
- result.add(fullAliasViewFactory.create((Alias) searchResult.getObj()));
+ } else if (searchResult.getObj() instanceof Element) {
+ result.add(fullAliasViewFactory.create((Element) searchResult.getObj()));
} else {
throw new InvalidStateException("Unknown class type: " + searchResult.getObj().getClass());
}
@@ -336,10 +336,10 @@ public class SearchService implements ISearchService {
List<Object> results = new ArrayList<Object>();
- Set<Alias> aliases = params.getModel().getAliases();
+ Set<Element> aliases = params.getModel().getAliases();
Point2D point = new Point2D.Double(params.getX(), params.getY());
- for (Alias alias : aliases) {
- if (alias instanceof SpeciesAlias) {
+ for (Element alias : aliases) {
+ if (alias instanceof Species) {
if (alias.contains(point)) {
if (isVisible(alias, params)) {
results.add(alias);
@@ -364,8 +364,8 @@ public class SearchService implements ISearchService {
result.addAll(reactionToResultList(r));
return result;
} else if (nested) {
- for (Alias alias : aliases) {
- if (alias instanceof CompartmentAlias) {
+ for (Element alias : aliases) {
+ if (alias instanceof Compartment) {
if (alias.contains(point)) {
if (isVisible(alias, params)) {
results.add(alias);
@@ -377,10 +377,10 @@ public class SearchService implements ISearchService {
}
if (results.size() > 1) {
- Alias alias = (Alias) results.get(0);
+ Element alias = (Element) results.get(0);
for (Object obj : results) {
- if (((Alias) (obj)).getSize() < alias.getSize()) {
- alias = (Alias) obj;
+ if (((Element) (obj)).getSize() < alias.getSize()) {
+ alias = (Element) obj;
}
}
results.clear();
@@ -390,8 +390,8 @@ public class SearchService implements ISearchService {
return result;
} else {
Object obj = results.get(0);
- if (obj instanceof Alias) {
- result.add(fullAliasViewFactory.create((Alias) obj));
+ if (obj instanceof Element) {
+ result.add(fullAliasViewFactory.create((Element) obj));
return result;
} else if (obj instanceof Reaction) {
result.addAll(reactionToResultList((Reaction) obj));
@@ -442,7 +442,7 @@ public class SearchService implements ISearchService {
* @return <code>true</code> if alias is visible for the user,
* <code>false</code> otherwise
*/
- private boolean isVisible(Alias alias, CoordinatesSearchParams params) {
+ private boolean isVisible(Element alias, CoordinatesSearchParams params) {
if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
return true;
}
@@ -462,7 +462,7 @@ public class SearchService implements ISearchService {
result.addAll(searchByMiriam(model, mt, limit));
} else {
String indexQuery = searchIndexer.getQueryStringForIndex(query, speciesSearchReversePrefix.keySet());
- Class<? extends Alias> type = searchIndexer.getTypeForQuery(query, speciesSearchReversePrefix);
+ Class<? extends Element> type = searchIndexer.getTypeForQuery(query, speciesSearchReversePrefix);
List<IHeavyView> partResult = searchByIndexedQuery(model, indexQuery, limit, perfectMatch, type);
@@ -498,8 +498,8 @@ public class SearchService implements ISearchService {
if (result.size() >= limit) {
break;
}
- if (obj instanceof Alias) {
- result.add(fullAliasViewFactory.create((Alias) obj));
+ if (obj instanceof Element) {
+ result.add(fullAliasViewFactory.create((Element) obj));
} else if (obj instanceof Reaction) {
result.addAll(reactionToResultList((Reaction) obj));
} else {
@@ -537,8 +537,8 @@ public class SearchService implements ISearchService {
for (Reaction reaction : model.getReactions()) {
tmpList.add(new DistanceToObject(reaction, point));
}
- for (Alias alias : model.getAliases()) {
- if (alias instanceof SpeciesAlias) {
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Species) {
tmpList.add(new DistanceToObject(alias, point));
}
}
@@ -589,7 +589,7 @@ public class SearchService implements ISearchService {
* @param point
* point from which the distance will be computed
*/
- DistanceToObject(Alias alias, Point2D point) {
+ DistanceToObject(Element alias, Point2D point) {
reference = alias;
distance = alias.getDistanceFromPoint(point);
@@ -660,14 +660,14 @@ public class SearchService implements ISearchService {
Map<String, List<String>> result = new HashMap<String, List<String>>();
Set<String> possibilities = new HashSet<String>();
- for (Alias alias : model.getAliases()) {
- if (alias instanceof SpeciesAlias) {
+ for (Element alias : model.getAliases()) {
+ if (alias instanceof Species) {
possibilities.addAll(getSearchPossibilitiesForAlias(alias));
}
}
for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- for (Alias alias : connection.getSubmodel().getModel().getAliases()) {
- if (alias instanceof SpeciesAlias) {
+ for (Element alias : connection.getSubmodel().getModel().getAliases()) {
+ if (alias instanceof Species) {
possibilities.addAll(getSearchPossibilitiesForAlias(alias));
}
}
@@ -715,7 +715,7 @@ public class SearchService implements ISearchService {
* object for which we look for a list of searchable strings
* @return the list of all human readable search possibilities for alias
*/
- private List<String> getSearchPossibilitiesForAlias(Alias element) {
+ private List<String> getSearchPossibilitiesForAlias(Element element) {
List<String> result = new ArrayList<String>();
result.add(element.getName().trim().toLowerCase().replace(",", ""));
for (String string : element.getSynonyms()) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataMiningService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataMiningService.java
index f0d7434918..231f5c6c88 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataMiningService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataMiningService.java
@@ -8,10 +8,10 @@ import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.model.map.graph.DataMining;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.graph.DataMiningType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.utils.InvalidDataMiningInputFile;
import lcsb.mapviewer.services.view.DataMiningSetView;
@@ -30,7 +30,7 @@ public interface IDataMiningService {
* alias to be investigated
* @return set of suggested connections
*/
- Collection<DataMining> getMissingConnections(Alias alias);
+ Collection<DataMining> getMissingConnections(Element alias);
/**
* Adds new suggested connection.
@@ -69,7 +69,7 @@ public interface IDataMiningService {
* model from which suggested connections should taken
* @return set of elements that has suggested connection to a geneName.
*/
- Collection<Alias> getSpeciesWithMissingConnectionsByGeneName(Model model, String geneName);
+ Collection<Element> getSpeciesWithMissingConnectionsByGeneName(Model model, String geneName);
/**
* Removes all suggested connections for model.
@@ -107,7 +107,7 @@ public interface IDataMiningService {
* @throws InvalidDataMiningInputFile
* thrown when the input file is invalid
*/
- Set<DataMining> parseData(String filename, DataMiningType type, Collection<Alias> nodes, Set<Reaction> reactions, IProgressUpdater updater)
+ Set<DataMining> parseData(String filename, DataMiningType type, Collection<Element> nodes, Set<Reaction> reactions, IProgressUpdater updater)
throws IOException, InvalidDataMiningInputFile;
/**
@@ -126,7 +126,7 @@ public interface IDataMiningService {
* @throws InvalidDataMiningInputFile
* thrown when the input file is invalid
*/
- Set<DataMining> parseData(DataMiningSet dataMiningSet, Collection<Alias> nodes, Set<Reaction> reactions, IProgressUpdater updater)
+ Set<DataMining> parseData(DataMiningSet dataMiningSet, Collection<Element> nodes, Set<Reaction> reactions, IProgressUpdater updater)
throws InvalidDataMiningInputFile;
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
index 0a33f3f3cb..83af2d42fc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExporterService.java
@@ -8,7 +8,7 @@ import java.util.List;
import java.util.Set;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.utils.data.ExportColumn;
import lcsb.mapviewer.services.utils.data.ExportFileType;
@@ -66,12 +66,12 @@ public interface IExporterService {
* List of compartment aliases that should be included in export (empty list
* means that everything should be included).
*/
- private Set<CompartmentAlias> includedAliases = new HashSet<CompartmentAlias>();
+ private Set<Compartment> includedAliases = new HashSet<Compartment>();
/**
* List of compartment aliases that should be excluded in export (empty list
* means that anything should be excluded).
*/
- private Set<CompartmentAlias> excludedAliases = new HashSet<CompartmentAlias>();
+ private Set<Compartment> excludedAliases = new HashSet<Compartment>();
/**
* If false default complex name will be used for exporting complexes. If
* true then the name will be a concatenated string of all complex
@@ -122,7 +122,7 @@ public interface IExporterService {
for (Model modelElement : models) {
includedAliases.clear();
for (String string : included) {
- for (CompartmentAlias alias : modelElement.getCompartmentsAliases()) {
+ for (Compartment alias : modelElement.getCompartmentsAliases()) {
if (alias.getName().equalsIgnoreCase(string)) {
includedAliases.add(alias);
}
@@ -131,7 +131,7 @@ public interface IExporterService {
excludedAliases.clear();
for (String string : excluded) {
- for (CompartmentAlias alias : modelElement.getCompartmentsAliases()) {
+ for (Compartment alias : modelElement.getCompartmentsAliases()) {
if (alias.getName().equalsIgnoreCase(string)) {
excludedAliases.add(alias);
}
@@ -153,7 +153,7 @@ public interface IExporterService {
if (models.size() > 0) {
for (Model model : models) {
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
if (alias.getName().equalsIgnoreCase(included)) {
includedAliases.add(alias);
}
@@ -189,7 +189,7 @@ public interface IExporterService {
if (models.size() > 0) {
for (Model model : models) {
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
if (alias.getName().equalsIgnoreCase(excluded)) {
excludedAliases.add(alias);
}
@@ -206,7 +206,7 @@ public interface IExporterService {
* new element in {@link #excluded}
* @return object with all parameters set
*/
- public ExporterParameters excluded(CompartmentAlias excluded) {
+ public ExporterParameters excluded(Compartment excluded) {
this.excluded.add(excluded.getName());
excludedAliases.add(excluded);
@@ -234,8 +234,8 @@ public interface IExporterService {
* list of elements to add to {@link #excluded}
* @return object with all parameters set
*/
- public ExporterParameters excluded(Collection<CompartmentAlias> excluded) {
- for (CompartmentAlias string : excluded) {
+ public ExporterParameters excluded(Collection<Compartment> excluded) {
+ for (Compartment string : excluded) {
excluded(string);
}
return this;
@@ -451,7 +451,7 @@ public interface IExporterService {
* @return the includedAliases
* @see #includedAliases
*/
- public Set<CompartmentAlias> getIncludedAliases() {
+ public Set<Compartment> getIncludedAliases() {
return includedAliases;
}
@@ -459,7 +459,7 @@ public interface IExporterService {
* @return the excludedAliases
* @see #excludedAliases
*/
- public Set<CompartmentAlias> getExcludedAliases() {
+ public Set<Compartment> getExcludedAliases() {
return excludedAliases;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
index 3ac6a7c631..98a3696f4e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -457,7 +457,7 @@ public interface ILayoutService {
List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId);
/**
- * Returns mapping between {@link lcsb.mapviewer.model.map.layout.alias.Alias
+ * Returns mapping between {@link lcsb.mapviewer.model.map.species.Element
* Alias}/ {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} and
* {@link ColorSchema} used for coloring object in the layout given in the
* parameter.
@@ -484,7 +484,7 @@ public interface ILayoutService {
* list of alias identifiers in a given submodel. Every {@link Pair}
* contains information about {@link Model#getId() model identifier}
* (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias#getId() alias
+ * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
* identifier} (in {@link Pair#right}).
* @return a list of {@link LightLayoutAliasView aliases} that are visualized
* in a {@link lcsb.mapviewer.model.map.layout.Layout}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
index b5ed240210..6dd73441b5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
@@ -1,145 +1,145 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.search.data.FullAliasView;
-import lcsb.mapviewer.services.search.data.LightAliasView;
-import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.view.ModelView;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * Service that manages models (maps).
- *
- * @author Piotr Gawron
- *
- */
-public interface IModelService {
-
- /**
- * Returns the newest model for the project identified by the
- * {@link lcsb.mapviewer.model.Project#projectId project identifier}.
- *
- * @param projectId
- * {@link lcsb.mapviewer.model.Project#projectId project identifier}
- * @return the newest model for the project
- */
- Model getLastModelByProjectId(String projectId);
-
- /**
- * Caches information about all pubmed articles for the given model.
- *
- * @param model
- * model in which we are caching the data
- * @param updater
- * callback interface that update progress information
- */
- void cacheAllPubmedIds(Model model, IProgressUpdater updater);
-
- /**
- * Updates information in the model with the one taken from selectedProject.
- *
- * @param model
- * model to update
- * @param selectedProject
- * source of data that should be used in the update
- */
- void updateModel(ModelData model, ProjectView selectedProject);
-
- /**
- * Removes model from application cache.
- *
- * @param model
- * model to remove
- */
- void removeModelFromCache(Model model);
-
- /**
- * Caches information about all miriam resources in the model.
- *
- * @param model
- * model in which we are caching the data
- * @param updater
- * callback interface that update progress information
- */
- void cacheAllMiriamLinks(Model model, IProgressUpdater updater);
-
- /**
- * Returns {@link ModelView} for the given model.
- *
- * @param model
- * model fgor which view is returned.
- * @param user
- * user for which custom layouts should be added
- * @return {@link ModelView} for the given {@link Model}
- */
- ModelView getModelView(Model model, User user);
-
- /**
- * Removes model from application cache.
- *
- * @param model
- * model to remove
- */
- void removeModelFromCache(ModelData model);
-
- /**
- * Removes model from application cache.
- *
- * @param projectId
- * identifier of the project
- */
- void removeModelFromCacheByProjectId(String projectId);
-
- /**
- * Returns list of {@link LightAliasView aliases} for given identifiers.
- *
- * @param model
- * model where aliases are located
- * @param identifiers
- * list of alias identifiers in a given submodel. Every {@link Pair}
- * contains information about {@link Model#getId() model identifier}
- * (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias#getId() alias
- * identifier} (in {@link Pair#right}).
- * @return list of {@link LightAliasView aliases} for given identifiers
- */
- List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers);
-
- /**
- * Returns list of {@link LightReactionView reactions} for given identifiers.
- *
- * @param model
- * model where aliases are located
- * @param identifiers
- * list of reaction identifiers in a given submodel. Every
- * {@link Pair} contains information about {@link Model#getId() model
- * identifier} (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.reaction.Reaction#getId() reaction
- * identifier} (in {@link Pair#right}).
- * @return list of {@link LightReactionView reactions} for given identifiers
- */
- List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers);
-
- /**
- * Returns list of {@link FullAliasView aliases} (with full information) for
- * given identifiers.
- *
- * @param model
- * model where aliases are located
- * @param identifiers
- * list of alias identifiers in a given submodel. Every {@link Pair}
- * contains information about {@link Model#getId() model identifier}
- * (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias#getId() alias
- * identifier} (in {@link Pair#right}).
- * @return list of {@link FullAliasView aliases} (with full information about
- * aliases) for given identifiers
- */
- List<FullAliasView> getFullAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers);
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.List;
+
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.search.data.FullAliasView;
+import lcsb.mapviewer.services.search.data.LightAliasView;
+import lcsb.mapviewer.services.search.data.LightReactionView;
+import lcsb.mapviewer.services.view.ModelView;
+import lcsb.mapviewer.services.view.ProjectView;
+
+/**
+ * Service that manages models (maps).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IModelService {
+
+ /**
+ * Returns the newest model for the project identified by the
+ * {@link lcsb.mapviewer.model.Project#projectId project identifier}.
+ *
+ * @param projectId
+ * {@link lcsb.mapviewer.model.Project#projectId project identifier}
+ * @return the newest model for the project
+ */
+ Model getLastModelByProjectId(String projectId);
+
+ /**
+ * Caches information about all pubmed articles for the given model.
+ *
+ * @param model
+ * model in which we are caching the data
+ * @param updater
+ * callback interface that update progress information
+ */
+ void cacheAllPubmedIds(Model model, IProgressUpdater updater);
+
+ /**
+ * Updates information in the model with the one taken from selectedProject.
+ *
+ * @param model
+ * model to update
+ * @param selectedProject
+ * source of data that should be used in the update
+ */
+ void updateModel(ModelData model, ProjectView selectedProject);
+
+ /**
+ * Removes model from application cache.
+ *
+ * @param model
+ * model to remove
+ */
+ void removeModelFromCache(Model model);
+
+ /**
+ * Caches information about all miriam resources in the model.
+ *
+ * @param model
+ * model in which we are caching the data
+ * @param updater
+ * callback interface that update progress information
+ */
+ void cacheAllMiriamLinks(Model model, IProgressUpdater updater);
+
+ /**
+ * Returns {@link ModelView} for the given model.
+ *
+ * @param model
+ * model fgor which view is returned.
+ * @param user
+ * user for which custom layouts should be added
+ * @return {@link ModelView} for the given {@link Model}
+ */
+ ModelView getModelView(Model model, User user);
+
+ /**
+ * Removes model from application cache.
+ *
+ * @param model
+ * model to remove
+ */
+ void removeModelFromCache(ModelData model);
+
+ /**
+ * Removes model from application cache.
+ *
+ * @param projectId
+ * identifier of the project
+ */
+ void removeModelFromCacheByProjectId(String projectId);
+
+ /**
+ * Returns list of {@link LightAliasView aliases} for given identifiers.
+ *
+ * @param model
+ * model where aliases are located
+ * @param identifiers
+ * list of alias identifiers in a given submodel. Every {@link Pair}
+ * contains information about {@link Model#getId() model identifier}
+ * (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
+ * identifier} (in {@link Pair#right}).
+ * @return list of {@link LightAliasView aliases} for given identifiers
+ */
+ List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers);
+
+ /**
+ * Returns list of {@link LightReactionView reactions} for given identifiers.
+ *
+ * @param model
+ * model where aliases are located
+ * @param identifiers
+ * list of reaction identifiers in a given submodel. Every
+ * {@link Pair} contains information about {@link Model#getId() model
+ * identifier} (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.reaction.Reaction#getId() reaction
+ * identifier} (in {@link Pair#right}).
+ * @return list of {@link LightReactionView reactions} for given identifiers
+ */
+ List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers);
+
+ /**
+ * Returns list of {@link FullAliasView aliases} (with full information) for
+ * given identifiers.
+ *
+ * @param model
+ * model where aliases are located
+ * @param identifiers
+ * list of alias identifiers in a given submodel. Every {@link Pair}
+ * contains information about {@link Model#getId() model identifier}
+ * (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
+ * identifier} (in {@link Pair#right}).
+ * @return list of {@link FullAliasView aliases} (with full information about
+ * aliases) for given identifiers
+ */
+ List<FullAliasView> getFullAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers);
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
index 5597b0a318..080f82df06 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -14,13 +14,13 @@ import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.GeneRow;
@@ -87,7 +87,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
return null;
} else if (ElementIdentifierType.ALIAS.getJsName().equalsIgnoreCase(element.getType())) {
Model m = model.getSubmodelById(element.getModelId());
- Alias alias = m.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ Element alias = m.getAliasByDbId(Integer.valueOf(element.getObjectId()));
if (alias == null) {
logger.warn("Alias with object id = " + element.getObjectId() + " is unknown.");
return null;
@@ -117,11 +117,11 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
* @param target
* drug target to check
* @param element
- * {@link Alias} to check
+ * {@link Element} to check
* @return <code>true</code> if drug target can target element,
* <code>false</code> otherwise
*/
- protected boolean elementMatch(TargetView target, Alias element) {
+ protected boolean elementMatch(TargetView target, Element element) {
if (target.getType().equals(TargetType.COMPLEX_PROTEIN.getCommonName())) {
MiriamData targetAnnotation = annotationViewFactory.viewToObject(target.getAnnotation());
if (MiriamType.CHEMBL_TARGET.equals(targetAnnotation.getDataType())) {
@@ -134,14 +134,14 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
ids.add(row.getAnnotation().getName());
}
- if (element instanceof ComplexAlias) {
- ComplexAlias complex = (ComplexAlias) element;
- Set<SpeciesAlias> speciesSet = complex.getAllSimpleChildren();
+ if (element instanceof Complex) {
+ Complex complex = (Complex) element;
+ Set<Species> speciesSet = complex.getAllSimpleChildren();
if (speciesSet.size() != ids.size()) {
return false;
}
- for (Alias id : speciesSet) {
+ for (Element id : speciesSet) {
if (!ids.contains(id.getName())) {
return false;
}
@@ -161,7 +161,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
if (targetAnnotation != null && element.getMiriamData().contains(targetAnnotation)) {
return true;
}
- if (element instanceof ProteinAlias || element instanceof RnaAlias || element instanceof GeneAlias) {
+ if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
if (target.getProteins().size() > 0) {
String hgncId = target.getProteins().get(0).getAnnotation().getName();
if (element.getName().equalsIgnoreCase(hgncId)) {
@@ -171,7 +171,7 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
}
return false;
} else if (target.getType().equals(TargetType.PROTEIN_FAMILY.getCommonName())) {
- if (element instanceof ProteinAlias || element instanceof RnaAlias || element instanceof GeneAlias) {
+ if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
String hgncId = target.getProteins().get(0).getAnnotation().getName();
if (element.getName().equalsIgnoreCase(hgncId)) {
return true;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/comment/FullCommentViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/comment/FullCommentViewFactory.java
index 8a5d4112be..928f736018 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/comment/FullCommentViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/comment/FullCommentViewFactory.java
@@ -11,9 +11,9 @@ import com.google.gson.Gson;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.overlay.IconManager;
import lcsb.mapviewer.services.search.SearchResultFactory;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
@@ -44,7 +44,7 @@ public class FullCommentViewFactory extends SearchResultFactory<List<Comment>, F
if (comment.getTableName().getName().contains("Reaction")) {
type = Reaction.class;
} else {
- type = Alias.class;
+ type = Element.class;
}
} else {
point.setLocation(comment.getCoordinates().getX(), comment.getCoordinates().getY());
@@ -71,7 +71,7 @@ public class FullCommentViewFactory extends SearchResultFactory<List<Comment>, F
if (Reaction.class.equals(comment.getType())) {
result
.add(new ElementIdentifier(comment.getIdObject(), comment.getModelId(), ElementIdentifierType.REACTION, IconManager.getInstance().getCommentIcon()));
- } else if (Alias.class.equals(comment.getType())) {
+ } else if (Element.class.equals(comment.getType())) {
result.add(new ElementIdentifier(comment.getIdObject(), comment.getModelId(), ElementIdentifierType.ALIAS, IconManager.getInstance().getCommentIcon()));
} else if (Point2D.class.equals(comment.getType())) {
result.add(new ElementIdentifier(comment.getIdObject(), comment.getModelId(), ElementIdentifierType.POINT, IconManager.getInstance().getCommentIcon()));
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/ElementIdentifier.java b/service/src/main/java/lcsb/mapviewer/services/search/data/ElementIdentifier.java
index 84ba728014..50cdc872bb 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/ElementIdentifier.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/ElementIdentifier.java
@@ -4,7 +4,7 @@ import java.io.Serializable;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Light class identifing element to visualize on map in a browser.
@@ -144,14 +144,14 @@ public class ElementIdentifier implements Serializable {
}
/**
- * Constructor creating object from {@link Alias}.
+ * Constructor creating object from {@link Element}.
*
* @param speciesAlias
- * {@link Alias} from which {@link ElementIdentifier} is created
+ * {@link Element} from which {@link ElementIdentifier} is created
* @param icon
* {@link #icon}
*/
- public ElementIdentifier(Alias speciesAlias, String icon) {
+ public ElementIdentifier(Element speciesAlias, String icon) {
this(speciesAlias.getId(), speciesAlias.getModel().getId(), ElementIdentifierType.ALIAS, icon);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
index 6c7cc8c1b9..05818c2851 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
@@ -8,8 +8,8 @@ import java.util.Map;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.search.IHeavyView;
import lcsb.mapviewer.services.view.AnnotationView;
@@ -94,113 +94,113 @@ public class FullAliasView extends LightAliasView implements IHeavyView {
/**
* Description.
*
- * @see Alias#notes
+ * @see Element#notes
*/
private String notes;
/**
* Type of the alias.
*
- * @see Alias#getStringType()
+ * @see Element#getStringType()
*/
private String type;
/**
* Symbol of the element.
*
- * @see Alias#symbol
+ * @see Element#symbol
*/
private String symbol;
/**
* Full name of the element.
*
- * @see Alias#fullName
+ * @see Element#fullName
*/
private String fullName;
/**
* Abbreviation of the element.
*
- * @see Alias#abbreviation
+ * @see Element#abbreviation
*/
private String abbreviation;
/**
* Formula describing the element.
*
- * @see Alias#formula
+ * @see Element#formula
*/
private String formula;
/**
* Charge of the element.
*
- * @see SpeciesAlias#charge
+ * @see Species#charge
*/
private Integer charge;
/**
* Initial amount of species.
*
- * @see SpeciesAlias#initialAmount
+ * @see Species#initialAmount
*/
private Integer initialAmount = null;
/**
* Initial concentration of species.
*
- * @see SpeciesAlias#initialConcentration
+ * @see Species#initialConcentration
*/
private Integer initialConcentration = null;
/**
* Is only substance units allowed in a species.
*
- * @see SpeciesAlias#onlySubstanceUnits
+ * @see Species#onlySubstanceUnits
*/
private Boolean onlySubstanceUnits = null;
/**
* Name of the element.
*
- * @see Alias#name
+ * @see Element#name
*/
private String name = "";
/**
- * Name of the {@link Alias#model}.
+ * Name of the {@link Element#model}.
*/
private String modelName;
/**
- * Name of the {@link Alias#submodel}.
+ * Name of the {@link Element#submodel}.
*/
private String submodelName;
/**
- * Id of the {@link Alias#submodel}.
+ * Id of the {@link Element#submodel}.
*/
private String submodelId;
/**
* List of synonyms of the element.
*
- * @see Alias#synonyms
+ * @see Element#synonyms
*/
private List<String> synonyms = new ArrayList<>();
/**
* List of former symbols used by the entity represented by this element.
*
- * @see Alias#formerSymbols
+ * @see Element#formerSymbols
*/
private List<String> formerSymbols = new ArrayList<>();
/**
* List of references for this element.
*
- * @see Alias#miriamData
+ * @see Element#miriamData
*/
private List<AnnotationView> references = new ArrayList<>();
@@ -218,7 +218,7 @@ public class FullAliasView extends LightAliasView implements IHeavyView {
* @param icon
* string with icon that should be used to visualize this alias
*/
- protected FullAliasView(Alias element, String icon) {
+ protected FullAliasView(Element element, String icon) {
super(element, icon);
setModelName(element.getModel().getName());
if (element != null) {
@@ -231,8 +231,8 @@ public class FullAliasView extends LightAliasView implements IHeavyView {
setSymbol(element.getSymbol());
addSynonyms(element.getSynonyms());
setType(element.getStringType());
- if (element instanceof SpeciesAlias) {
- SpeciesAlias species = (SpeciesAlias) element;
+ if (element instanceof Species) {
+ Species species = (Species) element;
setCharge(species.getCharge());
setInitialAmount(species.getInitialAmount());
setInitialConcentration(species.getInitialConcentration());
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java
index d50755877a..7a3b63d52e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java
@@ -24,10 +24,10 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.graph.DataMiningType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.services.interfaces.IDataMiningService;
import lcsb.mapviewer.services.overlay.ChebiTreeRow;
import lcsb.mapviewer.services.search.ElementViewFactory;
@@ -43,7 +43,7 @@ import lcsb.mapviewer.services.view.DataMiningViewFactory;
* @author Piotr Gawron
*
*/
-public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasView> {
+public class FullAliasViewFactory extends ElementViewFactory<Element, FullAliasView> {
/**
* How many rows with data mining information should be presented to the user.
@@ -86,12 +86,12 @@ public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasVie
private ChebiAnnotator chebiBackend;
@Override
- public FullAliasView create(Alias alias) {
+ public FullAliasView create(Element alias) {
return create(alias, null);
}
/**
- * Creates {@link FullAliasView} from given {@link Alias}.
+ * Creates {@link FullAliasView} from given {@link Element}.
*
* @param element
* alias for which view is created
@@ -99,7 +99,7 @@ public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasVie
* icon that should be assigned to the view
* @return {@link FullAliasView} for given alias
*/
- public FullAliasView create(Alias element, String icon) {
+ public FullAliasView create(Element element, String icon) {
FullAliasView result = new FullAliasView(element, icon);
if (element != null) {
result.addReferences(annotationViewFactory.createList(element.getMiriamData()));
@@ -153,7 +153,7 @@ public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasVie
}
}
}
- if (element instanceof ProteinAlias) {
+ if (element instanceof Protein) {
result.addOther("posttranslationalModifications", getPosttransationalModifications(element));
}
@@ -170,12 +170,12 @@ public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasVie
* @return list of {@link PosttransationalModification} objects for object
* alias
*/
- private List<PosttransationalModification> getPosttransationalModifications(Alias alias) {
+ private List<PosttransationalModification> getPosttransationalModifications(Element alias) {
List<PosttransationalModification> result = new ArrayList<PosttransationalModification>();
- if (alias instanceof ProteinAlias) {
- List<ModificationResidueAlias> modifications = ((ProteinAlias) alias).getModificationResidues();
+ if (alias instanceof Protein) {
+ List<ModificationResidue> modifications = ((Protein) alias).getModificationResidues();
if (modifications.size() > 0) {
- for (ModificationResidueAlias residue : modifications) {
+ for (ModificationResidue residue : modifications) {
if (residue.getState() != null) {
PosttransationalModification modification = new PosttransationalModification();
modification.setName(residue.getState().getFullName());
@@ -202,11 +202,11 @@ public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasVie
* max elements that should be presented
* @return html table with data mining information
*/
- protected List<List<DataMiningView>> getDataMiningInformation(Alias alias, int maxMissingConnections) {
+ protected List<List<DataMiningView>> getDataMiningInformation(Element alias, int maxMissingConnections) {
List<List<DataMiningView>> result = new ArrayList<>();
List<DataMiningView> enricoList = new ArrayList<>();
List<DataMiningView> mariaList = new ArrayList<>();
- if (!(alias instanceof SpeciesAlias)) {
+ if (!(alias instanceof Species)) {
return result;
}
if (dataMiningService != null) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasView.java
index aaa901ea9e..7c1c12657e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasView.java
@@ -1,104 +1,104 @@
-package lcsb.mapviewer.services.search.data;
-
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.services.search.ElementView;
-import lcsb.mapviewer.services.search.ILightView;
-
-/**
- * Light {@link ElementView view} for alias representing data that should be
- * send to client.
- *
- * @author Piotr Gawron
- *
- */
-public class LightAliasView extends ElementView implements ILightView {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Coordinates of the alias.
- */
- private Rectangle2D bounds;
-
- /**
- * Icon representing this alias on the map.
- */
- private String icon;
-
- /**
- * Default constructor.
- *
- * @param alias
- * original {@link Alias} from which the object is created
- * @param icon
- * {@link #icon} - icon representing this alias on the map
- */
- protected LightAliasView(Alias alias, String icon) {
- super(alias.getId(), alias.getModel().getId());
- if (alias != null) {
- this.bounds = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
- }
- setIcon(icon);
- }
-
- /**
- * Constructory copying data from the original object.
- *
- * @param original
- * original object from which data will be copied
- */
- protected LightAliasView(LightAliasView original) {
- super(original.getUniqueId(), original.getModelId());
- setBounds(
- new Rectangle2D.Double(original.getBounds().getX(), original.getBounds().getY(), original.getBounds().getWidth(), original.getBounds().getHeight()));
- setIcon(original.getIcon());
-
- }
-
- /**
- * Constructor that should be used only for (de)serialization.
- */
- protected LightAliasView() {
- super();
- }
-
- /**
- * @return the bounds
- * @see #bounds
- */
- public Rectangle2D getBounds() {
- return bounds;
- }
-
- /**
- * @param bounds
- * the bounds to set
- * @see #bounds
- */
- public void setBounds(Rectangle2D bounds) {
- this.bounds = bounds;
- }
-
- /**
- * @return the icon
- * @see #icon
- */
- public String getIcon() {
- return icon;
- }
-
- /**
- * @param icon
- * the icon to set
- * @see #icon
- */
- public void setIcon(String icon) {
- this.icon = icon;
- }
-
-}
+package lcsb.mapviewer.services.search.data;
+
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.search.ElementView;
+import lcsb.mapviewer.services.search.ILightView;
+
+/**
+ * Light {@link ElementView view} for alias representing data that should be
+ * send to client.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LightAliasView extends ElementView implements ILightView {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Coordinates of the alias.
+ */
+ private Rectangle2D bounds;
+
+ /**
+ * Icon representing this alias on the map.
+ */
+ private String icon;
+
+ /**
+ * Default constructor.
+ *
+ * @param alias
+ * original {@link Element} from which the object is created
+ * @param icon
+ * {@link #icon} - icon representing this alias on the map
+ */
+ protected LightAliasView(Element alias, String icon) {
+ super(alias.getId(), alias.getModel().getId());
+ if (alias != null) {
+ this.bounds = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ }
+ setIcon(icon);
+ }
+
+ /**
+ * Constructory copying data from the original object.
+ *
+ * @param original
+ * original object from which data will be copied
+ */
+ protected LightAliasView(LightAliasView original) {
+ super(original.getUniqueId(), original.getModelId());
+ setBounds(
+ new Rectangle2D.Double(original.getBounds().getX(), original.getBounds().getY(), original.getBounds().getWidth(), original.getBounds().getHeight()));
+ setIcon(original.getIcon());
+
+ }
+
+ /**
+ * Constructor that should be used only for (de)serialization.
+ */
+ protected LightAliasView() {
+ super();
+ }
+
+ /**
+ * @return the bounds
+ * @see #bounds
+ */
+ public Rectangle2D getBounds() {
+ return bounds;
+ }
+
+ /**
+ * @param bounds
+ * the bounds to set
+ * @see #bounds
+ */
+ public void setBounds(Rectangle2D bounds) {
+ this.bounds = bounds;
+ }
+
+ /**
+ * @return the icon
+ * @see #icon
+ */
+ public String getIcon() {
+ return icon;
+ }
+
+ /**
+ * @param icon
+ * the icon to set
+ * @see #icon
+ */
+ public void setIcon(String icon) {
+ this.icon = icon;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasViewFactory.java
index 8037197ab2..c3529e4861 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/LightAliasViewFactory.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.services.search.data;
-
-import org.apache.log4j.Logger;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.services.search.ElementViewFactory;
-import lcsb.mapviewer.services.search.ILightView;
-
-/**
- * Factory class for {@link LightAliasView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class LightAliasViewFactory extends ElementViewFactory<Alias, LightAliasView> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LightAliasViewFactory.class);
-
- @Override
- public LightAliasView create(Alias alias) {
- return create(alias, null);
- }
-
- /**
- * Creates {@link LightAliasView} for {@link Alias}.
- *
- * @param alias
- * alias for which view is created
- * @param icon
- * icon that should be assigned to the view
- * @return {@link LightAliasView} for {@link Alias}
- */
- public LightAliasView create(Alias alias, String icon) {
- LightAliasView result = new LightAliasView(alias, icon);
- return result;
- }
-
- @Override
- public String createGson(LightAliasView object) {
- return new Gson().toJson(object);
- }
-
- /**
- * Creates {@link ILightView} from {@link FullAliasView}.
- *
- * @param object
- * original object
- * @return new light object
- */
- public ILightView create(FullAliasView object) {
- return new LightAliasView(object);
- }
-}
+package lcsb.mapviewer.services.search.data;
+
+import org.apache.log4j.Logger;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.search.ElementViewFactory;
+import lcsb.mapviewer.services.search.ILightView;
+
+/**
+ * Factory class for {@link LightAliasView} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LightAliasViewFactory extends ElementViewFactory<Element, LightAliasView> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LightAliasViewFactory.class);
+
+ @Override
+ public LightAliasView create(Element alias) {
+ return create(alias, null);
+ }
+
+ /**
+ * Creates {@link LightAliasView} for {@link Element}.
+ *
+ * @param alias
+ * alias for which view is created
+ * @param icon
+ * icon that should be assigned to the view
+ * @return {@link LightAliasView} for {@link Element}
+ */
+ public LightAliasView create(Element alias, String icon) {
+ LightAliasView result = new LightAliasView(alias, icon);
+ return result;
+ }
+
+ @Override
+ public String createGson(LightAliasView object) {
+ return new Gson().toJson(object);
+ }
+
+ /**
+ * Creates {@link ILightView} from {@link FullAliasView}.
+ *
+ * @param object
+ * original object
+ * @return new light object
+ */
+ public ILightView create(FullAliasView object) {
+ return new LightAliasView(object);
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java
index 6f718f8d3c..ff80e74959 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/IDbSearchService.java
@@ -4,8 +4,8 @@ import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.view.AbstractView;
/**
@@ -54,7 +54,7 @@ public interface IDbSearchService<T extends AbstractView<?>> {
* {@link lcsb.mapviewer.model.map.model.Model Model})
* @return list of drugs that targets something from the elements collection
*/
- List<T> getForTargets(Collection<Alias> targetElements, DbSearchCriteria searchCriteria);
+ List<T> getForTargets(Collection<Element> targetElements, DbSearchCriteria searchCriteria);
/**
* Creates empty {@link T} object.
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
index 93f3f343eb..4b76eee0e9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
@@ -26,11 +26,11 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
@@ -231,11 +231,11 @@ public class ChemicalService implements IChemicalService {
}
@Override
- public List<ChemicalView> getForTargets(Collection<Alias> targets, DbSearchCriteria searchCriteria) {
+ public List<ChemicalView> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
List<Chemical> chemicalList = new ArrayList<>();
Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
- for (Alias alias : targets) {
- if (alias instanceof ProteinAlias || alias instanceof GeneAlias || alias instanceof RnaAlias) {
+ for (Element alias : targets) {
+ if (alias instanceof Protein || alias instanceof Gene || alias instanceof Rna) {
boolean hgncFound = false;
for (MiriamData md : alias.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
index 6e8bc8d619..f475b4cbfa 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalViewFactory.java
@@ -20,8 +20,8 @@ import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.overlay.IconManager;
import lcsb.mapviewer.services.overlay.IconType;
import lcsb.mapviewer.services.search.SearchResultFactory;
@@ -177,7 +177,7 @@ public class ChemicalViewFactory extends SearchResultFactory<Chemical, ChemicalV
for (Model model : models) {
for (TargetView target : chemical.getTargetRows()) {
if (target.getSelected() && target.getIcon() != null) {
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
if (elementMatch(target, element)) {
result.add(new ElementIdentifier(element, target.getIcon()));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index c483e52a73..83108406d9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -23,10 +23,10 @@ import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
@@ -242,11 +242,11 @@ public class DrugService implements IDrugService {
}
@Override
- public List<DrugView> getForTargets(Collection<Alias> targets, DbSearchCriteria searchCriteria) {
+ public List<DrugView> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
List<Drug> drugList = new ArrayList<Drug>();
Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
- for (Alias target : targets) {
- if (target instanceof ProteinAlias || target instanceof GeneAlias) {
+ for (Element target : targets) {
+ if (target instanceof Protein || target instanceof Gene) {
boolean hgncFound = false;
for (MiriamData md : target.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java
index 960958f958..074d19044c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactory.java
@@ -17,8 +17,8 @@ import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.data.Target;
import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.overlay.IconManager;
import lcsb.mapviewer.services.overlay.IconType;
import lcsb.mapviewer.services.search.SearchResultFactory;
@@ -147,8 +147,8 @@ public class DrugViewFactory extends SearchResultFactory<Drug, DrugView> {
List<ElementIdentifier> result = new ArrayList<>();
for (Model m : models) {
- List<Alias> species = m.getAliasByName(annotation.getName());
- for (Alias species2 : species) {
+ List<Element> species = m.getAliasByName(annotation.getName());
+ for (Element species2 : species) {
result.add(new ElementIdentifier(species2, icon));
}
}
@@ -169,7 +169,7 @@ public class DrugViewFactory extends SearchResultFactory<Drug, DrugView> {
List<ElementIdentifier> result = new ArrayList<>();
for (Model m : models) {
- for (Alias element : m.getAliases()) {
+ for (Element element : m.getAliases()) {
if (elementMatch(complexTarget, element)) {
result.add(new ElementIdentifier(element, complexTarget.getIcon()));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
index cf5cf744d9..4a5558bc49 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
@@ -23,11 +23,11 @@ import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
@@ -131,11 +131,11 @@ public class MiRNAService implements IMiRNAService {
}
@Override
- public List<MiRNAView> getForTargets(Collection<Alias> targets, DbSearchCriteria searchCriteria) {
+ public List<MiRNAView> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
List<MiRNA> mirnaList = new ArrayList<MiRNA>();
Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
- for (Alias element : targets) {
- if (element instanceof ProteinAlias || element instanceof GeneAlias || element instanceof RnaAlias) {
+ for (Element element : targets) {
+ if (element instanceof Protein || element instanceof Gene || element instanceof Rna) {
boolean hgncFound = false;
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
index 4940f74a6e..595ec33ca5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAViewFactory.java
@@ -11,8 +11,8 @@ import com.google.gson.Gson;
import lcsb.mapviewer.annotation.data.MiRNA;
import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.overlay.IconManager;
import lcsb.mapviewer.services.overlay.IconType;
import lcsb.mapviewer.services.search.SearchResultFactory;
@@ -102,7 +102,7 @@ public class MiRNAViewFactory extends SearchResultFactory<MiRNA, MiRNAView> {
for (Model model : models) {
for (TargetView target : searchResult.getTargetRows()) {
if (target.getSelected() && target.getIcon() != null) {
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
if (elementMatch(target, element)) {
result.add(new ElementIdentifier(element, target.getIcon()));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasView.java
index 01e111ea77..2e13086fc9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasView.java
@@ -7,7 +7,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GeneVariation;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.IHeavyView;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.utils.data.ColorSchemaType;
@@ -57,7 +57,7 @@ public class FullLayoutAliasView extends LightLayoutAliasView implements IHeavyV
* @param alias
* object for which vie is created
*/
- protected FullLayoutAliasView(Alias alias) {
+ protected FullLayoutAliasView(Element alias) {
super(alias);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
index 455cd161b0..d58e285eff 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactory.java
@@ -7,7 +7,7 @@ import com.google.gson.Gson;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.ElementViewFactory;
import lcsb.mapviewer.services.utils.data.ColorSchemaType;
@@ -17,7 +17,7 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaType;
* @author Piotr Gawron
*
*/
-public class FullLayoutAliasViewFactory extends ElementViewFactory<Pair<Alias, ColorSchema>, FullLayoutAliasView> {
+public class FullLayoutAliasViewFactory extends ElementViewFactory<Pair<Element, ColorSchema>, FullLayoutAliasView> {
/**
* Default class logger.
*/
@@ -25,7 +25,7 @@ public class FullLayoutAliasViewFactory extends ElementViewFactory<Pair<Alias, C
private static Logger logger = Logger.getLogger(FullLayoutAliasViewFactory.class);
@Override
- public FullLayoutAliasView create(Pair<Alias, ColorSchema> pair) {
+ public FullLayoutAliasView create(Pair<Element, ColorSchema> pair) {
ColorSchema schema = pair.getRight();
FullLayoutAliasView result = new FullLayoutAliasView(pair.getLeft());
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
index 00207463ec..bf8008175a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasView.java
@@ -1,93 +1,93 @@
-package lcsb.mapviewer.services.search.layout;
-
-import java.awt.Color;
-
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.services.search.ElementView;
-
-/**
- * Light {@link ElementView view} for alias representing data that should be
- * send to client about alias related to
- * {@link lcsb.mapviewer.model.map.layout.Layout}.
- *
- * @author Piotr Gawron
- *
- */
-public class LightLayoutAliasView extends ElementView {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Value used to highlight {@link Alias} in a a layout.
- */
- private Double value;
-
- /**
- * Color used to highlight {@link Alias} in a layout.
- */
- private Color color;
-
- /**
- * Default constructor.
- *
- * @param alias
- * original object from which this on is created
- */
- protected LightLayoutAliasView(Alias alias) {
- super(alias.getId(), alias.getModel().getId());
- }
-
- /**
- * Constructor that should be used only for (de)serialization.
- */
- protected LightLayoutAliasView() {
- super();
- }
-
- /**
- * @return the value
- * @see #value
- */
- public Double getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- * @see #value
- */
- public void setValue(Double value) {
- this.value = value;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- @Override
- public String toString() {
- return "[" + this.getClass().getSimpleName() + "] " + //
- "alias_id: " + getIdObject() + ", " + //
- "value: " + getValue() + ", " + //
- "color: " + getColor() + ", ";
-
- }
-
-}
+package lcsb.mapviewer.services.search.layout;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.search.ElementView;
+
+/**
+ * Light {@link ElementView view} for alias representing data that should be
+ * send to client about alias related to
+ * {@link lcsb.mapviewer.model.map.layout.Layout}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LightLayoutAliasView extends ElementView {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Value used to highlight {@link Element} in a a layout.
+ */
+ private Double value;
+
+ /**
+ * Color used to highlight {@link Element} in a layout.
+ */
+ private Color color;
+
+ /**
+ * Default constructor.
+ *
+ * @param alias
+ * original object from which this on is created
+ */
+ protected LightLayoutAliasView(Element alias) {
+ super(alias.getId(), alias.getModel().getId());
+ }
+
+ /**
+ * Constructor that should be used only for (de)serialization.
+ */
+ protected LightLayoutAliasView() {
+ super();
+ }
+
+ /**
+ * @return the value
+ * @see #value
+ */
+ public Double getValue() {
+ return value;
+ }
+
+ /**
+ * @param value
+ * the value to set
+ * @see #value
+ */
+ public void setValue(Double value) {
+ this.value = value;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + "] " + //
+ "alias_id: " + getIdObject() + ", " + //
+ "value: " + getValue() + ", " + //
+ "color: " + getColor() + ", ";
+
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
index c3666b448b..4d0c874fd4 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactory.java
@@ -6,7 +6,7 @@ import com.google.gson.Gson;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.ElementViewFactory;
/**
@@ -15,7 +15,7 @@ import lcsb.mapviewer.services.search.ElementViewFactory;
* @author Piotr Gawron
*
*/
-public class LightLayoutAliasViewFactory extends ElementViewFactory<Pair<Alias, ColorSchema>, LightLayoutAliasView> {
+public class LightLayoutAliasViewFactory extends ElementViewFactory<Pair<Element, ColorSchema>, LightLayoutAliasView> {
/**
* Default class logger.
*/
@@ -23,7 +23,7 @@ public class LightLayoutAliasViewFactory extends ElementViewFactory<Pair<Alias,
private static Logger logger = Logger.getLogger(LightLayoutAliasViewFactory.class);
@Override
- public LightLayoutAliasView create(Pair<Alias, ColorSchema> pair) {
+ public LightLayoutAliasView create(Pair<Element, ColorSchema> pair) {
LightLayoutAliasView result = new LightLayoutAliasView(pair.getLeft());
result.setColor(pair.getRight().getNormalizedColor());
result.setValue(pair.getRight().getValue());
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java b/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
index 26a19f2fd5..cb448f1dd0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
@@ -8,8 +8,8 @@ import java.util.Map.Entry;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.SearchIndex;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This class is responsible for seqrch queries. It allows to create an index
@@ -27,7 +27,7 @@ public class SearchIndexer {
private static final int SEARCH_SCORE_LEVEL_FOR_ALIAS_ID = 60;
/**
- * Base score of the index generated for {@link Alias#formerSymbols}. It will
+ * Base score of the index generated for {@link Element#formerSymbols}. It will
* be used as a shift for {@link SearchIndex#weight} value.
*/
private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_FORMER_SYMBOL = 75;
@@ -53,6 +53,7 @@ public class SearchIndexer {
/**
* Default class logger.
*/
+ @SuppressWarnings("unused")
private Logger logger = Logger.getLogger(SearchIndexer.class);
/**
@@ -72,7 +73,7 @@ public class SearchIndexer {
* object to be indexed
* @return list of indexes for an alias
*/
- public List<SearchIndex> createIndexForAlias(Alias species) {
+ public List<SearchIndex> createIndexForAlias(Element species) {
List<SearchIndex> result = new ArrayList<>();
String id1 = species.getAliasId();
result.add(new SearchIndex(getIndexStringForString(id1), SEARCH_SCORE_LEVEL_FOR_ALIAS_ID));
@@ -165,13 +166,13 @@ public class SearchIndexer {
* query
* @return class of the element that might exist in the result
*/
- public Class<? extends Alias> getTypeForQuery(String string, Map<String, Class<? extends Alias>> speciesSearchReversePrefix) {
+ public Class<? extends Element> getTypeForQuery(String string, Map<String, Class<? extends Element>> speciesSearchReversePrefix) {
String result = string;
- for (Entry<String, Class<? extends Alias>> entry : speciesSearchReversePrefix.entrySet()) {
+ for (Entry<String, Class<? extends Element>> entry : speciesSearchReversePrefix.entrySet()) {
if (result.startsWith(entry.getKey() + ":")) {
return entry.getValue();
}
}
- return Alias.class;
+ return Element.class;
}
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
index 259d006bce..93855824f8 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.services.utils.data;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This enum defines which columns are available in export function.
@@ -14,27 +14,27 @@ public enum ExportColumn {
/**
* Name of the species.
*/
- NAME("Name", SpeciesAlias.class), //
+ NAME("Name", Species.class), //
/**
* Name of compartment.
*/
- COMPARTMENT_NAME("Compartment", SpeciesAlias.class), //
+ COMPARTMENT_NAME("Compartment", Species.class), //
/**
* Name of compartment.
*/
- POSITION_TO_COMPARTMENT("Position to compartment", SpeciesAlias.class), //
+ POSITION_TO_COMPARTMENT("Position to compartment", Species.class), //
/**
* Name of pathway.
*/
- COMPONENT_NAME("Pathway", SpeciesAlias.class), //
+ COMPONENT_NAME("Pathway", Species.class), //
/**
* Type of the species.
*/
- TYPE("Type", SpeciesAlias.class), //
+ TYPE("Type", Species.class), //
/**
* Identifier.
@@ -44,12 +44,12 @@ public enum ExportColumn {
/**
* Complex in which element is localized.
*/
- COMPLEX("Parent complex", SpeciesAlias.class), //
+ COMPLEX("Parent complex", Species.class), //
/**
* Complex in which element is localized.
*/
- SUBMODEL("Submodel", SpeciesAlias.class), //
+ SUBMODEL("Submodel", Species.class), //
/**
* Reaction identifier.
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
index fb6d77531a..a16772c76b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/CommentViewFactory.java
@@ -9,9 +9,9 @@ import com.google.gson.Gson;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
/**
* Factory class for {@link CommentView} class.
@@ -78,7 +78,7 @@ public class CommentViewFactory extends AbstractViewFactory<Comment, CommentView
}
} else {
- Alias alias = model.getAliasByDbId(comment.getTableId());
+ Element alias = model.getAliasByDbId(comment.getTableId());
if (alias != null) {
title = alias.getName();
coordinates = alias.getCenter();
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
index 511c58f34a..e8a9acaae8 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
@@ -8,8 +8,8 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.impl.SearchService;
/**
@@ -92,8 +92,8 @@ public class PubmedAnnotatedElementsView extends AbstractView<MiriamData> {
* object to add
*/
public void addElement(AnnotatedObject annotatedObject) {
- if (annotatedObject instanceof Alias) {
- Alias alias = (Alias) annotatedObject;
+ if (annotatedObject instanceof Element) {
+ Element alias = (Element) annotatedObject;
elements.add(new Pair<String, String>(alias.getName(), SearchService.SPECIES_SEARCH_PREFIX + ":" + alias.getAliasId()));
} else if (annotatedObject instanceof Reaction) {
Reaction reaction = (Reaction) annotatedObject;
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
index d7307d9033..6c5d5baafb 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
@@ -17,10 +17,10 @@ import org.springframework.test.annotation.Rollback;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.comment.FullCommentView;
import lcsb.mapviewer.services.view.CommentView;
@@ -30,8 +30,8 @@ public class CommentServiceTest extends ServiceTestFunctions {
static Logger logger = Logger.getLogger(CommentServiceTest.class);
Model model;
Project project;
- Alias alias;
- Alias alias2;
+ Element alias;
+ Element alias2;
private String projectId = "Some_id";
@Before
@@ -47,10 +47,10 @@ public class CommentServiceTest extends ServiceTestFunctions {
model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
model.setMapVersion("tes");
model.setTileSize(128);
- Set<Alias> aliases = model.getAliases();
+ Set<Element> aliases = model.getAliases();
alias = null;
alias2 = null;
- for (Alias nAlias : aliases) {
+ for (Element nAlias : aliases) {
alias2 = alias;
alias = nAlias;
}
@@ -172,7 +172,7 @@ public class CommentServiceTest extends ServiceTestFunctions {
@Test
public void testAddCommentForAlias() throws Exception {
try {
- Alias alias = model.getAliasByAliasId("sa1");
+ Element alias = model.getAliasByAliasId("sa1");
long counter = commentService.getCommentCount();
Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), alias, false, model);
long counter2 = commentService.getCommentCount();
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
index ad5e461c1d..7c94ef9f11 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
@@ -28,10 +28,10 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.IDataMiningService;
@@ -41,8 +41,8 @@ public class DataMiningServiceTest extends ServiceTestFunctions {
private Model model;
private Project project;
- private Set<Alias> nodes;
- private Alias node;
+ private Set<Element> nodes;
+ private Element node;
@Autowired
IDataMiningService dm;
@@ -105,7 +105,7 @@ public class DataMiningServiceTest extends ServiceTestFunctions {
dataMiningService.addMissingConnection(connection);
- Collection<Alias> coll = dataMiningService.getSpeciesWithMissingConnectionsByGeneName(model, "ABLA");
+ Collection<Element> coll = dataMiningService.getSpeciesWithMissingConnectionsByGeneName(model, "ABLA");
assertNotNull(coll);
assertTrue(coll.size() > 0);
@@ -135,7 +135,7 @@ public class DataMiningServiceTest extends ServiceTestFunctions {
GenericLog log = logDao.getLastLog();
logDao.delete(log);
- Collection<Alias> elements = dataMiningService.getSpeciesWithMissingConnectionsByGeneName(model, "SOME2");
+ Collection<Element> elements = dataMiningService.getSpeciesWithMissingConnectionsByGeneName(model, "SOME2");
assertEquals(1, elements.size());
dataMiningService.deleteMissingConnection(connection, "No reason");
@@ -160,10 +160,10 @@ public class DataMiningServiceTest extends ServiceTestFunctions {
try {
DataMiningSet dm = new DataMiningSet();
dm.setInputData(IOUtils.toByteArray(new FileInputStream("testFiles/data_mining/sample_input.txt")));
- Set<Alias> set = new HashSet<>();
- ProteinAlias p1 = new GenericProteinAlias("id1");
+ Set<Element> set = new HashSet<>();
+ Protein p1 = new GenericProtein("id1");
p1.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- ProteinAlias p2 = new GenericProteinAlias("id2");
+ Protein p2 = new GenericProtein("id2");
p2.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
set.add(p1);
set.add(p2);
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest2.java
index ea458a4882..2f44610057 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest2.java
@@ -21,13 +21,13 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
import lcsb.mapviewer.model.map.graph.DataMiningType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.services.ServiceTestFunctions;
@Rollback(true)
@@ -45,14 +45,14 @@ public class DataMiningServiceTest2 extends ServiceTestFunctions {
@Test
public void testParseData() throws Exception {
try {
- Alias snca = new GenericProteinAlias("id1");
+ Element snca = new GenericProtein("id1");
snca.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- Alias park1 = new GenericProteinAlias("id2");
+ Element park1 = new GenericProtein("id2");
park1.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK1"));
- SimpleMoleculeAlias sm = new SimpleMoleculeAlias("id3");
+ SimpleMolecule sm = new SimpleMolecule("id3");
sm.addMiriamData(new MiriamData(MiriamType.CHEBI, "CHEBI:1234"));
- Collection<Alias> nodes = new ArrayList<>();
+ Collection<Element> nodes = new ArrayList<>();
nodes.add(snca);
nodes.add(park1);
@@ -108,10 +108,10 @@ public class DataMiningServiceTest2 extends ServiceTestFunctions {
@Test
public void testDataMiningMiriamDataFormat() throws Exception {
try {
- ProteinAlias snca = new GenericProteinAlias("id1");
+ Protein snca = new GenericProtein("id1");
snca.addMiriamData(new MiriamData(MiriamType.HGNC, "18618"));
- Collection<Alias> nodes = new ArrayList<>();
+ Collection<Element> nodes = new ArrayList<>();
nodes.add(snca);
Set<DataMining> res = dataMiningService
@@ -136,12 +136,12 @@ public class DataMiningServiceTest2 extends ServiceTestFunctions {
@Test
public void testParseDataWithFiltering() throws Exception {
try {
- ProteinAlias park7 = new GenericProteinAlias("id1");
+ Protein park7 = new GenericProtein("id1");
park7.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7"));
- ProteinAlias park1 = new GenericProteinAlias("id2");
+ Protein park1 = new GenericProtein("id2");
park1.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK1"));
- Collection<Alias> nodes = new ArrayList<>();
+ Collection<Element> nodes = new ArrayList<>();
nodes.add(park7);
nodes.add(park1);
@@ -170,12 +170,12 @@ public class DataMiningServiceTest2 extends ServiceTestFunctions {
@Test
public void testParseDataWithFiltering2() throws Exception {
try {
- ProteinAlias park7 = new GenericProteinAlias("id1");
+ Protein park7 = new GenericProtein("id1");
park7.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7"));
- ProteinAlias park1 = new GenericProteinAlias("id2");
+ Protein park1 = new GenericProtein("id2");
park1.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK1"));
- Collection<Alias> nodes = new ArrayList<>();
+ Collection<Element> nodes = new ArrayList<>();
nodes.add(park7);
nodes.add(park1);
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
index e4a866d808..893a4663a9 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
@@ -19,14 +19,14 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.IExporterService;
import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
@@ -69,7 +69,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
// only proteins for self-made modules
new CreateHierarchyCommand(model, 8, 80).execute();
- string = exporter.getExportSpeciesString(params.type(GenericProteinAlias.class));
+ string = exporter.getExportSpeciesString(params.type(GenericProtein.class));
lines = string.split("\n");
assertTrue(lines.length > 1);
@@ -81,7 +81,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
assertEquals(ExportColumn.TYPE.getTitle(), textColumns[4]);
} else {
textColumns = string2.split("\t");
- assertEquals(GenericProteinAlias.class.getSimpleName(), textColumns[4]);
+ assertEquals(GenericProtein.class.getSimpleName(), textColumns[4]);
if (!textColumns[2].equalsIgnoreCase(textColumns[3])) {
differenceBetweenComponentCompartmnet = true;
}
@@ -123,7 +123,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
try {
Model model = getModelForFile("testFiles/export/hsp70.xml", true);
- SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId("csa1");
+ Species alias = (Species) model.getAliasByAliasId("csa1");
ExportColumn columns[] = { ExportColumn.NAME };
ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
@@ -147,7 +147,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
assertTrue(string.contains("BAG1"));
// and now check complexes with mix of proteins and molecules
- alias = (SpeciesAlias) model.getAliasByAliasId("csa3");
+ alias = (Species) model.getAliasByAliasId("csa3");
elements = exporter.getExportStringForOneSpecies(alias, params);
assertTrue(elements.size() > 0);
@@ -156,7 +156,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
assertTrue(string.contains("UBA6"));
assertTrue(string.contains("AMP"));
- elements = exporter.getExportStringForOneSpecies(alias, params.type(ProteinAlias.class));
+ elements = exporter.getExportStringForOneSpecies(alias, params.type(Protein.class));
assertTrue(elements.size() > 0);
string = elements.get(0);
assertTrue(string.contains("UBA1"));
@@ -173,8 +173,8 @@ public class ExporterServiceTest extends ServiceTestFunctions {
public void testGetExportStringForOneReaction() throws Exception {
try {
Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<CompartmentAlias> aliases = new HashSet<>();
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ Set<Compartment> aliases = new HashSet<>();
+ for (Compartment alias : model.getCompartmentsAliases()) {
if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
aliases.add(alias);
}
@@ -183,8 +183,8 @@ public class ExporterServiceTest extends ServiceTestFunctions {
ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
fileType(ExportFileType.SIF).//
- type(ProteinAlias.class).//
- type(ComplexAlias.class).//
+ type(Protein.class).//
+ type(Complex.class).//
fileType(ExportFileType.SIF).//
complexElementsName(false).//
excluded(aliases);
@@ -197,7 +197,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
assertTrue(string.contains("trans-SNARE complex"));
assertFalse(string.contains("VAMP2"));
- params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF).type(ComplexAlias.class).type(ProteinAlias.class);
+ params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF).type(Complex.class).type(Protein.class);
string = exporter.getExportSingleInteractionString(reaction, params).get(0);
assertTrue(string.contains("VAMP2"));
@@ -216,7 +216,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
fileType(ExportFileType.SIF).//
complexElementsName(false).//
- type(ComplexAlias.class).type(ProteinAlias.class);
+ type(Complex.class).type(Protein.class);
String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
assertNotNull(string);
assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
@@ -245,8 +245,8 @@ public class ExporterServiceTest extends ServiceTestFunctions {
Reaction reaction = model.getReactionByReactionId("re11");
model.getReactions().clear();
model.addReaction(reaction);
- Set<CompartmentAlias> aliases = new HashSet<CompartmentAlias>();
- aliases.add((CompartmentAlias) model.getAliasByAliasId("ca1"));
+ Set<Compartment> aliases = new HashSet<Compartment>();
+ aliases.add((Compartment) model.getAliasByAliasId("ca1"));
ExporterParameters params = new IExporterService.ExporterParameters()
.model(model).fileType(ExportFileType.SIF).included("dopamine loaded synaptic vesicle");
assertEquals(0, exporter.getExportSingleInteractionString(reaction, params).size());
@@ -267,7 +267,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
for (Reaction reaction : model.getReactions()) {
String str = exporter
.getExportSingleInteractionString(
- reaction, new IExporterService.ExporterParameters().fileType(ExportFileType.TAB_SEPARATED).type(SpeciesAlias.class))
+ reaction, new IExporterService.ExporterParameters().fileType(ExportFileType.TAB_SEPARATED).type(Species.class))
.get(0);
List<String> strings = new ArrayList<String>();
@@ -297,14 +297,14 @@ public class ExporterServiceTest extends ServiceTestFunctions {
.model(model).fileType(ExportFileType.TAB_SEPARATED).column(ExportColumn.NAME).column(ExportColumn.COMPONENT_NAME)
.column(ExportColumn.COMPARTMENT_NAME);
- List<String> list = exporter.getExportStringForOneSpecies((SpeciesAlias) model.getAliasByAliasId("sa1"), params);
+ List<String> list = exporter.getExportStringForOneSpecies((Species) model.getAliasByAliasId("sa1"), params);
String desc = list.get(0);
String compartment = desc.split("\t")[2];
assertEquals("c1", compartment);
String component = desc.split("\t")[1];
assertEquals("Test3", component);
- list = exporter.getExportStringForOneSpecies((SpeciesAlias) model.getAliasByAliasId("sa2"), params);
+ list = exporter.getExportStringForOneSpecies((Species) model.getAliasByAliasId("sa2"), params);
desc = null;
for (String string : list) {
if (string.contains("Test 1")) {
@@ -336,7 +336,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
component = desc.split("\t")[1];
assertEquals("Test3", component);
- list = exporter.getExportStringForOneSpecies((SpeciesAlias) model.getAliasByAliasId("sa3"), params);
+ list = exporter.getExportStringForOneSpecies((Species) model.getAliasByAliasId("sa3"), params);
boolean ok = false;
for (String string : list) {
if (string.split("\t")[2].equals("null") && string.split("\t")[1].equals("Test2")) {
@@ -345,21 +345,21 @@ public class ExporterServiceTest extends ServiceTestFunctions {
}
assertTrue(ok);
- list = exporter.getExportStringForOneSpecies((SpeciesAlias) model.getAliasByAliasId("sa4"), params);
+ list = exporter.getExportStringForOneSpecies((Species) model.getAliasByAliasId("sa4"), params);
desc = list.get(0);
compartment = desc.split("\t")[2];
assertEquals("null", compartment);
component = desc.split("\t")[1];
assertEquals("Test3", component);
- list = exporter.getExportStringForOneSpecies((SpeciesAlias) model.getAliasByAliasId("sa5"), params);
+ list = exporter.getExportStringForOneSpecies((Species) model.getAliasByAliasId("sa5"), params);
desc = list.get(0);
compartment = desc.split("\t")[2];
assertEquals("c3", compartment);
component = desc.split("\t")[1];
assertEquals("null", component);
- list = exporter.getExportStringForOneSpecies((SpeciesAlias) model.getAliasByAliasId("sa6"), params);
+ list = exporter.getExportStringForOneSpecies((Species) model.getAliasByAliasId("sa6"), params);
desc = list.get(0);
compartment = desc.split("\t")[2];
assertEquals("null", compartment);
@@ -420,7 +420,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
List<ExportColumn> columns = new ArrayList<ExportColumn>();
for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(SpeciesAlias.class)) {
+ if (column.getClazz().isAssignableFrom(Species.class)) {
columns.add(column);
}
}
@@ -462,8 +462,8 @@ public class ExporterServiceTest extends ServiceTestFunctions {
public void testGetTabSeparatedReaction() throws Exception {
try {
Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<CompartmentAlias> aliases = new HashSet<>();
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ Set<Compartment> aliases = new HashSet<>();
+ for (Compartment alias : model.getCompartmentsAliases()) {
if (alias.getName().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
aliases.add(alias);
}
@@ -472,7 +472,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
fileType(ExportFileType.TAB_SEPARATED).//
column(ExportColumn.REACTION_ID).//
column(ExportColumn.REACTION_TYPE).//
- type(SpeciesAlias.class);
+ type(Species.class);
String string = exporter.getExportInteractionString(params);
assertTrue(string.indexOf("STATE_TRANSITION REACTANT") >= 0);
@@ -490,7 +490,7 @@ public class ExporterServiceTest extends ServiceTestFunctions {
Model model = getModelForFile("testFiles/export/new_line_file.xml", false);
List<ExportColumn> columns = new ArrayList<ExportColumn>();
for (ExportColumn column : ExportColumn.values()) {
- if (column.getClazz().isAssignableFrom(SpeciesAlias.class)) {
+ if (column.getClazz().isAssignableFrom(Species.class)) {
columns.add(column);
}
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index 222ab908db..d26b05ac51 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -27,8 +27,8 @@ import lcsb.mapviewer.model.map.layout.GeneVariation;
import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
@@ -70,7 +70,7 @@ public class LayoutServiceTest2 {
cs.setName("UUU");
cs.setReactionIdentifier("RE ID");
cs.setReverseReaction(true);
- cs.addType(GenericProteinAlias.class);
+ cs.addType(GenericProtein.class);
cs.setValue(1111.1111);
schemas.add(cs);
@@ -109,7 +109,7 @@ public class LayoutServiceTest2 {
cs.setName("UUU");
cs.setReactionIdentifier("RE ID");
cs.setReverseReaction(true);
- cs.addType(GenericProteinAlias.class);
+ cs.addType(GenericProtein.class);
cs.setValue(1111.1111);
GeneVariation gv = new GeneVariation();
gv.setModifiedDna("C");
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
index a29b4fb7f8..2049084f81 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
@@ -18,8 +18,8 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.log.GenericLog;
import lcsb.mapviewer.model.log.LogType;
import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
@@ -30,8 +30,8 @@ public class LogServiceTest extends ServiceTestFunctions {
private Model model;
private Project project;
- private Set<Alias> nodes;
- private Alias node;
+ private Set<Element> nodes;
+ private Element node;
private DataMining mc;
@Before
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
index 6430c72e62..f6cfdb028f 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
@@ -22,8 +22,8 @@ import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.search.data.LightAliasView;
@@ -83,8 +83,8 @@ public class ModelServiceTest extends ServiceTestFunctions {
try {
Model model = getModelForFile("testFiles/sample.xml", false);
int counter = 0;
- Alias alias0 = null;
- for (Alias alias : model.getAliases()) {
+ Element alias0 = null;
+ for (Element alias : model.getAliases()) {
if (counter == 0) {
alias0 = alias;
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index 74b3894831..3858e05830 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -37,11 +37,11 @@ import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
@@ -270,20 +270,20 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertNotNull(s2Model);
assertNotNull(s3Model);
- Alias al1 = model.getAliasByAliasId("sa1");
+ Element al1 = model.getAliasByAliasId("sa1");
assertNotNull(al1.getSubmodel());
assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
- Alias al2 = model.getAliasByAliasId("sa2");
+ Element al2 = model.getAliasByAliasId("sa2");
assertNull(al2.getSubmodel());
- Alias al4 = model.getAliasByAliasId("sa4");
+ Element al4 = model.getAliasByAliasId("sa4");
assertNotNull(al4.getSubmodel());
assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
- Alias s1_al1 = s1Model.getAliasByAliasId("sa1");
+ Element s1_al1 = s1Model.getAliasByAliasId("sa1");
assertNotNull(s1_al1.getSubmodel());
assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
@@ -520,7 +520,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
try {
super.createUser();
UserAnnotationSchema schema = new UserAnnotationSchema();
- schema.addClassAnnotator(new UserClassAnnotators(ProteinAlias.class, modelAnnotator.getAvailableAnnotatorNames(ProteinAlias.class)));
+ schema.addClassAnnotator(new UserClassAnnotators(Protein.class, modelAnnotator.getAvailableAnnotatorNames(Protein.class)));
user.setAnnotationSchema(schema);
userDao.update(user);
@@ -598,7 +598,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
try {
super.createUser();
UserAnnotationSchema schema = new UserAnnotationSchema();
- schema.addClassValidAnnotations(new UserClassValidAnnotations(ProteinAlias.class, MiriamType.values()));
+ schema.addClassValidAnnotations(new UserClassValidAnnotations(Protein.class, MiriamType.values()));
user.setAnnotationSchema(schema);
userDao.update(user);
userDao.flush();
@@ -645,7 +645,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
boolean dmFound = false;
- for (Alias element : model.getAliases()) {
+ for (Element element : model.getAliases()) {
if (dataMiningService.getMissingConnections(element).size() > 0) {
dmFound = true;
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index b39ff2b5a7..de566229ae 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -22,21 +22,21 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.ISearchService.CoordinatesSearchParams;
import lcsb.mapviewer.services.search.data.FullAliasView;
@@ -55,16 +55,16 @@ public class SearchServiceTest extends ServiceTestFunctions {
@Before
public void setUp() throws Exception {
- addSearchPrefix("complex", ComplexAlias.class);
- addSearchPrefix("degrded", DegradedAlias.class);
- addSearchPrefix("drug", DrugAlias.class);
- addSearchPrefix("gene", GeneAlias.class);
- addSearchPrefix("ion", IonAlias.class);
- addSearchPrefix("phenotype", PhenotypeAlias.class);
- addSearchPrefix("protein", ProteinAlias.class);
- addSearchPrefix("rna", RnaAlias.class);
- addSearchPrefix("molecule", SimpleMoleculeAlias.class);
- addSearchPrefix("unknown", UnknownAlias.class);
+ addSearchPrefix("complex", Complex.class);
+ addSearchPrefix("degrded", Degraded.class);
+ addSearchPrefix("drug", Drug.class);
+ addSearchPrefix("gene", Gene.class);
+ addSearchPrefix("ion", Ion.class);
+ addSearchPrefix("phenotype", Phenotype.class);
+ addSearchPrefix("protein", Protein.class);
+ addSearchPrefix("rna", Rna.class);
+ addSearchPrefix("molecule", SimpleMolecule.class);
+ addSearchPrefix("unknown", Unknown.class);
}
private void addSearchPrefix(String prefix, Class<?> clazz) {
@@ -234,20 +234,20 @@ public class SearchServiceTest extends ServiceTestFunctions {
List<Object> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5);
assertNotNull(elements);
assertEquals(5, elements.size());
- assertTrue(elements.get(0) instanceof SpeciesAlias);
- SpeciesAlias sAlias = (SpeciesAlias) elements.get(0);
+ assertTrue(elements.get(0) instanceof Species);
+ Species sAlias = (Species) elements.get(0);
assertEquals("s1", sAlias.getName());
assertTrue(elements.get(1) instanceof Reaction);
Reaction reaction = (Reaction) elements.get(1);
assertEquals("re1", reaction.getIdReaction());
- assertTrue(elements.get(2) instanceof SpeciesAlias);
- sAlias = (SpeciesAlias) elements.get(2);
+ assertTrue(elements.get(2) instanceof Species);
+ sAlias = (Species) elements.get(2);
assertEquals("s3", sAlias.getName());
assertTrue(elements.get(3) instanceof Reaction);
reaction = (Reaction) elements.get(3);
assertEquals("re2", reaction.getIdReaction());
- assertTrue(elements.get(4) instanceof SpeciesAlias);
- sAlias = (SpeciesAlias) elements.get(4);
+ assertTrue(elements.get(4) instanceof Species);
+ sAlias = (Species) elements.get(4);
assertEquals("s2", sAlias.getName());
} catch (Exception e) {
@@ -274,14 +274,14 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testGetAutocompleList() {
try {
Model model = new ModelFullIndexed(null);
- SpeciesAlias proteinAlias = new GenericProteinAlias("a");
+ Species proteinAlias = new GenericProtein("a");
proteinAlias.setName("PROT identifier");
proteinAlias.getSynonyms().add("PROT synonym");
proteinAlias.getSynonyms().add("another synonym");
proteinAlias.setFullName("Protein common name");
model.addAlias(proteinAlias);
- SimpleMoleculeAlias alias = new SimpleMoleculeAlias("a2");
+ SimpleMolecule alias = new SimpleMolecule("a2");
alias.setName("Molecule2");
model.addAlias(alias);
@@ -322,12 +322,12 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testGetAutocompleList2() {
try {
Model model = new ModelFullIndexed(null);
- GenericProteinAlias proteinAlias = new GenericProteinAlias("a1");
+ GenericProtein proteinAlias = new GenericProtein("a1");
proteinAlias.setName("PROT identifier");
proteinAlias.setNotes("Synonyms: PROT synonym, another synonym\nName: Protein common name");
model.addAlias(proteinAlias);
- SimpleMoleculeAlias alias = new SimpleMoleculeAlias("a2");
+ SimpleMolecule alias = new SimpleMolecule("a2");
alias.setName("Molecule2");
model.addAlias(alias);
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
index e0001fc278..86b87af933 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
@@ -10,8 +10,8 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.GeneRow;
@@ -51,7 +51,7 @@ public class SearchResultFactoryTest extends ServiceTestFunctions {
}
}
- Alias element = new RnaAlias("id");
+ Element element = new Rna("id");
element.setName(geneName);
assertTrue(factory.elementMatch(target, element));
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
index 69386a73bf..31df89988d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/data/FullAliasViewFactoryTest.java
@@ -25,17 +25,17 @@ import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.overlay.ChebiTreeRow;
@@ -47,15 +47,15 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
@Autowired
private ChebiAnnotator backend;
- private SpeciesAlias alias;
- private SpeciesAlias alias2;
+ private Species alias;
+ private Species alias2;
private Point2D midPoint;
private Reaction reaction;
- private SpeciesAlias alias3;
+ private Species alias3;
private Model model;
- private CompartmentAlias compartmentAlias;
+ private Compartment compartmentAlias;
@Before
public void setUp() throws Exception {
@@ -68,7 +68,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
model.addLayout(new Layout());
model.getModelData().setId(-12);
- alias = new GenericProteinAlias("AL1");
+ alias = new GenericProtein("AL1");
alias.setName("blablabla");
alias.setNotes("nottttttes");
alias.setX(10.0);
@@ -78,7 +78,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
model.addAlias(alias);
- alias2 = new GenericProteinAlias("AL2");
+ alias2 = new GenericProtein("AL2");
alias2.setName("blablabla2");
alias2.setX(100.0);
alias2.setY(120.0);
@@ -99,7 +99,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
model.addReaction(reaction);
- alias3 = new GenericProteinAlias("AL3");
+ alias3 = new GenericProtein("AL3");
alias3.setName("blablabla3");
alias3.setX(200.0);
alias3.setY(120.0);
@@ -111,7 +111,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
model.addReaction(reaction);
- compartmentAlias = new CompartmentAlias("AL4");
+ compartmentAlias = new Compartment("AL4");
compartmentAlias.setX(10);
compartmentAlias.setY(10);
compartmentAlias.setWidth(10);
@@ -126,7 +126,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
@Test
public void testCreateGson() {
try {
- Alias alias = new GenericProteinAlias("id");
+ Element alias = new GenericProtein("id");
alias.setName("12");
alias.setModel(new ModelFullIndexed(null));
FullAliasView object = fullAliasViewFactory.create(alias);
@@ -168,7 +168,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
try {
Model model = getModelForFile("testFiles/protein_with_modification.xml", true);
model.setTileSize(256);
- SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId("sa1");
+ Species alias = (Species) model.getAliasByAliasId("sa1");
FullAliasView marker = fullAliasViewFactory.create(alias);
List<?> list = (List<?>) marker.getOther("posttranslationalModifications");
assertNotNull(list);
@@ -216,12 +216,12 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
try {
Model model = getModelForFile("testFiles/graph_path_example3.xml", false);
model.setTileSize(256);
- SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId("sa4");
+ Species alias = (Species) model.getAliasByAliasId("sa4");
assertNotNull(alias);
FullAliasView result = fullAliasViewFactory.create(alias);
assertNotNull(result.getOther("chebiTree"));
- alias = (SpeciesAlias) model.getAliasByAliasId("sa3");
+ alias = (Species) model.getAliasByAliasId("sa3");
result = fullAliasViewFactory.create(alias);
assertNull(result.getOther("chebiTree"));
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/data/LightAliasViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/data/LightAliasViewFactoryTest.java
index 7671a2706b..74001678a2 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/data/LightAliasViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/data/LightAliasViewFactoryTest.java
@@ -7,9 +7,9 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class LightAliasViewFactoryTest {
Logger logger = Logger.getLogger(LightAliasViewFactoryTest.class);
@@ -27,7 +27,7 @@ public class LightAliasViewFactoryTest {
@Test
public void testCreateGson() throws Exception {
try {
- Alias alias = new GenericProteinAlias("id");
+ Element alias = new GenericProtein("id");
alias.setModel(new ModelFullIndexed(null));
LightAliasView object = lightAliasViewFactory.create(alias);
String gson = lightAliasViewFactory.createGson(object);
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java
index bda12a2d5b..bf03c7f2df 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/chemical/ChemicalServiceTest.java
@@ -14,8 +14,8 @@ import org.junit.Test;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
@@ -81,8 +81,8 @@ public class ChemicalServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByElements4() throws Exception {
try {
- List<Alias> elements = new ArrayList<>();
- RnaAlias protein = new RnaAlias("id");
+ List<Element> elements = new ArrayList<>();
+ Rna protein = new Rna("id");
protein.setName("GDNF");
elements.add(protein);
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java
index 1b5e3e4540..30989b7ad9 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugServiceTest.java
@@ -26,12 +26,12 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.GeneRow;
@@ -167,12 +167,12 @@ public class DrugServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByElements() throws Exception {
try {
- List<Alias> elements = new ArrayList<>();
+ List<Element> elements = new ArrayList<>();
List<DrugView> drugs = drugService.getForTargets(elements, new DbSearchCriteria());
assertNotNull(drugs);
assertEquals(0, drugs.size());
- ProteinAlias protein = new GenericProteinAlias("id");
+ Protein protein = new GenericProtein("id");
protein.setName("DRD2");
protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "DRD2"));
elements.add(protein);
@@ -190,8 +190,8 @@ public class DrugServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByElements2() throws Exception {
try {
- List<Alias> elements = new ArrayList<>();
- ProteinAlias protein = new GenericProteinAlias("id");
+ List<Element> elements = new ArrayList<>();
+ Protein protein = new GenericProtein("id");
protein.setName("DRD2");
protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "DRD2"));
elements.add(protein);
@@ -209,8 +209,8 @@ public class DrugServiceTest extends ServiceTestFunctions {
@Test
public void testSearchByElements3() throws Exception {
try {
- List<Alias> elements = new ArrayList<>();
- ProteinAlias protein = new GenericProteinAlias("id");
+ List<Element> elements = new ArrayList<>();
+ Protein protein = new GenericProtein("id");
protein.setName("GLUD1");
protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "GLUD1"));
protein.addMiriamData(new MiriamData(MiriamType.ENTREZ, "2746"));
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java
index 809ecc79d9..981396c266 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/db/drug/DrugViewFactoryTest.java
@@ -18,8 +18,8 @@ import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.data.Target;
import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.overlay.IconManager;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
@@ -109,7 +109,7 @@ public class DrugViewFactoryTest extends ServiceTestFunctions {
try {
Drug drug = chemblParser.findDrug("AMANTADINE");
Model model = getModelForFile("testFiles/drug_target.xml", false);
- Alias alias = model.getAliasByAliasId("sa9");
+ Element alias = model.getAliasByAliasId("sa9");
alias.setName("M");
alias.setId(12);
model.removeAlias(alias);
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactoryTest.java
index 17f59a8fc7..7c58a8a3db 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/layout/FullLayoutAliasViewFactoryTest.java
@@ -12,10 +12,10 @@ import org.junit.Test;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class FullLayoutAliasViewFactoryTest {
@@ -37,11 +37,11 @@ public class FullLayoutAliasViewFactoryTest {
public void testCreateGson() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- Alias alias = new GenericProteinAlias("id");
+ Element alias = new GenericProtein("id");
alias.setModel(model);
ColorSchema colorSchema = new GenericColorSchema();
colorSchema.setColor(Color.BLACK);
- FullLayoutAliasView object = factory.create(new Pair<Alias, ColorSchema>(alias, colorSchema));
+ FullLayoutAliasView object = factory.create(new Pair<Element, ColorSchema>(alias, colorSchema));
assertNotNull(factory.createGson(object));
} catch (Exception e) {
e.printStackTrace();
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactoryTest.java b/service/src/test/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactoryTest.java
index 895ea7d084..f3375530a2 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/layout/LightLayoutAliasViewFactoryTest.java
@@ -11,10 +11,10 @@ import org.junit.Test;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
public class LightLayoutAliasViewFactoryTest {
LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
@@ -31,11 +31,11 @@ public class LightLayoutAliasViewFactoryTest {
public void testCreateGson() throws Exception {
try {
Model model = new ModelFullIndexed(null);
- Alias alias = new GenericProteinAlias("id");
+ Element alias = new GenericProtein("id");
alias.setModel(model);
ColorSchema colorSchema = new GenericColorSchema();
colorSchema.setColor(Color.BLACK);
- LightLayoutAliasView object = factory.create(new Pair<Alias, ColorSchema>(alias, colorSchema));
+ LightLayoutAliasView object = factory.create(new Pair<Element, ColorSchema>(alias, colorSchema));
assertNotNull(factory.createGson(object));
} catch (Exception e) {
e.printStackTrace();
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java
index 48ac7727e5..d6b812bb0e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/graph/MissingConnectionDaoTest.java
@@ -16,15 +16,15 @@ import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
public class MissingConnectionDaoTest extends ServiceTestFunctions {
static Logger logger = Logger.getLogger(MissingConnectionDaoTest.class);
private Model model;
- private Collection<Alias> nodes;
+ private Collection<Element> nodes;
private Project project;
@@ -50,7 +50,7 @@ public class MissingConnectionDaoTest extends ServiceTestFunctions {
@Test
public void testGetMissingConnections() {
try {
- Alias node = nodes.iterator().next();
+ Element node = nodes.iterator().next();
DataMining mc = new DataMining();
mc.setDescription("desc a");
diff --git a/web/src/main/java/lcsb/mapviewer/bean/AbstractManagedBean.java b/web/src/main/java/lcsb/mapviewer/bean/AbstractManagedBean.java
index e657b1c4d1..8caa363dc1 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/AbstractManagedBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/AbstractManagedBean.java
@@ -1,547 +1,547 @@
-package lcsb.mapviewer.bean;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.beans.PropertyChangeSupport;
-import java.beans.PropertyVetoException;
-import java.beans.VetoableChangeListener;
-import java.beans.VetoableChangeSupport;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintStream;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.annotation.PostConstruct;
-import javax.faces.component.UIComponent;
-import javax.faces.context.ExternalContext;
-import javax.faces.context.FacesContext;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.bean.utils.IPrimefacesUtils;
-import lcsb.mapviewer.bean.utils.PrimefacesUtils;
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.events.Event;
-import lcsb.mapviewer.events.Listener;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Abstarct bean class containing basic functionality common for all beans
- * (property change listeners and vetoable property change listeners).
- *
- * @author Piotr Gawron
- *
- */
-public abstract class AbstractManagedBean implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Util class used to access information about current reqruest and general
- * information about P framework.
- */
- private transient IPrimefacesUtils primefacesUtils = new PrimefacesUtils();
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(AbstractManagedBean.class);
-
- /**
- * Set of verification listeners called when some property is changed. It's
- * marked transient because we don't want to store this in session. TODO it's
- * should be modified.
- */
- private final VetoableChangeSupport vchs = new VetoableChangeSupport(this);
-
- /**
- * Set of listeners called when some property is changed. It's marked
- * transient because we don't want to store this in session. TODO it's should
- * be modified.
- */
- private final PropertyChangeSupport pchs = new PropertyChangeSupport(this);
-
- /**
- * This map contains information about {@link Listener listeners} that should
- * be handled when {@link #callListeners(Event)} method is called. It's marked
- * transient because we don't want to store this in session. TODO it's should
- * be modified.
- */
- private transient Map<Class<? extends Event>, List<Listener<?>>> listeners = new HashMap<Class<? extends Event>, List<Listener<?>>>();
-
-
- /**
- * Default constructor. Adds generic log listener to property change
- * listeners.
- */
- public AbstractManagedBean() {
- // logger property listener
- PropertyChangeListener propertyChangeLogger = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: " + arg0.getOldValue() + " New: " + arg0.getNewValue());
- }
-
- };
- addPropertyChangeListener(propertyChangeLogger);
-
- }
-
- /**
- * Method run after creating all the beans. It's used for data initalization.
- */
- public abstract void init();
-
- /**
- * Initialize common data and call custom initializer of the bean.
- */
- @PostConstruct
- public void internalInit() {
- createSession();
- logger.debug("Initializing bean: " + this);
-
- // call init method for specific bean
- init();
- logger.debug("Bean: " + this + " initialized.");
- }
-
- /**
- * Creates http session if session hasn't been created yet.
- */
- public void createSession() {
- getPrimefacesUtils().createSession();
- }
-
- /**
- * Add property change listener that can VETO (cancel) the property change.
- *
- * @param listener
- * property listener
- */
- public final void addVetoablePropertyChangeListener(final VetoableChangeListener listener) {
- vchs.addVetoableChangeListener(listener);
- }
-
- /**
- * Removes property change l;istener that can VETO from the available
- * listeners.
- *
- * @param listener
- * listeren to be removed
- */
- public final void removeVetoablePropertyChangeListener(final VetoableChangeListener listener) {
- vchs.removeVetoableChangeListener(listener);
- }
-
- /**
- * Adds property change listener that is fired after property of a bean is
- * changed.
- *
- * @param listener
- * listener to be added
- */
- public final void addPropertyChangeListener(final PropertyChangeListener listener) {
- pchs.addPropertyChangeListener(listener);
- }
-
- /**
- * Removes property change listener from the list of all available listeners.
- *
- * @param listener
- * listener to be removed
- */
- public final void removePropertyChangeListener(final PropertyChangeListener listener) {
- pchs.removePropertyChangeListener(listener);
- }
-
- /**
- * Method that fires all vetoable property change listener for a given
- * property.
- *
- * @param propertyName
- * property that has changed
- * @param oldValue
- * old value of the property
- * @param newValue
- * new value of the property
- * @throws PropertyVetoException
- * if the change shouldn't be made this exception is thrown
- */
- protected final void fireVetoableChange(final String propertyName, final Object oldValue, final Object newValue) throws PropertyVetoException {
- vchs.fireVetoableChange(propertyName, oldValue, newValue);
- }
-
- /**
- * Method fires property change listener for a given property.
- *
- * @param propertyName
- * name of the property that has changed
- * @param oldValue
- * old value of the property
- * @param newValue
- * new value of the property
- */
- protected final void firePropertyChange(final String propertyName, final Object oldValue, final Object newValue) {
- if (oldValue != null || newValue != null) {
- pchs.firePropertyChange(propertyName, oldValue, newValue);
- }
- }
-
- /**
- * Returns list of all property change listeners for the bean (includes only
- * standard property change listeners, vetoable property change listeners are
- * excluded).
- *
- * @return list of property change listeners
- */
- protected final PropertyChangeListener[] getPropertyChangeListeners() {
- return pchs.getPropertyChangeListeners();
- }
-
- // TODO refactor these two methods to reduce copy-paste
-
- /**
- * Method sends to a client response with an attached file. The content of the
- * file is taken from the content param. Type defines MimeType of the content
- * (text file, xml, etc.) - this helps browser to properly handle response.
- *
- * @param content
- * - string with the file content
- * @param fileName
- * - name of the file that should popup in the client browser
- * @param type
- * - MIME type of the file
- * @throws IOException
- * exception thrown when there are some problems with sending file
- */
- protected final void sendFileAsResponse(String content, String fileName, MimeType type) throws IOException {
- // send the response to client
- FacesContext fc = FacesContext.getCurrentInstance();
- ExternalContext ec = fc.getExternalContext();
-
- ec.responseReset();
- ec.setResponseContentType(type.getTextRepresentation());
- ec.setResponseHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
- ec.addResponseHeader("Content-Type", type.getTextRepresentation());
-
- OutputStream output = ec.getResponseOutputStream();
- PrintStream printStream = new PrintStream(output);
- printStream.print(content);
-
- fc.responseComplete();
- }
-
- /**
- * Method sends to a client response with an attached file. Type defines
- * MimeType of the file content (text file, xml, etc.) - this helps browser to
- * properly handle response.
- *
- * @param file
- * - file which will be sent
- * @param fileName
- * - name of the file that should popup in the client browser
- * @param type
- * - MIME type of the file
- * @throws IOException
- * exception thrown when there are some problems with sending file
- */
- protected void sendFileAsResponse(File file, String fileName, MimeType type) throws IOException {
-
- // start sending
- FacesContext fc = FacesContext.getCurrentInstance();
- ExternalContext ec = fc.getExternalContext();
-
- ec.responseReset();
- ec.setResponseContentType(type.getTextRepresentation());
- ec.setResponseHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
-
- // attach file
- OutputStream output = ec.getResponseOutputStream();
- FileInputStream is = new FileInputStream(file);
- IOUtils.copy(is, output);
- fc.responseComplete();
-
- }
-
- /**
- * Clears whole data shared by this bean.
- */
- public abstract void clear();
-
- /**
- * Register new {@link Listener} in this bean.
- *
- * @param listener
- * listener that should be added
- */
- public void registerListener(Listener<?> listener) {
- List<Listener<?>> listenerList = getListeners().get(listener.getEventClass());
- if (listenerList == null) {
- listenerList = new ArrayList<Listener<?>>();
- listeners.put(listener.getEventClass(), listenerList);
- }
- listenerList.add(listener);
- }
-
- /**
- * This method will call all listeners associated with the specified
- * {@link Event}.
- *
- * @param event
- * {@link Event} for which listeners will be called
- */
- protected void callListeners(Event event) {
- List<Listener<?>> listenerList = getListeners().get(event.getClass());
- if (listenerList == null) {
- logger.warn("No listeners found for event: " + event);
- } else {
- for (Listener<?> listener : listenerList) {
- listener.handleEvent(event);
- }
- }
-
- }
-
- /**
- * Unregister {@link Listener} from this bean.
- *
- * @param listener
- * listener that should be removed
- */
- public void unregisterListener(Listener<?> listener) {
- List<Listener<?>> listenerList = listeners.get(listener.getEventClass());
- if (listenerList == null) {
- listenerList = new ArrayList<Listener<?>>();
- listeners.put(listener.getEventClass(), listenerList);
- }
- if (listenerList.contains(listener)) {
- listenerList.remove(listener);
- } else {
- throw new InvalidArgumentException("Listener " + listener + " wasn't registered.");
- }
-
- }
-
- /**
- * @param primefacesUtils
- * the primefacesUtils to set
- * @see #primefacesUtils
- */
- protected void setPrimefacesUtils(IPrimefacesUtils primefacesUtils) {
- this.primefacesUtils = primefacesUtils;
- }
-
- /**
- * Returns value of the parameter from http request call.
- *
- * @param name
- * name of the parameter
- * @return value of the request parameter
- */
- protected String getRequestParameter(String name) {
- return getPrimefacesUtils().getRequestParameter(name);
- }
-
- /**
- * Adds a parameter that will be stored in user session.
- *
- * @param key
- * name of the parameter
- * @param value
- * value of the parameter
- */
- protected void addSessionParam(String key, Object value) {
- getPrimefacesUtils().addSessionParam(key, value);
- }
-
- /**
- * Gets a value of the parameter stored in user session.
- *
- * @param key
- * name of the parameter
- * @return value of the user session parameter
- */
- protected Object getSessionParam(String key) {
- return getPrimefacesUtils().getSessionParam(key);
- }
-
- /**
- * @return the version of primefaces library
- */
- public String getPrimefacesVersion() {
- return getPrimefacesUtils().getVersion();
- }
-
- /**
- * Returns path on hard drive where the project is deplyed.
- *
- * @return path where the projest is running
- */
- public String getProjectDeployPath() {
- return getPrimefacesUtils().getPath();
- }
-
- /**
- * Sends an error message to the client.
- *
- * @param message
- * error message to be sent
- */
- protected void sendError(String message) {
- getPrimefacesUtils().error(message);
- }
-
- /**
- * Sends an error message to the client.
- *
- * @param message
- * error message to be sent
- * @param exception
- * exception which caused the error
- */
- protected void sendError(String message, Exception exception) {
- logger.error(message, exception);
- getPrimefacesUtils().error(message);
- }
-
- /**
- * Sends info message to the client.
- *
- * @param message
- * info message to be sent
- */
- protected void sendInfo(String message) {
- getPrimefacesUtils().info(message);
- }
-
- /**
- * Returns ip address of current client.
- *
- * @return IP addresss of the client
- */
- protected String getClientIpAddress() {
- return getPrimefacesUtils().getClientIpAddress();
- }
-
- /**
- * Returns a {@link UIComponent} corresponding to the client side component
- * with the identifier given in the parameter.
- *
- * @param id
- * identifier of a component
- * @return {@link UIComponent} corresponding to the client side component with
- * the identifier given in the parameter
- */
- protected UIComponent findComponent(String id) {
- return getPrimefacesUtils().findComponent(id);
- }
-
- /**
- * Returns bean identified by {@link Class}.
- *
- * @param clazz
- * class of the bean
- * @param <T>
- * class of the bean
- * @return bean identified by {@link Class}
- */
- public <T> T findBean(Class<T> clazz) {
- return getPrimefacesUtils().findBean(clazz);
- }
-
- /**
- * @return primefacesUtils.
- */
- public IPrimefacesUtils getPrimefacesUtils() {
- if (primefacesUtils == null) {
- primefacesUtils = new PrimefacesUtils();
- }
- return primefacesUtils;
- }
-
- /**
- * @return listeners.
- */
- public Map<Class<? extends Event>, List<Listener<?>>> getListeners() {
- if (listeners == null) {
- listeners = new HashMap<Class<? extends Event>, List<Listener<?>>>();
- }
- return listeners;
- }
-
- /**
- * @param listeners
- * general listeners.
- */
- public void setListeners(Map<Class<? extends Event>, List<Listener<?>>> listeners) {
- this.listeners = listeners;
- }
-
- /**
- * Executes javascript code on the client browser.
- *
- * @param javascript
- * javascript code
- */
- public void executeJavascript(String javascript) {
- getPrimefacesUtils().executeJavascript(javascript);
- }
-
- /**
- * Transform json string representing list of pairs with model and object id
- * (it can be list of alias ids or reaction ids) into a {@link List} of
- * {@link Pair pairs}.
- *
- * @param string
- * list containing pairs of identifiers
- * @return list of pairs with model and alias id: {@link Pair#left} contains
- * {@link Model#getId()} and {@link Pair#right} conatins
- * {@link lcsb.mapviewer.model.map.layout.alias.Alias#id}.
- *
- */
- protected List<Pair<Integer, Integer>> deserializeJsonIds(String string) {
- List<Pair<Integer, Integer>> result = new ArrayList<>();
- @SuppressWarnings("unchecked")
- List<List<?>> list = new Gson().fromJson(string, List.class);
- for (List<?> list2 : list) {
- Integer left = null;
- Object leftObj = list2.get(0);
- if (leftObj instanceof Double) {
- left = ((Double) leftObj).intValue();
- } else if (leftObj instanceof String) {
- left = Integer.valueOf((String) leftObj);
- } else {
- throw new InvalidArgumentException("Don't know how to handle class: " + leftObj.getClass());
- }
-
- Integer right = null;
- Object rightObj = list2.get(1);
- if (rightObj instanceof Double) {
- right = ((Double) rightObj).intValue();
- } else if (rightObj instanceof String) {
- right = Integer.valueOf((String) rightObj);
- } else {
- throw new InvalidArgumentException("Don't know how to handle class: " + rightObj.getClass());
- }
-
- result.add(new Pair<Integer, Integer>(left, right));
- }
- return result;
- }
-
-
-}
+package lcsb.mapviewer.bean;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.beans.PropertyVetoException;
+import java.beans.VetoableChangeListener;
+import java.beans.VetoableChangeSupport;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintStream;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.annotation.PostConstruct;
+import javax.faces.component.UIComponent;
+import javax.faces.context.ExternalContext;
+import javax.faces.context.FacesContext;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.bean.utils.IPrimefacesUtils;
+import lcsb.mapviewer.bean.utils.PrimefacesUtils;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.events.Event;
+import lcsb.mapviewer.events.Listener;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Abstarct bean class containing basic functionality common for all beans
+ * (property change listeners and vetoable property change listeners).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class AbstractManagedBean implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Util class used to access information about current reqruest and general
+ * information about P framework.
+ */
+ private transient IPrimefacesUtils primefacesUtils = new PrimefacesUtils();
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(AbstractManagedBean.class);
+
+ /**
+ * Set of verification listeners called when some property is changed. It's
+ * marked transient because we don't want to store this in session. TODO it's
+ * should be modified.
+ */
+ private final VetoableChangeSupport vchs = new VetoableChangeSupport(this);
+
+ /**
+ * Set of listeners called when some property is changed. It's marked
+ * transient because we don't want to store this in session. TODO it's should
+ * be modified.
+ */
+ private final PropertyChangeSupport pchs = new PropertyChangeSupport(this);
+
+ /**
+ * This map contains information about {@link Listener listeners} that should
+ * be handled when {@link #callListeners(Event)} method is called. It's marked
+ * transient because we don't want to store this in session. TODO it's should
+ * be modified.
+ */
+ private transient Map<Class<? extends Event>, List<Listener<?>>> listeners = new HashMap<Class<? extends Event>, List<Listener<?>>>();
+
+
+ /**
+ * Default constructor. Adds generic log listener to property change
+ * listeners.
+ */
+ public AbstractManagedBean() {
+ // logger property listener
+ PropertyChangeListener propertyChangeLogger = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: " + arg0.getOldValue() + " New: " + arg0.getNewValue());
+ }
+
+ };
+ addPropertyChangeListener(propertyChangeLogger);
+
+ }
+
+ /**
+ * Method run after creating all the beans. It's used for data initalization.
+ */
+ public abstract void init();
+
+ /**
+ * Initialize common data and call custom initializer of the bean.
+ */
+ @PostConstruct
+ public void internalInit() {
+ createSession();
+ logger.debug("Initializing bean: " + this);
+
+ // call init method for specific bean
+ init();
+ logger.debug("Bean: " + this + " initialized.");
+ }
+
+ /**
+ * Creates http session if session hasn't been created yet.
+ */
+ public void createSession() {
+ getPrimefacesUtils().createSession();
+ }
+
+ /**
+ * Add property change listener that can VETO (cancel) the property change.
+ *
+ * @param listener
+ * property listener
+ */
+ public final void addVetoablePropertyChangeListener(final VetoableChangeListener listener) {
+ vchs.addVetoableChangeListener(listener);
+ }
+
+ /**
+ * Removes property change l;istener that can VETO from the available
+ * listeners.
+ *
+ * @param listener
+ * listeren to be removed
+ */
+ public final void removeVetoablePropertyChangeListener(final VetoableChangeListener listener) {
+ vchs.removeVetoableChangeListener(listener);
+ }
+
+ /**
+ * Adds property change listener that is fired after property of a bean is
+ * changed.
+ *
+ * @param listener
+ * listener to be added
+ */
+ public final void addPropertyChangeListener(final PropertyChangeListener listener) {
+ pchs.addPropertyChangeListener(listener);
+ }
+
+ /**
+ * Removes property change listener from the list of all available listeners.
+ *
+ * @param listener
+ * listener to be removed
+ */
+ public final void removePropertyChangeListener(final PropertyChangeListener listener) {
+ pchs.removePropertyChangeListener(listener);
+ }
+
+ /**
+ * Method that fires all vetoable property change listener for a given
+ * property.
+ *
+ * @param propertyName
+ * property that has changed
+ * @param oldValue
+ * old value of the property
+ * @param newValue
+ * new value of the property
+ * @throws PropertyVetoException
+ * if the change shouldn't be made this exception is thrown
+ */
+ protected final void fireVetoableChange(final String propertyName, final Object oldValue, final Object newValue) throws PropertyVetoException {
+ vchs.fireVetoableChange(propertyName, oldValue, newValue);
+ }
+
+ /**
+ * Method fires property change listener for a given property.
+ *
+ * @param propertyName
+ * name of the property that has changed
+ * @param oldValue
+ * old value of the property
+ * @param newValue
+ * new value of the property
+ */
+ protected final void firePropertyChange(final String propertyName, final Object oldValue, final Object newValue) {
+ if (oldValue != null || newValue != null) {
+ pchs.firePropertyChange(propertyName, oldValue, newValue);
+ }
+ }
+
+ /**
+ * Returns list of all property change listeners for the bean (includes only
+ * standard property change listeners, vetoable property change listeners are
+ * excluded).
+ *
+ * @return list of property change listeners
+ */
+ protected final PropertyChangeListener[] getPropertyChangeListeners() {
+ return pchs.getPropertyChangeListeners();
+ }
+
+ // TODO refactor these two methods to reduce copy-paste
+
+ /**
+ * Method sends to a client response with an attached file. The content of the
+ * file is taken from the content param. Type defines MimeType of the content
+ * (text file, xml, etc.) - this helps browser to properly handle response.
+ *
+ * @param content
+ * - string with the file content
+ * @param fileName
+ * - name of the file that should popup in the client browser
+ * @param type
+ * - MIME type of the file
+ * @throws IOException
+ * exception thrown when there are some problems with sending file
+ */
+ protected final void sendFileAsResponse(String content, String fileName, MimeType type) throws IOException {
+ // send the response to client
+ FacesContext fc = FacesContext.getCurrentInstance();
+ ExternalContext ec = fc.getExternalContext();
+
+ ec.responseReset();
+ ec.setResponseContentType(type.getTextRepresentation());
+ ec.setResponseHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
+ ec.addResponseHeader("Content-Type", type.getTextRepresentation());
+
+ OutputStream output = ec.getResponseOutputStream();
+ PrintStream printStream = new PrintStream(output);
+ printStream.print(content);
+
+ fc.responseComplete();
+ }
+
+ /**
+ * Method sends to a client response with an attached file. Type defines
+ * MimeType of the file content (text file, xml, etc.) - this helps browser to
+ * properly handle response.
+ *
+ * @param file
+ * - file which will be sent
+ * @param fileName
+ * - name of the file that should popup in the client browser
+ * @param type
+ * - MIME type of the file
+ * @throws IOException
+ * exception thrown when there are some problems with sending file
+ */
+ protected void sendFileAsResponse(File file, String fileName, MimeType type) throws IOException {
+
+ // start sending
+ FacesContext fc = FacesContext.getCurrentInstance();
+ ExternalContext ec = fc.getExternalContext();
+
+ ec.responseReset();
+ ec.setResponseContentType(type.getTextRepresentation());
+ ec.setResponseHeader("Content-Disposition", "attachment; filename=\"" + fileName + "\"");
+
+ // attach file
+ OutputStream output = ec.getResponseOutputStream();
+ FileInputStream is = new FileInputStream(file);
+ IOUtils.copy(is, output);
+ fc.responseComplete();
+
+ }
+
+ /**
+ * Clears whole data shared by this bean.
+ */
+ public abstract void clear();
+
+ /**
+ * Register new {@link Listener} in this bean.
+ *
+ * @param listener
+ * listener that should be added
+ */
+ public void registerListener(Listener<?> listener) {
+ List<Listener<?>> listenerList = getListeners().get(listener.getEventClass());
+ if (listenerList == null) {
+ listenerList = new ArrayList<Listener<?>>();
+ listeners.put(listener.getEventClass(), listenerList);
+ }
+ listenerList.add(listener);
+ }
+
+ /**
+ * This method will call all listeners associated with the specified
+ * {@link Event}.
+ *
+ * @param event
+ * {@link Event} for which listeners will be called
+ */
+ protected void callListeners(Event event) {
+ List<Listener<?>> listenerList = getListeners().get(event.getClass());
+ if (listenerList == null) {
+ logger.warn("No listeners found for event: " + event);
+ } else {
+ for (Listener<?> listener : listenerList) {
+ listener.handleEvent(event);
+ }
+ }
+
+ }
+
+ /**
+ * Unregister {@link Listener} from this bean.
+ *
+ * @param listener
+ * listener that should be removed
+ */
+ public void unregisterListener(Listener<?> listener) {
+ List<Listener<?>> listenerList = listeners.get(listener.getEventClass());
+ if (listenerList == null) {
+ listenerList = new ArrayList<Listener<?>>();
+ listeners.put(listener.getEventClass(), listenerList);
+ }
+ if (listenerList.contains(listener)) {
+ listenerList.remove(listener);
+ } else {
+ throw new InvalidArgumentException("Listener " + listener + " wasn't registered.");
+ }
+
+ }
+
+ /**
+ * @param primefacesUtils
+ * the primefacesUtils to set
+ * @see #primefacesUtils
+ */
+ protected void setPrimefacesUtils(IPrimefacesUtils primefacesUtils) {
+ this.primefacesUtils = primefacesUtils;
+ }
+
+ /**
+ * Returns value of the parameter from http request call.
+ *
+ * @param name
+ * name of the parameter
+ * @return value of the request parameter
+ */
+ protected String getRequestParameter(String name) {
+ return getPrimefacesUtils().getRequestParameter(name);
+ }
+
+ /**
+ * Adds a parameter that will be stored in user session.
+ *
+ * @param key
+ * name of the parameter
+ * @param value
+ * value of the parameter
+ */
+ protected void addSessionParam(String key, Object value) {
+ getPrimefacesUtils().addSessionParam(key, value);
+ }
+
+ /**
+ * Gets a value of the parameter stored in user session.
+ *
+ * @param key
+ * name of the parameter
+ * @return value of the user session parameter
+ */
+ protected Object getSessionParam(String key) {
+ return getPrimefacesUtils().getSessionParam(key);
+ }
+
+ /**
+ * @return the version of primefaces library
+ */
+ public String getPrimefacesVersion() {
+ return getPrimefacesUtils().getVersion();
+ }
+
+ /**
+ * Returns path on hard drive where the project is deplyed.
+ *
+ * @return path where the projest is running
+ */
+ public String getProjectDeployPath() {
+ return getPrimefacesUtils().getPath();
+ }
+
+ /**
+ * Sends an error message to the client.
+ *
+ * @param message
+ * error message to be sent
+ */
+ protected void sendError(String message) {
+ getPrimefacesUtils().error(message);
+ }
+
+ /**
+ * Sends an error message to the client.
+ *
+ * @param message
+ * error message to be sent
+ * @param exception
+ * exception which caused the error
+ */
+ protected void sendError(String message, Exception exception) {
+ logger.error(message, exception);
+ getPrimefacesUtils().error(message);
+ }
+
+ /**
+ * Sends info message to the client.
+ *
+ * @param message
+ * info message to be sent
+ */
+ protected void sendInfo(String message) {
+ getPrimefacesUtils().info(message);
+ }
+
+ /**
+ * Returns ip address of current client.
+ *
+ * @return IP addresss of the client
+ */
+ protected String getClientIpAddress() {
+ return getPrimefacesUtils().getClientIpAddress();
+ }
+
+ /**
+ * Returns a {@link UIComponent} corresponding to the client side component
+ * with the identifier given in the parameter.
+ *
+ * @param id
+ * identifier of a component
+ * @return {@link UIComponent} corresponding to the client side component with
+ * the identifier given in the parameter
+ */
+ protected UIComponent findComponent(String id) {
+ return getPrimefacesUtils().findComponent(id);
+ }
+
+ /**
+ * Returns bean identified by {@link Class}.
+ *
+ * @param clazz
+ * class of the bean
+ * @param <T>
+ * class of the bean
+ * @return bean identified by {@link Class}
+ */
+ public <T> T findBean(Class<T> clazz) {
+ return getPrimefacesUtils().findBean(clazz);
+ }
+
+ /**
+ * @return primefacesUtils.
+ */
+ public IPrimefacesUtils getPrimefacesUtils() {
+ if (primefacesUtils == null) {
+ primefacesUtils = new PrimefacesUtils();
+ }
+ return primefacesUtils;
+ }
+
+ /**
+ * @return listeners.
+ */
+ public Map<Class<? extends Event>, List<Listener<?>>> getListeners() {
+ if (listeners == null) {
+ listeners = new HashMap<Class<? extends Event>, List<Listener<?>>>();
+ }
+ return listeners;
+ }
+
+ /**
+ * @param listeners
+ * general listeners.
+ */
+ public void setListeners(Map<Class<? extends Event>, List<Listener<?>>> listeners) {
+ this.listeners = listeners;
+ }
+
+ /**
+ * Executes javascript code on the client browser.
+ *
+ * @param javascript
+ * javascript code
+ */
+ public void executeJavascript(String javascript) {
+ getPrimefacesUtils().executeJavascript(javascript);
+ }
+
+ /**
+ * Transform json string representing list of pairs with model and object id
+ * (it can be list of alias ids or reaction ids) into a {@link List} of
+ * {@link Pair pairs}.
+ *
+ * @param string
+ * list containing pairs of identifiers
+ * @return list of pairs with model and alias id: {@link Pair#left} contains
+ * {@link Model#getId()} and {@link Pair#right} conatins
+ * {@link lcsb.mapviewer.model.map.species.Element#id}.
+ *
+ */
+ protected List<Pair<Integer, Integer>> deserializeJsonIds(String string) {
+ List<Pair<Integer, Integer>> result = new ArrayList<>();
+ @SuppressWarnings("unchecked")
+ List<List<?>> list = new Gson().fromJson(string, List.class);
+ for (List<?> list2 : list) {
+ Integer left = null;
+ Object leftObj = list2.get(0);
+ if (leftObj instanceof Double) {
+ left = ((Double) leftObj).intValue();
+ } else if (leftObj instanceof String) {
+ left = Integer.valueOf((String) leftObj);
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle class: " + leftObj.getClass());
+ }
+
+ Integer right = null;
+ Object rightObj = list2.get(1);
+ if (rightObj instanceof Double) {
+ right = ((Double) rightObj).intValue();
+ } else if (rightObj instanceof String) {
+ right = Integer.valueOf((String) rightObj);
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle class: " + rightObj.getClass());
+ }
+
+ result.add(new Pair<Integer, Integer>(left, right));
+ }
+ return result;
+ }
+
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java b/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
index dc92c1cc86..a0a0fd6a43 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
@@ -14,8 +14,8 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.ElementIdentifierDetails;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
@@ -239,8 +239,8 @@ public class ChemicalBean extends AbstractMarkerManagerBean<ChemicalView> implem
Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
- Alias alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
- List<Alias> list = new ArrayList<>();
+ Element alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ List<Element> list = new ArrayList<>();
list.add(alias);
List<ChemicalView> chemicals = chemicalService
.getForTargets(list, new DbSearchCriteria().model(getCurrentTopModel()).organisms(mapBean.getOrganism()).disease(getCurrentProject().getDisease()));
diff --git a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
index f1514b7ef7..dbd1bb3205 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
@@ -16,8 +16,8 @@ import lcsb.mapviewer.commands.SubModelCommand;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.interfaces.IUserService;
@@ -338,8 +338,8 @@ public class DrugBean extends AbstractMarkerManagerBean<DrugView> implements Ser
Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
- Alias alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
- List<Alias> list = new ArrayList<>();
+ Element alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ List<Element> list = new ArrayList<>();
list.add(alias);
List<DrugView> drugs = drugService.getForTargets(list, new DbSearchCriteria().model(getCurrentTopModel()).organisms(mapBean.getOrganism()));
for (DrugView drugView : drugs) {
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
index f289d8ad19..1f7734ae50 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
@@ -52,25 +52,25 @@ import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
-import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.services.interfaces.IExporterService;
import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
import lcsb.mapviewer.services.interfaces.ILayoutService;
@@ -289,7 +289,7 @@ public class ExportBean extends AbstractManagedBean {
annotations.put(mt, 0);
}
for (Model model2 : models) {
- for (Alias alias : model2.getAliases()) {
+ for (Element alias : model2.getAliases()) {
for (MiriamData md : alias.getMiriamData()) {
Integer amount = annotations.get(md.getDataType());
amount += 1;
@@ -699,11 +699,11 @@ public class ExportBean extends AbstractManagedBean {
}
Set<String> components = new HashSet<String>();
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ for (Compartment alias : model.getCompartmentsAliases()) {
components.add(alias.getName());
}
for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- for (CompartmentAlias alias : submodel.getSubmodel().getModel().getCompartmentsAliases()) {
+ for (Compartment alias : submodel.getSubmodel().getModel().getCompartmentsAliases()) {
components.add(alias.getName());
}
}
@@ -893,7 +893,7 @@ public class ExportBean extends AbstractManagedBean {
mapBean.addPropertyChangeListener(modelPropertyChangeListener);
for (ExportColumn type : ExportColumn.values()) {
- if (type.getClazz().isAssignableFrom(SpeciesAlias.class)) {
+ if (type.getClazz().isAssignableFrom(Species.class)) {
speciesColumnMap.put(type.getTitle(), type);
speciesColumnList.add(type.getTitle());
}
@@ -1056,18 +1056,18 @@ public class ExportBean extends AbstractManagedBean {
protected Map<String, Class<?>> getSpeciesTypeMap() {
if (speciesTypeMap == null) {
speciesTypeMap = new LinkedHashMap<>();
- speciesTypeMap.put("Antisense RNA", AntisenseRnaAlias.class);
- speciesTypeMap.put("Complex", ComplexAlias.class);
- speciesTypeMap.put("Degraded", DegradedAlias.class);
- speciesTypeMap.put("Drug", DrugAlias.class);
- speciesTypeMap.put("Gene", GeneAlias.class);
- speciesTypeMap.put("Ion", IonAlias.class);
- speciesTypeMap.put("Phenotype", PhenotypeAlias.class);
- speciesTypeMap.put("Protein", ProteinAlias.class);
- speciesTypeMap.put("RNA", RnaAlias.class);
- speciesTypeMap.put("Molecule", SimpleMoleculeAlias.class);
- speciesTypeMap.put("Unknown", UnknownAlias.class);
- speciesTypeMap.put("All", SpeciesAlias.class);
+ speciesTypeMap.put("Antisense RNA", AntisenseRna.class);
+ speciesTypeMap.put("Complex", Complex.class);
+ speciesTypeMap.put("Degraded", Degraded.class);
+ speciesTypeMap.put("Drug", Drug.class);
+ speciesTypeMap.put("Gene", Gene.class);
+ speciesTypeMap.put("Ion", Ion.class);
+ speciesTypeMap.put("Phenotype", Phenotype.class);
+ speciesTypeMap.put("Protein", Protein.class);
+ speciesTypeMap.put("RNA", Rna.class);
+ speciesTypeMap.put("Molecule", SimpleMolecule.class);
+ speciesTypeMap.put("Unknown", Unknown.class);
+ speciesTypeMap.put("All", Species.class);
}
return speciesTypeMap;
}
@@ -1149,7 +1149,7 @@ public class ExportBean extends AbstractManagedBean {
// if it's clean then remove coloring
new ColorModelCommand(colorModel, new HashSet<>()).execute();
}
- for (Alias alias : colorModel.getAliases()) {
+ for (Element alias : colorModel.getAliases()) {
alias.setVisibilityLevel(0);
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
index 054068c878..9932115018 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
@@ -20,12 +20,12 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.interfaces.ICommentService;
@@ -269,8 +269,8 @@ public class FeedbackBean extends AbstractMarkerManagerBean<FullCommentView> imp
public String getDescription(final Object object) {
if (object instanceof Reaction) {
return "Reaction: " + ((Reaction) object).getIdReaction();
- } else if (object instanceof Alias) {
- Alias alias = (Alias) object;
+ } else if (object instanceof Element) {
+ Element alias = (Element) object;
return alias.getStringType() + ": " + alias.getName();
} else {
throw new InvalidArgumentException("Unknown class type: " + object.getClass());
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java b/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
index b36c42ac14..3dd2136c55 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
@@ -851,7 +851,7 @@ public class MapBean extends AbstractManagedBean implements Serializable {
* Sends list of aliases (with given identifiers) to the browser. Identifiers
* are passed as a json string in request parameter <i>ids</i>. Each
* identifier is a pair containing information about {@link Model#getId()
- * model id} and {@link lcsb.mapviewer.model.map.layout.alias.Alias#id alias
+ * model id} and {@link lcsb.mapviewer.model.map.species.Element#id alias
* id}. Data is very light - contains only information about the location on
* the model.
*
@@ -868,7 +868,7 @@ public class MapBean extends AbstractManagedBean implements Serializable {
* Sends list of aliases (with given identifiers) to the browser. Identifiers
* are passed as a json string in request parameter <i>ids</i>. Each
* identifier is a pair containing information about {@link Model#getId()
- * model id} and {@link lcsb.mapviewer.model.map.layout.alias.Alias#id alias
+ * model id} and {@link lcsb.mapviewer.model.map.species.Element#id alias
* id}. Data is heavy - it contains all information related to the alias.
*
*/
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java b/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
index 074aa86431..6915f552c1 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
@@ -13,8 +13,8 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.search.ElementIdentifierDetails;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
@@ -186,8 +186,8 @@ public class MiRNABean extends AbstractMarkerManagerBean<MiRNAView> implements S
Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
- Alias alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
- List<Alias> list = new ArrayList<>();
+ Element alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ List<Element> list = new ArrayList<>();
list.add(alias);
List<MiRNAView> mirnas = miRNAService.getForTargets(list, new DbSearchCriteria().model(getCurrentTopModel()).organisms(mapBean.getOrganism()));
for (MiRNAView mirnaView : mirnas) {
--
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