From d357d2b275a4ea785cb8d3c73e01b04e1a08d38c Mon Sep 17 00:00:00 2001
From: "piotr.gawron" <piotr.gawron@uni-new>
Date: Fri, 30 Sep 2016 18:35:56 +0200
Subject: [PATCH] cell designer structures moved to celldesigner module, in
progress
---
.../annotators/BiocompendiumAnnotator.java | 6 +-
.../services/annotators/ChebiAnnotator.java | 2 +-
.../services/annotators/ElementAnnotator.java | 4 +-
.../services/annotators/EnsemblAnnotator.java | 8 +-
.../services/annotators/EntrezAnnotator.java | 2 +-
.../services/annotators/GoAnnotator.java | 6 +-
.../services/annotators/HgncAnnotator.java | 8 +-
.../services/annotators/ReconAnnotator.java | 8 +-
.../services/annotators/UniprotAnnotator.java | 6 +-
.../services/ImproperAnnotationsTest.java | 2 +-
.../services/MissingAnnotationTest.java | 2 +-
.../MissingRequiredAnnotationsTest.java | 2 +-
.../services/ModelAnnotatorTest.java | 4 +-
.../annotators/ChebiAnnotatorTest.java | 4 +-
.../annotators/ElementAnnotatorTest.java | 4 +-
.../annotators/EnsemblAnnotatorTest.java | 4 +-
.../annotators/EntrezAnnotatorTest.java | 2 +-
.../services/annotators/GoAnnotatorTest.java | 2 +-
.../annotators/HgncAnnotatorTest.java | 2 +-
.../annotators/ReconAnnotatorTest.java | 2 +-
.../annotators/UniprotAnnotatorTest.java | 2 +-
.../java/lcsb/mapviewer/run/BellExport.java | 2 +-
.../lcsb/mapviewer/run/ConsoleConverter.java | 8 +-
.../java/lcsb/mapviewer/run/DiabetesTest.java | 6 +-
.../mapviewer/run/ReactomeComparison.java | 4 +-
.../lcsb/mapviewer/run/ReactomeExport.java | 14 +-
.../java/lcsb/mapviewer/run/RunOptions.java | 2 +-
.../java/lcsb/mapviewer/run/Statistics.java | 8 +-
.../run/UnknownReactionInReactome.java | 2 +-
.../lcsb/mapviewer/run/VibineSnippet.java | 2 +-
.../CellDesignerElementCollection.java | 9 +-
.../celldesigner/CellDesignerXmlParser.java | 4 +-
.../alias/AbstractAliasXmlParser.java | 2 +-
.../alias/CompartmentAliasXmlParser.java | 2 +-
.../alias/ComplexAliasXmlParser.java | 2 +-
.../alias/SpeciesAliasXmlParser.java | 4 +-
.../celldesigner/annotation/NoteField.java | 4 +-
.../CompartmentCollectionXmlParser.java | 2 +-
.../compartment/CompartmentXmlParser.java | 2 +-
.../ProteinCellDesignerAliasConverter.java | 10 +-
.../UnknownCellDesignerAliasConverter.java | 86 +-
.../reaction/ReactionFromXml.java | 4 +-
.../celldesigner/reaction/ReactionToXml.java | 2 +-
.../species/AbstractElementXmlParser.java | 2 +-
.../species/AntisenseRnaXmlParser.java | 4 +-
.../celldesigner/species/GeneXmlParser.java | 4 +-
.../species/InternalModelSpeciesData.java | 428 ++--
.../celldesigner/species/ProteinMapping.java | 10 +-
.../species/ProteinXmlParser.java | 4 +-
.../celldesigner/species/RnaXmlParser.java | 4 +-
.../species/SpeciesCollection.java | 2 +-
.../species/SpeciesCollectionXmlParser.java | 14 +-
.../celldesigner/species/SpeciesMapping.java | 24 +-
.../species/SpeciesSbmlParser.java | 26 +-
.../celldesigner/structure}/AntisenseRna.java | 3 +-
.../structure}/AntisenseRnaComparator.java | 3 +-
.../structure}/AntisenseRnaRegion.java | 6 +-
.../celldesigner/structure}/Chemical.java | 2 +-
.../celldesigner/structure}/Compartment.java | 3 +-
.../structure}/CompartmentComparator.java | 179 +-
.../structure}/ComplexSpecies.java | 3 +-
.../structure}/ComplexSpeciesComparator.java | 5 +-
.../celldesigner/structure}/Degraded.java | 2 +-
.../structure}/DegradedComparator.java | 2 +-
.../model/celldesigner/structure}/Drug.java | 2 +-
.../structure}/DrugComparator.java | 2 +-
.../celldesigner/structure}/Element.java | 5 +-
.../structure}/ElementComparator.java | 7 +-
.../model/celldesigner/structure}/Gene.java | 3 +-
.../structure}/GeneComparator.java | 3 +-
.../structure}/GenericProtein.java | 2 +-
.../model/celldesigner/structure}/Ion.java | 2 +-
.../structure}/IonChannelProtein.java | 2 +-
.../structure}/IonComparator.java | 2 +-
.../structure}/ModificationResidue.java | 4 +-
.../celldesigner/structure/Phenotype.java | 62 +
.../structure}/PhenotypeComparator.java | 18 +-
.../celldesigner/structure}/Protein.java | 3 +-
.../structure}/ProteinComparator.java | 3 +-
.../structure}/ReceptorProtein.java | 2 +-
.../model/celldesigner/structure}/Rna.java | 3 +-
.../structure}/RnaComparator.java | 3 +-
.../celldesigner/structure}/RnaRegion.java | 6 +-
.../structure}/SimpleMolecule.java | 2 +-
.../structure}/SimpleMoleculeComparator.java | 2 +-
.../celldesigner/structure}/Species.java | 5 +-
.../structure}/SpeciesComparator.java | 3 +-
.../celldesigner/structure/SpeciesState.java | 7 -
.../structure}/TruncatedProtein.java | 2 +-
.../celldesigner/structure}/Unknown.java | 2 +-
.../structure}/UnknownComparator.java | 2 +-
.../celldesigner/types/ModifierTypeUtils.java | 2 +-
.../CellDesignerXmlParserTest.java | 8 +-
.../celldesigner/ComplexParserTests.java | 2 +-
.../celldesigner/LayerXmlParserTest.java | 2 +-
.../NestedComplexParsingTests.java | 4 +-
.../alias/AliasCollectionXmlParserTest.java | 8 +-
.../alias/CompartmentAliasXmlParserTest.java | 4 +-
.../alias/ComplexAliasXmlParserTest.java | 4 +-
.../alias/SpeciesAliasXmlParserTest.java | 8 +-
.../annotation/RestAnnotationParserTest.java | 4 +-
.../CompartmentCollectionXmlParserTest.java | 2 +-
.../compartment/CompartmentXmlParserTest.java | 2 +-
...bstractCellDesignerAliasConverterTest.java | 2 +-
.../IonCellDesignerAliasConverterTest.java | 2 +-
.../geometry/ProteinConverterTest.java | 2 +-
.../ReactionCollectionXmlParserTest.java | 2 +-
.../reaction/ReactionFromXmlTest.java | 2 +-
.../reaction/ReactionParserTests.java | 2 +-
.../reaction/ReactionToXmlTest.java | 4 +-
.../species/AntisenseRnaXmlParserTest.java | 4 +-
.../species/ComplexParserTest.java | 6 +-
.../species/GeneXmlParserTest.java | 6 +-
.../species/InternalModelSpeciesDataTest.java | 100 +-
.../model/celldesigner/species/ModelMock.java | 6 +-
.../species/ProteinMappingTest.java | 2 +-
.../species/ProteinXmlParserTest.java | 4 +-
.../species/RnaXmlParserTest.java | 2 +-
.../species/SpeciesCollectionTest.java | 10 +-
.../SpeciesCollectionXmlParserTest.java | 14 +-
.../species/SpeciesMappingTest.java | 2 +-
.../species/SpeciesSbmlParserTest.java | 34 +-
.../AntisenseRnaComparatorTest.java | 6 +-
.../structure}/AntisenseRnaRegionTest.java | 4 +-
.../structure}/AntisenseRnaTest.java | 5 +-
.../structure}/CompartmentComparatorTest.java | 2 +-
.../structure}/CompartmentTest.java | 4 +-
.../ComplexSpeciesComparatorTest.java | 10 +-
.../structure}/ComplexSpeciesTest.java | 6 +-
.../structure}/DegradedComparatorTest.java | 4 +-
.../celldesigner/structure}/DegradedTest.java | 4 +-
.../structure}/DrugComparatorTest.java | 4 +-
.../celldesigner/structure}/DrugTest.java | 4 +-
.../structure}/ElementComparatorTest.java | 10 +-
.../celldesigner/structure}/ElementTest.java | 7 +-
.../structure}/GeneComparatorTest.java | 9 +-
.../celldesigner/structure}/GeneTest.java | 6 +-
.../structure}/GenericProteinTest.java | 4 +-
.../structure}/IonChannelProteinTest.java | 4 +-
.../structure}/IonComparatorTest.java | 4 +-
.../celldesigner/structure}/IonTest.java | 4 +-
.../structure}/ModificationResidueTest.java | 310 +--
.../structure}/PhenotypeComparatorTest.java | 39 +-
.../structure}/PhenotypeTest.java | 27 +-
.../structure}/PositionToCompartmentTest.java | 76 +-
.../structure}/ProteinComparatorTest.java | 10 +-
.../celldesigner/structure}/ProteinTest.java | 7 +-
.../structure}/ReceptorProteinTest.java | 4 +-
.../structure}/RnaComparatorTest.java | 8 +-
.../structure}/RnaRegionTest.java | 270 +--
.../celldesigner/structure}/RnaTest.java | 337 +--
.../SimpleMoleculeComparatorTest.java | 4 +-
.../structure}/SimpleMoleculeTest.java | 4 +-
.../structure}/SpeciesComparatorTest.java | 13 +-
.../structure/SpeciesStateTest.java | 1 -
.../celldesigner/structure}/SpeciesTest.java | 3 +-
.../structure}/TruncatedProteinTest.java | 4 +-
.../structure}/UnknownComparatorTest.java | 4 +-
.../celldesigner/structure}/UnknownTest.java | 4 +-
.../types/ModifierTypeUtilsTest.java | 4 +-
.../model/sbgnml/SbgnmlXmlExporter.java | 6 +-
.../model/sbgnml/SbgnmlXmlParser.java | 26 +-
.../converter/graphics/AliasConverter.java | 81 +-
.../species/AntisenseRnaConverter.java | 11 +-
.../graphics/species/GeneConverter.java | 4 +-
.../graphics/species/IonConverter.java | 222 +-
.../graphics/species/PhenotypeConverter.java | 146 +-
.../graphics/species/ProteinConverter.java | 6 +-
.../graphics/species/RnaConverter.java | 9 +-
.../SBGNNucleicAcidFeatureConverter.java | 54 +-
.../species/SimpleMoleculeConverter.java | 28 +-
.../graphics/species/UnknownConverter.java | 140 +-
.../graphics/NormalImageGeneratorTest.java | 28 +-
.../graphics/PdfImageGeneratorTest.java | 19 +-
.../placefinder/AllPlaceFinderTest.java | 15 +-
.../species/SpeciesConverterTest.java | 10 +-
.../converter/ComplexZipConverterTest.java | 8 +-
.../CreateChangeFormerSymbolCommand.java | 98 +-
.../detailstab/CreateChangeNameCommand.java | 62 +-
.../CreateChangeSynonymCommand.java | 98 +-
.../gui/detailstab/ElementDetailsPanel.java | 46 +-
.../mapviewer/commands/ColorModelCommand.java | 2 +-
.../mapviewer/commands/SubModelCommand.java | 2 +-
.../AddElementFormerSymbolsCommand.java | 4 +-
.../AddElementMiriamDataCommand.java | 2 +-
.../AddElementPropertyListEntryCommand.java | 186 +-
.../properties/AddElementSynonymsCommand.java | 4 +-
.../ChangeElementFormerSymbolCommand.java | 6 +-
.../ChangeElementFormulaCommand.java | 2 +-
.../ChangeElementFullNameCommand.java | 2 +-
.../ChangeElementMiriamDataCommand.java | 2 +-
.../properties/ChangeElementNotesCommand.java | 2 +-
...ChangeElementPropertyListEntryCommand.java | 256 +--
.../ChangeElementSymbolCommand.java | 2 +-
.../ChangeElementSynonymCommand.java | 6 +-
.../RemoveElementFormerSymbolsCommand.java | 4 +-
.../RemoveElementMiriamDataCommand.java | 4 +-
...RemoveElementPropertyListEntryCommand.java | 186 +-
.../RemoveElementSynonymsCommand.java | 4 +-
.../commands/ColorModelCommandTest.java | 2 +-
.../commands/CommandTestFunctions.java | 6 +-
.../mapviewer/commands/CopyCommandTest.java | 8 +-
.../commands/MoveElementsCommandTest.java | 2 +-
.../lcsb/mapviewer/model/map/MiriamData.java | 2 -
.../lcsb/mapviewer/model/map/MiriamType.java | 8 -
.../model/map/agregator/package-info.java | 5 -
.../mapviewer/model/map/graph/DataMining.java | 424 ++--
.../model/map/layout/ColorSchema.java | 1086 ++++-----
.../map/layout/alias/AntisenseRnaAlias.java | 11 -
.../layout/alias/AntisenseRnaRegionAlias.java | 10 +-
.../model/map/layout/alias/ChemicalAlias.java | 14 +-
.../map/layout/alias/CompartmentAlias.java | 17 -
.../alias/CompartmentAliasComparator.java | 2 -
.../model/map/layout/alias/ComplexAlias.java | 16 -
.../model/map/layout/alias/DegradedAlias.java | 10 -
.../model/map/layout/alias/DrugAlias.java | 5 -
.../model/map/layout/alias/GeneAlias.java | 10 -
.../map/layout/alias/GenericProteinAlias.java | 9 -
.../model/map/layout/alias/IonAlias.java | 6 +-
.../layout/alias/IonChannelProteinAlias.java | 5 -
.../alias/ModificationResidueAlias.java | 1 -
.../alias}/ModificationState.java | 304 +--
.../map/layout/alias/PhenotypeAlias.java | 5 -
.../alias}/PositionToCompartment.java | 151 +-
.../model/map/layout/alias/ProteinAlias.java | 11 -
.../layout/alias/ReceptorProteinAlias.java | 5 -
.../model/map/layout/alias/RnaAlias.java | 7 +-
.../map/layout/alias/RnaRegionAlias.java | 7 +-
.../map/layout/alias/SimpleMoleculeAlias.java | 10 -
.../model/map/layout/alias/SpeciesAlias.java | 14 -
.../layout/alias/SpeciesAliasComparator.java | 6 +-
.../layout/alias/TruncatedProteinAlias.java | 5 -
.../model/map/layout/alias/UnknownAlias.java | 5 -
.../lcsb/mapviewer/model/map/model/Model.java | 9 +-
.../model/map/model/ModelComparator.java | 71 -
.../mapviewer/model/map/model/ModelData.java | 9 +-
.../model/map/model/ModelFullIndexed.java | 19 +-
.../model/map/modifier/Catalysis.java | 3 -
.../model/map/modifier/Inhibition.java | 2 -
.../model/map/modifier/Modulation.java | 5 +-
.../map/modifier/PhysicalStimulation.java | 3 -
.../mapviewer/model/map/modifier/Trigger.java | 5 +-
.../model/map/modifier/UnknownCatalysis.java | 3 -
.../model/map/modifier/UnknownInhibition.java | 3 -
.../model/map/reaction/Modifier.java | 7 +-
.../mapviewer/model/map/reaction/Product.java | 7 +-
.../model/map/reaction/Reactant.java | 7 +-
.../model/map/reaction/Reaction.java | 3 +-
.../model/map/reaction/ReactionNode.java | 16 +-
.../map/reaction/ReactionNodeComparator.java | 2 -
.../model/map/species/Phenotype.java | 117 -
.../map/species/fields/AssociatedElement.java | 150 --
.../fields/AssociatedElementComparator.java | 90 -
.../map/species/fields/package-info.java | 8 -
.../model/map/species/package-info.java | 11 -
.../modelutils/map/ElementUtils.java | 31 +-
.../modelutils/map/RequireAnnotationMap.java | 8 -
.../lcsb/mapviewer/model/map/AllMapTests.java | 6 -
.../mapviewer/model/map/MiriamDataTest.java | 5 +-
.../map/agregator/AllAgregatorTests.java | 13 -
.../model/map/graph/DataMiningTest.java | 187 +-
.../model/map/layout/ColorSchemaTest.java | 17 +-
.../map/layout/alias/AliasComparatorTest.java | 3 -
.../map/layout/alias/AliasGroupTest.java | 2 -
.../alias/CompartmentAliasComparatorTest.java | 2 -
.../layout/alias/CompartmentAliasTest.java | 7 +-
.../alias/ComplexAliasComparatorTest.java | 3 -
.../map/layout/alias/ComplexAliasTest.java | 1 -
.../alias}/ModificationStateTest.java | 78 +-
.../alias/SpeciesAliasComparatorTest.java | 24 +-
.../map/layout/alias/SpeciesAliasTest.java | 6 +-
...AliasSubmodelConnectionComparatorTest.java | 4 -
.../model/map/model/ModelComparatorTest.java | 11 +-
.../model/map/model/ModelDataTest.java | 3 -
.../model/map/model/ModelFullIndexedTest.java | 5 -
...ModelSubmodelConnectionComparatorTest.java | 2 -
.../mapviewer/model/map/model/ModelTest.java | 11 -
.../SubmodelConnectionComparatorTest.java | 2 -
.../model/map/modifier/CatalysisTest.java | 2 -
.../model/map/modifier/InhibitionTest.java | 1 -
.../model/map/modifier/ModulationTest.java | 1 -
.../map/modifier/PhysicalStimulationTest.java | 1 -
.../model/map/modifier/TriggerTest.java | 1 -
.../map/modifier/UnknownInhibitionTest.java | 1 -
.../reaction/NodeOperatorComparatorTest.java | 8 -
.../map/reaction/ReactionComparatorTest.java | 4 -
.../reaction/ReactionNodeComparatorTest.java | 5 -
.../model/map/reaction/ReactionTest.java | 5 +-
.../model/map/species/AllSpeciesTests.java | 42 -
.../species/fields/AllSpeciesFieldsTests.java | 19 -
.../AssociatedElementComparatorTest.java | 111 -
.../species/fields/AssociatedElementTest.java | 62 -
.../modelutils/map/ElementUtilsTest.java | 16 +-
.../wikipathway/XML/ModelContructor.java | 8 +-
.../model/GpmlModificationType.java | 272 +--
.../mapviewer/wikipathway/model/State.java | 516 ++---
.../wikipathway/XML/StateParserTest.java | 2 +-
.../persist/dao/map/graph/DataMiningDao.java | 110 +-
.../persist/dao/map/species/SpeciesDao.java | 42 +-
.../mapviewer/persist/dao/ProjectDaoTest.java | 6 +-
.../persist/dao/map/CommentDaoTest.java | 10 +-
.../persist/dao/map/LayoutDaoTest.java | 4 +-
.../persist/dao/map/ModelDaoTest.java | 14 +-
.../dao/map/graph/DataMiningDaoTest.java | 76 +-
.../dao/map/layout/alias/AliasDaoTest.java | 8 +-
.../dao/map/layout/alias/AliasDaoTest2.java | 4 +-
.../dao/map/species/AntisenseRnaTest.java | 6 +-
.../persist/dao/user/UserDaoTest.java | 562 ++---
.../reactome/utils/DataFormatter.java | 2 +-
.../mapviewer/reactome/utils/ElementUtil.java | 2 +-
.../reactome/utils/ReactionComparator.java | 2 +-
.../ComplexAndSimpleEntityComparator.java | 2 +-
...tityWithAccessionedSequenceComparator.java | 2 +-
.../DrugAndCatalystComparator.java | 2 +-
.../GeneAndDefinedSetComparator.java | 2 +-
.../GeneAndOtherEntityComparator.java | 2 +-
.../comparators/IonAndCatalystComparator.java | 2 +-
.../comparators/IonAndComplexComparator.java | 2 +-
.../IonAndDefinedSetComparator.java | 2 +-
...tityWithAccessionedSequenceComparator.java | 2 +-
.../IonAndSimpleEntityComparator.java | 2 +-
.../utils/comparators/MatchResult.java | 2 +-
.../MoleculeAndCatalystComparator.java | 2 +-
.../MoleculeAndComplexComparator.java | 2 +-
.../MoleculeAndDefinedSetComparator.java | 2 +-
...tityWithAccessionedSequenceComparator.java | 2 +-
.../MoleculeAndSimpleEntityComparator.java | 2 +-
.../utils/comparators/NodeComparator.java | 2 +-
.../ProteinAndCandidateSetComparator.java | 2 +-
.../ProteinAndCatalystComparator.java | 2 +-
.../ProteinAndComplexComparator.java | 2 +-
.../ProteinAndDefinedSetComparator.java | 2 +-
...tityWithAccessionedSequenceComparator.java | 2 +-
.../ProteinAndGenomeEncodedEntity.java | 2 +-
.../ProteinAndOtherEntityComparator.java | 2 +-
.../ProteinAndPolymerComparator.java | 2 +-
.../ProteinAndSimpleEntityComparator.java | 2 +-
.../UnknownAndCatalystComparator.java | 2 +-
...knownAndGenomeEncodedEntityComparator.java | 2 +-
.../services/impl/DataMiningService.java | 2 +-
.../services/impl/ExporterService.java | 34 +-
.../services/impl/LayoutService.java | 1952 ++++++++---------
.../mapviewer/services/impl/ModelService.java | 4 +-
.../services/impl/ProjectService.java | 2 +-
.../services/impl/SearchService.java | 22 +-
.../interfaces/IDataMiningService.java | 2 +-
.../services/search/SearchResultFactory.java | 12 +-
.../services/search/data/FullAliasView.java | 4 +-
.../search/data/FullAliasViewFactory.java | 8 +-
.../services/search/db/IDbSearchService.java | 2 +-
.../search/db/chemical/ChemicalService.java | 8 +-
.../db/chemical/ChemicalViewFactory.java | 2 +-
.../search/db/drug/DrugViewFactory.java | 4 +-
.../search/db/mirna/MiRNAService.java | 8 +-
.../search/db/mirna/MiRNAViewFactory.java | 238 +-
.../services/utils/SearchIndexer.java | 2 +-
.../services/utils/data/ExportColumn.java | 2 +-
.../view/PubmedAnnotatedElementsView.java | 2 +-
.../services/impl/DataMiningServiceTest.java | 6 +-
.../services/impl/DataMiningServiceTest2.java | 8 +-
.../services/impl/ExporterServiceTest.java | 1058 ++++-----
.../services/impl/LayoutServiceTest2.java | 494 ++---
.../services/impl/LogServiceTest.java | 268 +--
.../services/impl/ProjectServiceTest.java | 4 +-
.../services/impl/SearchServiceTest.java | 20 +-
.../search/SearchResultFactoryTest.java | 4 +-
.../search/data/FullAliasViewFactoryTest.java | 8 +-
.../db/chemical/ChemicalServiceTest.java | 202 +-
.../search/db/drug/DrugServiceTest.java | 6 +-
.../search/db/drug/DrugViewFactoryTest.java | 310 +--
.../utils/graph/MissingConnectionDaoTest.java | 206 +-
.../lcsb/mapviewer/bean/ChemicalBean.java | 2 +-
.../java/lcsb/mapviewer/bean/DrugBean.java | 842 +++----
.../java/lcsb/mapviewer/bean/ExportBean.java | 24 +-
.../lcsb/mapviewer/bean/FeedbackBean.java | 2 +-
.../java/lcsb/mapviewer/bean/MiRNABean.java | 2 +-
376 files changed, 7148 insertions(+), 8210 deletions(-)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/AntisenseRna.java (93%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/AntisenseRnaComparator.java (91%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species/fields => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/AntisenseRnaRegion.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Chemical.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/agregator => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Compartment.java (93%)
rename {model/src/main/java/lcsb/mapviewer/model/map/agregator => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/CompartmentComparator.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ComplexSpecies.java (94%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ComplexSpeciesComparator.java (93%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Degraded.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/DegradedComparator.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Drug.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/DrugComparator.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Element.java (98%)
rename {model/src/main/java/lcsb/mapviewer/model/map => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ElementComparator.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Gene.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/GeneComparator.java (91%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/GenericProtein.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Ion.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/IonChannelProtein.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/IonComparator.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species/fields => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ModificationResidue.java (93%)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/PhenotypeComparator.java (62%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Protein.java (94%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ProteinComparator.java (93%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ReceptorProtein.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Rna.java (93%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/RnaComparator.java (92%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species/fields => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/RnaRegion.java (91%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/SimpleMolecule.java (91%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/SimpleMoleculeComparator.java (94%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Species.java (94%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/SpeciesComparator.java (96%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/TruncatedProtein.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/Unknown.java (90%)
rename {model/src/main/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure}/UnknownComparator.java (92%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/AntisenseRnaComparatorTest.java (87%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species/fields => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/AntisenseRnaRegionTest.java (93%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/AntisenseRnaTest.java (91%)
rename {model/src/test/java/lcsb/mapviewer/model/map/agregator => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/CompartmentComparatorTest.java (93%)
rename {model/src/test/java/lcsb/mapviewer/model/map/agregator => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/CompartmentTest.java (91%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ComplexSpeciesComparatorTest.java (90%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ComplexSpeciesTest.java (87%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/DegradedComparatorTest.java (88%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/DegradedTest.java (83%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/DrugComparatorTest.java (86%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/DrugTest.java (83%)
rename {model/src/test/java/lcsb/mapviewer/model/map => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ElementComparatorTest.java (92%)
rename {model/src/test/java/lcsb/mapviewer/model/map => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ElementTest.java (89%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/GeneComparatorTest.java (90%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/GeneTest.java (86%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/GenericProteinTest.java (82%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/IonChannelProteinTest.java (82%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/IonComparatorTest.java (86%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/IonTest.java (83%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species/fields => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ModificationResidueTest.java (92%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/PhenotypeComparatorTest.java (62%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/PhenotypeTest.java (57%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species/fields => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/PositionToCompartmentTest.java (80%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ProteinComparatorTest.java (83%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ProteinTest.java (86%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/ReceptorProteinTest.java (82%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/RnaComparatorTest.java (84%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species/fields => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/RnaRegionTest.java (85%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/RnaTest.java (85%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/SimpleMoleculeComparatorTest.java (91%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/SimpleMoleculeTest.java (83%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/SpeciesComparatorTest.java (84%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/SpeciesTest.java (94%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/TruncatedProteinTest.java (82%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/UnknownComparatorTest.java (86%)
rename {model/src/test/java/lcsb/mapviewer/model/map/species => converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure}/UnknownTest.java (83%)
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/agregator/package-info.java
rename model/src/main/java/lcsb/mapviewer/model/map/{species/fields => layout/alias}/ModificationState.java (94%)
rename model/src/main/java/lcsb/mapviewer/model/map/{species/fields => layout/alias}/PositionToCompartment.java (78%)
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElement.java
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparator.java
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/fields/package-info.java
delete mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
delete mode 100644 model/src/test/java/lcsb/mapviewer/model/map/agregator/AllAgregatorTests.java
rename model/src/test/java/lcsb/mapviewer/model/map/{species/fields => layout/alias}/ModificationStateTest.java (81%)
delete mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
delete mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/fields/AllSpeciesFieldsTests.java
delete mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparatorTest.java
delete mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementTest.java
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 7fbe3d16ac..5a8ffbd541 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
@@ -32,13 +32,13 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+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.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.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
/**
* This class is responsible for connection to Vencata annotation service. The
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 319445dfea..0ac86df18d 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
@@ -20,13 +20,13 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
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.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;
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 64717722d7..af1b1e6f62 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
@@ -7,6 +7,8 @@ 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.Species;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -14,8 +16,6 @@ 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.Chemical;
-import lcsb.mapviewer.model.map.species.Species;
/**
* Interface that allows to annotate {@link AnnotatedObject elements} in the
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 ff43691925..e467af1db7 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
@@ -20,6 +20,10 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+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.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -28,10 +32,6 @@ 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.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;
/**
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 fe76c9d5d7..41c4c55270 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
@@ -23,6 +23,7 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -32,7 +33,6 @@ 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.GenericProtein;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
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 e232b856f0..5595d42818 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
@@ -21,17 +21,17 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
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.agregator.Compartment;
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.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Phenotype;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
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 2e6170a9bf..b734a9f78f 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
@@ -15,6 +15,10 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+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.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -24,10 +28,6 @@ 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.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;
/**
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 8bc93762e7..1d70b5b048 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
@@ -17,16 +17,16 @@ 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.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
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.Chemical;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
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 ae6cec46b1..6557299e04 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
@@ -17,15 +17,15 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+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.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;
/**
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 099744a303..dbad82e990 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ImproperAnnotationsTest.java
@@ -13,10 +13,10 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
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 {
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 5d3d0aa7e6..fe08330591 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingAnnotationTest.java
@@ -7,8 +7,8 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingAnnotationTest {
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 c6062c60c0..a743f67faf 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotationsTest.java
@@ -11,9 +11,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public class MissingRequiredAnnotationsTest {
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 eb03a32992..70e37ad8b3 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -29,6 +29,8 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -42,8 +44,6 @@ 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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.persist.dao.map.ModelDao;
public class ModelAnnotatorTest extends AnnotationTestFunctions {
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 5049a7a502..c395af2126 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
@@ -25,13 +25,13 @@ import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.data.Chebi;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Chemical;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
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.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.Chemical;
-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;
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 b355a0407f..1d5c8ad097 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
@@ -11,12 +11,12 @@ import org.junit.Test;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
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 {
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 24dc111f73..d46f769e80 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
@@ -24,12 +24,12 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
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 {
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 78352367bd..dde266a54c 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
@@ -28,11 +28,11 @@ import lcsb.mapviewer.annotation.data.EntrezData;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
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;
public class EntrezAnnotatorTest extends AnnotationTestFunctions {
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 a14942ea7c..39572ea55b 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
@@ -25,10 +25,10 @@ import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.data.Go;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
public class GoAnnotatorTest extends AnnotationTestFunctions {
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 1739fa2d83..0a774fba1f 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
@@ -16,11 +16,11 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
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;
public class HgncAnnotatorTest extends AnnotationTestFunctions {
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 e4b824ea69..95ba90d632 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
@@ -21,10 +21,10 @@ 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.converter.model.celldesigner.structure.SimpleMolecule;
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;
public class ReconAnnotatorTest extends AnnotationTestFunctions {
Logger logger = Logger.getLogger(ReconAnnotatorTest.class);
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 92e67a2fc7..100dca76ee 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
@@ -19,11 +19,11 @@ 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.converter.model.celldesigner.structure.GenericProtein;
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;
public class UniprotAnnotatorTest extends AnnotationTestFunctions {
diff --git a/console/src/main/java/lcsb/mapviewer/run/BellExport.java b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
index d280b38887..603295e43e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/BellExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/BellExport.java
@@ -4,8 +4,8 @@ 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.converter.model.celldesigner.structure.Species;
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;
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index c0b76acea0..9bab0dc4be 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -21,12 +21,14 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
@@ -37,8 +39,6 @@ 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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
diff --git a/console/src/main/java/lcsb/mapviewer/run/DiabetesTest.java b/console/src/main/java/lcsb/mapviewer/run/DiabetesTest.java
index 913b48991f..09c363daa0 100644
--- a/console/src/main/java/lcsb/mapviewer/run/DiabetesTest.java
+++ b/console/src/main/java/lcsb/mapviewer/run/DiabetesTest.java
@@ -12,11 +12,13 @@ import java.util.List;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
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.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
@@ -29,8 +31,6 @@ import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import org.apache.log4j.Logger;
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
index 74ea907a17..6d6cf330a4 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
@@ -17,10 +17,10 @@ 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.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
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;
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
index 556976542d..e68583c3ce 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
@@ -14,8 +14,13 @@ import java.util.Set;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
@@ -28,11 +33,6 @@ 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.ComplexSpecies;
-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;
diff --git a/console/src/main/java/lcsb/mapviewer/run/RunOptions.java b/console/src/main/java/lcsb/mapviewer/run/RunOptions.java
index 394f4238f0..c68686c26e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/RunOptions.java
+++ b/console/src/main/java/lcsb/mapviewer/run/RunOptions.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.run;
import java.util.List;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.modelutils.map.ElementUtils;
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index 90dbec74ed..1448d17aa6 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -20,14 +20,14 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+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.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import lcsb.mapviewer.persist.DbUtils;
diff --git a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
index c0f17f66b1..ba1845afc9 100644
--- a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
+++ b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
@@ -19,6 +19,7 @@ import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
@@ -26,7 +27,6 @@ import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
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;
import lcsb.mapviewer.persist.ApplicationContextLoader;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.utils.DataFormatter;
diff --git a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
index 32f4a07f0f..0d4e197c42 100644
--- a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
+++ b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
@@ -8,7 +8,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
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 2c71b7c21e..186ac05c5e 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
@@ -5,11 +5,11 @@ import java.util.List;
import java.util.Map;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class CellDesignerElementCollection {
@@ -44,7 +44,8 @@ public class CellDesignerElementCollection {
private void addElement(Element element, String id) {
if (elementById.get(id) != null) {
- throw new InvalidArgumentException(eu.getElementTag(element) + "Element with given id alread exists. ID: " + id);
+ throw new InvalidArgumentException(
+ "[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t" + "Element with given id alread exists. ID: " + id);
}
elementById.put(id, 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 2623c4cd0c..c672d69e48 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
@@ -33,9 +33,10 @@ 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.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
@@ -51,7 +52,6 @@ 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.Species;
/**
* This class is a parser for CellDesigner files. There are two typical use
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 ee9116d558..f32f4b8625 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.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.layout.alias.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 4768fc6e8d..44a1aafc9c 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
@@ -10,7 +10,7 @@ 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.species.SpeciesCollection;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+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;
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 d0b03bcfbc..6325587594 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
@@ -11,6 +11,7 @@ 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;
@@ -18,7 +19,6 @@ import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
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.species.ComplexSpecies;
/**
* Parser of CellDesigner xml used for parsing complex aliases. Important: Only
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 59e38e69ef..4fb76150be 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
@@ -7,6 +7,8 @@ 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;
@@ -14,8 +16,6 @@ import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
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.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
/**
* Parser of CellDesigner xml used for parsing SpeciesAlias.
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 b654b06476..f64ef822ac 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
@@ -1,10 +1,10 @@
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.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
/**
* Describes structural information that appears in the cell designer notes.
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 239e2c054c..eeeb3105ca 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
@@ -12,7 +12,7 @@ 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.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
/**
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 ea871ffcb6..fdb5c0e3cc 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
@@ -9,7 +9,7 @@ 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.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
/**
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 b794659117..d51a63d444 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
@@ -13,6 +13,11 @@ 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.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.Alias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.IonChannelProteinAlias;
@@ -20,11 +25,6 @@ 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.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;
/**
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 5e2c2eb783..719c38f3b8 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
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.PathIterator;
-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;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * {@link lcsb.mapviewer.db.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> {
- @Override
- public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getEllipseTransformation().getPointOnEllipseByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
-
- @Override
- public PathIterator getBoundPathIterator(SpeciesAlias alias) {
- throw new NotImplementedException("This class doesn't provide boundPath");
- }
-
- @Override
- public Point2D getAnchorPointCoordinates(SpeciesAlias alias, double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- return alias.getCenter();
- }
- Point2D result;
- result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
- return result;
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.PathIterator;
+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;
+
+/**
+ * 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
+ * conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SpeciesAlias> {
+ @Override
+ public Point2D getPointCoordinates(SpeciesAlias alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getEllipseTransformation().getPointOnEllipseByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(SpeciesAlias alias) {
+ throw new NotImplementedException("This class doesn't provide boundPath");
+ }
+
+ @Override
+ public Point2D getAnchorPointCoordinates(SpeciesAlias alias, double angle) {
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ return alias.getCenter();
+ }
+ Point2D result;
+ result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
+ return result;
+
+ }
+
+}
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 295e481344..3cb76024ff 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
@@ -27,7 +27,9 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerP
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.Element;
import lcsb.mapviewer.converter.model.celldesigner.structure.LineProperties;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
@@ -36,7 +38,6 @@ 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.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.model.Model;
@@ -62,7 +63,6 @@ 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.Species;
/**
* This is a part of {@link ReactionXmlParser} class functionality that allows
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 1a41106fac..629a3958b2 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
@@ -21,6 +21,7 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasCon
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerLineTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
@@ -38,7 +39,6 @@ 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.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
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 b276976c94..5dc3dea215 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
@@ -7,7 +7,7 @@ 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.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.layout.alias.Alias;
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 e822b78bf6..99878f25d4 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.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
/**
* Class that performs parsing of the CellDesigner xml for AntisenseRna object.
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 ed3050e1f7..5e14f7b498 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
@@ -8,11 +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.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.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
/**
* Class that performs parsing of the CellDesigner xml for {@link Gene} object.
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 d56085c958..df965befb1 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
@@ -1,214 +1,214 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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;
-
-/**
- * This class contains information about all species in model that are relevant
- * during parsing via CellDesigner parser.
- *
- * @author Piotr Gawron
- *
- */
-public class InternalModelSpeciesData {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(InternalModelSpeciesData.class);
-
- /**
- * Collection of proteins. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Protein> proteins;
-
- /**
- * Collection of genes. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Gene> genes;
-
- /**
- * Collection of genes. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Rna> rnas;
-
- /**
- * Collection of antisense rnas. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<AntisenseRna> antisenseRnas;
-
- /**
- * Collection of phenotypes. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Phenotype> phenotypes;
-
- /**
- * Collection of ions. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Ion> ions;
-
- /**
- * Collection of simple molecules. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<SimpleMolecule> simpleMolecules;
-
- /**
- * Collection of drugs. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Drug> drugs;
-
- /**
- * Collection of unknowns. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Unknown> unknowns;
-
- /**
- * Collection of degraded elements. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<Degraded> degradeds;
-
- /**
- * Collection of complexes.
- */
- private List<ComplexSpecies> complexes = new ArrayList<ComplexSpecies>();
-
- /**
- * Default constructor.
- */
- public InternalModelSpeciesData() {
- proteins = new SpeciesCollection<Protein>();
- genes = new SpeciesCollection<Gene>();
- rnas = new SpeciesCollection<Rna>();
- antisenseRnas = new SpeciesCollection<AntisenseRna>();
- phenotypes = new SpeciesCollection<Phenotype>();
- ions = new SpeciesCollection<Ion>();
- simpleMolecules = new SpeciesCollection<SimpleMolecule>();
- drugs = new SpeciesCollection<Drug>();
- unknowns = new SpeciesCollection<Unknown>();
- degradeds = new SpeciesCollection<Degraded>();
- }
-
- /**
- *
- * @return {@link #proteins}
- */
- public Collection<Protein> getProteins() {
- return proteins.getAll();
- }
-
- /**
- *
- * @return {@link #genes}
- */
- public Collection<Gene> getGenes() {
- return genes.getAll();
- }
-
- /**
- *
- * @return {@link #rnas}
- */
- public Collection<Rna> getRnas() {
- return rnas.getAll();
- }
-
- /**
- *
- * @return {@link #antisenseRnas}
- */
- public Collection<AntisenseRna> getAntisenseRnas() {
- return antisenseRnas.getAll();
- }
-
- /**
- * Updates information about species in the dataset.
- *
- * @param collection
- * 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) {
- updateSpecies(species.getRight(), species.getLeft());
- }
- }
-
- /**
- * Updates information about species in the dataset (identified by
- * celldesigner specific identifier).
- *
- * @param sp
- * species to be updated
- * @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);
- } else {
- throw new InvalidArgumentException("Unknown species type: " + sp.getClass().getName());
- }
- }
-
- /**
- * Returns list of all species in dataset.
- *
- * @return list of all species in dataset
- */
- public Collection<Species> getAll() {
- List<Species> result = new ArrayList<Species>();
-
- result.addAll(genes.getAll());
- result.addAll(rnas.getAll());
- result.addAll(antisenseRnas.getAll());
- result.addAll(phenotypes.getAll());
- result.addAll(ions.getAll());
- result.addAll(simpleMolecules.getAll());
- result.addAll(drugs.getAll());
- result.addAll(unknowns.getAll());
- result.addAll(degradeds.getAll());
- result.addAll(proteins.getAll());
- result.addAll(complexes);
-
- return result;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+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;
+
+/**
+ * This class contains information about all species in model that are relevant
+ * during parsing via CellDesigner parser.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InternalModelSpeciesData {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(InternalModelSpeciesData.class);
+
+ /**
+ * Collection of proteins. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Protein> proteins;
+
+ /**
+ * Collection of genes. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Gene> genes;
+
+ /**
+ * Collection of genes. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Rna> rnas;
+
+ /**
+ * Collection of antisense rnas. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<AntisenseRna> antisenseRnas;
+
+ /**
+ * Collection of phenotypes. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Phenotype> phenotypes;
+
+ /**
+ * Collection of ions. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Ion> ions;
+
+ /**
+ * Collection of simple molecules. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<SimpleMolecule> simpleMolecules;
+
+ /**
+ * Collection of drugs. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Drug> drugs;
+
+ /**
+ * Collection of unknowns. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Unknown> unknowns;
+
+ /**
+ * Collection of degraded elements. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<Degraded> degradeds;
+
+ /**
+ * Collection of complexes.
+ */
+ private List<ComplexSpecies> complexes = new ArrayList<ComplexSpecies>();
+
+ /**
+ * Default constructor.
+ */
+ public InternalModelSpeciesData() {
+ proteins = new SpeciesCollection<Protein>();
+ genes = new SpeciesCollection<Gene>();
+ rnas = new SpeciesCollection<Rna>();
+ antisenseRnas = new SpeciesCollection<AntisenseRna>();
+ phenotypes = new SpeciesCollection<Phenotype>();
+ ions = new SpeciesCollection<Ion>();
+ simpleMolecules = new SpeciesCollection<SimpleMolecule>();
+ drugs = new SpeciesCollection<Drug>();
+ unknowns = new SpeciesCollection<Unknown>();
+ degradeds = new SpeciesCollection<Degraded>();
+ }
+
+ /**
+ *
+ * @return {@link #proteins}
+ */
+ public Collection<Protein> getProteins() {
+ return proteins.getAll();
+ }
+
+ /**
+ *
+ * @return {@link #genes}
+ */
+ public Collection<Gene> getGenes() {
+ return genes.getAll();
+ }
+
+ /**
+ *
+ * @return {@link #rnas}
+ */
+ public Collection<Rna> getRnas() {
+ return rnas.getAll();
+ }
+
+ /**
+ *
+ * @return {@link #antisenseRnas}
+ */
+ public Collection<AntisenseRna> getAntisenseRnas() {
+ return antisenseRnas.getAll();
+ }
+
+ /**
+ * Updates information about species in the dataset.
+ *
+ * @param collection
+ * 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) {
+ updateSpecies(species.getRight(), species.getLeft());
+ }
+ }
+
+ /**
+ * Updates information about species in the dataset (identified by
+ * celldesigner specific identifier).
+ *
+ * @param sp
+ * species to be updated
+ * @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);
+ } else {
+ throw new InvalidArgumentException("Unknown species type: " + sp.getClass().getName());
+ }
+ }
+
+ /**
+ * Returns list of all species in dataset.
+ *
+ * @return list of all species in dataset
+ */
+ public Collection<Species> getAll() {
+ List<Species> result = new ArrayList<Species>();
+
+ result.addAll(genes.getAll());
+ result.addAll(rnas.getAll());
+ result.addAll(antisenseRnas.getAll());
+ result.addAll(phenotypes.getAll());
+ result.addAll(ions.getAll());
+ result.addAll(simpleMolecules.getAll());
+ result.addAll(drugs.getAll());
+ result.addAll(unknowns.getAll());
+ result.addAll(degradeds.getAll());
+ result.addAll(proteins.getAll());
+ result.addAll(complexes);
+
+ return result;
+ }
+}
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 4eab52ba7c..4e968b7396 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
@@ -3,16 +3,16 @@ 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.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
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 fc1c009314..3350a30611 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
@@ -8,10 +8,10 @@ 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.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
/**
* Class that performs parsing of the CellDesigner xml for {@link Protein}
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 9405829076..ffa563d00b 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
@@ -8,10 +8,10 @@ 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.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
/**
* Class that performs parsing of the CellDesigner xml for {@link Rna} object.
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 b6163eee5b..7594604db1 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.model.map.species.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
/**
* This collection performs some magic, so please try no to understand it :). It
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 61fe98c920..db98bc09d9 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
@@ -16,7 +16,13 @@ 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.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+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.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
@@ -26,12 +32,6 @@ 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.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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
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 981859c2c9..abe71c3ce1 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
@@ -1,6 +1,18 @@
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;
@@ -13,18 +25,6 @@ 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.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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;
/**
* This enum contains information about mapping between CellDesigner xml nodes
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 eebd2c75ab..38d6af5ff6 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
@@ -11,28 +11,28 @@ 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.InconsistentModelException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
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.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
-import lcsb.mapviewer.model.map.species.fields.PositionToCompartment;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
/**
* Parser for sbml part of CellDesigner format. It's used for retrieving Species
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
index 2486171748..dbe7dc37c5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRna.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
@@ -15,7 +15,6 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
/**
* Class representing antisense rna in the model.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparator.java
similarity index 91%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparator.java
index 0f0b0e3188..2bb9ff7cb0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
import java.util.HashSet;
@@ -7,7 +7,6 @@ import java.util.Set;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
/**
* This class implements comparator interface for AntisenseRna.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/fields/AntisenseRnaRegion.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
index 0fa6e0fa58..8966d67425 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AntisenseRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegion.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species.fields;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
@@ -19,13 +19,13 @@ import org.hibernate.annotations.CascadeType;
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.ModificationState;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaRegionAlias.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.species.Species;
/**
* This structure contains information about antisense rna region (rna fragment
* of interest) for a specific
- * {@link lcsb.mapviewer.model.map.species.AntisenseRna AntisenseRna}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna AntisenseRna}.
*
* @author Piotr Gawron
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
index 7de4104415..b99380b8be 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Chemical.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.Column;
import javax.persistence.DiscriminatorValue;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/agregator/Compartment.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/agregator/Compartment.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
index a60649bd67..0396a2a81f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/agregator/Compartment.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Compartment.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.agregator;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.HashSet;
import java.util.Set;
@@ -11,7 +11,6 @@ import javax.persistence.OneToMany;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/agregator/CompartmentComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparator.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/agregator/CompartmentComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparator.java
index 7b9fa190fd..0034469773 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/agregator/CompartmentComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparator.java
@@ -1,90 +1,89 @@
-package lcsb.mapviewer.model.map.agregator;
-
-import java.util.Comparator;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.model.map.ElementComparator;
-
-/**
- * This class implements comparator interface for Compartment.
- *
- * @author Piotr Gawron
- *
- * @see Compartment
- *
- */
-public class CompartmentComparator implements Comparator<Compartment> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public CompartmentComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public CompartmentComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Compartment arg0, Compartment 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(Compartment.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in Compartment class
- * in inheritence tree. By the design it calls also comparator of the upper
- * (Element) 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(Compartment arg0, Compartment arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
-
- int result = elementComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- if (!arg0.getElementId().equals(arg1.getElementId())) {
- return arg0.getElementId().compareTo(arg1.getElementId());
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.Comparator;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+
+/**
+ * This class implements comparator interface for Compartment.
+ *
+ * @author Piotr Gawron
+ *
+ * @see Compartment
+ *
+ */
+public class CompartmentComparator implements Comparator<Compartment> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public CompartmentComparator(double epsilon) {
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CompartmentComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public int compare(Compartment arg0, Compartment 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(Compartment.class)) {
+ return internalCompare(arg0, arg1);
+ } else {
+ throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
+ }
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * This method compares only the fields that are defined in Compartment class
+ * in inheritence tree. By the design it calls also comparator of the upper
+ * (Element) 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(Compartment arg0, Compartment arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+
+ int result = elementComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+
+ if (!arg0.getElementId().equals(arg1.getElementId())) {
+ return arg0.getElementId().compareTo(arg1.getElementId());
+ }
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
similarity index 94%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/ComplexSpecies.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
index db9107d2aa..35cceece6a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpecies.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.HashSet;
import java.util.Set;
@@ -12,7 +12,6 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexSpeciesComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparator.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/ComplexSpeciesComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparator.java
index 70c072161e..c8e398769a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexSpeciesComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
@@ -8,9 +8,6 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.ElementComparator;
-import lcsb.mapviewer.model.map.agregator.Compartment;
/**
* This class implements comparator interface for ComplexSpecies.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
index 6d4f86d5fb..3f4935ffb2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Degraded.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparator.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparator.java
index 341a95a1d6..c59ba6e2b4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
index b44732d671..977bca234d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Drug.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparator.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparator.java
index 722268f526..46522e97af 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/Element.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
similarity index 98%
rename from model/src/main/java/lcsb/mapviewer/model/map/Element.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
index 8279738bce..40e2c6bd2b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/Element.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Element.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
import java.util.ArrayList;
@@ -32,12 +32,11 @@ import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.IndexColumn;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+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.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
/**
* Generic element of the map. It is a root object in inheritence three for
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/ElementComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparator.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/ElementComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparator.java
index ee7fb16e3d..9e573a0ab8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/ElementComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
import java.util.HashSet;
@@ -9,10 +9,7 @@ import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringListComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.agregator.CompartmentComparator;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.SpeciesComparator;
+import lcsb.mapviewer.model.map.MiriamData;
import org.apache.log4j.Logger;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
index 3056fdea12..bd9660cdbb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Gene.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
@@ -14,7 +14,6 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
/**
* Class representing gene in the model.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparator.java
similarity index 91%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparator.java
index 2522cbdcd6..9f5ea4b31c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
import java.util.HashSet;
@@ -7,7 +7,6 @@ import java.util.Set;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
/**
* This class implements comparator interface for Gene.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
index 1d757016c5..7161bcfe86 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
index 4132566ff4..13198e509d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Ion.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
index 62cc3a6ea5..c0189b97eb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparator.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparator.java
index 8c35ad4a35..352ad337ba 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/ModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/fields/ModificationResidue.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
index 0470ff62b7..37e5683269 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/ModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidue.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species.fields;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
@@ -17,7 +17,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
/**
* This class represent modification residue in protein and gene. However, it is
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/Phenotype.java
new file mode 100644
index 0000000000..b43dac692f
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Phenotype.java
@@ -0,0 +1,62 @@
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
+
+/**
+ * Class representing phenotype in the model.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Phenotype")
+public class Phenotype extends Species<PhenotypeAlias> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor that initializes phenotype with the data passed in the
+ * argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public Phenotype(Species species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public Phenotype() {
+ }
+
+ @Override
+ 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());
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Phenotype";
+ }
+
+ @Override
+ public PhenotypeAlias createAlias(String aliasId) {
+ PhenotypeAlias result = new PhenotypeAlias(aliasId);
+ super.setAliasFields(result);
+ return result;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparator.java
similarity index 62%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparator.java
index 39318fab73..b0a691dc86 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparator.java
@@ -1,13 +1,11 @@
-package lcsb.mapviewer.model.map.species;
+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.IntegerComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.AssociatedElementComparator;
/**
* This class implements comparator interface for Phenotype.
@@ -86,20 +84,6 @@ public class PhenotypeComparator implements Comparator<Phenotype> {
return result;
}
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getAssociatedElements().size(), arg1.getAssociatedElements().size()) != 0) {
- logger.debug("number of associated elements different: " + arg0.getAssociatedElements().size() + ", " + arg1.getAssociatedElements().size());
- return integerComparator.compare(arg0.getAssociatedElements().size(), arg1.getAssociatedElements().size());
- }
-
- AssociatedElementComparator associatedElementComparator = new AssociatedElementComparator();
- for (int i = 0; i < arg0.getAssociatedElements().size(); i++) {
- if (associatedElementComparator.compare(arg0.getAssociatedElements().get(i), arg1.getAssociatedElements().get(i)) != 0) {
- logger.debug("Associated elements different");
- return associatedElementComparator.compare(arg0.getAssociatedElements().get(i), arg1.getAssociatedElements().get(i));
- }
- }
return 0;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
similarity index 94%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
index f53a79e3e7..4bfa7ab8d4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Protein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
@@ -17,7 +17,6 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.ModificationResidueAlias;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
/**
* Class representing protein in the model.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparator.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparator.java
index a102f6b7aa..0c3f33d7f0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
import java.util.HashSet;
@@ -10,7 +10,6 @@ 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.model.map.species.fields.ModificationResidue;
/**
* This class implements comparator interface for Protein.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
index 22b69af23c..82a4e23eb4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
similarity index 93%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
index 7f879606cb..e0bdfba4dd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Rna.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
@@ -15,7 +15,6 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.layout.alias.RnaAlias;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
/**
* Class representing rna in the model.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparator.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparator.java
index c1273dada2..d1982ef413 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
import java.util.HashSet;
@@ -7,7 +7,6 @@ import java.util.Set;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
/**
* This class implements comparator interface for Rna.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/RnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
similarity index 91%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/fields/RnaRegion.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
index dc681880cb..128dcfe834 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/RnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegion.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species.fields;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.io.Serializable;
@@ -15,12 +15,12 @@ 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.Species;
/**
* This structure contains information about rna region (rna fragment of
- * interest) for a specific {@link lcsb.mapviewer.model.map.species.Rna Rna}.
+ * interest) for a specific {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
*
* @author Piotr Gawron
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
similarity index 91%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
index d99677feb8..64ca650675 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMolecule.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparator.java
similarity index 94%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparator.java
index 24d954c4a3..bb24f976d6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
similarity index 94%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
index 1cb2b2f556..4a79d01566 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Species.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
@@ -9,10 +9,9 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
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.fields.PositionToCompartment;
/**
* Generic species of the map.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparator.java
similarity index 96%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparator.java
index b07ba68a12..486f9d6881 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
@@ -9,7 +9,6 @@ import lcsb.mapviewer.common.comparator.BooleanComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.model.map.ElementComparator;
/**
* This class implements comparator interface for Species. It calls comparator
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/SpeciesState.java
index dffaf038f6..41f82d6aa0 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/SpeciesState.java
@@ -13,13 +13,6 @@ 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.ComplexSpecies;
-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.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
/**
* Structure for storing the state of the Species in CellDesigner format.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
index bf3168b5b4..2a1ebc5dfe 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProtein.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
index dd10b378f3..1c1d8077a9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/Unknown.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparator.java
similarity index 92%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
rename to converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparator.java
index 5ec9093971..2e064d10ee 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparator.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.Comparator;
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 cc5784f1b3..9ef5fe9197 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
@@ -9,8 +9,8 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Modifier;
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 fdc24dab14..98712e479c 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
@@ -27,8 +27,11 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
@@ -42,9 +45,6 @@ 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.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(CellDesignerXmlParserTest.class);
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 774abcfd62..5cae4d2dd7 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
@@ -27,13 +27,13 @@ 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.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.fields.ModificationState;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class ComplexParserTests extends CellDesignerTestFunctions {
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 2c6a02437a..864e24d010 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
@@ -15,6 +15,7 @@ import org.junit.Test;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.graphics.PolylineDataComparator;
import lcsb.mapviewer.model.map.layout.alias.AliasGroup;
@@ -30,7 +31,6 @@ 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;
public class LayerXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(LayerXmlParserTest.class);
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 4a29655ff1..ccc01fb043 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
@@ -4,12 +4,12 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
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.model.Model;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
import org.junit.After;
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 f0ac6dcdc7..fc8482f9e8 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
@@ -17,15 +17,15 @@ 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.ModelMock;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+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.converter.model.celldesigner.structure.Species;
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.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
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 be613603e2..5a84ec35f8 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
@@ -17,7 +17,8 @@ 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.species.ModelMock;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
import lcsb.mapviewer.model.map.layout.alias.BottomSquareCompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.LeftSquareCompartmentAlias;
@@ -26,7 +27,6 @@ import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.TopSquareCompartmentAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
static Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class);
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 4e8cf26bce..fb303e53ac 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
@@ -11,11 +11,11 @@ import org.junit.Test;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.species.ModelMock;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
Model model;
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 199b98bc2b..eb0b36804b 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
@@ -21,16 +21,16 @@ 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.species.ModelMock;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+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.converter.model.celldesigner.structure.Species;
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.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
static Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class);
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 65815619db..c4e168099a 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
@@ -22,6 +22,8 @@ import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -31,8 +33,6 @@ 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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class RestAnnotationParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(RestAnnotationParserTest.class);
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 439b789a3c..f85656e82b 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
@@ -17,7 +17,7 @@ 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.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
public class CompartmentCollectionXmlParserTest extends CellDesignerTestFunctions {
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 1d15e75ad8..c045378475 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
@@ -23,7 +23,7 @@ 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.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.model.Model;
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 81d2959cfb..4dc677a758 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
@@ -17,10 +17,10 @@ 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.converter.model.celldesigner.structure.GenericProtein;
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;
public class AbstractCellDesignerAliasConverterTest {
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 9f2af55ad5..7ccdbdbbec 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
@@ -11,9 +11,9 @@ 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.model.map.layout.alias.IonAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.Ion;
public class IonCellDesignerAliasConverterTest {
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 8ed9d0a759..6973e8af94 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
@@ -11,8 +11,8 @@ import org.junit.Test;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
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);
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 f3def802ed..4b0c112fed 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
@@ -14,12 +14,12 @@ import org.w3c.dom.Node;
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.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;
public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ReactionCollectionXmlParserTest.class);
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 59b7ca63b1..0604c7d35c 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
@@ -12,6 +12,7 @@ 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.compartment.CompartmentCollectionXmlParser;
+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.model.map.model.Model;
@@ -21,7 +22,6 @@ 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;
public class ReactionFromXmlTest extends CellDesignerTestFunctions {
ReactionXmlParser parser;
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 17d7115f07..6da9140073 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
@@ -22,6 +22,7 @@ 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.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -56,7 +57,6 @@ 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.GenericProtein;
public class ReactionParserTests extends CellDesignerTestFunctions {
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 d3342c7c9b..2202e9cf5e 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
@@ -17,6 +17,8 @@ import org.junit.Test;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
@@ -32,8 +34,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public class ReactionToXmlTest {
Logger logger = Logger.getLogger(ReactionToXmlTest.class);
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 d4ec47fbdc..7fec98632d 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.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
protected Logger logger = Logger.getLogger(AntisenseRnaXmlParserTest.class.getName());
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 e1f3350f76..ec79d3196b 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
@@ -22,14 +22,14 @@ 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.model.map.Element;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
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.ComplexSpecies;
public class ComplexParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ComplexParserTest.class);
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 10fc0e353c..1aed0e229d 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
@@ -23,12 +23,12 @@ 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.converter.model.celldesigner.structure.ModificationResidue;
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.model.Model;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
public class GeneXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(GeneXmlParserTest.class.getName());
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 56033d7409..c3277a4455 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
@@ -1,50 +1,50 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class InternalModelSpeciesDataTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- InternalModelSpeciesData data = new InternalModelSpeciesData();
- assertNotNull(data.getAll());
- assertNotNull(data.getAntisenseRnas());
- assertNotNull(data.getGenes());
- assertNotNull(data.getProteins());
- assertNotNull(data.getRnas());
- }
-
- @Test
- public void testUpdateUnknownSpecies() {
- InternalModelSpeciesData data = new InternalModelSpeciesData();
- try {
- data.updateSpecies(new Species(), null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown species type"));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+
+public class InternalModelSpeciesDataTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ InternalModelSpeciesData data = new InternalModelSpeciesData();
+ assertNotNull(data.getAll());
+ assertNotNull(data.getAntisenseRnas());
+ assertNotNull(data.getGenes());
+ assertNotNull(data.getProteins());
+ assertNotNull(data.getRnas());
+ }
+
+ @Test
+ public void testUpdateUnknownSpecies() {
+ InternalModelSpeciesData data = new InternalModelSpeciesData();
+ try {
+ data.updateSpecies(new Species(), 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/ModelMock.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
index 0c414a753c..466f686c23 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModelMock.java
@@ -9,12 +9,13 @@ import java.util.Map;
import java.util.Set;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.alias.Alias;
@@ -29,7 +30,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
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 ea3672b708..2ba1853a76 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 +13,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
public class ProteinMappingTest {
Logger logger = Logger.getLogger(ProteinMappingTest.class);
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 0fa86025bd..19c2ab5083 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
@@ -23,10 +23,10 @@ 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.model.map.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
public class ProteinXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
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 69edb09f72..34757ada7c 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.model.map.species.Rna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
public class RnaXmlParserTest extends CellDesignerTestFunctions {
protected Logger logger = Logger.getLogger(RnaXmlParserTest.class.getName());
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 2893ddaeb9..07dde3ae48 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
@@ -12,11 +12,11 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-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.Species;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
+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.TruncatedProtein;
public class SpeciesCollectionTest {
Logger logger = Logger.getLogger(SpeciesCollectionTest.class);
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 bc35785af4..3b78eebfc6 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
@@ -24,6 +24,13 @@ 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.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.Alias;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
@@ -33,13 +40,6 @@ 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.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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.model.map.species.Species;
public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
static Logger logger = Logger.getLogger(SpeciesCollectionXmlParserTest.class);
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 633ad1af14..1d70306270 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 +11,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class SpeciesMappingTest {
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 4a32a89157..fd258d2988 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
@@ -27,30 +27,30 @@ 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.Compartment;
+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.InconsistentModelException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
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.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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.model.map.species.fields.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
@SuppressWarnings("unused")
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
similarity index 87%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
index e22fb2cb7e..fa649ac8af 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -9,8 +9,10 @@ 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.model.map.species.fields.AntisenseRnaRegion;
public class AntisenseRnaComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AntisenseRnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
similarity index 93%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/fields/AntisenseRnaRegionTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
index bce8a334db..0564a8bc98 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AntisenseRnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaRegionTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species.fields;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -14,7 +14,7 @@ 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.species.Species;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
public class AntisenseRnaRegionTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
similarity index 91%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
index a57f4364fc..4e4b7fa223 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AntisenseRnaTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -14,8 +14,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
public class AntisenseRnaTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/agregator/CompartmentComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
similarity index 93%
rename from model/src/test/java/lcsb/mapviewer/model/map/agregator/CompartmentComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
index 41f9c54ebb..5e52e347f9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/agregator/CompartmentComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.agregator;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/agregator/CompartmentTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
similarity index 91%
rename from model/src/test/java/lcsb/mapviewer/model/map/agregator/CompartmentTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
index 9c3f6451a6..4c2061915b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/agregator/CompartmentTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.agregator;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -12,8 +12,6 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public class CompartmentTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexSpeciesComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
similarity index 90%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/ComplexSpeciesComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
index 4bbaa3ab6c..8decad505f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexSpeciesComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -11,8 +11,12 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+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;
public class ComplexSpeciesComparatorTest {
Logger logger = Logger.getLogger(ComplexSpeciesComparatorTest.class);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexSpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
similarity index 87%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/ComplexSpeciesTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
index 1547c2f329..1c15f8cf5a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexSpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -14,7 +14,9 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class ComplexSpeciesTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
similarity index 88%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
index 793abb6410..0d15ec6b2a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -9,6 +9,8 @@ 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;
public class DegradedComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
index 495b9157da..fafbfa6f55 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.Degraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class DegradedTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
similarity index 86%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
index 2ca3baa4e2..84c3de7bec 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -9,6 +9,8 @@ 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;
public class DrugComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
index 57d7c4efc4..381663e7c4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.Drug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class DrugTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/ElementComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparatorTest.java
similarity index 92%
rename from model/src/test/java/lcsb/mapviewer/model/map/ElementComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparatorTest.java
index a8f10c4b6c..596a4ce353 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/ElementComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -10,10 +10,10 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.fields.PositionToCompartment;
+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;
public class ElementComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/ElementTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
similarity index 89%
rename from model/src/test/java/lcsb/mapviewer/model/map/ElementTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
index 9550d36991..4191dd34eb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/ElementTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -15,10 +15,13 @@ import org.junit.Test;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+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.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
public class ElementTest extends ModelTestFunctions {
Logger logger = Logger.getLogger(ElementTest.class);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
similarity index 90%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
index 69a1698416..d93122574d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneComparatorTest.java
@@ -1,17 +1,16 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
-
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+
public class GeneComparatorTest {
GeneComparator comparator = new GeneComparator();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
similarity index 86%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
index d1964f7db7..9cd00ce899 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -13,7 +13,9 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class GeneTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
similarity index 82%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
index a71219dde6..308a7a8341 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class GenericProteinTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
similarity index 82%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
index 211c9dd81c..df94d86afb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.IonChannelProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class IonChannelProteinTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
similarity index 86%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
index c81434ca60..a55e4fb58c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -9,6 +9,8 @@ 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;
public class IonComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
index 03de3ea919..d97de2bcb6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.Ion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class IonTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/ModificationResidueTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
similarity index 92%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/fields/ModificationResidueTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
index e3b41d4e7e..1690e144ac 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/ModificationResidueTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
@@ -1,155 +1,155 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-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.species.Species;
-
-public class ModificationResidueTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ModificationResidue());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- ModificationResidue original = new ModificationResidue();
- ModificationResidue copy = new ModificationResidue(original);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- ModificationResidue original = new ModificationResidue();
- ModificationResidue update = new ModificationResidue();
-
- String name = "n";
- String side = "s";
- ModificationState state = ModificationState.ACETYLATED;
- Double angle = 3.9;
- Double size = 5.0;
-
- update.setName(name);
- update.setSide(side);
- update.setAngle(angle);
- update.setSize(size);
- update.setState(state);
-
- original.update(update);
-
- assertEquals(name, original.getName());
- assertEquals(side, original.getSide());
- assertEquals(angle, original.getAngle());
- assertEquals(size, original.getSize());
- assertEquals(state, original.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ModificationResidue original = new ModificationResidue();
-
- String doubleStr = "2.0";
- String invalidDoubleStr = "a2.0";
- String nullStr = null;
- Double angle = 2.0;
- Species species = new Species();
- int id = 5;
-
- original.setAngle(doubleStr);
- assertEquals(angle, original.getAngle(), Configuration.EPSILON);
- try {
- original.setAngle(invalidDoubleStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- original.setAngle(nullStr);
- assertNull(original.getAngle());
-
- original.setSize(doubleStr);
- assertEquals(angle, original.getSize(), Configuration.EPSILON);
- try {
- original.setSize(invalidDoubleStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- original.setSize(doubleStr);
- original.setSize(nullStr);
- assertNull(original.getSize());
-
- original.setId(id);
- assertEquals(id, original.getId());
-
- original.setSpecies(species);
- assertEquals(species, original.getSpecies());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- ModificationResidue degraded = new ModificationResidue().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new ModificationResidue() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+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;
+
+public class ModificationResidueTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ModificationResidue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ ModificationResidue original = new ModificationResidue();
+ ModificationResidue copy = new ModificationResidue(original);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ ModificationResidue original = new ModificationResidue();
+ ModificationResidue update = new ModificationResidue();
+
+ String name = "n";
+ String side = "s";
+ ModificationState state = ModificationState.ACETYLATED;
+ Double angle = 3.9;
+ Double size = 5.0;
+
+ update.setName(name);
+ update.setSide(side);
+ update.setAngle(angle);
+ update.setSize(size);
+ update.setState(state);
+
+ original.update(update);
+
+ assertEquals(name, original.getName());
+ assertEquals(side, original.getSide());
+ assertEquals(angle, original.getAngle());
+ assertEquals(size, original.getSize());
+ assertEquals(state, original.getState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ModificationResidue original = new ModificationResidue();
+
+ String doubleStr = "2.0";
+ String invalidDoubleStr = "a2.0";
+ String nullStr = null;
+ Double angle = 2.0;
+ Species species = new Species();
+ int id = 5;
+
+ original.setAngle(doubleStr);
+ assertEquals(angle, original.getAngle(), Configuration.EPSILON);
+ try {
+ original.setAngle(invalidDoubleStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ original.setAngle(nullStr);
+ assertNull(original.getAngle());
+
+ original.setSize(doubleStr);
+ assertEquals(angle, original.getSize(), Configuration.EPSILON);
+ try {
+ original.setSize(invalidDoubleStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ original.setSize(doubleStr);
+ original.setSize(nullStr);
+ assertNull(original.getSize());
+
+ original.setId(id);
+ assertEquals(id, original.getId());
+
+ original.setSpecies(species);
+ assertEquals(species, original.getSpecies());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ ModificationResidue degraded = new ModificationResidue().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new ModificationResidue() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
similarity index 62%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
index 4f9f9861c1..1812f7a3ca 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -10,7 +10,6 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.fields.AssociatedElement;
public class PhenotypeComparatorTest {
@@ -39,11 +38,6 @@ public class PhenotypeComparatorTest {
assertEquals(0, comparator.compare(phenotype1, phenotype2));
assertEquals(0, comparator.compare(phenotype2, phenotype1));
- phenotype1.addAssociatedElement(new AssociatedElement());
- phenotype2.addAssociatedElement(new AssociatedElement());
- assertEquals(0, comparator.compare(phenotype1, phenotype2));
- assertEquals(0, comparator.compare(phenotype2, phenotype1));
-
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -99,35 +93,4 @@ public class PhenotypeComparatorTest {
return result;
}
- @Test
- public void testDifferentNewFields() throws Exception {
- try {
- Phenotype species1 = createPhenotype();
- Phenotype species2 = createPhenotype();
-
- AssociatedElement ae = new AssociatedElement();
-
- species1.addAssociatedElement(ae);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createPhenotype();
- species2 = createPhenotype();
-
- AssociatedElement ae1 = new AssociatedElement();
- AssociatedElement ae2 = new AssociatedElement();
-
- ae2.setSource(MiriamType.CHEMBL_COMPOUND);
-
- species1.addAssociatedElement(ae1);
- species2.addAssociatedElement(ae2);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
similarity index 57%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
index 2e8e9f5313..f137ee4d62 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
@@ -1,21 +1,14 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
-import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
-import java.util.ArrayList;
-import java.util.List;
-
import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.fields.AssociatedElement;
public class PhenotypeTest {
@@ -41,9 +34,6 @@ public class PhenotypeTest {
public void testConstructor1() {
try {
Phenotype original = new Phenotype();
- AssociatedElement ae = new AssociatedElement();
- ae.setData(new MiriamData(MiriamType.CCDS, "a"));
- original.addAssociatedElement(ae);
Phenotype copy = new Phenotype(original);
assertNotNull(copy);
} catch (Exception e) {
@@ -52,21 +42,6 @@ public class PhenotypeTest {
}
}
- @Test
- public void testGetters() {
- try {
- Phenotype phenotype = new Phenotype(new Species());
- assertNotNull(phenotype.getStringType());
- List<AssociatedElement> associatedElements = new ArrayList<>();
- phenotype.setAssociatedElements(associatedElements);
-
- assertEquals(associatedElements, phenotype.getAssociatedElements());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testCopy() {
try {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/PositionToCompartmentTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PositionToCompartmentTest.java
similarity index 80%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/fields/PositionToCompartmentTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PositionToCompartmentTest.java
index cc78192b32..95502105f0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/PositionToCompartmentTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PositionToCompartmentTest.java
@@ -1,37 +1,39 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PositionToCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (PositionToCompartment type : PositionToCompartment.values()) {
- assertNotNull(type);
- assertNotNull(type.getStringName());
-
- // for coverage tests
- PositionToCompartment.valueOf(type.toString());
- }
- }
-
- @Test
- public void testGetByString() {
- assertNotNull(PositionToCompartment.getByString("insideOfMembrane"));
- assertNull(PositionToCompartment.getByString("insideOfasdasdas"));
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.PositionToCompartment;
+
+public class PositionToCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (PositionToCompartment type : PositionToCompartment.values()) {
+ assertNotNull(type);
+ assertNotNull(type.getStringName());
+
+ // for coverage tests
+ PositionToCompartment.valueOf(type.toString());
+ }
+ }
+
+ @Test
+ public void testGetByString() {
+ assertNotNull(PositionToCompartment.getByString("insideOfMembrane"));
+ assertNull(PositionToCompartment.getByString("insideOfasdasdas"));
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
index dfdb3be78d..b980ff7263 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinComparatorTest.java
@@ -1,10 +1,14 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ProteinComparator;
import org.junit.After;
import org.junit.Before;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
similarity index 86%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
index deb6067334..6c7acf7e88 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@@ -13,7 +13,10 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
+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;
public class ProteinTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
similarity index 82%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
index ffc8af66eb..0f9fad6249 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.ReceptorProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class ReceptorProteinTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
similarity index 84%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
index beea204bb9..2466831932 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaComparatorTest.java
@@ -1,12 +1,14 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.RnaComparator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.RnaRegion;
import org.junit.After;
import org.junit.Before;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/RnaRegionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
similarity index 85%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/fields/RnaRegionTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
index 76651462d0..f0dc640df0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/RnaRegionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaRegionTest.java
@@ -1,134 +1,136 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class RnaRegionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new RnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- RnaRegion region = new RnaRegion(new RnaRegion());
- assertNotNull(region);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetSize() {
- try {
- RnaRegion region = new RnaRegion();
- try {
- region.setSize("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setSize("0.0");
- assertEquals(0.0, region.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetPos() {
- try {
- RnaRegion region = new RnaRegion();
- try {
- region.setPos("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setPos("1.0");
- assertEquals(1.0, region.getPos(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- RnaRegion region = new RnaRegion();
- RnaRegion region2 = new RnaRegion();
- region2.setState(ModificationState.ACETYLATED);
- region2.setName("asd");
- region2.setPos(2.2);
- region.update(region2);
- assertEquals(region2.getName(), region.getName());
- assertEquals(region2.getPos(), region.getPos());
- assertEquals(region2.getState(), region.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate2() {
- try {
- RnaRegion region = new RnaRegion();
- region.setIdRnaRegion("1");
- RnaRegion region2 = new RnaRegion();
- region2.setIdRnaRegion("2");
- region.update(region2);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- RnaRegion region = new RnaRegion();
- int id = 47;
- double size = 2.5;
- Species species = new GenericProtein();
- region.setId(id);
- region.setSize(size);
- region.setSpecies(species);
- assertEquals(id, region.getId());
- assertEquals(size, region.getSize(), Configuration.EPSILON);
- assertEquals(species, region.getSpecies());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.RnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+
+public class RnaRegionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new RnaRegion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ RnaRegion region = new RnaRegion(new RnaRegion());
+ assertNotNull(region);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetSize() {
+ try {
+ RnaRegion region = new RnaRegion();
+ try {
+ region.setSize("as");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ region.setSize("0.0");
+ assertEquals(0.0, region.getSize(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetPos() {
+ try {
+ RnaRegion region = new RnaRegion();
+ try {
+ region.setPos("as");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ region.setPos("1.0");
+ assertEquals(1.0, region.getPos(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ RnaRegion region = new RnaRegion();
+ RnaRegion region2 = new RnaRegion();
+ region2.setState(ModificationState.ACETYLATED);
+ region2.setName("asd");
+ region2.setPos(2.2);
+ region.update(region2);
+ assertEquals(region2.getName(), region.getName());
+ assertEquals(region2.getPos(), region.getPos());
+ assertEquals(region2.getState(), region.getState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate2() {
+ try {
+ RnaRegion region = new RnaRegion();
+ region.setIdRnaRegion("1");
+ RnaRegion region2 = new RnaRegion();
+ region2.setIdRnaRegion("2");
+ region.update(region2);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ RnaRegion region = new RnaRegion();
+ int id = 47;
+ double size = 2.5;
+ Species species = new GenericProtein();
+ region.setId(id);
+ region.setSize(size);
+ region.setSpecies(species);
+ assertEquals(id, region.getId());
+ assertEquals(size, region.getSize(), Configuration.EPSILON);
+ assertEquals(species, region.getSpecies());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
similarity index 85%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
index 63fbc0f06b..afc4f0748a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/RnaTest.java
@@ -1,167 +1,170 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
-
-public class RnaTest {
- Logger logger = Logger.getLogger(RnaTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Rna());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testConstructor1() {
- try {
- Rna rna = new Rna(new Species());
- assertNotNull(rna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Rna rna = new Rna(new Species());
- assertNotNull(rna.getStringType());
- List<RnaRegion> regions = new ArrayList<>();
-
- rna.setRegions(regions);
-
- assertEquals(regions, rna.getRegions());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Rna rna = new Rna().copy();
- assertNotNull(rna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new Rna() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testAddRnaRegion() {
- try {
- Rna original = new Rna();
- RnaRegion region = new RnaRegion();
- region.setIdRnaRegion("id1");
- original.addRegion(region);
-
- RnaRegion region2 = new RnaRegion();
- region2.setIdRnaRegion("id1");
- region2.setName("nam");
- original.addRegion(region2);
-
- assertEquals(1, original.getRegions().size());
-
- assertEquals("nam", original.getRegions().get(0).getName());
-
- RnaRegion region3 = new RnaRegion();
- region3.setIdRnaRegion("id2");
- region3.setName("nam");
- original.addRegion(region3);
-
- assertEquals(2, original.getRegions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- Rna original = new Rna();
- RnaRegion region2 = new RnaRegion();
- region2.setIdRnaRegion("id1");
- region2.setName("nam");
- original.addRegion(region2);
- RnaRegion region3 = new RnaRegion();
- region3.setIdRnaRegion("id2");
- region3.setName("nam");
- original.addRegion(region3);
-
- Rna copy = new Rna(original);
- copy.addRegion(new RnaRegion());
- copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
-
- logger.debug(copy.getRegions().size());
-
- original.update(copy);
-
- boolean acetylatedFound = false;
- for (RnaRegion region : copy.getRegions()) {
- if (ModificationState.ACETYLATED.equals(region.getState())) {
- acetylatedFound = true;
- }
- }
- assertTrue(acetylatedFound);
- assertEquals(3, original.getRegions().size());
- assertEquals(3, copy.getRegions().size());
-
- original.update(new GenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+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.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.RnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+
+public class RnaTest {
+ Logger logger = Logger.getLogger(RnaTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Rna());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Rna rna = new Rna(new Species());
+ assertNotNull(rna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Rna rna = new Rna(new Species());
+ assertNotNull(rna.getStringType());
+ List<RnaRegion> regions = new ArrayList<>();
+
+ rna.setRegions(regions);
+
+ assertEquals(regions, rna.getRegions());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Rna rna = new Rna().copy();
+ assertNotNull(rna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new Rna() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testAddRnaRegion() {
+ try {
+ Rna original = new Rna();
+ RnaRegion region = new RnaRegion();
+ region.setIdRnaRegion("id1");
+ original.addRegion(region);
+
+ RnaRegion region2 = new RnaRegion();
+ region2.setIdRnaRegion("id1");
+ region2.setName("nam");
+ original.addRegion(region2);
+
+ assertEquals(1, original.getRegions().size());
+
+ assertEquals("nam", original.getRegions().get(0).getName());
+
+ RnaRegion region3 = new RnaRegion();
+ region3.setIdRnaRegion("id2");
+ region3.setName("nam");
+ original.addRegion(region3);
+
+ assertEquals(2, original.getRegions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ Rna original = new Rna();
+ RnaRegion region2 = new RnaRegion();
+ region2.setIdRnaRegion("id1");
+ region2.setName("nam");
+ original.addRegion(region2);
+ RnaRegion region3 = new RnaRegion();
+ region3.setIdRnaRegion("id2");
+ region3.setName("nam");
+ original.addRegion(region3);
+
+ Rna copy = new Rna(original);
+ copy.addRegion(new RnaRegion());
+ copy.getRegions().get(0).setState(ModificationState.ACETYLATED);
+
+ logger.debug(copy.getRegions().size());
+
+ original.update(copy);
+
+ boolean acetylatedFound = false;
+ for (RnaRegion region : copy.getRegions()) {
+ if (ModificationState.ACETYLATED.equals(region.getState())) {
+ acetylatedFound = true;
+ }
+ }
+ assertTrue(acetylatedFound);
+ assertEquals(3, original.getRegions().size());
+ assertEquals(3, copy.getRegions().size());
+
+ original.update(new GenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
similarity index 91%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
index 729d959778..06e688cf76 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -9,6 +9,8 @@ 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;
public class SimpleMoleculeComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
index ade7b468f0..82db2cc5d4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.SimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
public class SimpleMoleculeTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparatorTest.java
similarity index 84%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparatorTest.java
index 70ef5263e9..418cbaf994 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -9,10 +9,19 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.PositionToCompartment;
+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.SpeciesComparator;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.fields.PositionToCompartment;
public class SpeciesComparatorTest {
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 8efc570bf1..882a0b0e68 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
@@ -15,7 +15,6 @@ 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.model.map.species.fields.ModificationResidue;
public class SpeciesStateTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
similarity index 94%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
index cb3b3ec810..611c1d97bc 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -14,6 +14,7 @@ import org.junit.Test;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.MiriamData;
public class SpeciesTest extends ModelTestFunctions {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
similarity index 82%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
index c0c0743d30..90ebc9489c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.TruncatedProtein;
public class TruncatedProteinTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
similarity index 86%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
index 87ae8c8b1a..009dd1d89e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownComparatorTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -9,6 +9,8 @@ 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;
public class UnknownComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
similarity index 83%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
index 5caa89237a..24ac6f9abf 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.model.map.species;
+package lcsb.mapviewer.converter.model.celldesigner.structure;
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.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
public class UnknownTest {
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 db4717bce5..e27cfaae40 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
@@ -16,8 +16,9 @@ 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.Species;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.AndOperator;
@@ -26,7 +27,6 @@ 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.Species;
public class ModifierTypeUtilsTest {
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 26b277c84f..a270247ead 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
@@ -28,8 +28,10 @@ import org.sbgn.bindings.Sbgn;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.AntisenseRnaAlias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
@@ -71,8 +73,6 @@ 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.Protein;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
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 888a736864..9e9b45f3a4 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
@@ -29,6 +29,18 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.graphics.species.SpeciesConverter;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+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.SimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
@@ -36,10 +48,10 @@ 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.agregator.Compartment;
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.ModificationState;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
import lcsb.mapviewer.model.map.model.Model;
@@ -64,18 +76,6 @@ 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.ComplexSpecies;
-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.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
/**
* This class is a parser for SBGN-ML files.
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 4d0ed68462..43255ebac4 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
@@ -27,33 +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.Element;
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.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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.model.map.layout.alias.TruncatedProteinAlias;
+import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
/**
* This class is designed to convert any type of alias into a graphic glyph that
@@ -68,7 +64,7 @@ public class AliasConverter implements IAliasConverter<Alias> {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(AliasConverter.class.getName());
+ private static Logger logger = Logger.getLogger(AliasConverter.class.getName());
// *****************************************************************
//
@@ -76,39 +72,31 @@ public class AliasConverter implements IAliasConverter<Alias> {
//
// *****************************************************************
- /**
- * Static map of graphic alias converters used for conversion of aliases. Key
- * in this map is a class of element to which alias reference to. Value is
- * instance of a converter that can process the alias with the specific
- * element type reference.
- */
- private static Map<Class<? extends Element>, IAliasConverter<?>> elementConverters = new HashMap<Class<? extends Element>, IAliasConverter<?>>();
-
/**
* Static map of graphic alias converters used for conversion of aliases. Key
* 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 Alias>, IAliasConverter<?>> aliasConverters = new HashMap<Class<? extends Alias>, IAliasConverter<?>>();
static {
// at the beginning lets add all implemented aliases
// for element reference
- addElementConverter(GenericProtein.class, new ProteinConverter());
- addElementConverter(IonChannelProtein.class, new ProteinConverter());
- addElementConverter(ReceptorProtein.class, new ProteinConverter());
- addElementConverter(TruncatedProtein.class, new ProteinConverter());
- addElementConverter(Degraded.class, new DegradedConverter());
- addElementConverter(ComplexSpecies.class, new ComplexConverter());
- addElementConverter(SimpleMolecule.class, new SimpleMoleculeConverter());
- addElementConverter(Drug.class, new DrugConverter());
- addElementConverter(Ion.class, new IonConverter());
- addElementConverter(Phenotype.class, new PhenotypeConverter());
- addElementConverter(Rna.class, new RnaConverter());
- addElementConverter(AntisenseRna.class, new AntisenseRnaConverter());
- addElementConverter(Gene.class, new GeneConverter());
- addElementConverter(Unknown.class, new UnknownConverter());
+ 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());
// for compartment aliases
addAliasConverter(SquareCompartmentAlias.class, new SquareCompartmentConverter());
@@ -121,21 +109,6 @@ public class AliasConverter implements IAliasConverter<Alias> {
}
- /**
- * Method that set a converter for element referenced by alias to process.
- *
- * @param clazz
- * class type of element referenced by alias
- * @param converter
- * converter that should be used for conversion of this alias
- */
- protected static void addElementConverter(final Class<? extends Element> clazz, final IAliasConverter<?> converter) {
- if (elementConverters.get(clazz) != null) {
- logger.warn("Converter for " + clazz + " has been already added");
- }
- elementConverters.put(clazz, converter);
- }
-
/**
* Method that set a converter for specific alias type.
*
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 b1ca0be507..ebfb0c2dcc 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
@@ -11,16 +11,13 @@ import java.awt.geom.Path2D;
import java.awt.geom.PathIterator;
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.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
-
-import org.apache.log4j.Logger;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
/**
* This class defines methods used for drawing Antisense Rna SpeciesAlias on the
@@ -35,7 +32,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRnaAlias> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
+ private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
@Override
public void drawAlias(final AntisenseRnaAlias alias, final Graphics2D graphics, final ConverterParams params) {
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 2419143dcd..fecd7d7777 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
@@ -17,7 +17,7 @@ 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.species.fields.ModificationState;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
/**
* This class defines methods used for drawing Gene SpeciesAlias on the
@@ -31,7 +31,7 @@ public class GeneConverter extends SpeciesConverter<GeneAlias> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GeneConverter.class.getName());
+ private static Logger logger = Logger.getLogger(GeneConverter.class.getName());
@Override
public void drawAlias(final GeneAlias alias, final Graphics2D graphics, final ConverterParams params) {
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 7f0f3e644c..1b0dd1ac47 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
@@ -1,111 +1,111 @@
-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.Ellipse2D;
-import java.awt.geom.PathIterator;
-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 org.apache.log4j.Logger;
-
-/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.db.model.map.species.Ion Ion} on the {@link Graphics2D}
- * object.
- *
- * @author Piotr Gawron
- *
- */
-public class IonConverter extends SpeciesConverter<SpeciesAlias> {
- /**
- * 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) {
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
- graphics.draw(shape);
- graphics.setStroke(stroke);
- drawText(alias, graphics, params);
- }
-
- /**
- * Returns transformed y coordinate for the ion 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();
- return y;
- }
-
- /**
- * Returns transformed x coordinate for the ion alias.
- *
- * @param alias
- * object alias to to which we are looking for x coordinate
- * @param diameter
- * diameter of circle representation of ion
- * @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;
- }
-
- /**
- * Returns diameter of circle representation of ion.
- *
- * @param alias
- * object alias to to which we are looking for diameter.
- * @return diameter of ion circle representation
- */
- private double getDiameter(final Alias alias) {
- double diameter = Math.min(alias.getWidth(), alias.getHeight());
- if (diameter < 0) {
- logger.warn("Something is wrong. Size cannot be negative");
- diameter = 0;
- }
-
- return diameter;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
- throw new InvalidStateException("This class doesn't have bound");
- }
-
- @Override
- public Point2D getPointCoordinatesOnBorder(final SpeciesAlias 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();
- }
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
- return result;
-
- }
-
-}
+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.Ellipse2D;
+import java.awt.geom.PathIterator;
+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 org.apache.log4j.Logger;
+
+/**
+ * This class defines methods used for drawing SpeciesAlias of
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Ion Ion} on the {@link Graphics2D}
+ * object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class IonConverter extends SpeciesConverter<SpeciesAlias> {
+ /**
+ * 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) {
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
+ Color c = graphics.getColor();
+ graphics.setColor(alias.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(alias));
+ graphics.draw(shape);
+ graphics.setStroke(stroke);
+ drawText(alias, graphics, params);
+ }
+
+ /**
+ * Returns transformed y coordinate for the ion 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();
+ return y;
+ }
+
+ /**
+ * Returns transformed x coordinate for the ion alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for x coordinate
+ * @param diameter
+ * diameter of circle representation of ion
+ * @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;
+ }
+
+ /**
+ * Returns diameter of circle representation of ion.
+ *
+ * @param alias
+ * object alias to to which we are looking for diameter.
+ * @return diameter of ion circle representation
+ */
+ private double getDiameter(final Alias alias) {
+ double diameter = Math.min(alias.getWidth(), alias.getHeight());
+ if (diameter < 0) {
+ logger.warn("Something is wrong. Size cannot be negative");
+ diameter = 0;
+ }
+
+ return diameter;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
+ throw new InvalidStateException("This class doesn't have bound");
+ }
+
+ @Override
+ public Point2D getPointCoordinatesOnBorder(final SpeciesAlias 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();
+ }
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
+ return result;
+
+ }
+
+}
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 3cacd381fb..217c3f630d 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
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.converter.graphics.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-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 org.apache.log4j.Logger;
-
-/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.db.model.map.species.Phenotype Phenotype} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class PhenotypeConverter extends SpeciesConverter<SpeciesAlias> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PhenotypeConverter.class.getName());
-
- @Override
- public void drawAlias(final SpeciesAlias alias, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getPhenotypePath(alias);
-
- Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
- graphics.fill(path);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(alias));
- graphics.draw(path);
- graphics.setStroke(stroke);
- drawText(alias, graphics, params);
- }
-
- /**
- * 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(final Alias alias) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(Path2D.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;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
- return getPhenotypePath(alias).getPathIterator(new AffineTransform());
- }
-
-}
+package lcsb.mapviewer.converter.graphics.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+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 org.apache.log4j.Logger;
+
+/**
+ * This class defines methods used for drawing SpeciesAlias of
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Phenotype Phenotype} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PhenotypeConverter extends SpeciesConverter<SpeciesAlias> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(PhenotypeConverter.class.getName());
+
+ @Override
+ public void drawAlias(final SpeciesAlias alias, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getPhenotypePath(alias);
+
+ Color c = graphics.getColor();
+ graphics.setColor(alias.getColor());
+ graphics.fill(path);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(alias));
+ graphics.draw(path);
+ graphics.setStroke(stroke);
+ drawText(alias, graphics, params);
+ }
+
+ /**
+ * 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(final Alias alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(Path2D.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;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final SpeciesAlias 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 9baf37c177..be62fa2f7b 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
@@ -25,15 +25,11 @@ 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.GenericProtein;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
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 177559f4fe..0e0c06e2b3 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
@@ -15,15 +15,14 @@ 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.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
/**
* This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.db.model.map.species.Rna Rna} on the {@link Graphics2D}
- * object.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Rna
+ * Rna} on the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -33,7 +32,7 @@ public class RnaConverter extends SpeciesConverter<RnaAlias> {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
+ private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
@Override
public void drawAlias(final RnaAlias alias, final Graphics2D graphics, final ConverterParams params) {
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 0eb77c8dbb..25252c4945 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
@@ -11,44 +11,40 @@ 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.Species;
/**
- * This class defines methods used for drawing SpeciesAlias of
- * nucleic acid feature in the SBGN way on the
- * {@link Graphics2D} object.
+ * This class defines methods used for drawing SpeciesAlias of nucleic acid
+ * feature in the SBGN way on the {@link Graphics2D} object.
*
* @author Michał Kuźma
*
*/
public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAlias> {
-
+
/**
- * How big should be the arc in rectangle for nucleic acid feature representation.
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
*/
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
/**
* Returns shape of SBGN Nucleic acid feature.
+ *
* @param alias
- * alias for which the shape should be returned
- * @return
- * shape of the SBGN Nucleic acid feature for given alias
+ * 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) {
GeneralPath bottomRoundedRectangle = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
double x = alias.getX(), y = alias.getY(), width = alias.getWidth(), height = alias.getHeight();
-
+
bottomRoundedRectangle.moveTo(x, y);
bottomRoundedRectangle.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- bottomRoundedRectangle.curveTo(x, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height,
- x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ bottomRoundedRectangle.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
bottomRoundedRectangle.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- bottomRoundedRectangle.curveTo(x + width, y + height,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE,
- x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ bottomRoundedRectangle
+ .curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
bottomRoundedRectangle.lineTo(x + width, y);
bottomRoundedRectangle.closePath();
return bottomRoundedRectangle;
@@ -56,7 +52,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAli
@Override
public void drawAlias(SpeciesAlias alias, Graphics2D graphics, ConverterParams params) {
- //Unit of information text - multimer cardinality
+ // Unit of information text - multimer cardinality
String unitOfInformationText = null;
if (alias.getAliasStatePrefix() != null && alias.getAliasStateLabel() != null) {
if (alias.getAliasStatePrefix().equals("free input")) {
@@ -65,15 +61,15 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAli
unitOfInformationText = alias.getAliasStatePrefix() + ":" + alias.getAliasStateLabel();
}
}
-
+
int homodir = alias.getHomodimer();
-
+
alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
-
+
alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
-
+
int glyphCount;
if (homodir > 1) {
glyphCount = 2;
@@ -83,19 +79,19 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAli
for (int i = 0; i < glyphCount; i++) {
alias.setX(alias.getX() - SpeciesConverter.HOMODIMER_OFFSET);
alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
-
+
Shape shape = getShape(alias);
-
+
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
graphics.fill(shape);
graphics.setColor(c);
-
+
Stroke stroke = graphics.getStroke();
graphics.setStroke(getBorderLine(alias));
graphics.draw(shape);
graphics.setStroke(stroke);
-
+
if (i == 1) {
if (homodir > 1 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
if (unitOfInformationText == null) {
@@ -106,12 +102,12 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<SpeciesAli
unitOfInformationText = unitOfInformationText.concat("N:").concat(Integer.toString(homodir));
}
}
-
+
}
-
+
drawUnitOfInformation(unitOfInformationText, alias, graphics);
drawText(alias, graphics, params);
-
+
alias.setWidth(alias.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
alias.setHeight(alias.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
}
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 f01f64b1a4..35fed2b238 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
@@ -8,18 +8,16 @@ import java.awt.geom.Ellipse2D;
import java.awt.geom.PathIterator;
import java.awt.geom.Point2D;
+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.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-
-import org.apache.log4j.Logger;
/**
* This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.db.model.map.species.SimpleMolecule SimpleMolecule} on the
- * {@link Graphics2D} object.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.SimpleMolecule
+ * SimpleMolecule} on the {@link Graphics2D} object.
*
* @author Piotr Gawron
*
@@ -28,13 +26,14 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMoleculeAlia
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(SimpleMoleculeConverter.class.getName());
+ private static Logger logger = Logger.getLogger(SimpleMoleculeConverter.class.getName());
@Override
public void drawAlias(final SimpleMoleculeAlias 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 glyphs
+ // If the SBGN display mode is set, multimer is shown as two stacked
+ // glyphs
if (alias.getHomodimer() > 1) {
homodir = 2;
} else {
@@ -43,16 +42,16 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMoleculeAlia
} else {
homodir = alias.getHomodimer();
}
-
+
alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
-
+
// SBGN view - simple molecules are represented as circles
if (params.isSbgnFormat()) {
alias.setX(alias.getX() + (alias.getWidth() - alias.getHeight()) / 2);
alias.setWidth(alias.getHeight());
}
-
+
alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
@@ -68,8 +67,9 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMoleculeAlia
graphics.setStroke(getBorderLine(alias));
graphics.draw(shape);
graphics.setStroke(stroke);
-
- // SBGN view - multimers are displayed with a unit of information containing cardinality
+
+ // SBGN view - multimers are displayed with a unit of information
+ // containing cardinality
if (params.isSbgnFormat() && (i == homodir - 1)) {
String unitOfInformationText = null;
if (alias.getAliasStatePrefix() != null && alias.getAliasStateLabel() != null) {
@@ -83,7 +83,7 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMoleculeAlia
}
unitOfInformationText += "N:" + alias.getHomodimer();
}
-
+
drawUnitOfInformation(unitOfInformationText, alias, graphics);
}
}
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 ac97a2a4f0..4337fe9367 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
@@ -1,70 +1,70 @@
-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.Ellipse2D;
-import java.awt.geom.PathIterator;
-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 org.apache.log4j.Logger;
-
-/**
- * This class defines methods used for drawing SpeciesAlias of
- * {@link lcsb.mapviewer.db.model.map.species.Unknown Unknown} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownConverter extends SpeciesConverter<SpeciesAlias> {
- /**
- * 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) {
- if (alias.getActivity()) {
- int border = ACTIVITY_BORDER_DISTANCE;
- alias.increaseBorder(border);
- Shape shape2 = new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(LineType.DOTTED.getStroke());
- graphics.draw(shape2);
- graphics.setStroke(stroke);
- alias.increaseBorder(-border);
- }
-
- Shape shape = new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
- Color c = graphics.getColor();
- graphics.setColor(alias.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- drawText(alias, graphics, params);
- }
-
- @Override
- public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
- throw new InvalidStateException("This class doesn't provide boundPath");
- }
-
- @Override
- public Point2D getPointCoordinatesOnBorder(final SpeciesAlias alias, final double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- logger.warn("Looking for coordinates for unknown of 0 size");
- return alias.getCenter();
- }
- Point2D result;
- result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
- return result;
-
- }
-
-}
+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.Ellipse2D;
+import java.awt.geom.PathIterator;
+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 org.apache.log4j.Logger;
+
+/**
+ * This class defines methods used for drawing SpeciesAlias of
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.db.model.map.species.Unknown Unknown} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownConverter extends SpeciesConverter<SpeciesAlias> {
+ /**
+ * 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) {
+ if (alias.getActivity()) {
+ int border = ACTIVITY_BORDER_DISTANCE;
+ alias.increaseBorder(border);
+ Shape shape2 = new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(LineType.DOTTED.getStroke());
+ graphics.draw(shape2);
+ graphics.setStroke(stroke);
+ alias.increaseBorder(-border);
+ }
+
+ Shape shape = new Ellipse2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ Color c = graphics.getColor();
+ graphics.setColor(alias.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ drawText(alias, graphics, params);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final SpeciesAlias alias) {
+ throw new InvalidStateException("This class doesn't provide boundPath");
+ }
+
+ @Override
+ public Point2D getPointCoordinatesOnBorder(final SpeciesAlias alias, final double angle) {
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ logger.warn("Looking for coordinates for unknown of 0 size");
+ return alias.getCenter();
+ }
+ Point2D result;
+ result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), angle);
+ return result;
+
+ }
+
+}
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 80f0a3bfa9..59817921e0 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
@@ -26,8 +26,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public class NormalImageGeneratorTest {
static Logger logger = Logger.getLogger(NormalImageGenerator.class);
@@ -66,7 +64,7 @@ public class NormalImageGeneratorTest {
public void testComplexConversion() throws Exception {
scale = null;
try {
- AliasConverter.addElementConverter(ComplexSpecies.class, new TmpComplexConverter());
+ AliasConverter.addAliasConverter(ComplexAlias.class, new TmpComplexConverter());
Model model = createComplexModel();
new CreateHierarchyCommand(model, 2, 2).execute();
@@ -86,24 +84,16 @@ public class NormalImageGeneratorTest {
model.setWidth(600);
model.setHeight(600);
- ComplexSpecies complex = new ComplexSpecies();
- complex.setName("a");
- complex.setElementId("c1");
-
- ComplexAlias alias = new ComplexAlias(complex);
- alias.setAliasId("1");
+ ComplexAlias alias = new ComplexAlias("1");
+ alias.setName("a");
alias.setX(10);
alias.setY(10);
alias.setWidth(200);
alias.setHeight(50);
model.addAlias(alias);
- GenericProtein protein = new GenericProtein();
- protein.setName("b");
- protein.setElementId("s1");
-
- SpeciesAlias a2 = new GenericProteinAlias(protein);
- a2.setAliasId("2");
+ SpeciesAlias a2 = new GenericProteinAlias("2");
+ a2.setName("b");
a2.setX(10);
a2.setY(100);
a2.setWidth(200);
@@ -159,12 +149,8 @@ public class NormalImageGeneratorTest {
layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
- ComplexSpecies complex = new ComplexSpecies();
- complex.setName("a");
- complex.setElementId("c1");
-
- ComplexAlias alias = new ComplexAlias(complex);
- alias.setAliasId("1");
+ ComplexAlias alias = new ComplexAlias("1");
+ alias.setName("a");
alias.setX(300);
alias.setY(90);
alias.setWidth(100);
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 574b4bc41d..eeef94d0f5 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
@@ -8,6 +8,10 @@ import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.io.File;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -16,11 +20,6 @@ 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.ComplexSpecies;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
public class PdfImageGeneratorTest {
@@ -41,7 +40,7 @@ public class PdfImageGeneratorTest {
if (f.exists()) {
f.delete();
}
-
+
assertFalse(f.exists());
Model model = createCompartmentModel();
@@ -89,12 +88,8 @@ public class PdfImageGeneratorTest {
layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
- ComplexSpecies complex = new ComplexSpecies();
- complex.setName("a");
- complex.setElementId("c1");
-
- ComplexAlias alias = new ComplexAlias(complex);
- alias.setAliasId("1");
+ ComplexAlias alias = new ComplexAlias("1");
+ alias.setName("a");
alias.setX(300);
alias.setY(90);
alias.setWidth(100);
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 303a4e3379..4acd4cebfd 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
@@ -7,22 +7,21 @@ import java.awt.geom.Rectangle2D;
import java.io.IOException;
import java.util.Arrays;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.SquareCompartmentAlias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
public class AllPlaceFinderTest {
- Logger logger = Logger.getLogger(AllPlaceFinderTest.class);
- final String out = "map_images/testOutput";
- final String folder = "testFiles/placeFinderFiles/";
+ Logger logger = Logger.getLogger(AllPlaceFinderTest.class);
+ final String out = "map_images/testOutput";
+ final String folder = "testFiles/placeFinderFiles/";
- int id = 10;
+ int id = 10;
@Test
public void oneEmptyCompartments() throws InvalidXmlSchemaException, IOException {
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 cb172341f1..1f93051927 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
@@ -19,8 +19,6 @@ 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.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public class SpeciesConverterTest {
@@ -40,8 +38,7 @@ public class SpeciesConverterTest {
return super.getResidueCoordinates(alias, angle);
}
}
- GenericProtein protein = new GenericProtein();
- GenericProteinAlias alias = new GenericProteinAlias(protein);
+ GenericProteinAlias alias = new GenericProteinAlias("id");
alias.setX(135);
alias.setY(194.0);
alias.setWidth(130);
@@ -180,9 +177,8 @@ public class SpeciesConverterTest {
}
private GenericProteinAlias createAlias() {
- GenericProtein protein = new GenericProtein();
- protein.setName("NAME_OF_THE_ELEMENT");
- GenericProteinAlias alias = new GenericProteinAlias(protein);
+ GenericProteinAlias alias = new GenericProteinAlias("id");
+ alias.setName("NAME_OF_THE_ELEMENT");
alias.setX(10);
alias.setY(20);
alias.setWidth(100);
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index ad071e1810..5abb11d212 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -22,6 +22,10 @@ import org.junit.Test;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.map.InconsistentModelException;
@@ -41,10 +45,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
public class ComplexZipConverterTest {
private static Logger logger = Logger.getLogger(ComplexZipConverterTest.class);
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 a0a7ccd0ee..e95dbc3021 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
@@ -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.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;
-
-/**
- * Class that creates commands that modifies
- * {@link lcsb.mapviewer.model.map.Element#formerSymbols} from gui input for
- * given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeFormerSymbolCommand extends CreateListPropertyChangeCommand<String> {
-
- /**
- * Default constructor.
- *
- * @param list
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeFormerSymbolCommand(JList<String> list) {
- super(list);
- }
-
- @Override
- protected ModelCommand createRemoveCommand(Model model, Alias alias, List<String> values) {
- return new RemoveElementFormerSymbolsCommand(model, alias, values);
- }
-
- @Override
- protected ModelCommand createChangeCommand(Model model, Alias alias, String newValue, String oldValue) {
- return new ChangeElementFormerSymbolCommand(model, alias, newValue, oldValue);
- }
-
- @Override
- protected ModelCommand createAddCommand(Model model, Alias alias, List<String> newValues) {
- return new AddElementFormerSymbolsCommand(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.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;
+
+/**
+ * Class that creates commands that modifies
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#formerSymbols} from gui input for
+ * given {@link Model} and {@link Alias}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeFormerSymbolCommand extends CreateListPropertyChangeCommand<String> {
+
+ /**
+ * Default constructor.
+ *
+ * @param list
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeFormerSymbolCommand(JList<String> list) {
+ super(list);
+ }
+
+ @Override
+ protected ModelCommand createRemoveCommand(Model model, Alias alias, List<String> values) {
+ return new RemoveElementFormerSymbolsCommand(model, alias, values);
+ }
+
+ @Override
+ protected ModelCommand createChangeCommand(Model model, Alias alias, String newValue, String oldValue) {
+ return new ChangeElementFormerSymbolCommand(model, alias, newValue, oldValue);
+ }
+
+ @Override
+ protected ModelCommand createAddCommand(Model model, Alias alias, List<String> newValues) {
+ return new AddElementFormerSymbolsCommand(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 693efb5cd6..fbfe2a23ad 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
@@ -1,31 +1,31 @@
-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.ChangeElementNameCommand;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class with method executed when text property of
- * {@link lcsb.mapviewer.model.map.Element} is changed.
- *
- */
-public class CreateChangeNameCommand extends CreatePropertyChangeCommand {
- /**
- * Default constructor.
- *
- * @param field
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeNameCommand(JTextField field) {
- super(field);
- }
-
- @Override
- public ModelCommand createCommand(Model model, Alias alias) {
- return new ChangeElementNameCommand(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.ChangeElementNameCommand;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Class with method executed when text property of
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element} is changed.
+ *
+ */
+public class CreateChangeNameCommand extends CreatePropertyChangeCommand {
+ /**
+ * Default constructor.
+ *
+ * @param field
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeNameCommand(JTextField field) {
+ super(field);
+ }
+
+ @Override
+ public ModelCommand createCommand(Model model, Alias alias) {
+ return new ChangeElementNameCommand(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 3ed3062e4a..e7aec33f5a 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
@@ -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.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;
-
-/**
- * Class that creates commands that modifies
- * {@link lcsb.mapviewer.model.map.Element#synonyms} from gui input for
- * given {@link Model} and {@link Alias}.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateChangeSynonymCommand extends CreateListPropertyChangeCommand<String> {
-
- /**
- * Default constructor.
- *
- * @param list
- * GUI input from which {@link ModelCommand} will be created
- */
- CreateChangeSynonymCommand(JList<String> list) {
- super(list);
- }
-
- @Override
- protected ModelCommand createRemoveCommand(Model model, Alias alias, List<String> values) {
- return new RemoveElementSynonymsCommand(model, alias, values);
- }
-
- @Override
- protected ModelCommand createChangeCommand(Model model, Alias alias, String newValue, String oldValue) {
- return new ChangeElementSynonymCommand(model, alias, newValue, oldValue);
- }
-
- @Override
- protected ModelCommand createAddCommand(Model model, Alias alias, List<String> newValues) {
- return new AddElementSynonymsCommand(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.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;
+
+/**
+ * Class that creates commands that modifies
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonyms} from gui input for
+ * given {@link Model} and {@link Alias}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateChangeSynonymCommand extends CreateListPropertyChangeCommand<String> {
+
+ /**
+ * Default constructor.
+ *
+ * @param list
+ * GUI input from which {@link ModelCommand} will be created
+ */
+ CreateChangeSynonymCommand(JList<String> list) {
+ super(list);
+ }
+
+ @Override
+ protected ModelCommand createRemoveCommand(Model model, Alias alias, List<String> values) {
+ return new RemoveElementSynonymsCommand(model, alias, values);
+ }
+
+ @Override
+ protected ModelCommand createChangeCommand(Model model, Alias alias, String newValue, String oldValue) {
+ return new ChangeElementSynonymCommand(model, alias, newValue, oldValue);
+ }
+
+ @Override
+ protected ModelCommand createAddCommand(Model model, Alias alias, List<String> newValues) {
+ return new AddElementSynonymsCommand(model, alias, newValues);
+ }
+
+}
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 e544119e74..5c02dce650 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
@@ -74,12 +74,12 @@ public class ElementDetailsPanel extends JPanel {
private final Logger logger = Logger.getLogger(ElementDetailsPanel.class);
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#name} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#name} parameter.
*/
private JLabel nameLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#getElementId()}
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#getElementId()}
* parameter.
*/
private JLabel idLabel;
@@ -105,53 +105,53 @@ public class ElementDetailsPanel extends JPanel {
private JLabel colorLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#notes} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#notes} parameter.
*/
private JLabel notesLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#symbol} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#symbol} parameter.
*/
private JLabel symbolLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#fullName} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#fullName} parameter.
*/
private JLabel fullNameLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#abbreviation} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#abbreviation} parameter.
*/
private JLabel abbreviationLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#formula} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#formula} parameter.
*/
private JLabel formulaLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#synonyms} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonyms} parameter.
*/
private JLabel synonymsLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#formerSymbols} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#formerSymbols} parameter.
*/
private JLabel formerSymbolsLabel;
/**
- * Label for {@link lcsb.mapviewer.model.map.Element#symbol} parameter.
+ * Label for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#symbol} parameter.
*/
private JLabel miriamDataLabel;
/**
- * {@link JTextField} for {@link lcsb.mapviewer.model.map.Element#name}
+ * {@link JTextField} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#name}
* parameter.
*/
private JTextField nameText;
/**
- * {@link JTextField} for {@link lcsb.mapviewer.model.map.Element#name}
+ * {@link JTextField} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#name}
* parameter.
*/
private JTextField idText;
@@ -177,69 +177,69 @@ public class ElementDetailsPanel extends JPanel {
private JButton colorButton;
/**
- * {@link JTextField} for {@link lcsb.mapviewer.model.map.Element#notes}
+ * {@link JTextField} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#notes}
* parameter.
*/
private JTextArea notesText;
/**
- * {@link JTextField} for {@link lcsb.mapviewer.model.map.Element#symbol}
+ * {@link JTextField} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#symbol}
* parameter.
*/
private JTextField symbolText;
/**
- * {@link JTextField} for {@link lcsb.mapviewer.model.map.Element#fullName}
+ * {@link JTextField} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#fullName}
* parameter.
*/
private JTextField fullNameText;
/**
* {@link JTextField} for
- * {@link lcsb.mapviewer.model.map.Element#abbreviation} parameter.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#abbreviation} parameter.
*/
private JTextField abbreviationText;
/**
- * {@link JTextField} for {@link lcsb.mapviewer.model.map.Element#formula}
+ * {@link JTextField} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#formula}
* parameter.
*/
private JTextField formulaText;
/**
- * {@link JList} for {@link lcsb.mapviewer.model.map.Element#synonyms}
+ * {@link JList} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonyms}
* parameter.
*/
private JList<String> synonymsList;
/**
* {@link JList} for
- * {@link lcsb.mapviewer.model.map.Element#formerSymbols} parameter.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#formerSymbols} parameter.
*/
private JList<String> formerSymbolsList;
/**
- * {@link JList} for {@link lcsb.mapviewer.model.map.Element#miriamData}
+ * {@link JList} for {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#miriamData}
* parameter.
*/
private JList<MiriamData> miriamDataList;
/**
- * List of synonyms in {@link lcsb.mapviewer.model.map.Element#synonyms}.
+ * List of synonyms in {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonyms}.
*
* @see {@link #synonymsList}
*/
private DefaultListModel<String> synonymsListModel = new DefaultListModel<>();
/**
- * List of synonyms in {@link lcsb.mapviewer.model.map.Element#formerSymbols}.
+ * List of synonyms in {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#formerSymbols}.
*
* @see {@link #formerSymbolsList}
*/
private DefaultListModel<String> formerSymbolsListModel = new DefaultListModel<>();
/**
- * List of synonyms in {@link lcsb.mapviewer.model.map.Element#miriamData}.
+ * List of synonyms in {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#miriamData}.
*
* @see {@link #miriamDataList}
*/
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 8453b5d165..fe7b37500c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -11,6 +11,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -26,7 +27,6 @@ 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.Species;
/**
* This {@link ModelCommand} colors a model (nodes and reactions) according to
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 08a50071aa..a5026776c0 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
@@ -7,7 +7,7 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
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 d9d57309a5..e1cf4f0d1a 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
@@ -10,7 +10,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * former sybmols of the {@link lcsb.mapviewer.model.map.Element Element} connected to
+ * former sybmols of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected to
* {@link Alias}.
*
* @author Piotr Gawron
@@ -32,7 +32,7 @@ public class AddElementFormerSymbolsCommand extends AddElementPropertyListEntryC
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * new {@link lcsb.mapviewer.model.map.Element#synonym} values to be
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} values to be
* added
*/
public AddElementFormerSymbolsCommand(Model model, Alias alias, List<String> 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 3e5b2440e9..2785204d23 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
@@ -12,7 +12,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
* {@link MiriamData annotations} of the
- * {@link lcsb.mapviewer.model.map.Element Element} connected to {@link Alias}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected to {@link Alias}.
*
* @author Piotr Gawron
*
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 2b52484c70..dd2f07fe56 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
@@ -1,93 +1,93 @@
-package lcsb.mapviewer.commands.properties;
-
-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;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that add entries
- * into a property of the {@link lcsb.mapviewer.model.map.Element Element} that
- * is list. {@link lcsb.mapviewer.model.map.Element Element} is connected to
- * {@link Alias}.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand {
-
- /**
- * List of new values that should be added to property.
- */
- private List<T> newValues;
-
- /**
- * {@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 newValues
- * new values of the element property that will be added
- *
- */
- public AddElementPropertyListEntryCommand(Model model, Alias alias, List<T> newValues) {
- super(model);
- this.alias = alias;
- this.newValues = newValues;
- }
-
- @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 newValue
- * @see #newValue
- */
- protected List<T> getNewValues() {
- return newValues;
- }
-
- /**
- * @param newValue
- * the newValue to set
- * @see #newValue
- */
- protected void setNewValues(List<T> newValue) {
- this.newValues = newValue;
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+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;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that add entries
+ * into a property of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} that
+ * is list. {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} is connected to
+ * {@link Alias}.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand {
+
+ /**
+ * List of new values that should be added to property.
+ */
+ private List<T> newValues;
+
+ /**
+ * {@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 newValues
+ * new values of the element property that will be added
+ *
+ */
+ public AddElementPropertyListEntryCommand(Model model, Alias alias, List<T> newValues) {
+ super(model);
+ this.alias = alias;
+ this.newValues = newValues;
+ }
+
+ @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 newValue
+ * @see #newValue
+ */
+ protected List<T> getNewValues() {
+ return newValues;
+ }
+
+ /**
+ * @param newValue
+ * the newValue to set
+ * @see #newValue
+ */
+ protected void setNewValues(List<T> newValue) {
+ this.newValues = newValue;
+ }
+}
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 059e33828f..41a529447c 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
@@ -10,7 +10,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * synonyms of the {@link lcsb.mapviewer.model.map.Element Element} connected to
+ * synonyms of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected to
* {@link Alias}.
*
* @author Piotr Gawron
@@ -32,7 +32,7 @@ public class AddElementSynonymsCommand extends AddElementPropertyListEntryComman
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * new {@link lcsb.mapviewer.model.map.Element#synonym} values to be
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} values to be
* added
*/
public AddElementSynonymsCommand(Model model, Alias alias, List<String> values) {
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 025c586f45..59c47fcbae 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
@@ -8,7 +8,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes former
- * symbol of the {@link lcsb.mapviewer.model.map.Element Element} connected to
+ * symbol of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected to
* {@link Alias}.
*
* @author Piotr Gawron
@@ -30,9 +30,9 @@ public class ChangeElementFormerSymbolCommand extends ChangeElementPropertyListE
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newValue
- * new {@link lcsb.mapviewer.model.map.Element#synonym} value
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} value
* @param oldValue
- * old {@link lcsb.mapviewer.model.map.Element#synonym} value
+ * old {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} value
*/
public ChangeElementFormerSymbolCommand(Model model, Alias 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 56f6a1c96b..6f21ab50ac 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
@@ -28,7 +28,7 @@ public class ChangeElementFormulaCommand extends ChangeElementPropertyCommand<St
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link lcsb.mapviewer.model.map.Element#formula} value
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#formula} value
*/
public ChangeElementFormulaCommand(Model model, Alias 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 7efafa6b99..915eee3dda 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
@@ -28,7 +28,7 @@ public class ChangeElementFullNameCommand extends ChangeElementPropertyCommand<S
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link lcsb.mapviewer.model.map.Element#fullName} value
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#fullName} value
*/
public ChangeElementFullNameCommand(Model model, Alias 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 26f59f8f10..dae2ea31ed 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
@@ -9,7 +9,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * annotations of the {@link lcsb.mapviewer.model.map.Element Element} connected
+ * annotations of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected
* to {@link Alias}.
*
* @author Piotr Gawron
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 0c1a544e0b..ecbf0aeadf 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
@@ -28,7 +28,7 @@ public class ChangeElementNotesCommand extends ChangeElementPropertyCommand<Stri
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link lcsb.mapviewer.model.map.Element#notes} value
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#notes} value
*/
public ChangeElementNotesCommand(Model model, Alias alias, String newName) {
super(model, alias, newName);
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 b83fa614b8..49fd7ec140 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
@@ -1,128 +1,128 @@
-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
- * entry in a property of the {@link lcsb.mapviewer.model.map.Element Element}
- * that is list. {@link lcsb.mapviewer.model.map.Element Element} is connected
- * to {@link Alias}.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ChangeElementPropertyListEntryCommand<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
- *
- * @param oldValue
- * old value of the element property
- */
- public ChangeElementPropertyListEntryCommand(Model model, Alias alias, T newValue, T oldValue) {
- super(model);
- this.alias = alias;
- this.oldValue = oldValue;
- this.newValue = newValue;
- }
-
- @Override
- protected void undoImplementation() throws CommandExecutionException {
- T tmpNewValue = newValue;
- T tmpOldValue = oldValue;
- newValue = tmpOldValue;
- oldValue = tmpNewValue;
- executeImplementation();
- newValue = tmpNewValue;
- oldValue = tmpOldValue;
- 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 T 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 T 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.layout.alias.Alias;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
+ * entry in a property of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element}
+ * that is list. {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} is connected
+ * to {@link Alias}.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ChangeElementPropertyListEntryCommand<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
+ *
+ * @param oldValue
+ * old value of the element property
+ */
+ public ChangeElementPropertyListEntryCommand(Model model, Alias alias, T newValue, T oldValue) {
+ super(model);
+ this.alias = alias;
+ this.oldValue = oldValue;
+ this.newValue = newValue;
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ T tmpNewValue = newValue;
+ T tmpOldValue = oldValue;
+ newValue = tmpOldValue;
+ oldValue = tmpNewValue;
+ executeImplementation();
+ newValue = tmpNewValue;
+ oldValue = tmpOldValue;
+ 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 T 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 T 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/ChangeElementSymbolCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java
index c54fd8d29f..1958015498 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
@@ -28,7 +28,7 @@ public class ChangeElementSymbolCommand extends ChangeElementPropertyCommand<Str
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newName
- * new {@link lcsb.mapviewer.model.map.Element#symbol} value
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#symbol} value
*/
public ChangeElementSymbolCommand(Model model, Alias 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 051f192af3..d9764839b3 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
@@ -8,7 +8,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * synonym of the {@link lcsb.mapviewer.model.map.Element Element} connected to
+ * synonym of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected to
* {@link Alias}.
*
* @author Piotr Gawron
@@ -30,9 +30,9 @@ public class ChangeElementSynonymCommand extends ChangeElementPropertyListEntryC
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param newValue
- * new {@link lcsb.mapviewer.model.map.Element#synonym} value
+ * new {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} value
* @param oldValue
- * old {@link lcsb.mapviewer.model.map.Element#synonym} value
+ * old {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} value
*/
public ChangeElementSynonymCommand(Model model, Alias 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 2bc7e0d99a..1fdc63b9d1 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
@@ -10,7 +10,7 @@ import lcsb.mapviewer.model.map.model.Model;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes former
- * symbols from {@link lcsb.mapviewer.model.map.Element Element} connected to
+ * symbols from {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected to
* {@link Alias}.
*
* @author Piotr Gawron
@@ -32,7 +32,7 @@ public class RemoveElementFormerSymbolsCommand extends RemoveElementPropertyList
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * {@link lcsb.mapviewer.model.map.Element#synonym} values to be
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} values to be
* removed
*/
public RemoveElementFormerSymbolsCommand(Model model, Alias alias, List<String> 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 619d01b113..b8264c8984 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
@@ -11,7 +11,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * annotations from {@link lcsb.mapviewer.model.map.Element Element} connected
+ * annotations from {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected
* to {@link Alias}.
*
* @author Piotr Gawron
@@ -33,7 +33,7 @@ public class RemoveElementMiriamDataCommand extends RemoveElementPropertyListEnt
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * {@link lcsb.mapviewer.model.map.Element#synonym} values to be
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} values to be
* removed
*/
public RemoveElementMiriamDataCommand(Model model, Alias alias, List<MiriamData> 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 49c57fcf6e..285c3bb702 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
@@ -1,93 +1,93 @@
-package lcsb.mapviewer.commands.properties;
-
-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;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * entries from a property of the {@link lcsb.mapviewer.model.map.Element
- * Element} that is list. {@link lcsb.mapviewer.model.map.Element Element} is
- * connected to {@link Alias}.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelCommand {
-
- /**
- * Rlement property values to be removed.
- */
- private List<T> values;
-
- /**
- * {@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 values
- * values of the element property to remove
- */
- public RemoveElementPropertyListEntryCommand(Model model, Alias alias, List<T> values) {
- super(model);
- this.alias = alias;
- this.values = values;
- }
-
- @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 values
- * @see #values
- */
- public List<T> getValues() {
- return values;
- }
-
- /**
- * @param values
- * the values to set
- * @see #values
- */
- public void setValues(List<T> values) {
- this.values = values;
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+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;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
+ * entries from a property of the {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element
+ * Element} that is list. {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} is
+ * connected to {@link Alias}.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelCommand {
+
+ /**
+ * Rlement property values to be removed.
+ */
+ private List<T> values;
+
+ /**
+ * {@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 values
+ * values of the element property to remove
+ */
+ public RemoveElementPropertyListEntryCommand(Model model, Alias alias, List<T> values) {
+ super(model);
+ this.alias = alias;
+ this.values = values;
+ }
+
+ @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 values
+ * @see #values
+ */
+ public List<T> getValues() {
+ return values;
+ }
+
+ /**
+ * @param values
+ * the values to set
+ * @see #values
+ */
+ public void setValues(List<T> values) {
+ this.values = values;
+ }
+
+}
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 f54b5bf560..31715dfab3 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
@@ -10,7 +10,7 @@ import org.apache.log4j.Logger;
/**
* {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * synonym from {@link lcsb.mapviewer.model.map.Element Element} connected to
+ * synonym from {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element Element} connected to
* {@link Alias}.
*
* @author Piotr Gawron
@@ -32,7 +32,7 @@ public class RemoveElementSynonymsCommand extends RemoveElementPropertyListEntry
* @param alias
* {@link ChangeElementPropertyCommand#alias}
* @param values
- * {@link lcsb.mapviewer.model.map.Element#synonym} values to be
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Element#synonym} values to be
* removed
*/
public RemoveElementSynonymsCommand(Model model, Alias alias, List<String> values) {
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 99607c7696..ffd2b86d58 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -16,6 +16,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -27,7 +28,6 @@ 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.GenericProtein;
public class ColorModelCommandTest extends CommandTestFunctions {
Logger logger = Logger.getLogger(ColorModelCommandTest.class);
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 7ba119a656..e99ef7701b 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -9,13 +9,13 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.agregator.Compartment;
+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.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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public abstract class CommandTestFunctions {
public double EPSILON = 1e-6;
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 d9eb113cfd..1463362ed6 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -14,9 +14,12 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+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.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
@@ -29,9 +32,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
public class CopyCommandTest extends CommandTestFunctions {
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 d239dfe232..72ba4c56ef 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
@@ -12,11 +12,11 @@ import java.util.List;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
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.Species;
import org.junit.After;
import org.junit.Before;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
index ca9957f456..df0c5393d3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
@@ -6,11 +6,9 @@ import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
-import javax.persistence.ManyToOne;
import javax.persistence.Table;
import javax.xml.bind.annotation.XmlRootElement;
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 fc08ab7123..875ba57f53 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -4,7 +4,6 @@ import java.util.ArrayList;
import java.util.List;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.ChemicalAlias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
@@ -14,13 +13,6 @@ 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.Chemical;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/agregator/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/agregator/package-info.java
deleted file mode 100644
index 168d49a4f5..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/agregator/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * Contains structures used for compartment modeling.
- */
-package lcsb.mapviewer.model.map.agregator;
-
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 360c1f1757..bbeaa6515f 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
@@ -1,212 +1,212 @@
-package lcsb.mapviewer.model.map.graph;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-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.JoinTable;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.IndexColumn;
-
-/**
- * Entity representing data mining entry.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-public class DataMining implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * For which element this entry was created.
- */
- @ManyToOne(optional = false)
- private Element element;
-
- /**
- * List of the suggested connection.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- @JoinTable(name = "datamining_suggested_connections")
- private List<MiriamData> suggestedConnections = new ArrayList<MiriamData>();
-
- /**
- * Short description of the connection.
- */
- @Column(columnDefinition = "TEXT")
- private String description;
-
- /**
- * Where the data comes from.
- */
- private DataMiningType type;
-
- /**
- * List of reference links for this entry.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<MiriamData> references = new ArrayList<MiriamData>();
-
- /**
- * Adds reference.
- *
- * @param md
- * new reference link
- * @see #references
- */
- public void addReference(MiriamData md) {
- references.add(md);
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<MiriamData> references) {
- this.references = references;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public DataMiningType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(DataMiningType type) {
- this.type = type;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public Integer getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(Integer id) {
- this.id = id;
- }
-
- /**
- * @return the element
- * @see #element
- */
- public Element getElement() {
- return element;
- }
-
- /**
- * @param element
- * the element to set
- * @see #element
- */
- public void setElement(Element element) {
- this.element = element;
- }
-
- /**
- * @return the suggestedConnections
- * @see #suggestedConnections
- */
- public List<MiriamData> getSuggestedConnections() {
- return suggestedConnections;
- }
-
- /**
- * @param suggestedConnections
- * the suggestedConnections to set
- * @see #suggestedConnections
- */
- public void setSuggestedConnections(List<MiriamData> suggestedConnections) {
- this.suggestedConnections = suggestedConnections;
- }
-
- /**
- * @param suggestedConnection
- * the suggestedConnection to add
- * @see #suggestedConnections
- */
- public void addSuggestedConnection(MiriamData suggestedConnection) {
- this.suggestedConnections.add(suggestedConnection);
- }
-
- /**
- * Adds references to {@link #references}.
- *
- * @param ref
- * references to add
- */
- public void addReferences(List<MiriamData> ref) {
- references.addAll(ref);
- }
-
-}
+package lcsb.mapviewer.model.map.graph;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+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.JoinTable;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.IndexColumn;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+
+/**
+ * Entity representing data mining entry.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+public class DataMining implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * For which element this entry was created.
+ */
+ @ManyToOne(optional = false)
+ private Alias element;
+
+ /**
+ * List of the suggested connection.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ @JoinTable(name = "datamining_suggested_connections")
+ private List<MiriamData> suggestedConnections = new ArrayList<MiriamData>();
+
+ /**
+ * Short description of the connection.
+ */
+ @Column(columnDefinition = "TEXT")
+ private String description;
+
+ /**
+ * Where the data comes from.
+ */
+ private DataMiningType type;
+
+ /**
+ * List of reference links for this entry.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ private List<MiriamData> references = new ArrayList<MiriamData>();
+
+ /**
+ * Adds reference.
+ *
+ * @param md
+ * new reference link
+ * @see #references
+ */
+ public void addReference(MiriamData md) {
+ references.add(md);
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<MiriamData> references) {
+ this.references = references;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public DataMiningType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(DataMiningType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the element
+ * @see #element
+ */
+ public Alias getElement() {
+ return element;
+ }
+
+ /**
+ * @param element
+ * the element to set
+ * @see #element
+ */
+ public void setElement(Alias element) {
+ this.element = element;
+ }
+
+ /**
+ * @return the suggestedConnections
+ * @see #suggestedConnections
+ */
+ public List<MiriamData> getSuggestedConnections() {
+ return suggestedConnections;
+ }
+
+ /**
+ * @param suggestedConnections
+ * the suggestedConnections to set
+ * @see #suggestedConnections
+ */
+ public void setSuggestedConnections(List<MiriamData> suggestedConnections) {
+ this.suggestedConnections = suggestedConnections;
+ }
+
+ /**
+ * @param suggestedConnection
+ * the suggestedConnection to add
+ * @see #suggestedConnections
+ */
+ public void addSuggestedConnection(MiriamData suggestedConnection) {
+ this.suggestedConnections.add(suggestedConnection);
+ }
+
+ /**
+ * Adds references to {@link #references}.
+ *
+ * @param ref
+ * references to add
+ */
+ public void addReferences(List<MiriamData> ref) {
+ references.addAll(ref);
+ }
+
+}
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 bbdb86ebfe..0493975e9a 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
@@ -1,543 +1,543 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.awt.Color;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Entry of coloring schema used for changing colors in the map. It allows to
- * identify some elements by use of the filters (by name, type, etcs.) and
- * contains information about the color that should be assigned to the fileter
- * elements.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ColorSchema implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Base of the hex representation.
- */
- private static final int HEX_BASE = 16;
-
- /**
- * Length of the string describing color in rgb: "#RRGGBB".
- */
- private static final int COLOR_STRING_LENGTH = 7;
-
- /**
- * Where starts description of red color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_RED = 1;
-
- /**
- * Where starts description of green color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_GREEN = 3;
-
- /**
- * Where starts description of blue color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_BLUE = 5;
-
- /**
- * Defines the maximum value of primary colors in RGB model (every color is
- * from range 0..255).
- */
- 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
- * then this field will be skiped.
- */
- private String name = null;
-
- /**
- * Identifier of the reaction to change the color.
- */
- private String reactionIdentifier = null;
-
- /**
- * Should the direction of highlighted reaction be reversed.
- */
- private Boolean reverseReaction = null;
-
- /**
- * Width of the line in the reaction.
- */
- private Double lineWidth = null;
-
- /**
- * In which compartments (identified by name) the element can occur.
- */
- private List<String> compartments = new ArrayList<String>();
-
- /**
- * What types of element should be identified by this entry.
- */
- private List<Class<? extends Species>> types = new ArrayList<Class<? extends Species>>();
-
- /**
- * Value (-1..1 range) that is assigned to filtered elements (it will be
- * transformed into color later on). Only one of the {@link #value} and
- * {@link #color} can be set.
- */
- private Double value = null;
-
- /**
- * Color that is assigned to filtered elements. Only one of the {@link #value}
- * and {@link #color} can be set.
- */
- private Color color = null;
-
- /**
- * General identifier that identifies the element.
- */
- private String generalIdentifier = null;
-
- /**
- * List of specific identifiers that filter the elements.
- */
- private List<Pair<MiriamType, String>> identifierColumns = new ArrayList<Pair<MiriamType, String>>();
-
- /**
- * Number of elements matched by this entry.
- */
- private int matches = 0;
-
- /**
- * Short description of the entry.
- */
- private String description;
-
- /**
- * Default constructor.
- */
- protected ColorSchema() {
- }
-
- /**
- * Initializes object by copying data from the parameter.
- *
- * @param original
- * original object used for initialization
- */
- protected ColorSchema(ColorSchema original) {
- this.setName(original.getName());
- this.setReactionIdentifier(original.getReactionIdentifier());
- this.setReverseReaction(original.getReverseReaction());
- this.setLineWidth(original.getLineWidth());
- this.addCompartments(original.getCompartments());
- this.addTypes(original.getTypes());
- this.setValue(original.getValue());
- this.setColor(original.getColor());
- this.setGeneralIdentifier(original.getGeneralIdentifier());
- this.addIdentifierColumns(original.getIdentifierColumns());
- this.setMatches(original.getMatches());
- this.setDescription(original.getDescription());
- }
-
- /**
- * Adds identifiers to {@link #identifierColumns} list.
- *
- * @param identifierColumnsList
- * list of pairs defining type of identifier and the identifier value
- */
- public void addIdentifierColumns(List<Pair<MiriamType, String>> identifierColumnsList) {
- for (Pair<MiriamType, String> pair : identifierColumnsList) {
- addIdentifierColumn(pair);
- }
-
- }
-
- /**
- * Adds class types to {@link #types} list.
- *
- * @param types2
- * list of classes to add
- */
- public void addTypes(List<Class<? extends Species>> types2) {
- for (Class<? extends Species> clazz : types2) {
- addType(clazz);
- }
- }
-
- /**
- * Adds compartment names to {@link #compartments} list.
- *
- * @param compartments2
- * elements to add
- */
- public void addCompartments(String[] compartments2) {
- for (String string : compartments2) {
- compartments.add(string);
- }
- }
-
- /**
- * Adds compartment names to {@link #compartments} list.
- *
- * @param compartments2
- * elements to add
- */
- public void addCompartments(Collection<String> compartments2) {
- for (String string : compartments2) {
- compartments.add(string);
- }
- }
-
- /**
- * Sets {@link #color} from the string.
- *
- * @param string
- * color in text representation
- * @throws InvalidColorSchemaException
- * thrown when string describing color is invalid
- */
- public void setColor(String string) throws InvalidColorSchemaException {
- if (string.length() != COLOR_STRING_LENGTH) {
- throw new InvalidColorSchemaException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
- }
- if (string.charAt(0) != '#') {
- throw new InvalidColorSchemaException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
-
- } else {
- setColor(new Color(Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE)));
- }
-
- }
-
- @Override
- public String toString() {
- StringBuilder result = new StringBuilder();
- result.append("[");
- if (name != null) {
- result.append(name + ",");
- }
- if (compartments.size() > 0) {
- result.append("(");
- for (String comp : compartments) {
- result.append(comp + ",");
- }
- result.append("),");
- }
- if (types.size() > 0) {
- result.append("(");
- for (Class<?> clazz : types) {
- result.append(clazz.getSimpleName() + ",");
- }
- result.append("),");
- }
- if (value != null) {
- result.append(value + ",");
- }
- if (color != null) {
- result.append(color + ",");
- }
- if (generalIdentifier != null) {
- result.append(generalIdentifier + ",");
- }
- if (types.size() > 0) {
- result.append("(");
- for (Pair<MiriamType, String> pair : identifierColumns) {
- result.append(pair.getLeft() + "-" + pair.getRight() + ",");
- }
- result.append("),");
- }
- result.append(matches + "]");
- return result.toString();
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- if (name == null) {
- this.name = null;
- } else {
- this.name = name.trim();
- }
- }
-
- /**
- * @return the compartments
- * @see #compartments
- */
- public List<String> getCompartments() {
- return compartments;
- }
-
- /**
- * @param compartments
- * the compartments to set
- * @see #compartments
- */
- public void setCompartments(List<String> compartments) {
- this.compartments = compartments;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public List<Class<? extends Species>> getTypes() {
- return types;
- }
-
- /**
- * @param types
- * the types to set
- * @see #types
- */
- public void setTypes(List<Class<? extends Species>> types) {
- this.types = types;
- }
-
- /**
- * @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;
- }
-
- /**
- * @return the generalIdentifier
- * @see #generalIdentifier
- */
- public String getGeneralIdentifier() {
- return generalIdentifier;
- }
-
- /**
- * @param generalIdentifier
- * the generalIdentifier to set
- * @see #generalIdentifier
- */
- public void setGeneralIdentifier(String generalIdentifier) {
- this.generalIdentifier = generalIdentifier;
- }
-
- /**
- * @return the identifierColumns
- * @see #identifierColumns
- */
- public List<Pair<MiriamType, String>> getIdentifierColumns() {
- return identifierColumns;
- }
-
- /**
- * @param identifierColumns
- * the identifierColumns to set
- * @see #identifierColumns
- */
- public void setIdentifierColumns(List<Pair<MiriamType, String>> identifierColumns) {
- this.identifierColumns = identifierColumns;
- }
-
- /**
- * @return the matches
- * @see #matches
- */
- public int getMatches() {
- return matches;
- }
-
- /**
- * @param matches
- * the matches to set
- * @see #matches
- */
- public void setMatches(int matches) {
- this.matches = matches;
- }
-
- /**
- * Adds identifier to {@link #identifierColumns} list.
- *
- * @param pair
- * pair defining type of identifier and the identifier value
- */
- public void addIdentifierColumn(Pair<MiriamType, String> pair) {
- identifierColumns.add(pair);
-
- }
-
- /**
- * @return the reactionIdentifier
- * @see #reactionIdentifier
- */
- public String getReactionIdentifier() {
- return reactionIdentifier;
- }
-
- /**
- * @param reactionIdentifier
- * the reactionIdentifier to set
- * @see #reactionIdentifier
- */
- public void setReactionIdentifier(String reactionIdentifier) {
- this.reactionIdentifier = reactionIdentifier;
- }
-
- /**
- * @return the lineWidth
- * @see #lineWidth
- */
- public Double getLineWidth() {
- return lineWidth;
- }
-
- /**
- * @param lineWidth
- * the lineWidth to set
- * @see #lineWidth
- */
- public void setLineWidth(Double lineWidth) {
- this.lineWidth = lineWidth;
- }
-
- /**
- * @return the reverseReaction
- * @see #reverseReaction
- */
- public Boolean getReverseReaction() {
- return reverseReaction;
- }
-
- /**
- * @param reverseReaction
- * the reverseReaction to set
- * @see #reverseReaction
- */
- public void setReverseReaction(Boolean reverseReaction) {
- this.reverseReaction = reverseReaction;
- }
-
- /**
- * Adds compartment name to {@link #compartments}.
- *
- * @param name
- * compartment name
- */
- public void addCompartment(String name) {
- compartments.add(name);
- }
-
- /**
- * Adds class type to {@link #types} list.
- *
- * @param clazz
- * class to add
- */
- public void addType(Class<? extends Species> clazz) {
- this.types.add(clazz);
- }
-
- /**
- * Extracts color from {@link ColorSchema} object.
- *
- * @return color from {@link ColorSchema} object
- */
- public Color getNormalizedColor() {
- if (getColor() != null) {
- return getColor();
- } else {
- return getColorForValue(getValue());
- }
- }
-
- /**
- * Returns color from red - green scale for the given normalized double value
- * (from range -1,1).
- *
- * @param value
- * double value that should be converted into color
- * @return color for the double value
- */
- protected Color getColorForValue(Double value) {
- if (value > 0) {
- int val = (int) ((1 - value) * MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT);
- return new Color(val, MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT, val);
- }
- if (value < 0) {
- int val = (int) ((1 + value) * MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT);
- return new Color(MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT, val, val);
- }
- return Color.WHITE;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * Creates a copy of this object.
- *
- * @return copy of the object
- */
- public abstract ColorSchema copy();
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.awt.Color;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+
+/**
+ * Entry of coloring schema used for changing colors in the map. It allows to
+ * identify some elements by use of the filters (by name, type, etcs.) and
+ * contains information about the color that should be assigned to the fileter
+ * elements.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ColorSchema implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Base of the hex representation.
+ */
+ private static final int HEX_BASE = 16;
+
+ /**
+ * Length of the string describing color in rgb: "#RRGGBB".
+ */
+ private static final int COLOR_STRING_LENGTH = 7;
+
+ /**
+ * Where starts description of red color in stirng representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_RED = 1;
+
+ /**
+ * Where starts description of green color in stirng representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_GREEN = 3;
+
+ /**
+ * Where starts description of blue color in stirng representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_BLUE = 5;
+
+ /**
+ * Defines the maximum value of primary colors in RGB model (every color is
+ * from range 0..255).
+ */
+ 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
+ * then this field will be skiped.
+ */
+ private String name = null;
+
+ /**
+ * Identifier of the reaction to change the color.
+ */
+ private String reactionIdentifier = null;
+
+ /**
+ * Should the direction of highlighted reaction be reversed.
+ */
+ private Boolean reverseReaction = null;
+
+ /**
+ * Width of the line in the reaction.
+ */
+ private Double lineWidth = null;
+
+ /**
+ * In which compartments (identified by name) the element can occur.
+ */
+ private List<String> compartments = new ArrayList<String>();
+
+ /**
+ * What types of element should be identified by this entry.
+ */
+ private List<Class<? extends Alias>> types = new ArrayList<>();
+
+ /**
+ * Value (-1..1 range) that is assigned to filtered elements (it will be
+ * transformed into color later on). Only one of the {@link #value} and
+ * {@link #color} can be set.
+ */
+ private Double value = null;
+
+ /**
+ * Color that is assigned to filtered elements. Only one of the {@link #value}
+ * and {@link #color} can be set.
+ */
+ private Color color = null;
+
+ /**
+ * General identifier that identifies the element.
+ */
+ private String generalIdentifier = null;
+
+ /**
+ * List of specific identifiers that filter the elements.
+ */
+ private List<Pair<MiriamType, String>> identifierColumns = new ArrayList<>();
+
+ /**
+ * Number of elements matched by this entry.
+ */
+ private int matches = 0;
+
+ /**
+ * Short description of the entry.
+ */
+ private String description;
+
+ /**
+ * Default constructor.
+ */
+ protected ColorSchema() {
+ }
+
+ /**
+ * Initializes object by copying data from the parameter.
+ *
+ * @param original
+ * original object used for initialization
+ */
+ protected ColorSchema(ColorSchema original) {
+ this.setName(original.getName());
+ this.setReactionIdentifier(original.getReactionIdentifier());
+ this.setReverseReaction(original.getReverseReaction());
+ this.setLineWidth(original.getLineWidth());
+ this.addCompartments(original.getCompartments());
+ this.addTypes(original.getTypes());
+ this.setValue(original.getValue());
+ this.setColor(original.getColor());
+ this.setGeneralIdentifier(original.getGeneralIdentifier());
+ this.addIdentifierColumns(original.getIdentifierColumns());
+ this.setMatches(original.getMatches());
+ this.setDescription(original.getDescription());
+ }
+
+ /**
+ * Adds identifiers to {@link #identifierColumns} list.
+ *
+ * @param identifierColumnsList
+ * list of pairs defining type of identifier and the identifier value
+ */
+ public void addIdentifierColumns(List<Pair<MiriamType, String>> identifierColumnsList) {
+ for (Pair<MiriamType, String> pair : identifierColumnsList) {
+ addIdentifierColumn(pair);
+ }
+
+ }
+
+ /**
+ * Adds class types to {@link #types} list.
+ *
+ * @param types2
+ * list of classes to add
+ */
+ public void addTypes(List<Class<? extends Alias>> types2) {
+ for (Class<? extends Alias> clazz : types2) {
+ addType(clazz);
+ }
+ }
+
+ /**
+ * Adds compartment names to {@link #compartments} list.
+ *
+ * @param compartments2
+ * elements to add
+ */
+ public void addCompartments(String[] compartments2) {
+ for (String string : compartments2) {
+ compartments.add(string);
+ }
+ }
+
+ /**
+ * Adds compartment names to {@link #compartments} list.
+ *
+ * @param compartments2
+ * elements to add
+ */
+ public void addCompartments(Collection<String> compartments2) {
+ for (String string : compartments2) {
+ compartments.add(string);
+ }
+ }
+
+ /**
+ * Sets {@link #color} from the string.
+ *
+ * @param string
+ * color in text representation
+ * @throws InvalidColorSchemaException
+ * thrown when string describing color is invalid
+ */
+ public void setColor(String string) throws InvalidColorSchemaException {
+ if (string.length() != COLOR_STRING_LENGTH) {
+ throw new InvalidColorSchemaException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
+ }
+ if (string.charAt(0) != '#') {
+ throw new InvalidColorSchemaException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
+
+ } else {
+ setColor(new Color(Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE)));
+ }
+
+ }
+
+ @Override
+ public String toString() {
+ StringBuilder result = new StringBuilder();
+ result.append("[");
+ if (name != null) {
+ result.append(name + ",");
+ }
+ if (compartments.size() > 0) {
+ result.append("(");
+ for (String comp : compartments) {
+ result.append(comp + ",");
+ }
+ result.append("),");
+ }
+ if (types.size() > 0) {
+ result.append("(");
+ for (Class<?> clazz : types) {
+ result.append(clazz.getSimpleName() + ",");
+ }
+ result.append("),");
+ }
+ if (value != null) {
+ result.append(value + ",");
+ }
+ if (color != null) {
+ result.append(color + ",");
+ }
+ if (generalIdentifier != null) {
+ result.append(generalIdentifier + ",");
+ }
+ if (types.size() > 0) {
+ result.append("(");
+ for (Pair<MiriamType, String> pair : identifierColumns) {
+ result.append(pair.getLeft() + "-" + pair.getRight() + ",");
+ }
+ result.append("),");
+ }
+ result.append(matches + "]");
+ return result.toString();
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ if (name == null) {
+ this.name = null;
+ } else {
+ this.name = name.trim();
+ }
+ }
+
+ /**
+ * @return the compartments
+ * @see #compartments
+ */
+ public List<String> getCompartments() {
+ return compartments;
+ }
+
+ /**
+ * @param compartments
+ * the compartments to set
+ * @see #compartments
+ */
+ public void setCompartments(List<String> compartments) {
+ this.compartments = compartments;
+ }
+
+ /**
+ * @return the types
+ * @see #types
+ */
+ public List<Class<? extends Alias>> getTypes() {
+ return types;
+ }
+
+ /**
+ * @param types
+ * the types to set
+ * @see #types
+ */
+ public void setTypes(List<Class<? extends Alias>> types) {
+ this.types = types;
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * @return the generalIdentifier
+ * @see #generalIdentifier
+ */
+ public String getGeneralIdentifier() {
+ return generalIdentifier;
+ }
+
+ /**
+ * @param generalIdentifier
+ * the generalIdentifier to set
+ * @see #generalIdentifier
+ */
+ public void setGeneralIdentifier(String generalIdentifier) {
+ this.generalIdentifier = generalIdentifier;
+ }
+
+ /**
+ * @return the identifierColumns
+ * @see #identifierColumns
+ */
+ public List<Pair<MiriamType, String>> getIdentifierColumns() {
+ return identifierColumns;
+ }
+
+ /**
+ * @param identifierColumns
+ * the identifierColumns to set
+ * @see #identifierColumns
+ */
+ public void setIdentifierColumns(List<Pair<MiriamType, String>> identifierColumns) {
+ this.identifierColumns = identifierColumns;
+ }
+
+ /**
+ * @return the matches
+ * @see #matches
+ */
+ public int getMatches() {
+ return matches;
+ }
+
+ /**
+ * @param matches
+ * the matches to set
+ * @see #matches
+ */
+ public void setMatches(int matches) {
+ this.matches = matches;
+ }
+
+ /**
+ * Adds identifier to {@link #identifierColumns} list.
+ *
+ * @param pair
+ * pair defining type of identifier and the identifier value
+ */
+ public void addIdentifierColumn(Pair<MiriamType, String> pair) {
+ identifierColumns.add(pair);
+
+ }
+
+ /**
+ * @return the reactionIdentifier
+ * @see #reactionIdentifier
+ */
+ public String getReactionIdentifier() {
+ return reactionIdentifier;
+ }
+
+ /**
+ * @param reactionIdentifier
+ * the reactionIdentifier to set
+ * @see #reactionIdentifier
+ */
+ public void setReactionIdentifier(String reactionIdentifier) {
+ this.reactionIdentifier = reactionIdentifier;
+ }
+
+ /**
+ * @return the lineWidth
+ * @see #lineWidth
+ */
+ public Double getLineWidth() {
+ return lineWidth;
+ }
+
+ /**
+ * @param lineWidth
+ * the lineWidth to set
+ * @see #lineWidth
+ */
+ public void setLineWidth(Double lineWidth) {
+ this.lineWidth = lineWidth;
+ }
+
+ /**
+ * @return the reverseReaction
+ * @see #reverseReaction
+ */
+ public Boolean getReverseReaction() {
+ return reverseReaction;
+ }
+
+ /**
+ * @param reverseReaction
+ * the reverseReaction to set
+ * @see #reverseReaction
+ */
+ public void setReverseReaction(Boolean reverseReaction) {
+ this.reverseReaction = reverseReaction;
+ }
+
+ /**
+ * Adds compartment name to {@link #compartments}.
+ *
+ * @param name
+ * compartment name
+ */
+ public void addCompartment(String name) {
+ compartments.add(name);
+ }
+
+ /**
+ * Adds class type to {@link #types} list.
+ *
+ * @param clazz
+ * class to add
+ */
+ public void addType(Class<? extends Alias> clazz) {
+ this.types.add(clazz);
+ }
+
+ /**
+ * Extracts color from {@link ColorSchema} object.
+ *
+ * @return color from {@link ColorSchema} object
+ */
+ public Color getNormalizedColor() {
+ if (getColor() != null) {
+ return getColor();
+ } else {
+ return getColorForValue(getValue());
+ }
+ }
+
+ /**
+ * Returns color from red - green scale for the given normalized double value
+ * (from range -1,1).
+ *
+ * @param value
+ * double value that should be converted into color
+ * @return color for the double value
+ */
+ protected Color getColorForValue(Double value) {
+ if (value > 0) {
+ int val = (int) ((1 - value) * MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT);
+ return new Color(val, MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT, val);
+ }
+ if (value < 0) {
+ int val = (int) ((1 + value) * MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT);
+ return new Color(MAX_SINGLE_COLOR_VALUE_IN_RGB_FORMAT, val, val);
+ }
+ return Color.WHITE;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * Creates a copy of this object.
+ *
+ * @return copy of the object
+ */
+ public abstract ColorSchema copy();
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAlias.java
index e678391031..6ceb4fcff9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaAlias.java
@@ -13,8 +13,6 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.fields.AntisenseRnaRegion;
@Entity
@DiscriminatorValue("ANTISENSE_RNA_ALIAS")
@@ -33,15 +31,6 @@ public class AntisenseRnaAlias extends SpeciesAlias {
AntisenseRnaAlias() {
}
- public AntisenseRnaAlias(AntisenseRna antisenseRna) {
- super(antisenseRna);
- }
-
- public AntisenseRnaAlias(String aliasId, AntisenseRna antisenseRna) {
- this(antisenseRna);
- super.setAliasId(aliasId);
- }
-
public AntisenseRnaAlias(AntisenseRnaAlias original) {
super(original);
for (AntisenseRnaRegionAlias region : original.getRegions()) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaRegionAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaRegionAlias.java
index 6e7eb8fd71..b2f96d7a56 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaRegionAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/AntisenseRnaRegionAlias.java
@@ -18,13 +18,12 @@ import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
/**
* This structure contains information about antisense rna region (rna fragment
* of interest) for a specific
- * {@link lcsb.mapviewer.model.map.species.AntisenseRna AntisenseRna}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna
+ * AntisenseRna}.
*
* @author Piotr Gawron
*
@@ -41,7 +40,8 @@ public class AntisenseRnaRegionAlias implements Serializable {
/**
* Enum that enlists types of available modification regions in
- * {@link lcsb.mapviewer.model.map.species.AntisenseRna AntisenseRna}.
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.AntisenseRna
+ * AntisenseRna}.
*
* @author Piotr Gawron
*
@@ -171,7 +171,7 @@ public class AntisenseRnaRegionAlias implements Serializable {
@Cascade({ CascadeType.ALL })
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "idSpeciesDb")
- private AntisenseRnaAlias species;
+ private AntisenseRnaAlias species;
/**
* Default constructor.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAlias.java
index 1f5c88463f..b9a0c730c2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ChemicalAlias.java
@@ -4,8 +4,6 @@ import javax.persistence.Column;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
-import lcsb.mapviewer.model.map.species.Chemical;
-
@Entity
@DiscriminatorValue("CHEMICAL_ALIAS")
public abstract class ChemicalAlias extends SpeciesAlias {
@@ -13,7 +11,7 @@ public abstract class ChemicalAlias extends SpeciesAlias {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* <a href=
@@ -21,7 +19,7 @@ public abstract class ChemicalAlias extends SpeciesAlias {
* >Smiles</a> parameter for the chemical.
*/
@Column(name = "smiles", columnDefinition = "TEXT")
- private String smiles;
+ private String smiles;
/**
* <a href= "http://en.wikipedia.org/wiki/International_Chemical_Identifier" >
@@ -29,7 +27,7 @@ public abstract class ChemicalAlias extends SpeciesAlias {
*/
@Column(name = "inchi", columnDefinition = "TEXT")
- private String inChI;
+ private String inChI;
/**
* <a href=
@@ -37,15 +35,11 @@ public abstract class ChemicalAlias extends SpeciesAlias {
* InChIKey</a> parameter for the chemical.
*/
- private String inChIKey;
+ private String inChIKey;
ChemicalAlias() {
}
- public ChemicalAlias(Chemical chemical) {
- super(chemical);
- }
-
public ChemicalAlias(ChemicalAlias original) {
super(original);
smiles = original.getSmiles();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAlias.java
index e5fa5e3f7c..1971655bdd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAlias.java
@@ -18,7 +18,6 @@ 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.agregator.Compartment;
/**
* This class defines alias for compartment in the model.
@@ -116,22 +115,6 @@ public class CompartmentAlias extends Alias {
setColor(DEFAULT_COLOR);
}
- /**
- * Constructor that points on the compartment.
- *
- * @param compartment
- * alias will reference to this compartment
- */
- public CompartmentAlias(Compartment compartment) {
- this();
- throw new NotImplementedException();
- }
-
- public CompartmentAlias(String aliasId, Compartment compartment) {
- this(compartment);
- setAliasId(aliasId);
- }
-
public CompartmentAlias(String aliasId) {
setAliasId(aliasId);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparator.java
index 014897a763..fc7b054678 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparator.java
@@ -11,8 +11,6 @@ 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.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.agregator.CompartmentComparator;
/**
* This class implements comparator interface for CompartmentAlias.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAlias.java
index c9f6e4459e..44adf66474 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ComplexAlias.java
@@ -15,7 +15,6 @@ import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
/**
* Class that represents alias of a complex in the model.
@@ -73,16 +72,6 @@ public class ComplexAlias extends SpeciesAlias {
this.structuralState = original.getStructuralState();
}
- /**
- * Constructor that creates alias with reference to species.
- *
- * @param species
- * rederence to this complex will be used by alias
- */
- public ComplexAlias(ComplexSpecies species) {
- super(species);
- }
-
/**
* Constructor that creates complex alias with given alias id.
*
@@ -93,11 +82,6 @@ public class ComplexAlias extends SpeciesAlias {
super(aliasId);
}
- public ComplexAlias(String aliasId, ComplexSpecies cSpecies) {
- this(cSpecies);
- setAliasId(aliasId);
- }
-
/**
* Adds alias to the complex.
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAlias.java
index 9fa2c266d5..02c923732c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DegradedAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Degraded;
@Entity
@DiscriminatorValue("DEGRADED_ALIAS")
@@ -12,19 +11,10 @@ public class DegradedAlias extends SpeciesAlias {
DegradedAlias() {
}
- public DegradedAlias(Degraded degraded) {
- super(degraded);
- }
-
public DegradedAlias(DegradedAlias original) {
super(original);
}
- public DegradedAlias(String aliasId, Degraded degraded) {
- super(degraded);
- super.setAliasId(aliasId);
- }
-
public DegradedAlias(String aliasId) {
super.setAliasId(aliasId);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAlias.java
index 7da88f1cf7..e54ed5fd71 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/DrugAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Drug;
@Entity
@DiscriminatorValue("DRUG_ALIAS")
@@ -12,10 +11,6 @@ public class DrugAlias extends SpeciesAlias {
DrugAlias() {
}
- public DrugAlias(Drug drug) {
- super(drug);
- }
-
public DrugAlias(DrugAlias original) {
super(original);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAlias.java
index 93f516a48d..04e3b1fdb8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GeneAlias.java
@@ -13,7 +13,6 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Gene;
@Entity
@DiscriminatorValue("GENE_ALIAS")
@@ -35,10 +34,6 @@ public class GeneAlias extends SpeciesAlias {
GeneAlias() {
}
- public GeneAlias(Gene gene) {
- super(gene);
- }
-
public GeneAlias(GeneAlias original) {
super(original);
for (ModificationResidueAlias mr : original.getModificationResidues()) {
@@ -52,11 +47,6 @@ public class GeneAlias extends SpeciesAlias {
}
- public GeneAlias(String aliasId, Gene gene) {
- super(gene);
- super.setAliasId(aliasId);
- }
-
public GeneAlias(String aliasId) {
setAliasId(aliasId);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAlias.java
index 20a95c4291..aa33839f1f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/GenericProteinAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
@Entity
@DiscriminatorValue("GENERIC_PROTEIN_ALIAS")
@@ -12,14 +11,6 @@ public class GenericProteinAlias extends ProteinAlias {
GenericProteinAlias() {
}
- public GenericProteinAlias(GenericProtein genericProtein) {
- super(genericProtein);
- }
-
- public GenericProteinAlias(String aliasId, GenericProtein genericProtein) {
- super(aliasId, genericProtein);
- }
-
public GenericProteinAlias(String aliasId) {
super(aliasId);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAlias.java
index 6bf65a70a4..9a76148e33 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Ion;
@Entity
@DiscriminatorValue("ION_ALIAS")
@@ -12,13 +11,10 @@ public class IonAlias extends ChemicalAlias {
IonAlias() {
}
- public IonAlias(Ion ion) {
- super(ion);
- }
-
public IonAlias(IonAlias original) {
super(original);
}
+
public IonAlias(String aliasId) {
setAliasId(aliasId);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAlias.java
index 1b90bc3a7a..820cfd5b95 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/IonChannelProteinAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
@Entity
@DiscriminatorValue("ION_CHANNEL_PROTEIN_ALIAS")
@@ -12,10 +11,6 @@ public class IonChannelProteinAlias extends ProteinAlias {
IonChannelProteinAlias() {
}
- public IonChannelProteinAlias(IonChannelProtein ionChannelProtein) {
- super(ionChannelProtein);
- }
-
public IonChannelProteinAlias(IonChannelProteinAlias original) {
super(original);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java
index cd0a2e7fbf..475464ccce 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationResidueAlias.java
@@ -16,7 +16,6 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
/**
* This class represent modification residue in protein and gene. However, it is
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/ModificationState.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationState.java
similarity index 94%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/fields/ModificationState.java
rename to model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationState.java
index f18e6182fe..5fa20a125a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/ModificationState.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ModificationState.java
@@ -1,152 +1,152 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-/**
- * Defines a type of modification (in protein or rna). Possible values are:
- * <ul>
- * <li>{@link ModificationState#ACETYLATED ACETYLATED},</li>
- * <li>{@link ModificationState#DONT_CARE DON'T CARE},</li>
- * <li>{@link ModificationState#EMPTY EMPTY},</li>
- * <li>{@link ModificationState#GLYCOSYLATED GLYCOSYLATED},</li>
- * <li>{@link ModificationState#HYDROXYLATED HYDROXYLATED},</li>
- * <li>{@link ModificationState#METHYLATED METHYLATED},</li>
- * <li>{@link ModificationState#MYRISTOYLATED MYRISTOYLATED},</li>
- * <li>{@link ModificationState#PALMYTOYLATED PALMYTOYLATED},</li>
- * <li>{@link ModificationState#PHOSPHORYLATED PHOSPHORYLATED},</li>
- * <li>{@link ModificationState#PRENYLATED PRENYLATED},</li>
- * <li>{@link ModificationState#PROTONATED PROTONATED},</li>
- * <li>{@link ModificationState#SULFATED SULFATED},</li>
- * <li>{@link ModificationState#UBIQUITINATED UBIQUITINATED},</li>
- * <li>{@link ModificationState#UNKNOWN UNKNOWN}.</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-public enum ModificationState {
-
- /**
- * Phosporylated state.
- */
- PHOSPHORYLATED("phosphorylated", "P"), //
-
- /**
- * Acetylated state.
- */
- ACETYLATED("acetylated", "Ac"), //
-
- /**
- * Ubiquitinated state.
- */
- UBIQUITINATED("ubiquitinated", "Ub"), //
-
- /**
- * Methylated state.
- */
- METHYLATED("methylated", "Me"), //
-
- /**
- * Hydroxylated state.
- */
- HYDROXYLATED("hydroxylated", "OH"), //
-
- /**
- * Myristoylated state.
- */
- MYRISTOYLATED("myristoylated", "My"), //
-
- /**
- * Sulfated state.
- */
- SULFATED("sulfated", "S"), //
-
- /**
- * Prenylated state.
- */
- PRENYLATED("prenylated", "Pr"), //
-
- /**
- * Glycosylated state.
- */
- GLYCOSYLATED("glycosylated", "G"), //
-
- /**
- * Palmytoylated state.
- */
- PALMYTOYLATED("palmytoylated", "Pa"), //
-
- /**
- * Unknown state.
- */
- UNKNOWN("unknown", "?"), //
-
- /**
- * Empty state.
- */
- EMPTY("empty", ""), //
-
- /**
- * Protonated state.
- */
- PROTONATED("protonated", "H"), //
-
- /**
- * We don't care in which state it is.
- */
- DONT_CARE("don't care", "*");
-
- /**
- * Full name of the modification.
- */
-
- private String fullName;
- /**
- * Abbreviation used for the modification.
- */
- private String abbreviation;
-
- /**
- * Default constructor with the name and abbreviation.
- *
- * @param name
- * name used for this state
- * @param abbreviation
- * abbreviation used in this state
- */
- ModificationState(String name, String abbreviation) {
- this.fullName = name;
- this.abbreviation = abbreviation;
- }
-
- /**
- * @return the fullName
- * @see #fullName
- */
- public String getFullName() {
- return fullName;
- }
-
- /**
- * @return the abbreviation
- * @see #abbreviation
- */
- public String getAbbreviation() {
- return abbreviation;
- }
-
- /**
- * Returns {@link ModificationState} identified by the full name.
- *
- * @param name
- * full name of the state
- * @return {@link ModificationState} identified by the full name
- */
- public static ModificationState getByName(String name) {
- for (ModificationState state : values()) {
- if (state.getFullName().equalsIgnoreCase(name)) {
- return state;
- }
- }
- return null;
- }
-
-}
+package lcsb.mapviewer.model.map.layout.alias;
+
+/**
+ * Defines a type of modification (in protein or rna). Possible values are:
+ * <ul>
+ * <li>{@link ModificationState#ACETYLATED ACETYLATED},</li>
+ * <li>{@link ModificationState#DONT_CARE DON'T CARE},</li>
+ * <li>{@link ModificationState#EMPTY EMPTY},</li>
+ * <li>{@link ModificationState#GLYCOSYLATED GLYCOSYLATED},</li>
+ * <li>{@link ModificationState#HYDROXYLATED HYDROXYLATED},</li>
+ * <li>{@link ModificationState#METHYLATED METHYLATED},</li>
+ * <li>{@link ModificationState#MYRISTOYLATED MYRISTOYLATED},</li>
+ * <li>{@link ModificationState#PALMYTOYLATED PALMYTOYLATED},</li>
+ * <li>{@link ModificationState#PHOSPHORYLATED PHOSPHORYLATED},</li>
+ * <li>{@link ModificationState#PRENYLATED PRENYLATED},</li>
+ * <li>{@link ModificationState#PROTONATED PROTONATED},</li>
+ * <li>{@link ModificationState#SULFATED SULFATED},</li>
+ * <li>{@link ModificationState#UBIQUITINATED UBIQUITINATED},</li>
+ * <li>{@link ModificationState#UNKNOWN UNKNOWN}.</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ModificationState {
+
+ /**
+ * Phosporylated state.
+ */
+ PHOSPHORYLATED("phosphorylated", "P"), //
+
+ /**
+ * Acetylated state.
+ */
+ ACETYLATED("acetylated", "Ac"), //
+
+ /**
+ * Ubiquitinated state.
+ */
+ UBIQUITINATED("ubiquitinated", "Ub"), //
+
+ /**
+ * Methylated state.
+ */
+ METHYLATED("methylated", "Me"), //
+
+ /**
+ * Hydroxylated state.
+ */
+ HYDROXYLATED("hydroxylated", "OH"), //
+
+ /**
+ * Myristoylated state.
+ */
+ MYRISTOYLATED("myristoylated", "My"), //
+
+ /**
+ * Sulfated state.
+ */
+ SULFATED("sulfated", "S"), //
+
+ /**
+ * Prenylated state.
+ */
+ PRENYLATED("prenylated", "Pr"), //
+
+ /**
+ * Glycosylated state.
+ */
+ GLYCOSYLATED("glycosylated", "G"), //
+
+ /**
+ * Palmytoylated state.
+ */
+ PALMYTOYLATED("palmytoylated", "Pa"), //
+
+ /**
+ * Unknown state.
+ */
+ UNKNOWN("unknown", "?"), //
+
+ /**
+ * Empty state.
+ */
+ EMPTY("empty", ""), //
+
+ /**
+ * Protonated state.
+ */
+ PROTONATED("protonated", "H"), //
+
+ /**
+ * We don't care in which state it is.
+ */
+ DONT_CARE("don't care", "*");
+
+ /**
+ * Full name of the modification.
+ */
+
+ private String fullName;
+ /**
+ * Abbreviation used for the modification.
+ */
+ private String abbreviation;
+
+ /**
+ * Default constructor with the name and abbreviation.
+ *
+ * @param name
+ * name used for this state
+ * @param abbreviation
+ * abbreviation used in this state
+ */
+ ModificationState(String name, String abbreviation) {
+ this.fullName = name;
+ this.abbreviation = abbreviation;
+ }
+
+ /**
+ * @return the fullName
+ * @see #fullName
+ */
+ public String getFullName() {
+ return fullName;
+ }
+
+ /**
+ * @return the abbreviation
+ * @see #abbreviation
+ */
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ /**
+ * Returns {@link ModificationState} identified by the full name.
+ *
+ * @param name
+ * full name of the state
+ * @return {@link ModificationState} identified by the full name
+ */
+ public static ModificationState getByName(String name) {
+ for (ModificationState state : values()) {
+ if (state.getFullName().equalsIgnoreCase(name)) {
+ return state;
+ }
+ }
+ return null;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAlias.java
index c9a84b72de..49526e06a8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PhenotypeAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Phenotype;
@Entity
@DiscriminatorValue("PHENTOYPE_ALIAS")
@@ -13,10 +12,6 @@ public class PhenotypeAlias extends SpeciesAlias {
PhenotypeAlias() {
}
- public PhenotypeAlias(Phenotype phenotype) {
- super(phenotype);
- }
-
public PhenotypeAlias(PhenotypeAlias original) {
super(original);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/PositionToCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartment.java
similarity index 78%
rename from model/src/main/java/lcsb/mapviewer/model/map/species/fields/PositionToCompartment.java
rename to model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartment.java
index a8467cae90..cb512ced9c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/PositionToCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/PositionToCompartment.java
@@ -1,75 +1,76 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-/**
- * Defines possible position of {@link lcsb.mapviewer.model.map.species.Species}
- * on {@link lcsb.mapviewer.model.map.agregator.Compartment}.
- *
- * @author Piotr Gawron
- *
- */
-public enum PositionToCompartment {
-
- /**
- * Species is inside compartment.
- */
- INSIDE("inside"),
-
- /**
- * Species is inside the border.
- */
- INSIDE_OF_MEMBRANE("insideOfMembrane"),
-
- /**
- * Species is crossing the border.
- */
- TRANSMEMBRANE("transmembrane"),
-
- /**
- * Species is on outer border of compartment.
- */
- OUTER_SURFACE("outerSurface"),
-
- /**
- * Species is on inner border of compartment.
- */
- INNER_SURFACE("innerSurface");
-
- /**
- * String representing the position.
- */
- private String stringName;
-
- /**
- * Default constructor.
- *
- * @param stringName
- * {@link #stringName}
- */
- PositionToCompartment(String stringName) {
- this.stringName = stringName;
- }
-
- /**
- * @return the stringName
- * @see #stringName
- */
- public String getStringName() {
- return stringName;
- }
-
- /**
- * Returns {@link PositionToCompartment} based on the {@link #stringName}.
- *
- * @param string
- * {@link #stringName}
- * @return {@link PositionToCompartment} based on the {@link #stringName}
- */
- public static PositionToCompartment getByString(String string) {
- for (PositionToCompartment pos : PositionToCompartment.values()) {
- if (pos.getStringName().equalsIgnoreCase(string)) {
- return pos;
- }
- }
- return null;
- }
-}
+package lcsb.mapviewer.model.map.layout.alias;
+
+/**
+ * Defines possible position of
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Species} on
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Compartment}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum PositionToCompartment {
+
+ /**
+ * Species is inside compartment.
+ */
+ INSIDE("inside"),
+
+ /**
+ * Species is inside the border.
+ */
+ INSIDE_OF_MEMBRANE("insideOfMembrane"),
+
+ /**
+ * Species is crossing the border.
+ */
+ TRANSMEMBRANE("transmembrane"),
+
+ /**
+ * Species is on outer border of compartment.
+ */
+ OUTER_SURFACE("outerSurface"),
+
+ /**
+ * Species is on inner border of compartment.
+ */
+ INNER_SURFACE("innerSurface");
+
+ /**
+ * String representing the position.
+ */
+ private String stringName;
+
+ /**
+ * Default constructor.
+ *
+ * @param stringName
+ * {@link #stringName}
+ */
+ PositionToCompartment(String stringName) {
+ this.stringName = stringName;
+ }
+
+ /**
+ * @return the stringName
+ * @see #stringName
+ */
+ public String getStringName() {
+ return stringName;
+ }
+
+ /**
+ * Returns {@link PositionToCompartment} based on the {@link #stringName}.
+ *
+ * @param string
+ * {@link #stringName}
+ * @return {@link PositionToCompartment} based on the {@link #stringName}
+ */
+ public static PositionToCompartment getByString(String string) {
+ for (PositionToCompartment pos : PositionToCompartment.values()) {
+ if (pos.getStringName().equalsIgnoreCase(string)) {
+ return pos;
+ }
+ }
+ return null;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAlias.java
index 82ff459246..673f8b0b68 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ProteinAlias.java
@@ -12,8 +12,6 @@ import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
-import lcsb.mapviewer.model.map.species.Protein;
-
@Entity
@DiscriminatorValue("PROTEIN_ALIAS")
public abstract class ProteinAlias extends SpeciesAlias {
@@ -39,15 +37,6 @@ public abstract class ProteinAlias extends SpeciesAlias {
ProteinAlias() {
}
- public ProteinAlias(String aliasId, Protein protein) {
- super(protein);
- this.setAliasId(aliasId);
- }
-
- public ProteinAlias(Protein protein) {
- super(protein);
- }
-
public ProteinAlias(ProteinAlias original) {
super(original);
this.structuralState = original.getStructuralState();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAlias.java
index 9b5bdb4aa6..ea4ed55217 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/ReceptorProteinAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
@Entity
@DiscriminatorValue("RECEPTOR_PROTEIN_ALIAS")
@@ -12,10 +11,6 @@ public class ReceptorProteinAlias extends ProteinAlias {
ReceptorProteinAlias() {
}
- public ReceptorProteinAlias(ReceptorProtein receptorProtein) {
- super(receptorProtein);
- }
-
public ReceptorProteinAlias(ReceptorProteinAlias original) {
super(original);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAlias.java
index 79cbbd71a4..38ce0e289b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaAlias.java
@@ -13,7 +13,6 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Rna;
@Entity
@DiscriminatorValue("RNA_ALIAS")
@@ -23,7 +22,7 @@ public class RnaAlias extends SpeciesAlias {
*
*/
private static final long serialVersionUID = 1L;
-
+
/**
* List of rna regions (some rna sequences) in this object.
*/
@@ -35,10 +34,6 @@ public class RnaAlias extends SpeciesAlias {
RnaAlias() {
}
- public RnaAlias(Rna rna) {
- super(rna);
- }
-
public RnaAlias(RnaAlias original) {
super(original);
for (RnaRegionAlias region : original.getRegions()) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java
index e2200da4d1..ee5053a324 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/RnaRegionAlias.java
@@ -15,12 +15,11 @@ import javax.persistence.Table;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
/**
* This structure contains information about rna region (rna fragment of
- * interest) for a specific {@link lcsb.mapviewer.model.map.species.Rna Rna}.
+ * interest) for a specific
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Rna Rna}.
*
* @author Piotr Gawron
*
@@ -103,7 +102,7 @@ public class RnaRegionAlias implements Serializable {
*/
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "idSpeciesDb")
- private RnaAlias species;
+ private RnaAlias species;
/**
* Default constructor.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAlias.java
index 8072a549ae..95a4002f7e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SimpleMoleculeAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
@Entity
@DiscriminatorValue("SIMPLE_MOLECULE_ALIAS")
@@ -12,19 +11,10 @@ public class SimpleMoleculeAlias extends ChemicalAlias {
SimpleMoleculeAlias() {
}
- public SimpleMoleculeAlias(SimpleMolecule simpleMolecule) {
- super(simpleMolecule);
- }
-
public SimpleMoleculeAlias(SimpleMoleculeAlias original) {
super(original);
}
- public SimpleMoleculeAlias(String aliasId, SimpleMolecule species) {
- super(species);
- super.setAliasId(aliasId);
- }
-
public SimpleMoleculeAlias(String aliasId) {
setAliasId(aliasId);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAlias.java
index 9104251a21..d5c353c94b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAlias.java
@@ -16,10 +16,7 @@ import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.fields.PositionToCompartment;
/**
* {@link Alias} structure used for representing {@link Species}.
@@ -145,17 +142,6 @@ public abstract class SpeciesAlias extends Alias {
state = "usual";
}
- /**
- * Constructor with species to which alias will refer.
- *
- * @param species
- * {@link #species}
- */
- public SpeciesAlias(Species species) {
- this();
- throw new NotImplementedException();
- }
-
/**
* Constructor that initializes data with the information given in the
* parameter.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparator.java
index fd18b76c3d..d9ebdf31f6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparator.java
@@ -10,8 +10,6 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.ElementComparator;
-import lcsb.mapviewer.model.map.species.SpeciesComparator;
/**
* This class implements comparator interface for SpeciesAlias. It also handles
@@ -133,7 +131,6 @@ public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
BooleanComparator booleanComparator = new BooleanComparator();
- SpeciesComparator speciesComparator = new SpeciesComparator(epsilon);
IntegerComparator integerComparator = new IntegerComparator();
if (booleanComparator.compare(arg0.getActivity(), arg1.getActivity()) != 0) {
@@ -156,7 +153,6 @@ public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
return stringComparator.compare(arg0.getAliasStatePrefix(), arg1.getAliasStatePrefix());
}
-
if (integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
return integerComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
@@ -196,7 +192,7 @@ public class SpeciesAliasComparator implements Comparator<SpeciesAlias> {
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/TruncatedProteinAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAlias.java
index e2d5eb4c9b..2e14310c2e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/TruncatedProteinAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
@Entity
@DiscriminatorValue("TRUNCATED_PROTEIN_ALIAS")
@@ -12,10 +11,6 @@ public class TruncatedProteinAlias extends ProteinAlias {
TruncatedProteinAlias() {
}
- public TruncatedProteinAlias(TruncatedProtein truncateProtein) {
- super(truncateProtein);
- }
-
public TruncatedProteinAlias(TruncatedProteinAlias original) {
super(original);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAlias.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAlias.java
index 85e8f6fa8e..40eb909880 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAlias.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/alias/UnknownAlias.java
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Unknown;
@Entity
@DiscriminatorValue("UNKNOWN_ALIAS")
@@ -12,10 +11,6 @@ public class UnknownAlias extends SpeciesAlias {
UnknownAlias() {
}
- public UnknownAlias(Unknown degraded) {
- super(degraded);
- }
-
public UnknownAlias(UnknownAlias original) {
super(original);
}
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 2c8deaf5f4..29676b3210 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
@@ -10,10 +10,8 @@ import org.apache.log4j.Appender;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.alias.Alias;
@@ -24,7 +22,6 @@ 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.Species;
/**
* This interface defines functionality that the model container class should
@@ -342,7 +339,7 @@ public interface Model {
* @return collection of species aliases
*/
Collection<SpeciesAlias> getNotComplexSpeciesAliases();
-
+
List<SpeciesAlias> getSpeciesAliases();
/**
@@ -368,7 +365,7 @@ public interface Model {
* @return list of elements
*/
Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData);
-
+
List<Alias> getAliasByName(String name);
/**
@@ -660,7 +657,7 @@ public interface Model {
/**
* Return list od all {@link AnnotatedObject} in the map. This includes all
- * {@link Reaction reactions} and {@link Element elements}.
+ * {@link Reaction reactions} and {@link Alias 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 0c47df44c7..7eba1e40b5 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
@@ -14,13 +14,8 @@ import lcsb.mapviewer.common.comparator.BooleanComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.ElementComparator;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewImageComparator;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSetComparator;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.LayoutComparator;
@@ -30,7 +25,6 @@ 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.Species;
/**
* Comparator for {@link Model} class.
@@ -266,71 +260,6 @@ public class ModelComparator implements Comparator<Model> {
return 0;
}
- /**
- * Compares two sets of elements.
- *
- * @param elements
- * first set of elements
- * @param elements2
- * second set of elements
- * @return if sets are equal then returns 0. If they are different then -1/1
- * is returned.
- */
- private int compareElements(Set<Element> elements, Set<Element> elements2) {
- ElementComparator comparator = new ElementComparator(epsilon);
-
- Map<String, Element> map = new HashMap<String, Element>();
- Map<String, Element> map2 = new HashMap<String, Element>();
- for (Element element : elements) {
- if (element instanceof Species) {
- map.put(((Species) element).getElementId(), element);
- } else if (element instanceof Compartment) {
- map.put(((Compartment) element).getElementId(), element);
- } else {
- throw new InvalidClassException("Unknown class type...");
- }
- }
-
- for (Element element : elements2) {
- if (element instanceof Species) {
- map2.put(((Species) element).getElementId(), element);
- } else if (element instanceof Compartment) {
- map2.put(((Compartment) element).getElementId(), element);
- } else {
- throw new InvalidClassException("Unknown class type...");
- }
- }
-
- for (Element element : elements) {
- String id = "";
- if (element instanceof Species) {
- id = ((Species) element).getElementId();
- } else if (element instanceof Compartment) {
- id = ((Compartment) element).getElementId();
- }
- int status = comparator.compare(element, map2.get(id));
- if (status != 0) {
- logger.debug("Element with id " + id + " (" + element.getClass() + ") different");
- return status;
- }
- }
-
- for (Element element : elements2) {
- String id = "";
- if (element instanceof Species) {
- id = ((Species) element).getElementId();
- } else if (element instanceof Compartment) {
- id = ((Compartment) element).getElementId();
- }
- int status = comparator.compare(element, map.get(id));
- if (status != 0) {
- logger.debug("Element with id " + id + "(" + element.getClass() + ") different");
- return status;
- }
- }
- return 0;
- }
-
/**
* Compares two sets of layers.
*
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 21a88ba3d0..6041b05312 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
@@ -21,9 +21,12 @@ import javax.persistence.Table;
import javax.persistence.Transient;
import javax.xml.bind.annotation.XmlTransient;
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
@@ -33,10 +36,6 @@ import lcsb.mapviewer.model.map.layout.alias.BlockDiagram;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
/**
* Representation of the model data. It contains all information about single
* map:
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 27c547eb3d..b04c10636f 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
@@ -17,25 +17,20 @@ import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
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.agregator.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.AliasGroup;
-import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
/**
* This class implemets {@link Model} interface. It's is very simple
@@ -50,35 +45,35 @@ public class ModelFullIndexed implements Model {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ModelFullIndexed.class);
+ private static Logger logger = Logger.getLogger(ModelFullIndexed.class);
/**
* Object that map {@link Alias#aliasId alias identifier} into {@link Alias}.
*/
- private Map<String, Alias> aliasByAliasId = new HashMap<String, Alias>();
+ private Map<String, Alias> aliasByAliasId = new HashMap<String, Alias>();
/**
* Object that map {@link Alias#id alias database identifier} into
* {@link Alias}.
*/
- private Map<Integer, Alias> aliasByDbId = new HashMap<Integer, Alias>();
+ private Map<Integer, Alias> aliasByDbId = new HashMap<Integer, Alias>();
/**
* Object that map {@link Reaction#idReaction reaction identifier} into
* {@link Reaction}.
*/
- private Map<String, Reaction> reactionByReactionId = new HashMap<String, Reaction>();
+ private Map<String, Reaction> reactionByReactionId = new HashMap<String, Reaction>();
/**
* Object that map {@link Reaction#id reaction database identifier} into
* {@link Reaction}.
*/
- private Map<Integer, Reaction> reactionByDbId = new HashMap<Integer, Reaction>();
+ private Map<Integer, Reaction> reactionByDbId = new HashMap<Integer, Reaction>();
/**
* {@link ModelData} object containing "raw" data about the model.
*/
- private ModelData modelData = null;
+ private ModelData modelData = null;
/**
* Default constructor.
@@ -471,7 +466,7 @@ public class ModelFullIndexed implements Model {
CompartmentAlias ca = alias.getCompartmentAlias();
ca.removeAlias(alias);
}
-
+
if (alias instanceof SpeciesAlias) {
SpeciesAlias al = (SpeciesAlias) alias;
if (al.getComplexAlias() != null) {
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 e5060d5914..616e6fa843 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
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -35,8 +34,6 @@ public class Catalysis extends Modifier {
*
* @param alias
* alias object to which this modifiar is assigned
- * @param element
- * element to which this modifier is assigned
*/
public Catalysis(SpeciesAlias 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 d70b8c5083..d6e36305cc 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
@@ -34,8 +34,6 @@ public class Inhibition extends Modifier {
*
* @param alias
* alias object to which this modifiar is assigned
- * @param element
- * element to which this modifier is assigned
*/
public Inhibition(SpeciesAlias 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 f3f6f141c5..7a5d19d33a 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
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -21,7 +20,7 @@ public class Modulation extends Modifier {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default constructor.
@@ -35,8 +34,6 @@ public class Modulation extends Modifier {
*
* @param alias
* alias object to which this modifiar is assigned
- * @param element
- * element to which this modifier is assigned
*/
public Modulation(SpeciesAlias 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 28ae11af87..187bc27cb0 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
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -36,8 +35,6 @@ public class PhysicalStimulation extends Modifier {
*
* @param alias
* alias object to which this modifiar is assigned
- * @param element
- * element to which this modifier is assigned
*/
public PhysicalStimulation(SpeciesAlias 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 9739ea7983..877a6d7147 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
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -21,7 +20,7 @@ public class Trigger extends Modifier {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default constructor.
@@ -35,8 +34,6 @@ public class Trigger extends Modifier {
*
* @param alias
* alias object to which this modifiar is assigned
- * @param element
- * element to which this modifier is assigned
*/
public Trigger(SpeciesAlias 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 c57d25336d..3e2b0d8fb4 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
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -36,8 +35,6 @@ public class UnknownCatalysis extends Modifier {
*
* @param alias
* alias object to which this modifiar is assigned
- * @param element
- * element to which this modifier is assigned
*/
public UnknownCatalysis(SpeciesAlias 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 112a10b019..511ebf6877 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
@@ -4,7 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -36,8 +35,6 @@ public class UnknownInhibition extends Modifier {
*
* @param alias
* alias object to which this modifiar is assigned
- * @param element
- * element to which this modifier is assigned
*/
public UnknownInhibition(SpeciesAlias 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 a9c922226a..f61570b290 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 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
/**
@@ -31,15 +30,13 @@ public class Modifier extends ReactionNode {
}
/**
- * Constructor that creates modifier for given {@link SpeciesAlias} and
- * {@link Element}. These elements reference to the objects in the
+ * Constructor that creates modifier for given {@link SpeciesAlias}. These
+ * elements reference to the objects in the
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this modifier.
*
* @param alias
* alias that represent this modifier
- * @param element
- * element that represent this modifier
*/
public Modifier(SpeciesAlias 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 df3298b930..2e7c9dbbd1 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 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
/**
@@ -30,15 +29,13 @@ public class Product extends ReactionNode {
}
/**
- * Constructor that creates product for given {@link SpeciesAlias} and
- * {@link Element}. These elements reference to the objects in the
+ * Constructor that creates product for given {@link SpeciesAlias}. These
+ * elements reference to the objects in the
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this product.
*
* @param alias
* alias that represent this product
- * @param element
- * element that represent this product
*/
public Product(SpeciesAlias 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 dcbe8da7e1..f553d769f5 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 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
/**
@@ -30,15 +29,13 @@ public class Reactant extends ReactionNode {
}
/**
- * Constructor that creates reactant for a given {@link SpeciesAlias} and
- * {@link Element}. These elements reference to the objects in the
+ * Constructor that creates reactant for a given {@link SpeciesAlias}. These
+ * elements reference to the objects in the
* {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
* represents this reactant.
*
* @param alias
* alias that represent this reactant
- * @param element
- * element that represent this reactant
*/
public Reactant(SpeciesAlias 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 0f3de039cc..16fa2d5e4c 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
@@ -39,7 +39,6 @@ import org.hibernate.annotations.IndexColumn;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
@@ -517,7 +516,7 @@ public class Reaction implements AnnotatedObject {
/**
* Check if one of the nodes reference to the element.
*
- * @param element
+ * @param alias
* element to be checked
* @return <code>true</code> if element is part of the reaction,
* <code>false</code> otherwise
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 4902211d6f..23643d2030 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 +4,6 @@ import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import javax.persistence.ManyToOne;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
/**
@@ -13,9 +12,9 @@ import lcsb.mapviewer.model.map.layout.alias.Alias;
* {@link #alias} define which element on the map correspond to this node. There
* are three known subclasses:
* <ul>
- * <li> {@link Reactant} - input of the reaction,</li>
- * <li> {@link Product} - output of the reaction,</li>
- * <li> {@link Modifier} - some modifier of the reaction.</li>
+ * <li>{@link Reactant} - input of the reaction,</li>
+ * <li>{@link Product} - output of the reaction,</li>
+ * <li>{@link Modifier} - some modifier of the reaction.</li>
* </ul>
*
*
@@ -29,13 +28,13 @@ public abstract class ReactionNode extends AbstractNode {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* {@link SpecisAlias} that represents this node in the model.
*/
@ManyToOne
- private Alias alias;
+ private Alias alias;
/**
* Default constructor.
@@ -61,8 +60,6 @@ public abstract class ReactionNode extends AbstractNode {
*
* @param alias
* {@link Alias} to which this node refer to
- * @param element
- * {@link Element} to which this node refer to
*/
public ReactionNode(Alias alias) {
this.alias = alias;
@@ -77,7 +74,8 @@ public abstract class ReactionNode extends AbstractNode {
}
/**
- * @param alias the alias to set
+ * @param alias
+ * the alias to set
* @see #alias
*/
public void setAlias(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 25dd159e5b..1efc5fba81 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 +5,6 @@ import java.util.Comparator;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.ElementComparator;
import lcsb.mapviewer.model.map.layout.alias.AliasComparator;
/**
@@ -78,7 +77,6 @@ public class ReactionNodeComparator implements Comparator<ReactionNode> {
*/
private int internalCompare(ReactionNode arg0, ReactionNode arg1) {
AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
- ElementComparator elementComparator = new ElementComparator(epsilon);
AliasComparator aliasComparator = new AliasComparator(epsilon);
int result = anComparator.internalCompare(arg0, arg1);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
deleted file mode 100644
index ccac5bd6f0..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
+++ /dev/null
@@ -1,117 +0,0 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.alias.PhenotypeAlias;
-import lcsb.mapviewer.model.map.species.fields.AssociatedElement;
-
-/**
- * Class representing phenotype in the model.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Phenotype")
-public class Phenotype extends Species<PhenotypeAlias> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of associated with this phenotape elements.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "phenotype", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<AssociatedElement> associatedElements = new ArrayList<AssociatedElement>();
-
- /**
- * Constructor that initializes phenotype with the data passed in the
- * argument.
- *
- * @param species
- * original species used for data initialization
- */
- public Phenotype(Species species) {
- super(species);
- if (species instanceof Phenotype) {
- Phenotype phenotype = (Phenotype) species;
- for (AssociatedElement ae : phenotype.getAssociatedElements()) {
- addAssociatedElement(new AssociatedElement(ae));
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public Phenotype() {
- }
-
- @Override
- 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());
- }
- }
-
- @Override
- public String getStringType() {
- return "Phenotype";
- }
-
- /**
- * Adds associated element to the phenotype.
- *
- * @param ae
- * associated element to add
- */
- public void addAssociatedElement(AssociatedElement ae) {
- associatedElements.add(ae);
- ae.setPhenotype(this);
- }
-
- /**
- * @return the associatedElements
- * @see #associatedElements
- */
- public List<AssociatedElement> getAssociatedElements() {
- return associatedElements;
- }
-
- /**
- * @param associatedElements
- * the associatedElements to set
- * @see #associatedElements
- */
- public void setAssociatedElements(List<AssociatedElement> associatedElements) {
- this.associatedElements = associatedElements;
- }
-
- @Override
- public PhenotypeAlias createAlias(String aliasId) {
- PhenotypeAlias result = new PhenotypeAlias(aliasId);
- if (associatedElements.size() > 0) {
- throw new NotImplementedException();
- }
- super.setAliasFields(result);
- return result;
- }
-
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElement.java b/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElement.java
deleted file mode 100644
index 72065eeb78..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElement.java
+++ /dev/null
@@ -1,150 +0,0 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Phenotype;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-/**
- * This class defines object that is associated with the phenotype. By
- * definition phenotype can contain set of elements with whom there is a kind of
- * association. This association are taken from different databases (or are
- * curated by human).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "associated_phenotype_element_table")
-public class AssociatedElement implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Where this association comes from.
- */
- private MiriamType source = MiriamType.UNKNOWN;
-
- /**
- * Description of this association in the form of Miriam object.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private MiriamData data;
-
- /**
- * Parent Phenotype object that contains this association.
- */
- @ManyToOne
- private Phenotype phenotype;
-
- /**
- * Default constructor.
- */
- public AssociatedElement() {
- }
-
- /**
- * Constructor that initialize the object with the data given in parameter.
- *
- * @param ae
- * object from which the data is initialized
- */
- public AssociatedElement(AssociatedElement ae) {
- this.source = ae.source;
- this.data = new MiriamData(ae.getData());
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the source
- * @see #source
- */
- public MiriamType getSource() {
- return source;
- }
-
- /**
- * @param source
- * the source to set
- * @see #source
- */
- public void setSource(MiriamType source) {
- this.source = source;
- }
-
- /**
- * @return the data
- * @see #data
- */
- public MiriamData getData() {
- return data;
- }
-
- /**
- * @param data
- * the data to set
- * @see #data
- */
- public void setData(MiriamData data) {
- this.data = data;
- }
-
- /**
- * @return the phenotype
- * @see #phenotype
- */
- public Phenotype getPhenotype() {
- return phenotype;
- }
-
- /**
- * @param phenotype
- * the phenotype to set
- * @see #phenotype
- */
- public void setPhenotype(Phenotype phenotype) {
- this.phenotype = phenotype;
- }
-
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparator.java
deleted file mode 100644
index 31dabfe521..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparator.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import java.util.Comparator;
-
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class implements comparator interface for AssociatedElement. It compares
- * the content, but skip database identifier and parent object reference.
- *
- * @author Piotr Gawron
- *
- */
-public class AssociatedElementComparator implements Comparator<AssociatedElement> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(AssociatedElementComparator.class);
-
- @Override
- public int compare(AssociatedElement arg0, AssociatedElement 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(AssociatedElement.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new InvalidClassException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in AssociatedElement
- * class in inheritence tree.
- *
- * @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(AssociatedElement arg0, AssociatedElement arg1) {
- if (arg0.getSource() != arg1.getSource()) {
- logger.debug("Source different: \"" + arg0.getSource() + "\", \"" + arg1.getSource() + "\"");
- if (arg0.getSource() == null) {
- return -1;
- } else {
- return arg0.getSource().compareTo(arg1.getSource());
- }
- }
-
- if (arg0.getData() == null) {
- if (arg1.getData() == null) {
- return 0;
- } else {
- logger.debug("Miriam data different");
- return 1;
- }
- } else {
- if (arg1.getData() == null) {
- logger.debug("Miriam data different");
- return -1;
- } else {
- String hash1 = arg0.getData().getRelationType() + " " + arg0.getData().getDataType() + " " + arg0.getData().getResource();
- String hash2 = arg1.getData().getRelationType() + " " + arg1.getData().getDataType() + " " + arg1.getData().getResource();
- StringComparator stringComparator = new StringComparator();
- if (stringComparator.compare(hash1, hash2) != 0) {
- logger.debug("Miriam data different: \n" + hash1 + "\n" + hash2);
- return stringComparator.compare(hash1, hash2);
- }
- }
- }
- return 0;
- }
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/species/fields/package-info.java
deleted file mode 100644
index 9fc9c50361..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/fields/package-info.java
+++ /dev/null
@@ -1,8 +0,0 @@
-/**
- * Provides data structure for complicated
- * {@link lcsb.mapviewer.model.map.species.Species Species} implementation.
- * These structures contain some additional structural information about
- * elements.
- */
-package lcsb.mapviewer.model.map.species.fields;
-
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
deleted file mode 100644
index e67728b252..0000000000
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
+++ /dev/null
@@ -1,11 +0,0 @@
-/**
- * Provides data structure for species on the map. The generic class from which
- * all element classes inherit data is
- * {@link lcsb.mapviewer.db.model.map.Element Element}. However, for species
- * there is another class that inherits from this class:
- * {@link lcsb.mapviewer.model.map.species.Species}. The package also
- * contains comparators for these elements that compare the data of the
- * structures, but ignore database-related information (like identifiers).
- */
-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 61e1ead208..0ed029d9d2 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -13,7 +13,6 @@ import org.reflections.Reflections;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -33,9 +32,9 @@ public final class ElementUtils {
/**
* Map between class names (used as user input) and implementation of
- * {@link Element} class.
+ * {@link Alias} class.
*/
- private static Map<String, Class<? extends Element>> elementClasses = null;
+ private static Map<String, Class<? extends Alias>> elementClasses = null;
/**
* Map between class names (used as user input) and implementation of
@@ -144,14 +143,14 @@ public final class ElementUtils {
}
/**
- * Returns list of classes that extends {@link Element} class, but don't have
+ * Returns list of classes that extends {@link Alias} class, but don't have
* children (leaves in the hierarchy tree).
*
- * @return list of classes that extends {@link Element} class, but don't have
+ * @return list of classes that extends {@link Alias} class, but don't have
* children (leaves in the hierarchy tree)
*/
- public List<Class<? extends Element>> getAvailableElementSubclasses() {
- List<Class<? extends Element>> result = new ArrayList<Class<? extends Element>>();
+ public List<Class<? extends Alias>> getAvailableElementSubclasses() {
+ List<Class<? extends Alias>> result = new ArrayList<Class<? extends Alias>>();
if (elementClasses == null) {
refreshClasses();
}
@@ -161,18 +160,18 @@ public final class ElementUtils {
}
/**
- * Refresh list of known implementation of {@link Element} class.
+ * Refresh list of known implementation of {@link Alias} class.
*/
protected void refreshClasses() {
- List<Class<? extends Element>> tmp = new ArrayList<Class<? extends Element>>();
+ List<Class<? extends Alias>> tmp = new ArrayList<>();
Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
- elementClasses = new HashMap<String, Class<? extends Element>>();
- Set<Class<? extends Element>> classes = reflections.getSubTypesOf(Element.class);
+ elementClasses = new HashMap<String, Class<? extends Alias>>();
+ Set<Class<? extends Alias>> classes = reflections.getSubTypesOf(Alias.class);
Set<Class<?>> toRemove = new HashSet<Class<?>>();
- for (Class<? extends Element> class1 : classes) {
+ for (Class<? extends Alias> class1 : classes) {
if (class1.isAnonymousClass() || class1.isMemberClass() || class1.isLocalClass()) {
continue;
}
@@ -182,7 +181,7 @@ public final class ElementUtils {
for (Class<?> clazz : toRemove) {
tmp.remove(clazz);
}
- for (Class<? extends Element> class1 : tmp) {
+ for (Class<? extends Alias> class1 : tmp) {
elementClasses.put(class1.getSimpleName(), class1);
}
@@ -249,7 +248,7 @@ public final class ElementUtils {
* the elementClasses to set
* @see #elementClasses
*/
- protected static void setElementClasses(Map<String, Class<? extends Element>> elementClasses) {
+ protected static void setElementClasses(Map<String, Class<? extends Alias>> elementClasses) {
ElementUtils.elementClasses = elementClasses;
}
@@ -262,8 +261,4 @@ public final class ElementUtils {
ElementUtils.reactionClasses = reactionClasses;
}
- public String getElementTag(Element element) {
- return "[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t";
- }
-
}
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 f1ec89c13e..14364ccac3 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
@@ -10,14 +10,6 @@ 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.ComplexSpecies;
-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
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 f0d48eeb97..d56d039a13 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
@@ -4,30 +4,24 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
-import lcsb.mapviewer.model.map.agregator.AllAgregatorTests;
import lcsb.mapviewer.model.map.graph.AllGraphTests;
import lcsb.mapviewer.model.map.layout.AllLayoutTests;
import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
import lcsb.mapviewer.model.map.model.AllModelTests;
import lcsb.mapviewer.model.map.modifier.AllModifierTests;
import lcsb.mapviewer.model.map.reaction.AllReactionTests;
-import lcsb.mapviewer.model.map.species.AllSpeciesTests;
import lcsb.mapviewer.model.map.statistics.AllStatisticsTests;
@RunWith(Suite.class)
@SuiteClasses({ AliasInFewParentsExceptionTest.class, //
- AllAgregatorTests.class, //
AllGraphTests.class, //
AllGraphicsTests.class, //
AllLayoutTests.class, //
AllModelTests.class, //
AllModifierTests.class, //
AllReactionTests.class, //
- AllSpeciesTests.class, //
AllStatisticsTests.class, //
CommentTest.class, //
- ElementComparatorTest.class, //
- ElementTest.class, //
InconsistentModelExceptionTest.class, //
LayoutComparatorTest.class, //
MiriamDataTest.class, //
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java
index e2da6fcea2..c17ab9a40b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java
@@ -13,7 +13,6 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Species;
public class MiriamDataTest {
@@ -76,7 +75,7 @@ public class MiriamDataTest {
MiriamData md = new MiriamData();
md.setResource(null);
assertNull(md.getResource());
-
+
md.setId(id);
assertEquals(id, md.getId());
@@ -90,7 +89,7 @@ public class MiriamDataTest {
public void testToString() {
try {
assertNotNull(new MiriamData().toString());
- assertNotNull(new MiriamData(MiriamType.CAS,"a").toString());
+ assertNotNull(new MiriamData(MiriamType.CAS, "a").toString());
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/agregator/AllAgregatorTests.java b/model/src/test/java/lcsb/mapviewer/model/map/agregator/AllAgregatorTests.java
deleted file mode 100644
index e344d0983f..0000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/agregator/AllAgregatorTests.java
+++ /dev/null
@@ -1,13 +0,0 @@
-package lcsb.mapviewer.model.map.agregator;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CompartmentComparatorTest.class,//
- CompartmentTest.class,//
-})
-public class AllAgregatorTests {
-
-}
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 c93c0dd1ef..bd6ed6c44c 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
@@ -1,93 +1,94 @@
-package lcsb.mapviewer.model.map.graph;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class DataMiningTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new DataMining());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- DataMining dm = new DataMining();
- String description = "xdg";
- Element element = new Species();
- Integer id = 61;
- List<MiriamData> references = new ArrayList<>();
- List<MiriamData> suggestedConnections = new ArrayList<>();
- DataMiningType type = DataMiningType.STRUCTURE_ANALYSIS;
-
- dm.setDescription(description);
- assertEquals(description, dm.getDescription());
- dm.setElement(element);
- assertEquals(element, dm.getElement());
- dm.setId(id);
- assertEquals(id, dm.getId());
- dm.setReferences(references);
- assertEquals(references, dm.getReferences());
- dm.setSuggestedConnections(suggestedConnections);
- assertEquals(suggestedConnections, dm.getSuggestedConnections());
- dm.setType(type);
- assertEquals(type, dm.getType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddReference() {
- try {
- DataMining dm = new DataMining();
- List<MiriamData> references = new ArrayList<>();
- references.add(new MiriamData());
- references.add(new MiriamData());
- dm.addReferences(references);
- assertEquals(2, dm.getReferences().size());
- dm.addReference(new MiriamData());
- assertEquals(3, dm.getReferences().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testAddSuggestedConnections() {
- try {
- DataMining dm = new DataMining();
- dm.addSuggestedConnection(new MiriamData());
- assertEquals(1, dm.getSuggestedConnections().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.graph;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+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;
+
+public class DataMiningTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new DataMining());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ DataMining dm = new DataMining();
+ String description = "xdg";
+ Alias element = new GenericProteinAlias("id");
+ Integer id = 61;
+ List<MiriamData> references = new ArrayList<>();
+ List<MiriamData> suggestedConnections = new ArrayList<>();
+ DataMiningType type = DataMiningType.STRUCTURE_ANALYSIS;
+
+ dm.setDescription(description);
+ assertEquals(description, dm.getDescription());
+ dm.setElement(element);
+ assertEquals(element, dm.getElement());
+ dm.setId(id);
+ assertEquals(id, dm.getId());
+ dm.setReferences(references);
+ assertEquals(references, dm.getReferences());
+ dm.setSuggestedConnections(suggestedConnections);
+ assertEquals(suggestedConnections, dm.getSuggestedConnections());
+ dm.setType(type);
+ assertEquals(type, dm.getType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddReference() {
+ try {
+ DataMining dm = new DataMining();
+ List<MiriamData> references = new ArrayList<>();
+ references.add(new MiriamData());
+ references.add(new MiriamData());
+ dm.addReferences(references);
+ assertEquals(2, dm.getReferences().size());
+ dm.addReference(new MiriamData());
+ assertEquals(3, dm.getReferences().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddSuggestedConnections() {
+ try {
+ DataMining dm = new DataMining();
+ dm.addSuggestedConnection(new MiriamData());
+ assertEquals(1, dm.getSuggestedConnections().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
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 7262b65932..b16bec7df7 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
@@ -14,8 +14,9 @@ import org.junit.Test;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
+import lcsb.mapviewer.model.map.layout.alias.SpeciesAlias;
public class ColorSchemaTest {
@@ -32,7 +33,7 @@ public class ColorSchemaTest {
try {
ColorSchema cs = new GenericColorSchema();
List<String> compartments = new ArrayList<>();
- List<Class<? extends Species>> types = new ArrayList<>();
+ List<Class<? extends Alias>> types = new ArrayList<>();
String name = "S";
String generalIdentifier = "id";
List<Pair<MiriamType, String>> identifierColumns = new ArrayList<>();
@@ -148,7 +149,7 @@ public class ColorSchemaTest {
assertNotNull(cs.toString());
cs.setName("gene name");
cs.addCompartment("A");
- cs.addType(Species.class);
+ cs.addType(SpeciesAlias.class);
cs.setValue(1.2);
cs.setColor(Color.BLACK);
cs.setGeneralIdentifier("a");
@@ -191,7 +192,7 @@ public class ColorSchemaTest {
public void testAddIdentifgierColumns() throws Exception {
try {
ColorSchema cs = new GenericColorSchema();
- List<Pair<MiriamType,String>> compartments = new ArrayList<>();
+ List<Pair<MiriamType, String>> compartments = new ArrayList<>();
compartments.add(new Pair<MiriamType, String>(MiriamType.CAS, "x"));
cs.addIdentifierColumns(compartments);
assertEquals(1, cs.getIdentifierColumns().size());
@@ -205,9 +206,9 @@ public class ColorSchemaTest {
public void testAddTypes() throws Exception {
try {
ColorSchema cs = new GenericColorSchema();
- List<Class<? extends Species>> compartments = new ArrayList<>();
- compartments.add(Species.class);
- compartments.add(Protein.class);
+ List<Class<? extends Alias>> compartments = new ArrayList<>();
+ compartments.add(SpeciesAlias.class);
+ compartments.add(ProteinAlias.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/AliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasComparatorTest.java
index 10cc64c503..802c590322 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasComparatorTest.java
@@ -11,16 +11,13 @@ import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
-import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.agregator.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.GenericProtein;
public class AliasComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasGroupTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasGroupTest.java
index 048cf4261e..d9502c7273 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasGroupTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/AliasGroupTest.java
@@ -10,8 +10,6 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
public class AliasGroupTest {
@Before
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparatorTest.java
index b9acbc1fab..1cf0304bcf 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasComparatorTest.java
@@ -12,8 +12,6 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
-import lcsb.mapviewer.model.map.species.GenericProtein;
public class CompartmentAliasComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasTest.java
index 2434709faa..6600e5b85a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/CompartmentAliasTest.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.model.map.layout.alias;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
@@ -20,12 +19,8 @@ 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.agregator.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
public class CompartmentAliasTest {
Logger logger = Logger.getLogger(CompartmentAliasTest.class);
@@ -137,7 +132,7 @@ public class CompartmentAliasTest {
alias.setName("AS");
assertFalse(alias.containsIdenticalSpecies());
-
+
SpeciesAlias sAlias = new GenericProteinAlias();
sAlias.setName("AS");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparatorTest.java
index 82996f5f7c..2577ab598d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasComparatorTest.java
@@ -12,9 +12,6 @@ import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class ComplexAliasComparatorTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasTest.java
index 2bacb3a01b..2390121c6d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ComplexAliasTest.java
@@ -10,7 +10,6 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
public class ComplexAliasTest {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/ModificationStateTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ModificationStateTest.java
similarity index 81%
rename from model/src/test/java/lcsb/mapviewer/model/map/species/fields/ModificationStateTest.java
rename to model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ModificationStateTest.java
index 7e292cc131..d122a41327 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/ModificationStateTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/ModificationStateTest.java
@@ -1,38 +1,40 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ModificationStateTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ModificationState type : ModificationState.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ModificationState.valueOf(type.toString());
- assertNotNull(type.getFullName());
- assertNotNull(type.getAbbreviation());
- }
- }
-
- @Test
- public void testGetByName() {
- assertNull(ModificationState.getByName("Adasd"));
- assertNotNull(ModificationState.getByName("protonated"));
- }
-
-}
+package lcsb.mapviewer.model.map.layout.alias;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationState;
+
+public class ModificationStateTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ModificationState type : ModificationState.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ModificationState.valueOf(type.toString());
+ assertNotNull(type.getFullName());
+ assertNotNull(type.getAbbreviation());
+ }
+ }
+
+ @Test
+ public void testGetByName() {
+ assertNull(ModificationState.getByName("Adasd"));
+ assertNotNull(ModificationState.getByName("protonated"));
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparatorTest.java
index 95a5881589..ffbafe9f43 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasComparatorTest.java
@@ -9,10 +9,9 @@ import java.awt.Color;
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.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class SpeciesAliasComparatorTest {
@@ -47,22 +46,9 @@ public class SpeciesAliasComparatorTest {
@Test
public void testCompareInvalid() {
try {
- class Tmp extends GenericProteinAlias {
-
- public Tmp() {
- super(null, null);
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }
- ;
-
- Tmp alias1 = new Tmp();
- Tmp alias2 = new Tmp();
- comparator.compare(alias1, alias2);
+
+ SpeciesAlias alias = Mockito.mock(SpeciesAlias.class);
+ comparator.compare(alias, alias);
fail("Exception expected");
} catch (NotImplementedException e) {
@@ -75,7 +61,7 @@ public class SpeciesAliasComparatorTest {
private SpeciesAlias createSpeciesAlias() {
GenericProteinAlias result = new GenericProteinAlias();
result.setName("a");
-
+
result.setAliasId("asd");
result.setX(12.0);
result.setY(123.0);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasTest.java
index 10ade68cb5..d2aa04e7f6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/alias/SpeciesAliasTest.java
@@ -1,18 +1,14 @@
package lcsb.mapviewer.model.map.layout.alias;
import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
import java.util.HashSet;
import java.util.Set;
-import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
public class SpeciesAliasTest {
@@ -29,7 +25,7 @@ public class SpeciesAliasTest {
public void testGetter() {
try {
SpeciesAlias alias = new SpeciesAlias() {
-
+
@Override
public SpeciesAlias copy() {
return null;
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 a8260e5706..3649aed846 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
@@ -9,15 +9,11 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.agregator.Compartment;
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.layout.graphics.Layer;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
public class AliasSubmodelConnectionComparatorTest {
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 0b23a9932f..c2076026bb 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
@@ -11,14 +11,11 @@ import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
-import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
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.agregator.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
@@ -28,9 +25,6 @@ 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.Protein;
-import lcsb.mapviewer.model.map.species.Species;
public class ModelComparatorTest {
Logger logger = Logger.getLogger(ModelComparatorTest.class);
@@ -151,10 +145,10 @@ public class ModelComparatorTest {
Model model1 = getModel();
Model model2 = getModel();
- SpeciesAlias mockAlias =Mockito.mock(SpeciesAlias.class);
+ SpeciesAlias mockAlias = Mockito.mock(SpeciesAlias.class);
when(mockAlias.getAliasId()).thenReturn("1");
model1.addAlias(mockAlias);
-
+
model2.addAlias(mockAlias);
try {
@@ -177,7 +171,6 @@ public class ModelComparatorTest {
}
}
-
@Test
public void testDifferent() throws Exception {
try {
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 9d768b0fa4..56c1808e30 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
@@ -18,7 +18,6 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
@@ -27,7 +26,6 @@ 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.Species;
public class ModelDataTest {
@@ -326,7 +324,6 @@ public class ModelDataTest {
try {
ModelData md = new ModelData();
Set<Alias> aliases = new HashSet<>();
- Set<Element> elements = 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 14cba9e260..bcadff7289 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
@@ -25,12 +25,10 @@ import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
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.agregator.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.alias.Alias;
@@ -44,9 +42,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.User;
public class ModelFullIndexedTest {
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 63ee6dfd8d..ad3ac46f5e 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
@@ -7,13 +7,11 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.agregator.Compartment;
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.species.GenericProtein;
public class ModelSubmodelConnectionComparatorTest {
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 26065e19ba..6d33781d45 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
@@ -14,12 +14,10 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
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.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
@@ -27,9 +25,6 @@ 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.species.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class ModelTest {
Logger logger = Logger.getLogger(ModelTest.class);
@@ -161,28 +156,23 @@ public class ModelTest {
private Model createModel() {
Model model = new ModelFullIndexed(null);
-
SpeciesAlias proteinAlias = new GenericProteinAlias("sa1");
proteinAlias.setName("s1");
model.addAlias(proteinAlias);
-
SpeciesAlias proteinAlias2 = new GenericProteinAlias("sa2");
proteinAlias2.setName("s1");
model.addAlias(proteinAlias2);
-
SpeciesAlias proteinAlias3 = new GenericProteinAlias("sa3");
proteinAlias3.setName("s1");
model.addAlias(proteinAlias3);
-
SpeciesAlias proteinAlias4 = new GenericProteinAlias("sa4");
proteinAlias4.setName("s5");
proteinAlias4.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEMBL_TARGET, "CHEMBL12345"));
model.addAlias(proteinAlias4);
-
CompartmentAlias compartmentAlias = new CompartmentAlias("cca");
compartmentAlias.setName("c1");
compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEBI, "CHEBI:12"));
@@ -197,7 +187,6 @@ public class ModelTest {
try {
Model model = new ModelFullIndexed(null);
-
SpeciesAlias alias = new GenericProteinAlias("2");
alias.setWidth(100);
alias.setHeight(100);
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 70566deae5..daf95263a3 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
@@ -9,13 +9,11 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.agregator.Compartment;
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.species.GenericProtein;
public class SubmodelConnectionComparatorTest {
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 a4dfad66ad..0d8269a0e6 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
@@ -11,8 +11,6 @@ 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.layout.alias.SpeciesAlias;
-import lcsb.mapviewer.model.map.species.Species;
public class CatalysisTest {
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 11824c36dd..c3818fc0da 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
@@ -11,7 +11,6 @@ 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.Species;
public class InhibitionTest {
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 db46dc85f4..5508d9c5a4 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
@@ -11,7 +11,6 @@ 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.Species;
public class ModulationTest {
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 7cacc0a727..b6f2ca0e75 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
@@ -11,7 +11,6 @@ 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.Species;
public class PhysicalStimulationTest {
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 89726e7ee0..f6ea1e96e4 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
@@ -11,7 +11,6 @@ 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.Species;
public class TriggerTest {
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 b04c967961..9d6214a920 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
@@ -11,7 +11,6 @@ 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.Species;
public class UnknownInhibitionTest {
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 3550a0a748..3b161e9152 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
@@ -2,7 +2,6 @@ package lcsb.mapviewer.model.map.reaction;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
import java.awt.geom.Point2D;
@@ -14,10 +13,6 @@ 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.Protein;
-import lcsb.mapviewer.model.map.species.Species;
public class NodeOperatorComparatorTest {
@@ -105,7 +100,6 @@ public class NodeOperatorComparatorTest {
private NodeOperator createNodeOperator() {
AndOperator result = new AndOperator();
-
SpeciesAlias alias0 = new GenericProteinAlias("id0");
alias0.setName("protein a");
alias0.setX(12.0);
@@ -117,7 +111,6 @@ public class NodeOperatorComparatorTest {
result.addOutput(product);
-
SpeciesAlias alias1 = new GenericProteinAlias("id1");
alias1.setName("protein b");
alias1.setX(120.0);
@@ -129,7 +122,6 @@ public class NodeOperatorComparatorTest {
result.addInput(reactant);
-
SpeciesAlias alias2 = new GeneAlias("id2");
alias2.setName("gene b");
alias2.setX(320.0);
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 c159a40985..1c987b9b18 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
@@ -2,7 +2,6 @@ package lcsb.mapviewer.model.map.reaction;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
import java.awt.geom.Point2D;
@@ -21,9 +20,6 @@ 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.Unknown;
public class ReactionComparatorTest {
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 b43140b0aa..89c180e1e8 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
@@ -2,7 +2,6 @@ package lcsb.mapviewer.model.map.reaction;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
import java.awt.geom.Point2D;
@@ -14,10 +13,6 @@ 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.Protein;
-import lcsb.mapviewer.model.map.species.Species;
public class ReactionNodeComparatorTest {
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 53c0047ccf..11cf8a18e8 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
@@ -34,13 +34,12 @@ 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.GenericProtein;
public class ReactionTest extends ModelTestFunctions {
- Logger logger = Logger.getLogger(ReactantTest.class);
+ Logger logger = Logger.getLogger(ReactantTest.class);
- private SpeciesAlias alias;
+ private SpeciesAlias alias;
@Before
public void setUp() throws Exception {
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
deleted file mode 100644
index 48cabcfeb5..0000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
+++ /dev/null
@@ -1,42 +0,0 @@
-package lcsb.mapviewer.model.map.species;
-
-import lcsb.mapviewer.model.map.species.fields.AllSpeciesFieldsTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllSpeciesFieldsTests.class,//
- AntisenseRnaComparatorTest.class, //
- AntisenseRnaTest.class, //
- ComplexSpeciesComparatorTest.class, //
- ComplexSpeciesTest.class,//
- DegradedComparatorTest.class, //
- DegradedTest.class, //
- DrugComparatorTest.class, //
- DrugTest.class, //
- GeneComparatorTest.class, //
- GenericProteinTest.class,//
- GeneTest.class, //
- IonChannelProteinTest.class, //
- IonComparatorTest.class, //
- IonTest.class, //
- PhenotypeComparatorTest.class, //
- PhenotypeTest.class,//
- ProteinComparatorTest.class, //
- ProteinTest.class, //
- ReceptorProteinTest.class, //
- RnaComparatorTest.class, //
- RnaTest.class, //
- SimpleMoleculeComparatorTest.class,//
- SimpleMoleculeTest.class, //
- SpeciesComparatorTest.class, //
- SpeciesTest.class, //
- TruncatedProteinTest.class, //
- UnknownComparatorTest.class, //
- UnknownTest.class,//
-})
-public class AllSpeciesTests {
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AllSpeciesFieldsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AllSpeciesFieldsTests.java
deleted file mode 100644
index a6a40ca862..0000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AllSpeciesFieldsTests.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AntisenseRnaRegionTest.class, //
- AssociatedElementComparatorTest.class, //
- AssociatedElementTest.class, //
- ModificationResidueTest.class, //
- ModificationStateTest.class, //
- PositionToCompartmentTest.class, //
- RnaRegionTest.class,//
-
-})
-public class AllSpeciesFieldsTests {
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparatorTest.java
deleted file mode 100644
index 983ff68bbf..0000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementComparatorTest.java
+++ /dev/null
@@ -1,111 +0,0 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-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 lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class AssociatedElementComparatorTest {
-
- AssociatedElementComparator comparator = new AssociatedElementComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCompareEquals() {
- try {
- AssociatedElement ae1 = new AssociatedElement();
- AssociatedElement ae2 = new AssociatedElement();
- assertTrue(comparator.compare(ae1, ae2) == 0);
-
- ae1 = new AssociatedElement();
- ae2 = new AssociatedElement();
- ae1.setData(new MiriamData(MiriamType.CAS,"TE"));
- ae2.setData(new MiriamData(MiriamType.CAS,"TE"));
- assertTrue(comparator.compare(ae1, ae2) == 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testCompareDifferent() {
- try {
- AssociatedElement ae1 = new AssociatedElement();
- AssociatedElement ae2 = new AssociatedElement();
- ae2.setSource(MiriamType.CHEBI);
- assertTrue(comparator.compare(ae1, ae2) != 0);
- assertTrue(comparator.compare(ae2, ae1) != 0);
- assertTrue(comparator.compare(null, ae2) != 0);
- assertTrue(comparator.compare(ae1, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- ae1 = new AssociatedElement();
- ae2 = new AssociatedElement();
- ae1.setSource(null);
- assertTrue(comparator.compare(ae1, ae2) != 0);
-
- ae1 = new AssociatedElement();
- ae2 = new AssociatedElement();
- ae1.setData(new MiriamData(MiriamType.CAS,"TE"));
- assertTrue(comparator.compare(ae1, ae2) != 0);
- assertTrue(comparator.compare(ae2, ae1) != 0);
-
- ae1 = new AssociatedElement();
- ae2 = new AssociatedElement();
- ae1.setData(new MiriamData(MiriamType.CAS,"TE"));
- ae2.setData(new MiriamData(MiriamType.CAS,"TE2"));
- assertTrue(comparator.compare(ae1, ae2) != 0);
- assertTrue(comparator.compare(ae2, ae1) != 0);
-
- AssociatedElement ae3 = new AssociatedElement() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
- assertTrue(comparator.compare(ae1, ae3) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testCompareInvalid() {
- try {
- AssociatedElement ae3 = new AssociatedElement() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
- comparator.compare(ae3, ae3);
- fail("Exception expected");
- } catch (InvalidClassException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementTest.java
deleted file mode 100644
index 543436256d..0000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/fields/AssociatedElementTest.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package lcsb.mapviewer.model.map.species.fields;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.species.Phenotype;
-
-public class AssociatedElementTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new AssociatedElement());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- AssociatedElement original = new AssociatedElement();
- original.setData(new MiriamData());
- AssociatedElement copy = new AssociatedElement(original);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testGetters() {
- try {
- AssociatedElement copy = new AssociatedElement();
- int id = 23;
- Phenotype phenotype = new Phenotype();
- copy.setId(id);
- copy.setPhenotype(phenotype);
-
- assertEquals(id, copy.getId());
- assertEquals(phenotype, copy.getPhenotype());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
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 742bf31236..0bc877fd6c 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
@@ -16,10 +16,12 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.Element;
+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.Ion;
public class ElementUtilsTest {
Logger logger = Logger.getLogger(ElementUtilsTest.class);
@@ -91,9 +93,9 @@ public class ElementUtilsTest {
try {
ElementUtils elementUtils = new ElementUtils();
- List<Class<? extends Element>> list = elementUtils.getAvailableElementSubclasses();
- assertTrue(list.contains(lcsb.mapviewer.model.map.species.IonChannelProtein.class));
- assertFalse(list.contains(lcsb.mapviewer.model.map.species.Protein.class));
+ List<Class<? extends Alias>> list = elementUtils.getAvailableElementSubclasses();
+ assertTrue(list.contains(IonChannelProteinAlias.class));
+ assertFalse(list.contains(ProteinAlias.class));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -104,8 +106,8 @@ public class ElementUtilsTest {
public void tesClassByName() throws Exception {
try {
ElementUtils elementUtils = new ElementUtils();
- assertEquals(Ion.class, elementUtils.getClassByName(Ion.class.getSimpleName()));
- assertEquals(Ion.class, elementUtils.getClassByName("Ion"));
+ assertEquals(IonAlias.class, elementUtils.getClassByName(IonAlias.class.getSimpleName()));
+ assertEquals(IonAlias.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 1c7ad10861..10756d049d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -22,11 +22,14 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
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.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
@@ -61,9 +64,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.wikipathway.model.DataNode;
import lcsb.mapviewer.wikipathway.model.Edge;
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 8be4928858..28c1614bd0 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
@@ -1,136 +1,136 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
-
-/**
- * This enum represents type of line in GPML format.
- *
- * @author Piotr Gawron
- *
- */
-public enum GpmlModificationType {
-
- /**
- * Gpml type representing: {@link ModificationState#PHOSPHORYLATED}.
- */
- PHOSPHORYLATED("P", ModificationState.PHOSPHORYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#ACETYLATED}.
- */
- ACETYLATED("Ac", ModificationState.ACETYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#UBIQUITINATED}.
- */
- UBIQUITINATED("Ub", ModificationState.UBIQUITINATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#METHYLATED}.
- */
- METHYLATED("Me", ModificationState.METHYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#HYDROXYLATED}.
- */
- HYDROXYLATED("OH", ModificationState.HYDROXYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#MYRISTOYLATED}.
- */
- MYRISTOYLATED("My", ModificationState.MYRISTOYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#SULFATED}.
- */
- SULFATED("S", ModificationState.SULFATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#PRENYLATED}.
- */
- PRENYLATED("Pr", ModificationState.PRENYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#GLYCOSYLATED}.
- */
- GLYCOSYLATED("G", ModificationState.GLYCOSYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#PALMYTOYLATED}.
- */
- PALMYTOYLATED("Pa", ModificationState.PALMYTOYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#UNKNOWN}.
- */
- UNKOWN("", ModificationState.UNKNOWN), //
-
- /**
- * Gpml type representing: {@link ModificationState#PROTONATED}.
- */
- PROTONATED("H", ModificationState.PROTONATED);
-
- /**
- * Default constructor.
- *
- * @param gpmlString
- * {@link #gpmlString}
- * @param correspondingModificationState
- * {@link #correspondingModificationState}
- */
- GpmlModificationType(String gpmlString, ModificationState correspondingModificationState) {
- this.gpmlString = gpmlString;
- this.correspondingModificationState = correspondingModificationState;
- }
-
- /**
- * String in GPML format representig this type.
- */
- private String gpmlString;
-
- /**
- * Which {@link ModificationState} in our model should be used for this GPML
- * modification type.
- */
- private ModificationState correspondingModificationState;
-
- /**
- * @return the gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
-
- /**
- * Returns {@link GpmlModificationType type} identified by {@link #gpmlName
- * gpml string} identifing the type.
- *
- * @param gpmlName
- * {@link #gpmlString}
- * @return {@link GpmlModificationType type} identified by {@link #gpmlName
- * gpml string} identifing the type
- * @throws UnknownTypeException
- * thrown when type cannot be found
- */
- public static GpmlModificationType getByGpmlName(String gpmlName) throws UnknownTypeException {
- for (GpmlModificationType type : values()) {
- if (type.getGpmlString() == null) {
- if (gpmlName == null) {
- return type;
- }
- } else if (type.getGpmlString().equalsIgnoreCase(gpmlName)) {
- return type;
- }
- }
- throw new UnknownTypeException("Unknown state type: " + gpmlName);
- }
-
- /**
- * @return the correspondingModificationState
- * @see #correspondingModificationState
- */
- public ModificationState getCorrespondingModificationState() {
- return correspondingModificationState;
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+
+/**
+ * This enum represents type of line in GPML format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum GpmlModificationType {
+
+ /**
+ * Gpml type representing: {@link ModificationState#PHOSPHORYLATED}.
+ */
+ PHOSPHORYLATED("P", ModificationState.PHOSPHORYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#ACETYLATED}.
+ */
+ ACETYLATED("Ac", ModificationState.ACETYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#UBIQUITINATED}.
+ */
+ UBIQUITINATED("Ub", ModificationState.UBIQUITINATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#METHYLATED}.
+ */
+ METHYLATED("Me", ModificationState.METHYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#HYDROXYLATED}.
+ */
+ HYDROXYLATED("OH", ModificationState.HYDROXYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#MYRISTOYLATED}.
+ */
+ MYRISTOYLATED("My", ModificationState.MYRISTOYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#SULFATED}.
+ */
+ SULFATED("S", ModificationState.SULFATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#PRENYLATED}.
+ */
+ PRENYLATED("Pr", ModificationState.PRENYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#GLYCOSYLATED}.
+ */
+ GLYCOSYLATED("G", ModificationState.GLYCOSYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#PALMYTOYLATED}.
+ */
+ PALMYTOYLATED("Pa", ModificationState.PALMYTOYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#UNKNOWN}.
+ */
+ UNKOWN("", ModificationState.UNKNOWN), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#PROTONATED}.
+ */
+ PROTONATED("H", ModificationState.PROTONATED);
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @param correspondingModificationState
+ * {@link #correspondingModificationState}
+ */
+ GpmlModificationType(String gpmlString, ModificationState correspondingModificationState) {
+ this.gpmlString = gpmlString;
+ this.correspondingModificationState = correspondingModificationState;
+ }
+
+ /**
+ * String in GPML format representig this type.
+ */
+ private String gpmlString;
+
+ /**
+ * Which {@link ModificationState} in our model should be used for this GPML
+ * modification type.
+ */
+ private ModificationState correspondingModificationState;
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * Returns {@link GpmlModificationType type} identified by {@link #gpmlName
+ * gpml string} identifing the type.
+ *
+ * @param gpmlName
+ * {@link #gpmlString}
+ * @return {@link GpmlModificationType type} identified by {@link #gpmlName
+ * gpml string} identifing the type
+ * @throws UnknownTypeException
+ * thrown when type cannot be found
+ */
+ public static GpmlModificationType getByGpmlName(String gpmlName) throws UnknownTypeException {
+ for (GpmlModificationType type : values()) {
+ if (type.getGpmlString() == null) {
+ if (gpmlName == null) {
+ return type;
+ }
+ } else if (type.getGpmlString().equalsIgnoreCase(gpmlName)) {
+ return type;
+ }
+ }
+ throw new UnknownTypeException("Unknown state type: " + gpmlName);
+ }
+
+ /**
+ * @return the correspondingModificationState
+ * @see #correspondingModificationState
+ */
+ public ModificationState getCorrespondingModificationState() {
+ return correspondingModificationState;
+ }
+}
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 915754779e..d0023f4715 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
@@ -1,258 +1,258 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
-
-/**
- * Class used to store data about {@link DataNode} state from .gpml.
- *
- * @author Piotr Gawron
- *
- */
-public class State extends GraphicalPathwayElement {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Shape of the element.
- */
- private String shape;
-
- /**
- * References for given edge.
- */
- private List<MiriamData> references = new ArrayList<>();
-
- /**
- * Object where this state is placed.
- */
- private String graphRef;
-
- /**
- * State correspondig to {@link lcsb.mapviewer.model.map.species.Protein#structuralState protein structural state}.
- */
- private String structuralState;
-
- /**
- * Type of the modification.
- */
- private ModificationState type;
-
- /**
- * X position on {@link #graphRef} element.
- */
- private Double relX;
-
- /**
- * Y position on {@link #graphRef} element.
- */
- private Double relY;
-
- /**
- * Width of the element.
- */
- private Double width;
-
- /**
- * Heightof the element.
- */
- private Double height;
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link PathwayElement#graphId}
- */
- public State(String graphId) {
- super(graphId);
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected State() {
- }
-
- @Override
- String getName() {
- throw new NotImplementedException();
- }
-
- @Override
- public Rectangle2D getRectangle() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the shape
- * @see #shape
- */
- public String getShape() {
- return shape;
- }
-
- /**
- * @param shape
- * the shape to set
- * @see #shape
- */
- public void setShape(String shape) {
- this.shape = shape;
- }
-
- /**
- * @return the relX
- * @see #relX
- */
- public Double getRelX() {
- return relX;
- }
-
- /**
- * @param relX
- * the relX to set
- * @see #relX
- */
- public void setRelX(Double relX) {
- this.relX = relX;
- }
-
- /**
- * @return the relY
- * @see #relY
- */
- public Double getRelY() {
- return relY;
- }
-
- /**
- * @param relY
- * the relY to set
- * @see #relY
- */
- public void setRelY(Double relY) {
- this.relY = relY;
- }
-
- /**
- * @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;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Double getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Double height) {
- this.height = height;
- }
-
- /**
- * @return the graphRef
- * @see #graphRef
- */
- public String getGraphRef() {
- return graphRef;
- }
-
- /**
- * @param graphRef
- * the graphRef to set
- * @see #graphRef
- */
- public void setGraphRef(String graphRef) {
- this.graphRef = graphRef;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<MiriamData> references) {
- this.references = references;
- }
-
- /**
- * Adds reference to object.
- *
- * @param reference
- * reference to add
- */
- public void addReference(MiriamData reference) {
- this.references.add(reference);
- }
-
- /**
- * @return the type
- * @see #type
- */
- public ModificationState getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(ModificationState type) {
- this.type = type;
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
+
+/**
+ * Class used to store data about {@link DataNode} state from .gpml.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class State extends GraphicalPathwayElement {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Shape of the element.
+ */
+ private String shape;
+
+ /**
+ * References for given edge.
+ */
+ private List<MiriamData> references = new ArrayList<>();
+
+ /**
+ * Object where this state is placed.
+ */
+ private String graphRef;
+
+ /**
+ * State correspondig to {@link lcsb.mapviewer.converter.model.celldesigner.structure.Protein#structuralState protein structural state}.
+ */
+ private String structuralState;
+
+ /**
+ * Type of the modification.
+ */
+ private ModificationState type;
+
+ /**
+ * X position on {@link #graphRef} element.
+ */
+ private Double relX;
+
+ /**
+ * Y position on {@link #graphRef} element.
+ */
+ private Double relY;
+
+ /**
+ * Width of the element.
+ */
+ private Double width;
+
+ /**
+ * Heightof the element.
+ */
+ private Double height;
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link PathwayElement#graphId}
+ */
+ public State(String graphId) {
+ super(graphId);
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected State() {
+ }
+
+ @Override
+ String getName() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public Rectangle2D getRectangle() {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * @return the shape
+ * @see #shape
+ */
+ public String getShape() {
+ return shape;
+ }
+
+ /**
+ * @param shape
+ * the shape to set
+ * @see #shape
+ */
+ public void setShape(String shape) {
+ this.shape = shape;
+ }
+
+ /**
+ * @return the relX
+ * @see #relX
+ */
+ public Double getRelX() {
+ return relX;
+ }
+
+ /**
+ * @param relX
+ * the relX to set
+ * @see #relX
+ */
+ public void setRelX(Double relX) {
+ this.relX = relX;
+ }
+
+ /**
+ * @return the relY
+ * @see #relY
+ */
+ public Double getRelY() {
+ return relY;
+ }
+
+ /**
+ * @param relY
+ * the relY to set
+ * @see #relY
+ */
+ public void setRelY(Double relY) {
+ this.relY = relY;
+ }
+
+ /**
+ * @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;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Double getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Double height) {
+ this.height = height;
+ }
+
+ /**
+ * @return the graphRef
+ * @see #graphRef
+ */
+ public String getGraphRef() {
+ return graphRef;
+ }
+
+ /**
+ * @param graphRef
+ * the graphRef to set
+ * @see #graphRef
+ */
+ public void setGraphRef(String graphRef) {
+ this.graphRef = graphRef;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<MiriamData> references) {
+ this.references = references;
+ }
+
+ /**
+ * Adds reference to object.
+ *
+ * @param reference
+ * reference to add
+ */
+ public void addReference(MiriamData reference) {
+ this.references.add(reference);
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public ModificationState getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(ModificationState type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ this.structuralState = structuralState;
+ }
+
+}
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 5332f30cbf..e4b453e25b 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.species.fields.ModificationState;
+import lcsb.mapviewer.model.map.layout.alias.ModificationState;
import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
import lcsb.mapviewer.wikipathway.model.State;
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 7d9262afd6..0348b5ed20 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
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.persist.dao.map.graph;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-import org.apache.log4j.Logger;
-import org.hibernate.Query;
-
-/**
- * Data access object for {@link DataMining} class.
- *
- * @author Piotr Gawron
- *
- */
-public class DataMiningDao extends BaseDao<DataMining> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DataMiningDao.class);
-
- /**
- * Default constructor.
- */
-
- public DataMiningDao() {
- super(DataMining.class);
- }
-
- /**
- * Returns the data mining elements for unified node.
- *
- * @param node
- * node for which data mining entries should be returned
- * @return the data mining elements for unified node
- */
- public Collection<DataMining> getMissingConnectionForElement(Element node) {
- if (node.getId() == 0) {
- return new ArrayList<DataMining>();
- } else {
- String queryString = "from " + this.getClazz().getSimpleName() + " where element=:node";
- Query query = getSession().createQuery(queryString);
- @SuppressWarnings("unchecked")
- List<DataMining> list = query.setParameter("node", node).list();
- return list;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.graph;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.model.map.graph.DataMining;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+import org.apache.log4j.Logger;
+import org.hibernate.Query;
+
+/**
+ * Data access object for {@link DataMining} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DataMiningDao extends BaseDao<DataMining> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DataMiningDao.class);
+
+ /**
+ * Default constructor.
+ */
+
+ public DataMiningDao() {
+ super(DataMining.class);
+ }
+
+ /**
+ * Returns the data mining elements for unified node.
+ *
+ * @param node
+ * node for which data mining entries should be returned
+ * @return the data mining elements for unified node
+ */
+ public Collection<DataMining> getMissingConnectionForElement(Element node) {
+ if (node.getId() == 0) {
+ return new ArrayList<DataMining>();
+ } else {
+ String queryString = "from " + this.getClazz().getSimpleName() + " where element=:node";
+ Query query = getSession().createQuery(queryString);
+ @SuppressWarnings("unchecked")
+ List<DataMining> list = query.setParameter("node", node).list();
+ return list;
+ }
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/SpeciesDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/SpeciesDao.java
index 5682bd9724..44c220b83d 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/SpeciesDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/SpeciesDao.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.persist.dao.map.species;
-
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for {@link Species} class.
- *
- * @author Piotr Gawron
- *
- */
-public class SpeciesDao extends BaseDao<Species> {
-
- /**
- * Default constructor.
- */
- public SpeciesDao() {
- super(Species.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.species;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for {@link Species} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SpeciesDao extends BaseDao<Species> {
+
+ /**
+ * Default constructor.
+ */
+ public SpeciesDao() {
+ super(Species.class);
+ }
+
+}
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 2d82e972ef..cbead2d998 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -11,10 +11,12 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
@@ -22,8 +24,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ProjectDaoTest extends PersistTestFunctions {
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 76ef37ae06..6f1fe10e3e 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
@@ -8,12 +8,16 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+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.converter.model.celldesigner.structure.ModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.Project;
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.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
import lcsb.mapviewer.model.map.layout.alias.GenericProteinAlias;
@@ -27,10 +31,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class CommentDaoTest extends PersistTestFunctions {
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 a492589bc4..a4895a8953 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
@@ -13,12 +13,13 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
import lcsb.mapviewer.model.Project;
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.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
@@ -34,7 +35,6 @@ 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.ComplexSpecies;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class LayoutDaoTest extends PersistTestFunctions {
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 3f11429473..4cefbcc14f 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
@@ -13,12 +13,17 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+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.model.Project;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.alias.Alias;
@@ -37,11 +42,6 @@ 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.ComplexSpecies;
-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.fields.ModificationResidue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ModelDaoTest extends PersistTestFunctions {
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 3e03f099b2..7b6ada7d53 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
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.persist.dao.map.graph;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class DataMiningDaoTest extends PersistTestFunctions {
-
- @Autowired
- private DataMiningDao dataMiningDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetConnections() {
- assertEquals(0, dataMiningDao.getMissingConnectionForElement(new Species()).size());
- }
-
- @Test
- public void testGetConnections2() {
- Species species = new Species();
- species.setId(1);
- assertEquals(0, dataMiningDao.getMissingConnectionForElement(species).size());
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.graph;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class DataMiningDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ private DataMiningDao dataMiningDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetConnections() {
+ assertEquals(0, dataMiningDao.getMissingConnectionForElement(new Species()).size());
+ }
+
+ @Test
+ public void testGetConnections2() {
+ Species species = new Species();
+ 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 88a87b9c05..b3a651bda4 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
@@ -7,8 +7,11 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.ComplexAlias;
@@ -19,9 +22,6 @@ 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.ComplexSpecies;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class AliasDaoTest extends PersistTestFunctions {
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 19ad3cdfb5..5f5e3fabad 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
@@ -10,6 +10,8 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ModificationState;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Phenotype;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -26,8 +28,6 @@ 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.Phenotype;
-import lcsb.mapviewer.model.map.species.fields.ModificationState;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class AliasDaoTest2 extends PersistTestFunctions {
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/species/AntisenseRnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/species/AntisenseRnaTest.java
index 630962b826..82f3c6ee31 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/species/AntisenseRnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/species/AntisenseRnaTest.java
@@ -10,16 +10,16 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.test.annotation.Rollback;
+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.model.Project;
-import lcsb.mapviewer.model.map.agregator.Compartment;
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.SpeciesAlias;
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.fields.AntisenseRnaRegion;
import lcsb.mapviewer.persist.PersistTestFunctions;
@Rollback(true)
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 ea4ad85954..64af4ecedf 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
@@ -1,281 +1,281 @@
-package lcsb.mapviewer.persist.dao.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-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.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;
-import lcsb.mapviewer.model.user.UserClassValidAnnotations;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class UserDaoTest extends PersistTestFunctions {
-
- @Autowired
- protected PasswordEncoder passwordEncoder;
-
- protected Logger logger = Logger.getLogger(UserDaoTest.class.getName());
- String testLogin = "test_login123";
- String testEmail = "a@a.pl";
- String testPasswd = "pwd";
- String testLogin2 = "test_login_tmp";
- String testName = "John";
- String testSurname = "Doe";
-
- @Before
- public void setUp() throws Exception {
- Map<String, Object> params = new HashMap<String, Object>();
- params.put("login_param", testLogin);
- params.put("login_param2", testLogin2);
- dbUtils.executeSqlQuery("delete from user_table where login = :login_param or login = :login_param2", params);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAddUpdateDelete() {
- try {
- User user = userDao.getUserByLogin(testLogin);
- assertNull(user);
-
- long counter = userDao.getCount();
-
- user = new User();
- user.setLogin(testLogin);
- userDao.add(user);
-
- long counter2 = userDao.getCount();
- assertEquals(counter + 1, counter2);
-
- user.setLogin(testLogin2);
- userDao.update(user);
-
- User user2 = userDao.getUserByLogin(testLogin2);
- assertNotNull(user2);
-
- userDao.delete(user);
-
- user2 = userDao.getUserByLogin(testLogin2);
- assertNull(user2);
- counter2 = userDao.getCount();
- assertEquals(counter, counter2);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception occured");
- }
- }
-
- @Test
- public void testAddDeleteAdd() {
- try {
- User user = userDao.getUserByLogin(testLogin);
- assertNull(user);
-
- long counter = userDao.getCount();
-
- user = new User();
- user.setLogin(testLogin);
- userDao.add(user);
-
- long counter2 = userDao.getCount();
- assertEquals(counter + 1, counter2);
-
- userDao.delete(user);
-
- User user2 = userDao.getUserByLogin(testLogin);
- assertNull(user2);
-
- user2 = new User();
- user2.setLogin(testLogin);
- userDao.add(user2);
-
- assertNotNull(userDao.getUserByLogin(testLogin));
-
- userDao.delete(user2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByLoginAndPassword() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- userDao.add(user);
- User user2 = userDao.getUserByLoginAndPassword(testLogin, testPasswd);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- userDao.delete(user);
- // after we remove it we shouldn't be able to get it
- User user3 = userDao.getUserByLoginAndPassword(testLogin, testPasswd);
- assertNull(user3);
-
- // after we remove it we shouldn't be able to get the removed and modified
- // object
- User user4 = userDao.getUserByLoginAndPassword(user2.getLogin(), testPasswd);
- assertNull(user4);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByLoginAndEmptyPassword() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- userDao.add(user);
- User user2 = userDao.getUserByLoginAndPassword(testLogin, null);
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByLogin() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- userDao.add(user);
- User user2 = userDao.getUserByLogin(testLogin);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- user2 = userDao.getUserByLogin(testLogin2);
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByEmail() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- user.setEmail(testEmail);
- userDao.add(user);
- User user2 = userDao.getUserByEmail(testEmail);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- user2 = userDao.getUserByEmail(testEmail + "sadas");
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByNameSurname() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- user.setEmail(testEmail);
- user.setName(testName);
- user.setSurname(testSurname);
- userDao.add(user);
- User user2 = userDao.getUserByNameSurname(testName + " " + testSurname);
- assertNotNull(user2);
- user2 = userDao.getUserByNameSurname(testName + " " + testSurname);
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAll() throws Exception {
- try {
- assertTrue(userDao.getAll().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUserWithAnnotatorSchema() throws Exception {
- try {
- User user = new User();
- UserAnnotationSchema uas = new UserAnnotationSchema();
- uas.setValidateMiriamTypes(true);
- UserClassAnnotators ca = new UserClassAnnotators();
- ca.setClassName(Species.class);
- ca.addAnnotator(String.class);
- ca.addAnnotator(Integer.class);
- uas.addClassAnnotator(ca);
- uas.addClassAnnotator(new UserClassAnnotators(String.class, new ArrayList<String>()));
- UserClassValidAnnotations cva = new UserClassValidAnnotations();
- cva.setClassName(Reaction.class);
- cva.addValidMiriamType(MiriamType.HGNC);
- cva.addValidMiriamType(MiriamType.HGNC_SYMBOL);
- uas.addClassValidAnnotations(cva);
- uas.addClassValidAnnotations(new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>()));
- uas.addClassValidAnnotations(new UserClassValidAnnotations(Integer.class, new ArrayList<MiriamType>()));
- user.setAnnotationSchema(uas);
- userDao.add(user);
- userDao.evict(user);
- User user2 = userDao.getById(user.getId());
- assertNotNull(user2);
- UserAnnotationSchema uas2 = user2.getAnnotationSchema();
- assertNotNull(uas2);
- assertEquals(2, uas2.getClassAnnotators().size());
- assertEquals(3, uas2.getClassValidAnnotators().size());
- 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());
- assertEquals(MiriamType.HGNC, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(0));
- assertEquals(MiriamType.HGNC_SYMBOL, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(1));
-
- userDao.delete(user2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.model.user.UserClassValidAnnotations;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class UserDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ protected PasswordEncoder passwordEncoder;
+
+ protected Logger logger = Logger.getLogger(UserDaoTest.class.getName());
+ String testLogin = "test_login123";
+ String testEmail = "a@a.pl";
+ String testPasswd = "pwd";
+ String testLogin2 = "test_login_tmp";
+ String testName = "John";
+ String testSurname = "Doe";
+
+ @Before
+ public void setUp() throws Exception {
+ Map<String, Object> params = new HashMap<String, Object>();
+ params.put("login_param", testLogin);
+ params.put("login_param2", testLogin2);
+ dbUtils.executeSqlQuery("delete from user_table where login = :login_param or login = :login_param2", params);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAddUpdateDelete() {
+ try {
+ User user = userDao.getUserByLogin(testLogin);
+ assertNull(user);
+
+ long counter = userDao.getCount();
+
+ user = new User();
+ user.setLogin(testLogin);
+ userDao.add(user);
+
+ long counter2 = userDao.getCount();
+ assertEquals(counter + 1, counter2);
+
+ user.setLogin(testLogin2);
+ userDao.update(user);
+
+ User user2 = userDao.getUserByLogin(testLogin2);
+ assertNotNull(user2);
+
+ userDao.delete(user);
+
+ user2 = userDao.getUserByLogin(testLogin2);
+ assertNull(user2);
+ counter2 = userDao.getCount();
+ assertEquals(counter, counter2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception occured");
+ }
+ }
+
+ @Test
+ public void testAddDeleteAdd() {
+ try {
+ User user = userDao.getUserByLogin(testLogin);
+ assertNull(user);
+
+ long counter = userDao.getCount();
+
+ user = new User();
+ user.setLogin(testLogin);
+ userDao.add(user);
+
+ long counter2 = userDao.getCount();
+ assertEquals(counter + 1, counter2);
+
+ userDao.delete(user);
+
+ User user2 = userDao.getUserByLogin(testLogin);
+ assertNull(user2);
+
+ user2 = new User();
+ user2.setLogin(testLogin);
+ userDao.add(user2);
+
+ assertNotNull(userDao.getUserByLogin(testLogin));
+
+ userDao.delete(user2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByLoginAndPassword() throws Exception {
+ try {
+ User user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(testPasswd));
+ user.setLogin(testLogin);
+ userDao.add(user);
+ User user2 = userDao.getUserByLoginAndPassword(testLogin, testPasswd);
+ assertNotNull(user2);
+ assertEquals(user2.getId(), user.getId());
+ assertEquals(user2.getLogin(), user.getLogin());
+ assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
+ userDao.delete(user);
+ // after we remove it we shouldn't be able to get it
+ User user3 = userDao.getUserByLoginAndPassword(testLogin, testPasswd);
+ assertNull(user3);
+
+ // after we remove it we shouldn't be able to get the removed and modified
+ // object
+ User user4 = userDao.getUserByLoginAndPassword(user2.getLogin(), testPasswd);
+ assertNull(user4);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByLoginAndEmptyPassword() throws Exception {
+ try {
+ User user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(testPasswd));
+ user.setLogin(testLogin);
+ userDao.add(user);
+ User user2 = userDao.getUserByLoginAndPassword(testLogin, null);
+ assertNull(user2);
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByLogin() throws Exception {
+ try {
+ User user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(testPasswd));
+ user.setLogin(testLogin);
+ userDao.add(user);
+ User user2 = userDao.getUserByLogin(testLogin);
+ assertNotNull(user2);
+ assertEquals(user2.getId(), user.getId());
+ assertEquals(user2.getLogin(), user.getLogin());
+ assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
+ user2 = userDao.getUserByLogin(testLogin2);
+ assertNull(user2);
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByEmail() throws Exception {
+ try {
+ User user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(testPasswd));
+ user.setLogin(testLogin);
+ user.setEmail(testEmail);
+ userDao.add(user);
+ User user2 = userDao.getUserByEmail(testEmail);
+ assertNotNull(user2);
+ assertEquals(user2.getId(), user.getId());
+ assertEquals(user2.getLogin(), user.getLogin());
+ assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
+ user2 = userDao.getUserByEmail(testEmail + "sadas");
+ assertNull(user2);
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByNameSurname() throws Exception {
+ try {
+ User user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(testPasswd));
+ user.setLogin(testLogin);
+ user.setEmail(testEmail);
+ user.setName(testName);
+ user.setSurname(testSurname);
+ userDao.add(user);
+ User user2 = userDao.getUserByNameSurname(testName + " " + testSurname);
+ assertNotNull(user2);
+ user2 = userDao.getUserByNameSurname(testName + " " + testSurname);
+ assertNull(user2);
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAll() throws Exception {
+ try {
+ assertTrue(userDao.getAll().size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUserWithAnnotatorSchema() throws Exception {
+ try {
+ User user = new User();
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ uas.setValidateMiriamTypes(true);
+ UserClassAnnotators ca = new UserClassAnnotators();
+ ca.setClassName(Species.class);
+ ca.addAnnotator(String.class);
+ ca.addAnnotator(Integer.class);
+ uas.addClassAnnotator(ca);
+ uas.addClassAnnotator(new UserClassAnnotators(String.class, new ArrayList<String>()));
+ UserClassValidAnnotations cva = new UserClassValidAnnotations();
+ cva.setClassName(Reaction.class);
+ cva.addValidMiriamType(MiriamType.HGNC);
+ cva.addValidMiriamType(MiriamType.HGNC_SYMBOL);
+ uas.addClassValidAnnotations(cva);
+ uas.addClassValidAnnotations(new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>()));
+ uas.addClassValidAnnotations(new UserClassValidAnnotations(Integer.class, new ArrayList<MiriamType>()));
+ user.setAnnotationSchema(uas);
+ userDao.add(user);
+ userDao.evict(user);
+ User user2 = userDao.getById(user.getId());
+ assertNotNull(user2);
+ UserAnnotationSchema uas2 = user2.getAnnotationSchema();
+ assertNotNull(uas2);
+ assertEquals(2, uas2.getClassAnnotators().size());
+ assertEquals(3, uas2.getClassValidAnnotators().size());
+ 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());
+ assertEquals(MiriamType.HGNC, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(0));
+ assertEquals(MiriamType.HGNC_SYMBOL, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(1));
+
+ userDao.delete(user2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
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 b321d7e705..e356ed0072 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/DataFormatter.java
@@ -10,10 +10,10 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
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.ComplexSpecies;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
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 cfb4df2a77..d6a7c2f07b 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
@@ -12,8 +12,8 @@ import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.Alias;
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 0355531f6e..f15afd32f9 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactionComparator.java
@@ -7,11 +7,11 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
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.Species;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomePhysicalEntity;
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 ed6766fed3..30589675b7 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
@@ -3,11 +3,11 @@ package lcsb.mapviewer.reactome.utils.comparators;
import java.util.HashSet;
import java.util.Set;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
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.ComplexSpecies;
import lcsb.mapviewer.reactome.model.ReactomeReferenceEntity;
import lcsb.mapviewer.reactome.model.ReactomeReferenceMolecule;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
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 1b3710a693..5562adf399 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
import lcsb.mapviewer.model.map.layout.alias.DegradedAlias;
-import lcsb.mapviewer.model.map.species.Degraded;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
/**
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 de0b223f9b..9aa4d9a618 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
@@ -2,8 +2,8 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
import lcsb.mapviewer.model.map.layout.alias.DrugAlias;
-import lcsb.mapviewer.model.map.species.Drug;
import lcsb.mapviewer.reactome.model.ReactomeCatalystActivity;
/**
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 c739522629..29897ec770 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
@@ -2,8 +2,8 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.reactome.model.ReactomeDefinedSet;
/**
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 4ece8e2ef0..394d3051ef 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
import lcsb.mapviewer.model.map.layout.alias.GeneAlias;
-import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
import org.apache.log4j.Logger;
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 2e578b812c..d13b28ace0 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
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;
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 b8271459f7..773e5130f2 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
@@ -4,9 +4,9 @@ import java.util.List;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
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;
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 0caa0ffe90..057f32b4e2 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
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;
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 871429bf1d..ccfdc73c01 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
import lcsb.mapviewer.model.map.layout.alias.IonAlias;
-import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
/**
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 2bfcd947f6..fc671bff37 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
@@ -4,9 +4,9 @@ import java.util.List;
import java.util.Set;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Ion;
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;
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 ffa4d378d1..730e0b08f4 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
@@ -5,9 +5,9 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
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 c01ede4f8e..8f3a22a1aa 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
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;
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 20e3484717..0692c746ce 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
@@ -2,9 +2,9 @@ package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
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;
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 e889654e18..746163c93f 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
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;
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 842e30f390..bd267ad0df 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
import lcsb.mapviewer.model.map.layout.alias.SimpleMoleculeAlias;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.reactome.model.ReactomeEntityWithAccessionedSequence;
/**
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 6621dca93a..65f000e50f 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
@@ -4,9 +4,9 @@ import java.util.List;
import java.util.Set;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.SimpleMolecule;
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;
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 96ec98a48a..290fabe72a 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
@@ -6,9 +6,9 @@ import java.util.Map;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.persist.SpringApplicationContext;
import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
import lcsb.mapviewer.reactome.utils.ComparatorException;
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 33d87198fd..0f5e16047a 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
@@ -4,8 +4,8 @@ import java.util.HashSet;
import java.util.Set;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
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;
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 a9485d3662..87e47f4d2d 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
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;
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 6c25ff64cc..13d5a90f66 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
@@ -5,10 +5,10 @@ import java.util.Set;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
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;
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 574e97672c..36d9b30bfd 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
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;
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 c2be3f4611..5ec9507444 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
@@ -5,10 +5,10 @@ import java.util.Set;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
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;
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 d9c0066728..0d8b91ae44 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
@@ -2,8 +2,8 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeGenomeEncodedEntity;
/**
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 4682b93e6b..e65d79b6fb 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
@@ -2,8 +2,8 @@ package lcsb.mapviewer.reactome.utils.comparators;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeOtherEntity;
/**
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 f18d40805c..9a3f909753 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
@@ -5,10 +5,10 @@ import java.util.List;
import java.util.Set;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
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;
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 1c8c70d0e2..997349c0ec 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.model.map.layout.alias.ProteinAlias;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.reactome.model.ReactomeSimpleEntity;
/**
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 3170fe8459..6a4d62232f 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
@@ -1,8 +1,8 @@
package lcsb.mapviewer.reactome.utils.comparators;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
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;
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 efd684fa11..5daaf4ad10 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.reactome.utils.comparators;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Unknown;
import lcsb.mapviewer.model.map.layout.alias.UnknownAlias;
-import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.reactome.model.ReactomeGenomeEncodedEntity;
/**
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 6fdfc8fdaf..7b10d88a22 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/DataMiningService.java
@@ -25,8 +25,8 @@ import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
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 f8fda6c140..33000680fe 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
@@ -17,10 +17,25 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
-import lcsb.mapviewer.model.map.Element;
+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.Degraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Drug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Gene;
+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.Unknown;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.ArtifitialCompartmentAlias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
@@ -32,21 +47,6 @@ 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.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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.fields.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
-import lcsb.mapviewer.model.map.species.fields.RnaRegion;
import lcsb.mapviewer.services.interfaces.IExporterService;
import lcsb.mapviewer.services.utils.data.ExportColumn;
import lcsb.mapviewer.services.utils.data.ExportFileType;
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 66297481ef..97bc8dd86b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -1,976 +1,976 @@
-package lcsb.mapviewer.services.impl;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.mail.MessagingException;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.commands.ColorModelCommand;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.TextFileUtils;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.MapGenerator;
-import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-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.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.Species;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.map.LayoutDao;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.ILogService;
-import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
-import lcsb.mapviewer.services.search.layout.FullLayoutAliasViewFactory;
-import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
-import lcsb.mapviewer.services.search.layout.LightLayoutAliasViewFactory;
-import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
-import lcsb.mapviewer.services.search.layout.LightLayoutReactionViewFactory;
-import lcsb.mapviewer.services.utils.ColorSchemaReader;
-import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
-import lcsb.mapviewer.services.view.LayoutView;
-import lcsb.mapviewer.services.view.LayoutViewFactory;
-
-/**
- * Implementation of the layout service.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class LayoutService implements ILayoutService {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(LayoutService.class);
-
- /**
- * Layout data access object.
- */
- @Autowired
- private LayoutDao layoutDao;
-
- /**
- * Factory object used for creation of {@link LayoutView} elements.
- */
- @Autowired
- private LayoutViewFactory layoutViewFactory;
-
- /**
- * Service that manages and gives access to user information.
- */
- @Autowired
- private IUserService userService;
-
- /**
- * Service used to access logs.
- *
- * @see ILogService
- */
- @Autowired
- private ILogService logService;
-
- /**
- * Service that manages and gives access to configuration parameters.
- */
- @Autowired
- private IConfigurationService configurationService;
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- @Override
- public boolean userCanAddLayout(Model model, User user) {
- // if we don't have privileges to view the object then we cannot add layouts
- if (!userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, model.getProject())) {
- return false;
- }
- long count = getAvailableCustomLayoutsNumber(user);
- return count > 0;
- }
-
- @Override
- public long getAvailableCustomLayoutsNumber(User user) {
- long level = userService.getUserPrivilegeLevel(user, PrivilegeType.CUSTOM_LAYOUTS);
- long layouts = layoutDao.getCountByUser(user);
- return level - layouts;
-
- }
-
- @Override
- public boolean userCanRemoveLayout(LayoutView layout, User user) {
- Layout originalLayout = layoutDao.getById(layout.getIdObject());
- User creator = originalLayout.getCreator();
- Project project = originalLayout.getModel().getProject();
- if (creator == null) {
- return userService.userHasPrivilege(user, PrivilegeType.LAYOUT_MANAGEMENT, project);
- } else {
- return creator.getId().equals(user.getId()) || userService.userHasPrivilege(user, PrivilegeType.LAYOUT_MANAGEMENT, project);
- }
- }
-
- @Override
- public List<LayoutView> getCustomLayouts(Model model, User user) {
- List<LayoutView> result = new ArrayList<LayoutView>();
- if (model == null || user == null) {
- return result;
- }
- List<Layout> layouts = layoutDao.getLayoutsByModel(model);
- for (Layout layout : layouts) {
- if (!layout.isPublicLayout() && layout.getCreator() != null) {
- if (layout.getCreator().getLogin().equals(user.getLogin())) {
- result.add(layoutViewFactory.create(layout));
- } else if (userService.userHasPrivilege(user, PrivilegeType.LAYOUT_VIEW, layout)) {
- result.add(layoutViewFactory.create(layout));
- }
- }
- }
- Collections.sort(result, LayoutView.ID_COMPARATOR);
- return result;
- }
-
- @Override
- public List<LayoutView> getGeneralLayouts(Model model) {
- List<LayoutView> result = new ArrayList<LayoutView>();
- if (model == null) {
- return result;
- }
- List<Layout> layouts = layoutDao.getLayoutsByModel(model);
- for (Layout layout : layouts) {
- if (layout.isPublicLayout()) {
- result.add(layoutViewFactory.create(layout));
- }
- }
- Collections.sort(result, LayoutView.ID_COMPARATOR);
- return result;
- }
-
- @Override
- public void removeLayout(LayoutView layout, final String homeDir) throws IOException {
- final String dir;
- final Layout dbLayout = layoutDao.getById(layout.getIdObject());
- if (homeDir != null) {
- if (dbLayout.getModel().getProject().getDirectory() != null) {
- dir = homeDir + "/../map_images/" + dbLayout.getModel().getProject().getDirectory() + "/";
- } else {
- dir = homeDir + "/../map_images/";
- }
- } else {
- dir = null;
- }
-
- String projectId = dbLayout.getModel().getProject().getProjectId();
- String email = null;
- User user = dbLayout.getCreator();
- if (user != null) {
- email = user.getEmail();
- }
-
- dbLayout.getModel().removeLayout(dbLayout);
- layoutDao.delete(dbLayout);
-
- LogParams params = new LogParams().object(dbLayout).type(LogType.LAYOUT_REMOVED);
- logService.log(params);
-
- if (email != null) {
- try {
- sendSuccesfullRemoveEmail(projectId, layout.getName(), email);
- } catch (MessagingException e) {
- logger.error(e);
- }
- }
- Thread computations = new Thread(new Runnable() {
- @Override
- public void run() {
- MapGenerator generator = new MapGenerator();
- try {
- generator.removeLayout(dbLayout, dir);
- } catch (IOException e) {
- logger.error(e);
- }
-
- }
- });
- computations.start();
- }
-
- @Override
- public void updateLayout(LayoutView layout) {
- Layout dbLayout = layoutDao.getById(layout.getIdObject());
- dbLayout.setTitle(layout.getName());
- dbLayout.setDescription(layout.getDescription());
- if (layout.getCreator().isEmpty()) {
- dbLayout.setCreator(null);
- dbLayout.setPublicLayout(true);
- } else {
- User user = userService.getUserByNameSurname(layout.getCreator());
- dbLayout.setCreator(user);
- dbLayout.setPublicLayout(false);
- }
-
- layoutDao.update(dbLayout);
- }
-
- @Override
- public void addViewPrivilegeToLayout(LayoutView layout, User user) {
- ObjectPrivilege privilege = new ObjectPrivilege();
- privilege.setIdObject(layout.getIdObject());
- privilege.setLevel(1);
- privilege.setType(PrivilegeType.LAYOUT_VIEW);
- privilege.setUser(user);
- userService.setUserPrivilege(user, privilege);
- }
-
- @Override
- public void dropViewPrivilegeFromLayout(LayoutView layout, User user) {
- ObjectPrivilege privilege = new ObjectPrivilege();
- privilege.setIdObject(layout.getIdObject());
- privilege.setLevel(0);
- privilege.setType(PrivilegeType.LAYOUT_VIEW);
- privilege.setUser(user);
- userService.setUserPrivilege(user, privilege);
- }
-
- @Override
- public LayoutView createLayoutWithImages(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException, CommandExecutionException {
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader
- .readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
- final Model colorModel = new CopyCommand(params.getModel()).execute();
- new ColorModelCommand(params.getModel(), schemas).execute();
- final EmailSender sender = new EmailSender(configurationService);
- String[] tmp = params.getDirectory().split("[\\\\/]");
- String simpleDir = tmp[tmp.length - 1];
-
- layoutDao.flush();
-
- boolean customSession = false;
- if (params.isAsync()) {
- customSession = !dbUtils.isCustomSessionForCurrentThread();
- if (customSession) {
- dbUtils.createSessionForCurrentThread();
- }
- }
- final Map<Model, Integer> layoutIdByModel = new HashMap<Model, Integer>();
-
- Layout topLayout = new Layout(params.getName(), simpleDir, false);
- if (params.getUser() == null) {
- topLayout.setPublicLayout(true);
- } else {
- topLayout.setPublicLayout(false);
- }
- topLayout.setStatus(LayoutStatus.NA);
- topLayout.setProgress(0.0);
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
- fileEntry.setOriginalFileName(params.getLayoutFileName());
- topLayout.setInputData(fileEntry);
- topLayout.setDescription(params.getDescription());
- params.getModel().addLayout(topLayout);
- topLayout.setCreator(params.getUser());
- layoutDao.add(topLayout);
- topLayout.setDirectory(simpleDir + topLayout.getId());
-
- layoutDao.update(topLayout);
-
- layoutIdByModel.put(colorModel, topLayout.getId());
-
- for (ModelSubmodelConnection connection : params.getModel().getSubmodelConnections()) {
- Layout layout = new Layout(params.getName(), simpleDir, false);
- layout.setStatus(LayoutStatus.NA);
- layout.setProgress(0.0);
- connection.getSubmodel().getModel().addLayout(layout);
- layout.setCreator(params.getUser());
- layout.setPublicLayout(false);
- topLayout.addLayout(layout);
- layoutDao.add(layout);
- layout.setDirectory(simpleDir + layout.getId());
-
- layoutDao.update(layout);
-
- layoutIdByModel.put(colorModel.getSubmodelByConnectionName(connection.getName()), layout.getId());
- }
-
- if (params.isAsync()) {
- if (customSession) {
- dbUtils.closeSessionForCurrentThread();
- } else {
- layoutDao.commit();
- }
- }
- final int layoutId = layoutIdByModel.get(colorModel);
-
- Thread computations = new Thread(new Runnable() {
- @Override
- public void run() {
- if (params.isAsync()) {
- // open transaction for this thread
- dbUtils.createSessionForCurrentThread();
- }
-
- try {
- MapGenerator generator = new MapGenerator();
- final int models = layoutIdByModel.entrySet().size();
-
- int count = 0;
- for (Model m : layoutIdByModel.keySet()) {
- final int counted = count;
- int id = layoutIdByModel.get(m);
- MapGeneratorParams imgParams = generator.new MapGeneratorParams().model(m).directory(params.getDirectory() + id).updater(new IProgressUpdater() {
- private int lastProgress = -1;
-
- @Override
- public void setProgress(double progress) {
- progress = progress / ((double) models) + ((double) counted * MAX_PROGRESS) / ((double) models);
- if (((int) progress) != lastProgress) {
- Layout layout = layoutDao.getById(layoutId);
- lastProgress = (int) progress;
- layout.setProgress(progress);
- layout.setStatus(LayoutStatus.GENERATING);
- layoutDao.update(layout);
- if (params.isAsync()) {
- layoutDao.commit();
- }
- }
- }
- });
- generator.generateMapImages(imgParams);
- count++;
- }
- Layout layout = layoutDao.getById(layoutId);
- layout.setProgress(IProgressUpdater.MAX_PROGRESS);
- layout.setStatus(LayoutStatus.OK);
- layoutDao.update(layout);
- if (params.isAsync()) {
- layoutDao.commit();
- }
-
- try {
- sendSuccessfullGenerationEmail(params, schemas);
- } catch (MessagingException e) {
- logger.error("Problem with sending email", e);
- }
- logService.log(new LogParams().object(layout).description("Created successfully.").type(LogType.LAYOUT_CREATED));
- } catch (Exception e) {
- logger.error("Problem with creating layout", e);
-
- Layout layout = layoutDao.getById(layoutId);
- layout.setProgress(IProgressUpdater.MAX_PROGRESS);
- layout.setStatus(LayoutStatus.FAILURE);
- layoutDao.update(layout);
-
- try {
- sender.sendEmail(
- "MapViewer status", "There was a problem with generating layout " + params.getName() + ". Contact administrator to solve this issue.",
- params.getUser());
- } catch (MessagingException e1) {
- logger.error("Problem with sending email", e1);
- }
- logService.log(new LogParams().object(layout).description("Problem during creation.").type(LogType.LAYOUT_CREATED));
- }
- if (params.isAsync()) {
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- }
- }
- });
-
- if (params.isAsync()) {
- computations.start();
- } else {
- computations.run();
- }
- return layoutViewFactory.create(topLayout);
- }
-
- @Override
- public LayoutView createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader
- .readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
-
- // check if we can color our model using this schema,
- // if not then exception will be thrown and passed up
- try {
- new ColorModelCommand(params.getModel(), schemas).execute();
- } catch (CommandExecutionException e) {
- throw new InvalidColorSchemaException(e);
- }
-
- String[] tmp = params.getDirectory().split("[\\\\/]");
- String simpleDir = tmp[tmp.length - 1];
-
- layoutDao.flush();
-
- boolean customSession = false;
-
- if (params.isAsync()) {
- customSession = !dbUtils.isCustomSessionForCurrentThread();
- if (customSession) {
- dbUtils.createSessionForCurrentThread();
- }
- }
-
- Layout topLayout = new Layout(params.getName(), simpleDir, false);
- if (params.getUser() == null) {
- topLayout.setPublicLayout(true);
- } else {
- topLayout.setPublicLayout(false);
- }
- topLayout.setStatus(LayoutStatus.OK);
- topLayout.setProgress(0.0);
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
- fileEntry.setOriginalFileName(params.getLayoutFileName());
- topLayout.setInputData(fileEntry);
- topLayout.setDescription(params.getDescription());
- params.getModel().addLayout(topLayout);
- topLayout.setCreator(params.getUser());
- layoutDao.add(topLayout);
- topLayout.setDirectory(simpleDir + topLayout.getId());
-
- layoutDao.update(topLayout);
-
- for (ModelSubmodelConnection connection : params.getModel().getSubmodelConnections()) {
- Layout layout = new Layout(params.getName(), simpleDir, false);
- layout.setStatus(LayoutStatus.OK);
- layout.setProgress(0.0);
- connection.getSubmodel().getModel().addLayout(layout);
- layout.setCreator(params.getUser());
- layout.setPublicLayout(false);
- topLayout.addLayout(layout);
- layoutDao.add(layout);
- layout.setDirectory(simpleDir + layout.getId());
-
- layoutDao.update(layout);
- }
-
- if (params.isAsync()) {
- if (customSession) {
- dbUtils.closeSessionForCurrentThread();
- } else {
- layoutDao.commit();
- }
- }
- Thread computations = new Thread(new Runnable() {
- @Override
- public void run() {
- if (params.isAsync()) {
- // open transaction for this thread
- dbUtils.createSessionForCurrentThread();
- }
-
- try {
- sendSuccessfullGenerationEmail(params, schemas);
- } catch (MessagingException e) {
- logger.error("Problem with sending email", e);
- }
-
- if (params.isAsync()) {
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- }
- }
- });
-
- LogParams logParams = new LogParams().object(topLayout).description("Created successfully.").type(LogType.LAYOUT_CREATED);
- logService.log(logParams);
-
- if (params.isAsync()) {
- computations.start();
- } else {
- computations.run();
- }
- return layoutViewFactory.create(topLayout);
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the dbUtils
- * @see #dbUtils
- */
- public DbUtils getDbUtils() {
- return dbUtils;
- }
-
- /**
- * @param dbUtils
- * the dbUtils to set
- * @see #dbUtils
- */
- public void setDbUtils(DbUtils dbUtils) {
- this.dbUtils = dbUtils;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- @Override
- public LayoutView getLayoutByName(Model model, String name) {
- if (model == null) {
- return null;
- }
- Layout layout = layoutDao.getLayoutByName(model, name);
- if (layout != null) {
- return layoutViewFactory.create(layout);
- } else {
- return null;
- }
- }
-
- /**
- * Sends notification email that layout was removed.
- *
- * @param projectId
- * identifier of the project
- * @param layoutName
- * name of the layout
- * @param email
- * otification email
- * @throws MessagingException
- * thrown when there is a problem with sending email
- */
- protected void sendSuccesfullRemoveEmail(String projectId, String layoutName, String email) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("Layout " + layoutName + " in map " + projectId + " was successfully removed.<br/>");
- emailSender.sendEmail("MapViewer notification", content.toString(), email);
- }
-
- /**
- * Sends notification email that layout was generated.
- *
- * @param params
- * list of {@link CreateLayoutParams params} used for layout creation
- * @param schemas
- * set of schemas used in coloring
- * @throws MessagingException
- * thrown when there is a problem with sending email
- */
- protected void sendSuccessfullGenerationEmail(final CreateLayoutParams params, final Collection<ColorSchema> schemas) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("Layout " + params.getName() + " generated successfully.\n");
- content.append("Result of coloring:<br/>");
-
- String table = prepareTableResult(schemas, new ColorSchemaReader());
- content.append(table);
- if (params.getUser() != null) { // send email to a user who owns the layout
- emailSender.sendEmail("MapViewer notification", content.toString(), params.getUser());
-
- // send email to the model owner
- String email = params.getModel().getNotifyEmail();
- if (email != null && !email.equals(params.getUser().getEmail())) {
- content = new StringBuilder("");
- String username = "UNKNOWN";
- if (params.getUser() != null) {
- username = params.getUser().getLogin();
- }
- content.append("User " + username + " created layout in " + params.getModel().getProject().getProjectId() + " map.");
-
- emailSender.sendEmail("MapViewer notification", content.toString(), email);
- }
- } else if (params.getModel().getNotifyEmail() != null) {
- // if nobody owns the layout then send it to the model owner
- emailSender.sendEmail("MapViewer notification", content.toString(), params.getModel().getNotifyEmail());
- }
- }
-
- /**
- * Prepares table with statistics about coloring.
- *
- * @param schemas
- * schemas that were used for coloring
- * @param scr
- * interface that returns list of columns that should be printed
- * @return table with statistics about coloring
- */
- protected String prepareTableResult(Collection<ColorSchema> schemas, ColorSchemaReader scr) {
- StringBuilder sb = new StringBuilder("");
-
- Collection<ColorSchemaColumn> columns = scr.getSetColorSchemaColumns(schemas);
-
- for (ColorSchemaColumn column : ColorSchemaColumn.values()) {
- if (columns.contains(column)) {
- sb.append(column.getTitle() + "\t");
- }
- }
- sb.append("matches<br/>\n");
-
- for (ColorSchema originalSchema : schemas) {
- for (ColorSchema schema : splitColorSchema(originalSchema)) {
- sb.append(prepareTableRow(columns, schema));
- }
- }
-
- return sb.toString();
- }
-
- /**
- * {@link ColorSchema} sometimes contains merged value from few rows. This
- * method split single {@link ColorSchema} object to simple flat objects that
- * can be serialiazed in a simple tab separated file.
- *
- * @param originalSchema
- * original {@link ColorSchema} objcet that we want to spli into flat
- * objects
- * @return {@link List} of flat schema objects obtained from input
- */
- private List<ColorSchema> splitColorSchema(ColorSchema originalSchema) {
- List<ColorSchema> result = new ArrayList<>();
- if (originalSchema instanceof GenericColorSchema) {
- result.add(originalSchema);
- } else if (originalSchema instanceof GeneVariationColorSchema) {
- for (GeneVariation gv : ((GeneVariationColorSchema) originalSchema).getGeneVariations()) {
- GeneVariationColorSchema copy = (GeneVariationColorSchema) originalSchema.copy();
- copy.getGeneVariations().clear();
- copy.addGeneVariation(gv.copy());
- result.add(copy);
- }
- } else {
- throw new InvalidArgumentException("Unknown class type: " + originalSchema.getClass());
- }
- return result;
- }
-
- /**
- * Prepares tab separated {@link String} represenation of {@link ColorSchema}.
- *
- * @param columns
- * columns that should be outputed in the result String
- * @param schema
- * input ColorSchema that is going to be transformed into String
- * representation
- * @return tab separated {@link String} represenation of {@link ColorSchema}
- */
- protected String prepareTableRow(Collection<ColorSchemaColumn> columns, ColorSchema schema) {
- StringBuilder sb = new StringBuilder();
- for (ColorSchemaColumn column : ColorSchemaColumn.values()) {
- if (columns.contains(column)) {
- if (schema instanceof GenericColorSchema) {
- sb.append(prepareTableCellForGenericSchema((GenericColorSchema) schema, column));
- } else if (schema instanceof GeneVariationColorSchema) {
- sb.append(prepareTableCellForGeneVariationSchema((GeneVariationColorSchema) schema, column));
- } else {
- throw new InvalidArgumentException("Unknown schema type: " + schema.getClass());
- }
- }
- }
- sb.append(schema.getMatches() + "<br/>\n");
- return sb.toString();
- }
-
- /**
- * Returns String representing data of {@link GenericColorSchema} that should
- * appear in a given {@link ColorSchemaColumn}.
- *
- * @param schema
- * object for which data will be returned
- * @param column
- * column for which data should be returned
- * @return {@link String} representing data of {@link GenericColorSchema} that
- * should appear in a given {@link ColorSchemaColumn}
- */
- protected String prepareTableCellForGenericSchema(GenericColorSchema schema, ColorSchemaColumn column) {
- StringBuilder sb = new StringBuilder();
- if (column.equals(ColorSchemaColumn.COLOR)) {
- if (schema.getColor() != null) {
- sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.NAME)) {
- sb.append(schema.getName() + "\t");
- } else if (column.equals(ColorSchemaColumn.VALUE)) {
- sb.append(schema.getValue() + "\t");
- } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
- for (String str : schema.getCompartments()) {
- sb.append(str + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.TYPE)) {
- for (Class<? extends Species> str : schema.getTypes()) {
- sb.append(str.getSimpleName() + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().trim().equals("")) {
- sb.append(pair.getLeft().getCommonName() + ": " + pair.getRight() + ", ");
- }
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
- sb.append(schema.getReactionIdentifier() + "\t");
- } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
- sb.append(schema.getLineWidth() + "\t");
- } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
- sb.append(schema.getReverseReaction() + "\t");
- } else if (column.equals(ColorSchemaColumn.POSITION)) {
- sb.append(schema.getReverseReaction() + "\t");
- } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
- sb.append(schema.getDescription() + "\t");
- } else {
- throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
- }
- return sb.toString();
- }
-
- /**
- * Returns String representing data of {@link GeneVariationColorSchema} that
- * should appear in a given {@link ColorSchemaColumn}.
- *
- * @param schema
- * object for which data will be returned
- * @param column
- * column for which data should be returned
- * @return {@link String} representing data of
- * {@link GeneVariationColorSchema} that should appear in a given
- * {@link ColorSchemaColumn}
- */
- protected String prepareTableCellForGeneVariationSchema(GeneVariationColorSchema schema, ColorSchemaColumn column) {
- StringBuilder sb = new StringBuilder();
- if (column.equals(ColorSchemaColumn.COLOR)) {
- if (schema.getColor() != null) {
- sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.NAME)) {
- sb.append(schema.getName() + "\t");
- } else if (column.equals(ColorSchemaColumn.VALUE)) {
- sb.append(schema.getValue() + "\t");
- } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
- for (String str : schema.getCompartments()) {
- sb.append(str + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.TYPE)) {
- for (Class<? extends Species> str : schema.getTypes()) {
- sb.append(str.getSimpleName() + ", ");
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().trim().equals("")) {
- sb.append(pair.getLeft().getCommonName() + ": " + pair.getRight() + ", ");
- }
- }
- sb.append("\t");
- } else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
- sb.append(schema.getReactionIdentifier() + "\t");
- } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
- sb.append(schema.getLineWidth() + "\t");
- } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
- sb.append(schema.getReverseReaction() + "\t");
- } else if (column.equals(ColorSchemaColumn.POSITION)) {
- sb.append(schema.getGeneVariations().get(0).getPosition() + "\t");
- } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
- sb.append(schema.getDescription() + "\t");
- } else if (column.equals(ColorSchemaColumn.ORIGINAL_DNA)) {
- sb.append(schema.getGeneVariations().get(0).getOriginalDna() + "\t");
- } else if (column.equals(ColorSchemaColumn.ALTERNATIVE_DNA)) {
- sb.append(schema.getGeneVariations().get(0).getModifiedDna() + "\t");
- } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_TYPE)) {
- sb.append(schema.getGeneVariations().get(0).getReferenceGenomeType() + "\t");
- } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_VERSION)) {
- sb.append(schema.getGeneVariations().get(0).getReferenceGenomeVersion() + "\t");
- } else if (column.equals(ColorSchemaColumn.CONTIG)) {
- sb.append(schema.getGeneVariations().get(0).getContig() + "\t");
- } else if (column.equals(ColorSchemaColumn.REFERENCES)) {
- MiriamConnector mc = new MiriamConnector();
- for (MiriamData md : schema.getGeneVariations().get(0).getReferences()) {
- sb.append(mc.miriamDataToUri(md) + "\t");
- }
- } else {
- throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
- }
- return sb.toString();
- }
-
- @Override
- public byte[] getInputDataForLayout(LayoutView layoutView) {
- return getInputDataForLayout(layoutView.getIdObject());
- }
-
- /**
- * Returns byte array containing data from original input file that was used
- * to generate the layout.
- *
- * @param layoutId
- * identifier of layout for which we want to retrieve original file
- * data
- * @return original data file for given layout, if such file is not stored in
- * database (compatibility reasons) then null is returned
- */
- private byte[] getInputDataForLayout(int layoutId) {
- Layout layout = layoutDao.getById(layoutId);
- if (layout == null) {
- return null;
- } else {
- if (layout.getInputData() != null) {
- return layout.getInputData().getFileContent();
- } else {
- return null;
- }
- }
- }
-
- @Override
- public List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId) {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
- 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())));
- }
- }
- return result;
- } catch (InvalidColorSchemaException e) {
- throw new InvalidStateException(e);
- } catch (IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId) {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
- LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
- List<LightLayoutReactionView> result = new ArrayList<>();
- for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
- if (entry.getKey() instanceof Reaction) {
- result.add(factory.create(new Pair<Reaction, ColorSchema>((Reaction) entry.getKey(), entry.getValue())));
- }
- }
- return result;
- } catch (InvalidColorSchemaException e) {
- throw new InvalidStateException(e);
- } catch (IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId) {
- try {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
- return command.getModifiedElements();
- } catch (InvalidColorSchemaException e) {
- throw new InvalidStateException(e);
- } catch (IOException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers, int layoutId) {
- try {
- Set<Integer> ids = new HashSet<>();
- for (Pair<Integer, Integer> pair : identifiers) {
- ids.add(pair.getRight());
- }
-
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
- ColorModelCommand command = new ColorModelCommand(model, schemas);
- FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
- List<FullLayoutAliasView> result = new ArrayList<>();
-
- // 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 (ids.contains(alias.getId())) {
- result.add(factory.create(new Pair<Alias, ColorSchema>(alias, entry.getValue())));
- }
- }
- }
- return result;
- } catch (InvalidColorSchemaException e) {
- throw new InvalidStateException(e);
- } catch (IOException e) {
- throw new InvalidStateException(e);
- }
- }
-}
+package lcsb.mapviewer.services.impl;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.mail.MessagingException;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.commands.ColorModelCommand;
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.MapGenerator;
+import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.log.LogType;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+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.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.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.map.LayoutDao;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.interfaces.ILogService;
+import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.layout.FullLayoutAliasView;
+import lcsb.mapviewer.services.search.layout.FullLayoutAliasViewFactory;
+import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
+import lcsb.mapviewer.services.search.layout.LightLayoutAliasViewFactory;
+import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
+import lcsb.mapviewer.services.search.layout.LightLayoutReactionViewFactory;
+import lcsb.mapviewer.services.utils.ColorSchemaReader;
+import lcsb.mapviewer.services.utils.EmailSender;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
+import lcsb.mapviewer.services.view.LayoutView;
+import lcsb.mapviewer.services.view.LayoutViewFactory;
+
+/**
+ * Implementation of the layout service.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class LayoutService implements ILayoutService {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(LayoutService.class);
+
+ /**
+ * Layout data access object.
+ */
+ @Autowired
+ private LayoutDao layoutDao;
+
+ /**
+ * Factory object used for creation of {@link LayoutView} elements.
+ */
+ @Autowired
+ private LayoutViewFactory layoutViewFactory;
+
+ /**
+ * Service that manages and gives access to user information.
+ */
+ @Autowired
+ private IUserService userService;
+
+ /**
+ * Service used to access logs.
+ *
+ * @see ILogService
+ */
+ @Autowired
+ private ILogService logService;
+
+ /**
+ * Service that manages and gives access to configuration parameters.
+ */
+ @Autowired
+ private IConfigurationService configurationService;
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ @Override
+ public boolean userCanAddLayout(Model model, User user) {
+ // if we don't have privileges to view the object then we cannot add layouts
+ if (!userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, model.getProject())) {
+ return false;
+ }
+ long count = getAvailableCustomLayoutsNumber(user);
+ return count > 0;
+ }
+
+ @Override
+ public long getAvailableCustomLayoutsNumber(User user) {
+ long level = userService.getUserPrivilegeLevel(user, PrivilegeType.CUSTOM_LAYOUTS);
+ long layouts = layoutDao.getCountByUser(user);
+ return level - layouts;
+
+ }
+
+ @Override
+ public boolean userCanRemoveLayout(LayoutView layout, User user) {
+ Layout originalLayout = layoutDao.getById(layout.getIdObject());
+ User creator = originalLayout.getCreator();
+ Project project = originalLayout.getModel().getProject();
+ if (creator == null) {
+ return userService.userHasPrivilege(user, PrivilegeType.LAYOUT_MANAGEMENT, project);
+ } else {
+ return creator.getId().equals(user.getId()) || userService.userHasPrivilege(user, PrivilegeType.LAYOUT_MANAGEMENT, project);
+ }
+ }
+
+ @Override
+ public List<LayoutView> getCustomLayouts(Model model, User user) {
+ List<LayoutView> result = new ArrayList<LayoutView>();
+ if (model == null || user == null) {
+ return result;
+ }
+ List<Layout> layouts = layoutDao.getLayoutsByModel(model);
+ for (Layout layout : layouts) {
+ if (!layout.isPublicLayout() && layout.getCreator() != null) {
+ if (layout.getCreator().getLogin().equals(user.getLogin())) {
+ result.add(layoutViewFactory.create(layout));
+ } else if (userService.userHasPrivilege(user, PrivilegeType.LAYOUT_VIEW, layout)) {
+ result.add(layoutViewFactory.create(layout));
+ }
+ }
+ }
+ Collections.sort(result, LayoutView.ID_COMPARATOR);
+ return result;
+ }
+
+ @Override
+ public List<LayoutView> getGeneralLayouts(Model model) {
+ List<LayoutView> result = new ArrayList<LayoutView>();
+ if (model == null) {
+ return result;
+ }
+ List<Layout> layouts = layoutDao.getLayoutsByModel(model);
+ for (Layout layout : layouts) {
+ if (layout.isPublicLayout()) {
+ result.add(layoutViewFactory.create(layout));
+ }
+ }
+ Collections.sort(result, LayoutView.ID_COMPARATOR);
+ return result;
+ }
+
+ @Override
+ public void removeLayout(LayoutView layout, final String homeDir) throws IOException {
+ final String dir;
+ final Layout dbLayout = layoutDao.getById(layout.getIdObject());
+ if (homeDir != null) {
+ if (dbLayout.getModel().getProject().getDirectory() != null) {
+ dir = homeDir + "/../map_images/" + dbLayout.getModel().getProject().getDirectory() + "/";
+ } else {
+ dir = homeDir + "/../map_images/";
+ }
+ } else {
+ dir = null;
+ }
+
+ String projectId = dbLayout.getModel().getProject().getProjectId();
+ String email = null;
+ User user = dbLayout.getCreator();
+ if (user != null) {
+ email = user.getEmail();
+ }
+
+ dbLayout.getModel().removeLayout(dbLayout);
+ layoutDao.delete(dbLayout);
+
+ LogParams params = new LogParams().object(dbLayout).type(LogType.LAYOUT_REMOVED);
+ logService.log(params);
+
+ if (email != null) {
+ try {
+ sendSuccesfullRemoveEmail(projectId, layout.getName(), email);
+ } catch (MessagingException e) {
+ logger.error(e);
+ }
+ }
+ Thread computations = new Thread(new Runnable() {
+ @Override
+ public void run() {
+ MapGenerator generator = new MapGenerator();
+ try {
+ generator.removeLayout(dbLayout, dir);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+
+ }
+ });
+ computations.start();
+ }
+
+ @Override
+ public void updateLayout(LayoutView layout) {
+ Layout dbLayout = layoutDao.getById(layout.getIdObject());
+ dbLayout.setTitle(layout.getName());
+ dbLayout.setDescription(layout.getDescription());
+ if (layout.getCreator().isEmpty()) {
+ dbLayout.setCreator(null);
+ dbLayout.setPublicLayout(true);
+ } else {
+ User user = userService.getUserByNameSurname(layout.getCreator());
+ dbLayout.setCreator(user);
+ dbLayout.setPublicLayout(false);
+ }
+
+ layoutDao.update(dbLayout);
+ }
+
+ @Override
+ public void addViewPrivilegeToLayout(LayoutView layout, User user) {
+ ObjectPrivilege privilege = new ObjectPrivilege();
+ privilege.setIdObject(layout.getIdObject());
+ privilege.setLevel(1);
+ privilege.setType(PrivilegeType.LAYOUT_VIEW);
+ privilege.setUser(user);
+ userService.setUserPrivilege(user, privilege);
+ }
+
+ @Override
+ public void dropViewPrivilegeFromLayout(LayoutView layout, User user) {
+ ObjectPrivilege privilege = new ObjectPrivilege();
+ privilege.setIdObject(layout.getIdObject());
+ privilege.setLevel(0);
+ privilege.setType(PrivilegeType.LAYOUT_VIEW);
+ privilege.setUser(user);
+ userService.setUserPrivilege(user, privilege);
+ }
+
+ @Override
+ public LayoutView createLayoutWithImages(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException, CommandExecutionException {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader
+ .readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
+ final Model colorModel = new CopyCommand(params.getModel()).execute();
+ new ColorModelCommand(params.getModel(), schemas).execute();
+ final EmailSender sender = new EmailSender(configurationService);
+ String[] tmp = params.getDirectory().split("[\\\\/]");
+ String simpleDir = tmp[tmp.length - 1];
+
+ layoutDao.flush();
+
+ boolean customSession = false;
+ if (params.isAsync()) {
+ customSession = !dbUtils.isCustomSessionForCurrentThread();
+ if (customSession) {
+ dbUtils.createSessionForCurrentThread();
+ }
+ }
+ final Map<Model, Integer> layoutIdByModel = new HashMap<Model, Integer>();
+
+ Layout topLayout = new Layout(params.getName(), simpleDir, false);
+ if (params.getUser() == null) {
+ topLayout.setPublicLayout(true);
+ } else {
+ topLayout.setPublicLayout(false);
+ }
+ topLayout.setStatus(LayoutStatus.NA);
+ topLayout.setProgress(0.0);
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
+ fileEntry.setOriginalFileName(params.getLayoutFileName());
+ topLayout.setInputData(fileEntry);
+ topLayout.setDescription(params.getDescription());
+ params.getModel().addLayout(topLayout);
+ topLayout.setCreator(params.getUser());
+ layoutDao.add(topLayout);
+ topLayout.setDirectory(simpleDir + topLayout.getId());
+
+ layoutDao.update(topLayout);
+
+ layoutIdByModel.put(colorModel, topLayout.getId());
+
+ for (ModelSubmodelConnection connection : params.getModel().getSubmodelConnections()) {
+ Layout layout = new Layout(params.getName(), simpleDir, false);
+ layout.setStatus(LayoutStatus.NA);
+ layout.setProgress(0.0);
+ connection.getSubmodel().getModel().addLayout(layout);
+ layout.setCreator(params.getUser());
+ layout.setPublicLayout(false);
+ topLayout.addLayout(layout);
+ layoutDao.add(layout);
+ layout.setDirectory(simpleDir + layout.getId());
+
+ layoutDao.update(layout);
+
+ layoutIdByModel.put(colorModel.getSubmodelByConnectionName(connection.getName()), layout.getId());
+ }
+
+ if (params.isAsync()) {
+ if (customSession) {
+ dbUtils.closeSessionForCurrentThread();
+ } else {
+ layoutDao.commit();
+ }
+ }
+ final int layoutId = layoutIdByModel.get(colorModel);
+
+ Thread computations = new Thread(new Runnable() {
+ @Override
+ public void run() {
+ if (params.isAsync()) {
+ // open transaction for this thread
+ dbUtils.createSessionForCurrentThread();
+ }
+
+ try {
+ MapGenerator generator = new MapGenerator();
+ final int models = layoutIdByModel.entrySet().size();
+
+ int count = 0;
+ for (Model m : layoutIdByModel.keySet()) {
+ final int counted = count;
+ int id = layoutIdByModel.get(m);
+ MapGeneratorParams imgParams = generator.new MapGeneratorParams().model(m).directory(params.getDirectory() + id).updater(new IProgressUpdater() {
+ private int lastProgress = -1;
+
+ @Override
+ public void setProgress(double progress) {
+ progress = progress / ((double) models) + ((double) counted * MAX_PROGRESS) / ((double) models);
+ if (((int) progress) != lastProgress) {
+ Layout layout = layoutDao.getById(layoutId);
+ lastProgress = (int) progress;
+ layout.setProgress(progress);
+ layout.setStatus(LayoutStatus.GENERATING);
+ layoutDao.update(layout);
+ if (params.isAsync()) {
+ layoutDao.commit();
+ }
+ }
+ }
+ });
+ generator.generateMapImages(imgParams);
+ count++;
+ }
+ Layout layout = layoutDao.getById(layoutId);
+ layout.setProgress(IProgressUpdater.MAX_PROGRESS);
+ layout.setStatus(LayoutStatus.OK);
+ layoutDao.update(layout);
+ if (params.isAsync()) {
+ layoutDao.commit();
+ }
+
+ try {
+ sendSuccessfullGenerationEmail(params, schemas);
+ } catch (MessagingException e) {
+ logger.error("Problem with sending email", e);
+ }
+ logService.log(new LogParams().object(layout).description("Created successfully.").type(LogType.LAYOUT_CREATED));
+ } catch (Exception e) {
+ logger.error("Problem with creating layout", e);
+
+ Layout layout = layoutDao.getById(layoutId);
+ layout.setProgress(IProgressUpdater.MAX_PROGRESS);
+ layout.setStatus(LayoutStatus.FAILURE);
+ layoutDao.update(layout);
+
+ try {
+ sender.sendEmail(
+ "MapViewer status", "There was a problem with generating layout " + params.getName() + ". Contact administrator to solve this issue.",
+ params.getUser());
+ } catch (MessagingException e1) {
+ logger.error("Problem with sending email", e1);
+ }
+ logService.log(new LogParams().object(layout).description("Problem during creation.").type(LogType.LAYOUT_CREATED));
+ }
+ if (params.isAsync()) {
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+ });
+
+ if (params.isAsync()) {
+ computations.start();
+ } else {
+ computations.run();
+ }
+ return layoutViewFactory.create(topLayout);
+ }
+
+ @Override
+ public LayoutView createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader
+ .readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
+
+ // check if we can color our model using this schema,
+ // if not then exception will be thrown and passed up
+ try {
+ new ColorModelCommand(params.getModel(), schemas).execute();
+ } catch (CommandExecutionException e) {
+ throw new InvalidColorSchemaException(e);
+ }
+
+ String[] tmp = params.getDirectory().split("[\\\\/]");
+ String simpleDir = tmp[tmp.length - 1];
+
+ layoutDao.flush();
+
+ boolean customSession = false;
+
+ if (params.isAsync()) {
+ customSession = !dbUtils.isCustomSessionForCurrentThread();
+ if (customSession) {
+ dbUtils.createSessionForCurrentThread();
+ }
+ }
+
+ Layout topLayout = new Layout(params.getName(), simpleDir, false);
+ if (params.getUser() == null) {
+ topLayout.setPublicLayout(true);
+ } else {
+ topLayout.setPublicLayout(false);
+ }
+ topLayout.setStatus(LayoutStatus.OK);
+ topLayout.setProgress(0.0);
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(IOUtils.toByteArray(params.getColorInputStream()));
+ fileEntry.setOriginalFileName(params.getLayoutFileName());
+ topLayout.setInputData(fileEntry);
+ topLayout.setDescription(params.getDescription());
+ params.getModel().addLayout(topLayout);
+ topLayout.setCreator(params.getUser());
+ layoutDao.add(topLayout);
+ topLayout.setDirectory(simpleDir + topLayout.getId());
+
+ layoutDao.update(topLayout);
+
+ for (ModelSubmodelConnection connection : params.getModel().getSubmodelConnections()) {
+ Layout layout = new Layout(params.getName(), simpleDir, false);
+ layout.setStatus(LayoutStatus.OK);
+ layout.setProgress(0.0);
+ connection.getSubmodel().getModel().addLayout(layout);
+ layout.setCreator(params.getUser());
+ layout.setPublicLayout(false);
+ topLayout.addLayout(layout);
+ layoutDao.add(layout);
+ layout.setDirectory(simpleDir + layout.getId());
+
+ layoutDao.update(layout);
+ }
+
+ if (params.isAsync()) {
+ if (customSession) {
+ dbUtils.closeSessionForCurrentThread();
+ } else {
+ layoutDao.commit();
+ }
+ }
+ Thread computations = new Thread(new Runnable() {
+ @Override
+ public void run() {
+ if (params.isAsync()) {
+ // open transaction for this thread
+ dbUtils.createSessionForCurrentThread();
+ }
+
+ try {
+ sendSuccessfullGenerationEmail(params, schemas);
+ } catch (MessagingException e) {
+ logger.error("Problem with sending email", e);
+ }
+
+ if (params.isAsync()) {
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+ });
+
+ LogParams logParams = new LogParams().object(topLayout).description("Created successfully.").type(LogType.LAYOUT_CREATED);
+ logService.log(logParams);
+
+ if (params.isAsync()) {
+ computations.start();
+ } else {
+ computations.run();
+ }
+ return layoutViewFactory.create(topLayout);
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ /**
+ * @return the dbUtils
+ * @see #dbUtils
+ */
+ public DbUtils getDbUtils() {
+ return dbUtils;
+ }
+
+ /**
+ * @param dbUtils
+ * the dbUtils to set
+ * @see #dbUtils
+ */
+ public void setDbUtils(DbUtils dbUtils) {
+ this.dbUtils = dbUtils;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ @Override
+ public LayoutView getLayoutByName(Model model, String name) {
+ if (model == null) {
+ return null;
+ }
+ Layout layout = layoutDao.getLayoutByName(model, name);
+ if (layout != null) {
+ return layoutViewFactory.create(layout);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Sends notification email that layout was removed.
+ *
+ * @param projectId
+ * identifier of the project
+ * @param layoutName
+ * name of the layout
+ * @param email
+ * otification email
+ * @throws MessagingException
+ * thrown when there is a problem with sending email
+ */
+ protected void sendSuccesfullRemoveEmail(String projectId, String layoutName, String email) throws MessagingException {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("Layout " + layoutName + " in map " + projectId + " was successfully removed.<br/>");
+ emailSender.sendEmail("MapViewer notification", content.toString(), email);
+ }
+
+ /**
+ * Sends notification email that layout was generated.
+ *
+ * @param params
+ * list of {@link CreateLayoutParams params} used for layout creation
+ * @param schemas
+ * set of schemas used in coloring
+ * @throws MessagingException
+ * thrown when there is a problem with sending email
+ */
+ protected void sendSuccessfullGenerationEmail(final CreateLayoutParams params, final Collection<ColorSchema> schemas) throws MessagingException {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("Layout " + params.getName() + " generated successfully.\n");
+ content.append("Result of coloring:<br/>");
+
+ String table = prepareTableResult(schemas, new ColorSchemaReader());
+ content.append(table);
+ if (params.getUser() != null) { // send email to a user who owns the layout
+ emailSender.sendEmail("MapViewer notification", content.toString(), params.getUser());
+
+ // send email to the model owner
+ String email = params.getModel().getNotifyEmail();
+ if (email != null && !email.equals(params.getUser().getEmail())) {
+ content = new StringBuilder("");
+ String username = "UNKNOWN";
+ if (params.getUser() != null) {
+ username = params.getUser().getLogin();
+ }
+ content.append("User " + username + " created layout in " + params.getModel().getProject().getProjectId() + " map.");
+
+ emailSender.sendEmail("MapViewer notification", content.toString(), email);
+ }
+ } else if (params.getModel().getNotifyEmail() != null) {
+ // if nobody owns the layout then send it to the model owner
+ emailSender.sendEmail("MapViewer notification", content.toString(), params.getModel().getNotifyEmail());
+ }
+ }
+
+ /**
+ * Prepares table with statistics about coloring.
+ *
+ * @param schemas
+ * schemas that were used for coloring
+ * @param scr
+ * interface that returns list of columns that should be printed
+ * @return table with statistics about coloring
+ */
+ protected String prepareTableResult(Collection<ColorSchema> schemas, ColorSchemaReader scr) {
+ StringBuilder sb = new StringBuilder("");
+
+ Collection<ColorSchemaColumn> columns = scr.getSetColorSchemaColumns(schemas);
+
+ for (ColorSchemaColumn column : ColorSchemaColumn.values()) {
+ if (columns.contains(column)) {
+ sb.append(column.getTitle() + "\t");
+ }
+ }
+ sb.append("matches<br/>\n");
+
+ for (ColorSchema originalSchema : schemas) {
+ for (ColorSchema schema : splitColorSchema(originalSchema)) {
+ sb.append(prepareTableRow(columns, schema));
+ }
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * {@link ColorSchema} sometimes contains merged value from few rows. This
+ * method split single {@link ColorSchema} object to simple flat objects that
+ * can be serialiazed in a simple tab separated file.
+ *
+ * @param originalSchema
+ * original {@link ColorSchema} objcet that we want to spli into flat
+ * objects
+ * @return {@link List} of flat schema objects obtained from input
+ */
+ private List<ColorSchema> splitColorSchema(ColorSchema originalSchema) {
+ List<ColorSchema> result = new ArrayList<>();
+ if (originalSchema instanceof GenericColorSchema) {
+ result.add(originalSchema);
+ } else if (originalSchema instanceof GeneVariationColorSchema) {
+ for (GeneVariation gv : ((GeneVariationColorSchema) originalSchema).getGeneVariations()) {
+ GeneVariationColorSchema copy = (GeneVariationColorSchema) originalSchema.copy();
+ copy.getGeneVariations().clear();
+ copy.addGeneVariation(gv.copy());
+ result.add(copy);
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + originalSchema.getClass());
+ }
+ return result;
+ }
+
+ /**
+ * Prepares tab separated {@link String} represenation of {@link ColorSchema}.
+ *
+ * @param columns
+ * columns that should be outputed in the result String
+ * @param schema
+ * input ColorSchema that is going to be transformed into String
+ * representation
+ * @return tab separated {@link String} represenation of {@link ColorSchema}
+ */
+ protected String prepareTableRow(Collection<ColorSchemaColumn> columns, ColorSchema schema) {
+ StringBuilder sb = new StringBuilder();
+ for (ColorSchemaColumn column : ColorSchemaColumn.values()) {
+ if (columns.contains(column)) {
+ if (schema instanceof GenericColorSchema) {
+ sb.append(prepareTableCellForGenericSchema((GenericColorSchema) schema, column));
+ } else if (schema instanceof GeneVariationColorSchema) {
+ sb.append(prepareTableCellForGeneVariationSchema((GeneVariationColorSchema) schema, column));
+ } else {
+ throw new InvalidArgumentException("Unknown schema type: " + schema.getClass());
+ }
+ }
+ }
+ sb.append(schema.getMatches() + "<br/>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Returns String representing data of {@link GenericColorSchema} that should
+ * appear in a given {@link ColorSchemaColumn}.
+ *
+ * @param schema
+ * object for which data will be returned
+ * @param column
+ * column for which data should be returned
+ * @return {@link String} representing data of {@link GenericColorSchema} that
+ * should appear in a given {@link ColorSchemaColumn}
+ */
+ protected String prepareTableCellForGenericSchema(GenericColorSchema schema, ColorSchemaColumn column) {
+ StringBuilder sb = new StringBuilder();
+ if (column.equals(ColorSchemaColumn.COLOR)) {
+ if (schema.getColor() != null) {
+ sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.NAME)) {
+ sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.VALUE)) {
+ sb.append(schema.getValue() + "\t");
+ } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
+ for (String str : schema.getCompartments()) {
+ sb.append(str + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.TYPE)) {
+ for (Class<? extends Species> str : schema.getTypes()) {
+ sb.append(str.getSimpleName() + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
+ for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+ if (pair.getRight() != null && !pair.getRight().trim().equals("")) {
+ sb.append(pair.getLeft().getCommonName() + ": " + pair.getRight() + ", ");
+ }
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
+ sb.append(schema.getReactionIdentifier() + "\t");
+ } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
+ sb.append(schema.getLineWidth() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
+ sb.append(schema.getReverseReaction() + "\t");
+ } else if (column.equals(ColorSchemaColumn.POSITION)) {
+ sb.append(schema.getReverseReaction() + "\t");
+ } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
+ sb.append(schema.getDescription() + "\t");
+ } else {
+ throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns String representing data of {@link GeneVariationColorSchema} that
+ * should appear in a given {@link ColorSchemaColumn}.
+ *
+ * @param schema
+ * object for which data will be returned
+ * @param column
+ * column for which data should be returned
+ * @return {@link String} representing data of
+ * {@link GeneVariationColorSchema} that should appear in a given
+ * {@link ColorSchemaColumn}
+ */
+ protected String prepareTableCellForGeneVariationSchema(GeneVariationColorSchema schema, ColorSchemaColumn column) {
+ StringBuilder sb = new StringBuilder();
+ if (column.equals(ColorSchemaColumn.COLOR)) {
+ if (schema.getColor() != null) {
+ sb.append("#" + Integer.toHexString(schema.getColor().getRGB()).substring(2).toUpperCase());
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.NAME)) {
+ sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.VALUE)) {
+ sb.append(schema.getValue() + "\t");
+ } else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
+ for (String str : schema.getCompartments()) {
+ sb.append(str + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.TYPE)) {
+ for (Class<? extends Species> str : schema.getTypes()) {
+ sb.append(str.getSimpleName() + ", ");
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.IDENTIFIER)) {
+ for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+ if (pair.getRight() != null && !pair.getRight().trim().equals("")) {
+ sb.append(pair.getLeft().getCommonName() + ": " + pair.getRight() + ", ");
+ }
+ }
+ sb.append("\t");
+ } else if (column.equals(ColorSchemaColumn.REACTION_IDENTIFIER)) {
+ sb.append(schema.getReactionIdentifier() + "\t");
+ } else if (column.equals(ColorSchemaColumn.LINE_WIDTH)) {
+ sb.append(schema.getLineWidth() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REVERSE_REACTION)) {
+ sb.append(schema.getReverseReaction() + "\t");
+ } else if (column.equals(ColorSchemaColumn.POSITION)) {
+ sb.append(schema.getGeneVariations().get(0).getPosition() + "\t");
+ } else if (column.equals(ColorSchemaColumn.DESCRIPTION)) {
+ sb.append(schema.getDescription() + "\t");
+ } else if (column.equals(ColorSchemaColumn.ORIGINAL_DNA)) {
+ sb.append(schema.getGeneVariations().get(0).getOriginalDna() + "\t");
+ } else if (column.equals(ColorSchemaColumn.ALTERNATIVE_DNA)) {
+ sb.append(schema.getGeneVariations().get(0).getModifiedDna() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_TYPE)) {
+ sb.append(schema.getGeneVariations().get(0).getReferenceGenomeType() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REFERENCE_GENOME_VERSION)) {
+ sb.append(schema.getGeneVariations().get(0).getReferenceGenomeVersion() + "\t");
+ } else if (column.equals(ColorSchemaColumn.CONTIG)) {
+ sb.append(schema.getGeneVariations().get(0).getContig() + "\t");
+ } else if (column.equals(ColorSchemaColumn.REFERENCES)) {
+ MiriamConnector mc = new MiriamConnector();
+ for (MiriamData md : schema.getGeneVariations().get(0).getReferences()) {
+ sb.append(mc.miriamDataToUri(md) + "\t");
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
+ }
+ return sb.toString();
+ }
+
+ @Override
+ public byte[] getInputDataForLayout(LayoutView layoutView) {
+ return getInputDataForLayout(layoutView.getIdObject());
+ }
+
+ /**
+ * Returns byte array containing data from original input file that was used
+ * to generate the layout.
+ *
+ * @param layoutId
+ * identifier of layout for which we want to retrieve original file
+ * data
+ * @return original data file for given layout, if such file is not stored in
+ * database (compatibility reasons) then null is returned
+ */
+ private byte[] getInputDataForLayout(int layoutId) {
+ Layout layout = layoutDao.getById(layoutId);
+ if (layout == null) {
+ return null;
+ } else {
+ if (layout.getInputData() != null) {
+ return layout.getInputData().getFileContent();
+ } else {
+ return null;
+ }
+ }
+ }
+
+ @Override
+ public List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId) {
+ try {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas;
+ schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ ColorModelCommand command = new ColorModelCommand(model, schemas);
+ 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())));
+ }
+ }
+ return result;
+ } catch (InvalidColorSchemaException e) {
+ throw new InvalidStateException(e);
+ } catch (IOException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ @Override
+ public List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId) {
+ try {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas;
+ schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ ColorModelCommand command = new ColorModelCommand(model, schemas);
+ LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
+ List<LightLayoutReactionView> result = new ArrayList<>();
+ for (Map.Entry<Object, ColorSchema> entry : command.getModifiedElements().entrySet()) {
+ if (entry.getKey() instanceof Reaction) {
+ result.add(factory.create(new Pair<Reaction, ColorSchema>((Reaction) entry.getKey(), entry.getValue())));
+ }
+ }
+ return result;
+ } catch (InvalidColorSchemaException e) {
+ throw new InvalidStateException(e);
+ } catch (IOException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ @Override
+ public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId) {
+ try {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas;
+ schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ ColorModelCommand command = new ColorModelCommand(model, schemas);
+ return command.getModifiedElements();
+ } catch (InvalidColorSchemaException e) {
+ throw new InvalidStateException(e);
+ } catch (IOException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ @Override
+ public List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers, int layoutId) {
+ try {
+ Set<Integer> ids = new HashSet<>();
+ for (Pair<Integer, Integer> pair : identifiers) {
+ ids.add(pair.getRight());
+ }
+
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas;
+ schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ ColorModelCommand command = new ColorModelCommand(model, schemas);
+ FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
+ List<FullLayoutAliasView> result = new ArrayList<>();
+
+ // 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 (ids.contains(alias.getId())) {
+ result.add(factory.create(new Pair<Alias, ColorSchema>(alias, entry.getValue())));
+ }
+ }
+ }
+ return result;
+ } catch (InvalidColorSchemaException e) {
+ throw new InvalidStateException(e);
+ } catch (IOException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+}
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 28375a5c04..6a1d8e58d5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -23,7 +23,8 @@ import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.Layout;
@@ -32,7 +33,6 @@ 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.Species;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ILayoutService;
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 a6bfe23fb5..25cc9a4e3f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -53,13 +53,13 @@ import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.log.LogType;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
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 95083039b9..99869b8ae6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -18,8 +18,18 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.InvalidStateException;
+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.Element;
+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.Unknown;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.Alias;
@@ -30,16 +40,6 @@ 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.ComplexSpecies;
-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;
import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
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 ba81f380e5..1c087cc40e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataMiningService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IDataMiningService.java
@@ -5,7 +5,7 @@ import java.util.Collection;
import java.util.Set;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.graph.DataMining;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.graph.DataMiningType;
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 060d242ccb..3f3d223863 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -12,16 +12,16 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Article;
import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+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.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.ComplexSpecies;
-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;
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 8268fbbb96..de97a53dfa 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
@@ -8,10 +8,10 @@ import java.util.Map;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.search.IHeavyView;
import lcsb.mapviewer.services.view.AnnotationView;
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 7fd70377fc..9457e4eae7 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
@@ -18,7 +18,10 @@ import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+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.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -26,9 +29,6 @@ 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.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
import lcsb.mapviewer.services.interfaces.IDataMiningService;
import lcsb.mapviewer.services.overlay.ChebiTreeRow;
import lcsb.mapviewer.services.search.ElementViewFactory;
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 a74deb1edd..75f84bb111 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
@@ -4,7 +4,7 @@ import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.view.AbstractView;
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 e82b7af3ec..a2c1eaa67e 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
@@ -23,8 +23,11 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+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.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.Alias;
@@ -32,9 +35,6 @@ 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.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;
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 69f2559cdd..402a083a15 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
@@ -18,7 +18,7 @@ import lcsb.mapviewer.annotation.services.MeSHParser;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.Alias;
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 a372abb9bc..5dabb9d7d2 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
@@ -16,11 +16,11 @@ import com.google.gson.Gson;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.annotation.data.Target;
import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.MiriamData;
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.services.overlay.IconManager;
import lcsb.mapviewer.services.overlay.IconType;
import lcsb.mapviewer.services.search.SearchResultFactory;
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 47810a2bf4..98ba29b6fa 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
@@ -20,8 +20,11 @@ import lcsb.mapviewer.annotation.services.MiRNASearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
+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.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.alias.Alias;
@@ -29,9 +32,6 @@ 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.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;
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 ed03c735fe..ca77e51f1d 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
@@ -1,119 +1,119 @@
-package lcsb.mapviewer.services.search.db.mirna;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.overlay.IconManager;
-import lcsb.mapviewer.services.overlay.IconType;
-import lcsb.mapviewer.services.search.SearchResultFactory;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.search.db.DrugTargetViewVisibilityComparator;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.search.db.TargetViewFactory;
-
-/**
- * Factory class for {@link MiRNAView} class.
- *
- * @author Ayan Rota
- *
- */
-public class MiRNAViewFactory extends SearchResultFactory<MiRNA, MiRNAView> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(MiRNAViewFactory.class);
-
- /**
- * Factory object for {@link TargetView} elements.
- */
- @Autowired
- private TargetViewFactory drugTargetViewFactory;
-
- @Override
- public MiRNAView create(MiRNA miRNA) {
- return create(miRNA, null, 0);
- }
-
- /**
- * Creates {@link MiRNAView}.
- *
- * @param miRNA
- * original MiRNA from which the data will be initialized
- * @param model
- * model where the view will be presented
- * @param set
- * which set of icons should be used
- *
- * @return {@link MiRNAView} object for given miRNA. links are placed
- * according to model given in the parameter.
- */
- public MiRNAView create(MiRNA miRNA, Model model, int set) {
- MiRNAView miRNAView = new MiRNAView(miRNA);
- if (miRNA == null) {
- return miRNAView;
- }
-
- miRNAView.setName(miRNA.getName());
-
- List<TargetView> targetsRows = new ArrayList<>();
- int differentNames = 0;
- for (Target geneEntry : miRNA.getTargets()) {
- targetsRows.add(drugTargetViewFactory.create(geneEntry, model));
- }
-
- Collections.sort(targetsRows, new DrugTargetViewVisibilityComparator());
-
- for (TargetView geneTargetView : targetsRows) {
- if (geneTargetView.getSelectable()) {
- String icon = IconManager.getInstance().getIconForIndex(differentNames++, IconType.MI_RNA, set);
- geneTargetView.setIcon(icon);
- geneTargetView.setSelected(true);
- }
- }
- miRNAView.setTargetRows(targetsRows);
- return miRNAView;
-
- }
-
- @Override
- public String createGson(MiRNAView object) {
- return new Gson().toJson(object);
- }
-
- @Override
- public List<ElementIdentifier> searchResultToElementIdentifier(MiRNAView searchResult, Model inputModel) {
- List<ElementIdentifier> result = new ArrayList<>();
-
- List<Model> models = new ArrayList<>();
- models.addAll(inputModel.getSubmodels());
- models.add(inputModel);
- for (Model model : models) {
- for (TargetView target : searchResult.getTargetRows()) {
- if (target.getSelected() && target.getIcon() != null) {
- for (Element element : model.getElements()) {
- if (elementMatch(target, element)) {
- for (Alias alias : model.getAliasesForElement(element)) {
- result.add(new ElementIdentifier(alias, target.getIcon()));
- }
- }
- }
- }
- }
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.services.search.db.mirna;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.overlay.IconManager;
+import lcsb.mapviewer.services.overlay.IconType;
+import lcsb.mapviewer.services.search.SearchResultFactory;
+import lcsb.mapviewer.services.search.data.ElementIdentifier;
+import lcsb.mapviewer.services.search.db.DrugTargetViewVisibilityComparator;
+import lcsb.mapviewer.services.search.db.TargetView;
+import lcsb.mapviewer.services.search.db.TargetViewFactory;
+
+/**
+ * Factory class for {@link MiRNAView} class.
+ *
+ * @author Ayan Rota
+ *
+ */
+public class MiRNAViewFactory extends SearchResultFactory<MiRNA, MiRNAView> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(MiRNAViewFactory.class);
+
+ /**
+ * Factory object for {@link TargetView} elements.
+ */
+ @Autowired
+ private TargetViewFactory drugTargetViewFactory;
+
+ @Override
+ public MiRNAView create(MiRNA miRNA) {
+ return create(miRNA, null, 0);
+ }
+
+ /**
+ * Creates {@link MiRNAView}.
+ *
+ * @param miRNA
+ * original MiRNA from which the data will be initialized
+ * @param model
+ * model where the view will be presented
+ * @param set
+ * which set of icons should be used
+ *
+ * @return {@link MiRNAView} object for given miRNA. links are placed
+ * according to model given in the parameter.
+ */
+ public MiRNAView create(MiRNA miRNA, Model model, int set) {
+ MiRNAView miRNAView = new MiRNAView(miRNA);
+ if (miRNA == null) {
+ return miRNAView;
+ }
+
+ miRNAView.setName(miRNA.getName());
+
+ List<TargetView> targetsRows = new ArrayList<>();
+ int differentNames = 0;
+ for (Target geneEntry : miRNA.getTargets()) {
+ targetsRows.add(drugTargetViewFactory.create(geneEntry, model));
+ }
+
+ Collections.sort(targetsRows, new DrugTargetViewVisibilityComparator());
+
+ for (TargetView geneTargetView : targetsRows) {
+ if (geneTargetView.getSelectable()) {
+ String icon = IconManager.getInstance().getIconForIndex(differentNames++, IconType.MI_RNA, set);
+ geneTargetView.setIcon(icon);
+ geneTargetView.setSelected(true);
+ }
+ }
+ miRNAView.setTargetRows(targetsRows);
+ return miRNAView;
+
+ }
+
+ @Override
+ public String createGson(MiRNAView object) {
+ return new Gson().toJson(object);
+ }
+
+ @Override
+ public List<ElementIdentifier> searchResultToElementIdentifier(MiRNAView searchResult, Model inputModel) {
+ List<ElementIdentifier> result = new ArrayList<>();
+
+ List<Model> models = new ArrayList<>();
+ models.addAll(inputModel.getSubmodels());
+ models.add(inputModel);
+ for (Model model : models) {
+ for (TargetView target : searchResult.getTargetRows()) {
+ if (target.getSelected() && target.getIcon() != null) {
+ for (Element element : model.getElements()) {
+ if (elementMatch(target, element)) {
+ for (Alias alias : model.getAliasesForElement(element)) {
+ result.add(new ElementIdentifier(alias, target.getIcon()));
+ }
+ }
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+}
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 b7bc490f3d..d9d2d8ba36 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
@@ -8,7 +8,7 @@ import java.util.Map.Entry;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.SearchIndex;
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 e38aea2294..d95592e179 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.converter.model.celldesigner.structure.Species;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
/**
* This enum defines which columns are available in export function.
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 53198e9f73..4bde13627c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
@@ -6,8 +6,8 @@ import java.util.List;
import lcsb.mapviewer.annotation.data.Article;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.reaction.Reaction;
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 a1b51aa31d..a1a75c7e9b 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest.java
@@ -22,16 +22,16 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.annotation.Rollback;
import lcsb.mapviewer.common.IProgressUpdater;
+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.model.Project;
import lcsb.mapviewer.model.log.GenericLog;
-import lcsb.mapviewer.model.map.Element;
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.model.Model;
-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;
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 6a0ec1ed15..3c3f6b35a1 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/DataMiningServiceTest2.java
@@ -11,7 +11,10 @@ import java.util.HashSet;
import java.util.Set;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.Element;
+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.SimpleMolecule;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
@@ -19,9 +22,6 @@ import lcsb.mapviewer.model.map.graph.DataMiningType;
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.Protein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.services.ServiceTestFunctions;
import org.apache.log4j.Logger;
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 50700a9a30..688d103d32 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ExporterServiceTest.java
@@ -1,529 +1,529 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-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.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.ComplexSpecies;
-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;
-import lcsb.mapviewer.services.utils.data.ExportColumn;
-import lcsb.mapviewer.services.utils.data.ExportFileType;
-import lcsb.mapviewer.services.view.PubmedAnnotatedElementsView;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-public class ExporterServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ExporterServiceTest.class);
- @Autowired
- IExporterService exporter2;
-
- ExporterService exporter;
-
- @Before
- public void setUp() throws Exception {
- exporter = (ExporterService) exporter2;
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetExportSpeciesStringForTabSeparatedFile() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME, ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length > 1);
-
- String response = lines[0];
- String textColumns[] = response.split("\t");
- assertEquals(5, textColumns.length);
-
- // only proteins for self-made modules
- new CreateHierarchyCommand(model, 8, 80).execute();
- string = exporter.getExportSpeciesString(params.type(GenericProtein.class));
- lines = string.split("\n");
- assertTrue(lines.length > 1);
-
- boolean differenceBetweenComponentCompartmnet = false;
- int lineCount = 0;
- for (String string2 : lines) {
- if (lineCount == 0) {
- textColumns = string2.split("\t");
- assertEquals(ExportColumn.TYPE.getTitle(), textColumns[4]);
- } else {
- textColumns = string2.split("\t");
- assertEquals(GenericProtein.class.getSimpleName(), textColumns[4]);
- if (!textColumns[2].equalsIgnoreCase(textColumns[3])) {
- differenceBetweenComponentCompartmnet = true;
- }
- }
- lineCount++;
- }
- assertTrue(differenceBetweenComponentCompartmnet);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDuplicatesInGetExportSpeciesString() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_duplicate_elements.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.COMPONENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
-
- String lines[] = string.split("\n");
- Set<String> uniqueNames = new HashSet<String>();
- for (String string2 : lines) {
- uniqueNames.add(string2);
- }
- assertEquals(uniqueNames.size(), lines.length);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportStringForOneSpecies_Complex() {
- try {
- Model model = getModelForFile("testFiles/export/hsp70.xml", true);
-
- SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId("csa1");
- ExportColumn columns[] = { ExportColumn.NAME };
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- column(columns).//
- complexElementsName(false).//
- fileType(ExportFileType.TAB_SEPARATED);
-
- List<String> elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.contains("HSP70:chaperon"));
-
- // now the results are concatenated children
- params.complexElementsName(true);
-
- elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.size() > 0);
- String string = elements.get(0);
- assertFalse(string.equals("HSP70:chaperon"));
- assertTrue(string.contains("HSP70"));
- assertTrue(string.contains("STUB1"));
- assertTrue(string.contains("DNAJB2"));
- assertTrue(string.contains("BAG1"));
-
- // and now check complexes with mix of proteins and molecules
- alias = (SpeciesAlias) model.getAliasByAliasId("csa3");
-
- elements = exporter.getExportStringForOneSpecies(alias, params);
- assertTrue(elements.size() > 0);
- string = elements.get(0);
- assertTrue(string.contains("UBA1"));
- assertTrue(string.contains("UBA6"));
- assertTrue(string.contains("AMP"));
-
- elements = exporter.getExportStringForOneSpecies(alias, params.type(Protein.class));
- assertTrue(elements.size() > 0);
- string = elements.get(0);
- assertTrue(string.contains("UBA1"));
- assertTrue(string.contains("UBA6"));
- assertFalse(string.contains("AMP"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
- }
-
- @Test
- public void testGetExportStringForOneReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<CompartmentAlias> aliases = new HashSet<CompartmentAlias>();
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
- if (alias.getTitle().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
- aliases.add(alias);
- }
-
- Reaction reaction = model.getReactionByReactionId("re2");
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.SIF).//
- type(Protein.class).//
- type(ComplexSpecies.class).//
- fileType(ExportFileType.SIF).//
- complexElementsName(false).//
- excluded(aliases);
-
- String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertNotNull(string);
- assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
- assertTrue(string.contains("CSP:Hsc70:SGT"));
- assertTrue(string.contains("SNCA"));
- assertTrue(string.contains("trans-SNARE complex"));
- assertFalse(string.contains("VAMP2"));
-
- params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF).type(ComplexSpecies.class).type(Protein.class);
- string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertTrue(string.contains("VAMP2"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetExportStringForOneReactionInGeneral() {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", true);
- Reaction reaction = model.getReactionByReactionId("re2");
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.SIF).//
- complexElementsName(false).//
- type(ComplexSpecies.class).type(Protein.class);
- String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertNotNull(string);
- assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
- assertTrue(string.contains("CSP:Hsc70:SGT"));
- assertTrue(string.contains("SNCA"));
- assertTrue(string.contains("trans-SNARE complex"));
- assertTrue(string.contains("SNAP25"));
- assertFalse(string.contains("RAB3A"));
-
- params.complexElementsName(true);
- string = exporter.getExportSingleInteractionString(reaction, params).get(0);
- assertFalse(string.contains("trans-SNARE complex"));
- assertTrue(string.contains("RAB3A"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
-
- }
-
- @Test
- public void testGetExportStringForOneReactionInGeneralWithOnlyOneElement() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Reaction reaction = model.getReactionByReactionId("re11");
- model.getReactions().clear();
- model.addReaction(reaction);
- Set<CompartmentAlias> aliases = new HashSet<CompartmentAlias>();
- aliases.add((CompartmentAlias) 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());
-
- params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF);
- assertEquals(1, exporter.getExportSingleInteractionString(reaction, params).size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportSingleInteractionString_text() {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- for (Reaction reaction : model.getReactions()) {
- String str = exporter.getExportSingleInteractionString(
- reaction, new IExporterService.ExporterParameters().fileType(ExportFileType.TAB_SEPARATED).type(Species.class)).get(0);
-
- List<String> strings = new ArrayList<String>();
- strings.add(ReactionLineData.getByReactionType(reaction.getClass()).getCellDesignerString());
- strings.add(reaction.getIdReaction());
- for (ReactionNode node : reaction.getReactionNodes()) {
- strings.add(((Species) node.getElement()).getName());
-
- }
- for (String string : strings) {
- assertTrue("Description \"" + str + "\" doesn't contain " + string + ". reactionId=" + reaction.getIdReaction(), str.contains(string));
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured");
- }
- }
-
- @Test
- public void testGetExportComponentAndCompartments() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/export_model.xml", false);
- new CreateHierarchyCommand(model, 7, 80).execute();
- ExporterParameters params = new IExporterService.ExporterParameters()
- .model(model).fileType(ExportFileType.TAB_SEPARATED).column(ExportColumn.NAME).column(ExportColumn.COMPONENT_NAME)
- .column(ExportColumn.COMPARTMENT_NAME);
-
- List<String> list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s1").get(0), 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(model.getAliasesBySpeciesId("s2").get(0), params);
- desc = null;
- for (String string : list) {
- if (string.contains("Test 1")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test 1", component);
-
- for (String string : list) {
- if (string.contains("Test2")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test2", component);
-
- for (String string : list) {
- if (string.contains("Test3")) {
- desc = string;
- }
- }
- compartment = desc.split("\t")[2];
- assertEquals("c2", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s3").get(0), params);
- boolean ok = false;
- for (String string : list) {
- if (string.split("\t")[2].equals("null") && string.split("\t")[1].equals("Test2")) {
- ok = true;
- }
- }
- assertTrue(ok);
-
- list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s4").get(0), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("null", compartment);
- component = desc.split("\t")[1];
- assertEquals("Test3", component);
-
- list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s5").get(0), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("c3", compartment);
- component = desc.split("\t")[1];
- assertEquals("null", component);
-
- list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s6").get(0), params);
- desc = list.get(0);
- compartment = desc.split("\t")[2];
- assertEquals("null", compartment);
- component = desc.split("\t")[1];
- assertEquals("null", component);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportSpeciesStringForTabSeparatedFile2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
- ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME, ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
-
- ExporterParameters params = new IExporterService.ExporterParameters()
- .model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length > 1);
-
- String response = lines[0];
- String textColumns[] = response.split("\t");
- assertEquals(columns.length, textColumns.length);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetExportCompartmentsString() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/export_compartments.xml", false);
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
-
- // full export (all compartments)
- String string = exporter.getExportCompartmentsString(params);
- String lines[] = string.split("\n");
- assertTrue("Not enough elements in the result file", lines.length >= 2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAllExportColumnsSpecies() throws Exception {
- try {
- 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(Species.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAllExportColumnsReaction() throws Exception {
- try {
- 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(Reaction.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportInteractionString(params);
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTabSeparatedReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- Set<CompartmentAlias> aliases = new HashSet<CompartmentAlias>();
- for (CompartmentAlias alias : model.getCompartmentsAliases()) {
- if (alias.getTitle().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
- aliases.add(alias);
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
- fileType(ExportFileType.TAB_SEPARATED).//
- column(ExportColumn.REACTION_ID).//
- column(ExportColumn.REACTION_TYPE).//
- type(Species.class);
-
- String string = exporter.getExportInteractionString(params);
- assertTrue(string.indexOf("STATE_TRANSITION REACTANT") >= 0);
- assertTrue(string.indexOf("s2240") >= 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test() throws Exception {
- try {
- 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(Species.class)) {
- columns.add(column);
- }
- }
-
- ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
-
- // full export (all elements)
- String string = exporter.getExportSpeciesString(params);
- String tmp[] = string.split("\n");
- for (String string2 : tmp) {
- assertTrue(string2,columns.size()<=string2.split("\t",-1).length);
- }
- assertNotNull(string);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPubmedSummary() throws Exception {
- try {
- Model model = getModelForFile("testFiles/export/reaction.xml", false);
- List<PubmedAnnotatedElementsView> result = exporter.getPublicationModelSummary(model);
- assertNotNull(result);
- for (PubmedAnnotatedElementsView pubmedAnnotatedElementsView : result) {
- assertNotNull(pubmedAnnotatedElementsView.getArticle());
- assertNotNull(pubmedAnnotatedElementsView.getArticle().getTitle());
- assertTrue(pubmedAnnotatedElementsView.getElements().size()>0);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+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.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.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.interfaces.IExporterService;
+import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
+import lcsb.mapviewer.services.utils.data.ExportColumn;
+import lcsb.mapviewer.services.utils.data.ExportFileType;
+import lcsb.mapviewer.services.view.PubmedAnnotatedElementsView;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+public class ExporterServiceTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(ExporterServiceTest.class);
+ @Autowired
+ IExporterService exporter2;
+
+ ExporterService exporter;
+
+ @Before
+ public void setUp() throws Exception {
+ exporter = (ExporterService) exporter2;
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetExportSpeciesStringForTabSeparatedFile() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME, ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ String lines[] = string.split("\n");
+ assertTrue("Not enough elements in the result file", lines.length > 1);
+
+ String response = lines[0];
+ String textColumns[] = response.split("\t");
+ assertEquals(5, textColumns.length);
+
+ // only proteins for self-made modules
+ new CreateHierarchyCommand(model, 8, 80).execute();
+ string = exporter.getExportSpeciesString(params.type(GenericProtein.class));
+ lines = string.split("\n");
+ assertTrue(lines.length > 1);
+
+ boolean differenceBetweenComponentCompartmnet = false;
+ int lineCount = 0;
+ for (String string2 : lines) {
+ if (lineCount == 0) {
+ textColumns = string2.split("\t");
+ assertEquals(ExportColumn.TYPE.getTitle(), textColumns[4]);
+ } else {
+ textColumns = string2.split("\t");
+ assertEquals(GenericProtein.class.getSimpleName(), textColumns[4]);
+ if (!textColumns[2].equalsIgnoreCase(textColumns[3])) {
+ differenceBetweenComponentCompartmnet = true;
+ }
+ }
+ lineCount++;
+ }
+ assertTrue(differenceBetweenComponentCompartmnet);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDuplicatesInGetExportSpeciesString() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_duplicate_elements.xml", false);
+ ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.COMPONENT_NAME, ExportColumn.TYPE };
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+
+ String lines[] = string.split("\n");
+ Set<String> uniqueNames = new HashSet<String>();
+ for (String string2 : lines) {
+ uniqueNames.add(string2);
+ }
+ assertEquals(uniqueNames.size(), lines.length);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportStringForOneSpecies_Complex() {
+ try {
+ Model model = getModelForFile("testFiles/export/hsp70.xml", true);
+
+ SpeciesAlias alias = (SpeciesAlias) model.getAliasByAliasId("csa1");
+ ExportColumn columns[] = { ExportColumn.NAME };
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ column(columns).//
+ complexElementsName(false).//
+ fileType(ExportFileType.TAB_SEPARATED);
+
+ List<String> elements = exporter.getExportStringForOneSpecies(alias, params);
+ assertTrue(elements.contains("HSP70:chaperon"));
+
+ // now the results are concatenated children
+ params.complexElementsName(true);
+
+ elements = exporter.getExportStringForOneSpecies(alias, params);
+ assertTrue(elements.size() > 0);
+ String string = elements.get(0);
+ assertFalse(string.equals("HSP70:chaperon"));
+ assertTrue(string.contains("HSP70"));
+ assertTrue(string.contains("STUB1"));
+ assertTrue(string.contains("DNAJB2"));
+ assertTrue(string.contains("BAG1"));
+
+ // and now check complexes with mix of proteins and molecules
+ alias = (SpeciesAlias) model.getAliasByAliasId("csa3");
+
+ elements = exporter.getExportStringForOneSpecies(alias, params);
+ assertTrue(elements.size() > 0);
+ string = elements.get(0);
+ assertTrue(string.contains("UBA1"));
+ assertTrue(string.contains("UBA6"));
+ assertTrue(string.contains("AMP"));
+
+ elements = exporter.getExportStringForOneSpecies(alias, params.type(Protein.class));
+ assertTrue(elements.size() > 0);
+ string = elements.get(0);
+ assertTrue(string.contains("UBA1"));
+ assertTrue(string.contains("UBA6"));
+ assertFalse(string.contains("AMP"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occured");
+ }
+ }
+
+ @Test
+ public void testGetExportStringForOneReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ Set<CompartmentAlias> aliases = new HashSet<CompartmentAlias>();
+ for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ if (alias.getTitle().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
+ aliases.add(alias);
+ }
+
+ Reaction reaction = model.getReactionByReactionId("re2");
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ fileType(ExportFileType.SIF).//
+ type(Protein.class).//
+ type(ComplexSpecies.class).//
+ fileType(ExportFileType.SIF).//
+ complexElementsName(false).//
+ excluded(aliases);
+
+ String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertNotNull(string);
+ assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
+ assertTrue(string.contains("CSP:Hsc70:SGT"));
+ assertTrue(string.contains("SNCA"));
+ assertTrue(string.contains("trans-SNARE complex"));
+ assertFalse(string.contains("VAMP2"));
+
+ params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF).type(ComplexSpecies.class).type(Protein.class);
+ string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertTrue(string.contains("VAMP2"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetExportStringForOneReactionInGeneral() {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", true);
+ Reaction reaction = model.getReactionByReactionId("re2");
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ fileType(ExportFileType.SIF).//
+ complexElementsName(false).//
+ type(ComplexSpecies.class).type(Protein.class);
+ String string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertNotNull(string);
+ assertTrue(string.contains("Calcium channel:RIMBP:RIM:MUNC13:RAB"));
+ assertTrue(string.contains("CSP:Hsc70:SGT"));
+ assertTrue(string.contains("SNCA"));
+ assertTrue(string.contains("trans-SNARE complex"));
+ assertTrue(string.contains("SNAP25"));
+ assertFalse(string.contains("RAB3A"));
+
+ params.complexElementsName(true);
+ string = exporter.getExportSingleInteractionString(reaction, params).get(0);
+ assertFalse(string.contains("trans-SNARE complex"));
+ assertTrue(string.contains("RAB3A"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occured");
+ }
+
+ }
+
+ @Test
+ public void testGetExportStringForOneReactionInGeneralWithOnlyOneElement() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ Reaction reaction = model.getReactionByReactionId("re11");
+ model.getReactions().clear();
+ model.addReaction(reaction);
+ Set<CompartmentAlias> aliases = new HashSet<CompartmentAlias>();
+ aliases.add((CompartmentAlias) 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());
+
+ params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.SIF);
+ assertEquals(1, exporter.getExportSingleInteractionString(reaction, params).size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportSingleInteractionString_text() {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ for (Reaction reaction : model.getReactions()) {
+ String str = exporter.getExportSingleInteractionString(
+ reaction, new IExporterService.ExporterParameters().fileType(ExportFileType.TAB_SEPARATED).type(Species.class)).get(0);
+
+ List<String> strings = new ArrayList<String>();
+ strings.add(ReactionLineData.getByReactionType(reaction.getClass()).getCellDesignerString());
+ strings.add(reaction.getIdReaction());
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ strings.add(((Species) node.getElement()).getName());
+
+ }
+ for (String string : strings) {
+ assertTrue("Description \"" + str + "\" doesn't contain " + string + ". reactionId=" + reaction.getIdReaction(), str.contains(string));
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occured");
+ }
+ }
+
+ @Test
+ public void testGetExportComponentAndCompartments() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/export_model.xml", false);
+ new CreateHierarchyCommand(model, 7, 80).execute();
+ ExporterParameters params = new IExporterService.ExporterParameters()
+ .model(model).fileType(ExportFileType.TAB_SEPARATED).column(ExportColumn.NAME).column(ExportColumn.COMPONENT_NAME)
+ .column(ExportColumn.COMPARTMENT_NAME);
+
+ List<String> list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s1").get(0), 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(model.getAliasesBySpeciesId("s2").get(0), params);
+ desc = null;
+ for (String string : list) {
+ if (string.contains("Test 1")) {
+ desc = string;
+ }
+ }
+ compartment = desc.split("\t")[2];
+ assertEquals("c2", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test 1", component);
+
+ for (String string : list) {
+ if (string.contains("Test2")) {
+ desc = string;
+ }
+ }
+ compartment = desc.split("\t")[2];
+ assertEquals("c2", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test2", component);
+
+ for (String string : list) {
+ if (string.contains("Test3")) {
+ desc = string;
+ }
+ }
+ compartment = desc.split("\t")[2];
+ assertEquals("c2", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test3", component);
+
+ list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s3").get(0), params);
+ boolean ok = false;
+ for (String string : list) {
+ if (string.split("\t")[2].equals("null") && string.split("\t")[1].equals("Test2")) {
+ ok = true;
+ }
+ }
+ assertTrue(ok);
+
+ list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s4").get(0), params);
+ desc = list.get(0);
+ compartment = desc.split("\t")[2];
+ assertEquals("null", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("Test3", component);
+
+ list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s5").get(0), params);
+ desc = list.get(0);
+ compartment = desc.split("\t")[2];
+ assertEquals("c3", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("null", component);
+
+ list = exporter.getExportStringForOneSpecies(model.getAliasesBySpeciesId("s6").get(0), params);
+ desc = list.get(0);
+ compartment = desc.split("\t")[2];
+ assertEquals("null", compartment);
+ component = desc.split("\t")[1];
+ assertEquals("null", component);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportSpeciesStringForTabSeparatedFile2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export_with_artifitial_comp.xml", false);
+ ExportColumn columns[] = { ExportColumn.NAME, ExportColumn.ID, ExportColumn.COMPONENT_NAME, ExportColumn.COMPARTMENT_NAME, ExportColumn.TYPE };
+
+ ExporterParameters params = new IExporterService.ExporterParameters()
+ .model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ String lines[] = string.split("\n");
+ assertTrue("Not enough elements in the result file", lines.length > 1);
+
+ String response = lines[0];
+ String textColumns[] = response.split("\t");
+ assertEquals(columns.length, textColumns.length);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetExportCompartmentsString() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/export_compartments.xml", false);
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).fileType(ExportFileType.TAB_SEPARATED).type(Object.class);
+
+ // full export (all compartments)
+ String string = exporter.getExportCompartmentsString(params);
+ String lines[] = string.split("\n");
+ assertTrue("Not enough elements in the result file", lines.length >= 2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAllExportColumnsSpecies() throws Exception {
+ try {
+ 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(Species.class)) {
+ columns.add(column);
+ }
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ assertNotNull(string);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAllExportColumnsReaction() throws Exception {
+ try {
+ 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(Reaction.class)) {
+ columns.add(column);
+ }
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportInteractionString(params);
+ assertNotNull(string);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTabSeparatedReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ Set<CompartmentAlias> aliases = new HashSet<CompartmentAlias>();
+ for (CompartmentAlias alias : model.getCompartmentsAliases()) {
+ if (alias.getTitle().equalsIgnoreCase("Dopamine loaded synaptic vesicle"))
+ aliases.add(alias);
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).//
+ fileType(ExportFileType.TAB_SEPARATED).//
+ column(ExportColumn.REACTION_ID).//
+ column(ExportColumn.REACTION_TYPE).//
+ type(Species.class);
+
+ String string = exporter.getExportInteractionString(params);
+ assertTrue(string.indexOf("STATE_TRANSITION REACTANT") >= 0);
+ assertTrue(string.indexOf("s2240") >= 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test() throws Exception {
+ try {
+ 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(Species.class)) {
+ columns.add(column);
+ }
+ }
+
+ ExporterParameters params = new IExporterService.ExporterParameters().model(model).column(columns).fileType(ExportFileType.TAB_SEPARATED);
+
+ // full export (all elements)
+ String string = exporter.getExportSpeciesString(params);
+ String tmp[] = string.split("\n");
+ for (String string2 : tmp) {
+ assertTrue(string2,columns.size()<=string2.split("\t",-1).length);
+ }
+ assertNotNull(string);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPubmedSummary() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/export/reaction.xml", false);
+ List<PubmedAnnotatedElementsView> result = exporter.getPublicationModelSummary(model);
+ assertNotNull(result);
+ for (PubmedAnnotatedElementsView pubmedAnnotatedElementsView : result) {
+ assertNotNull(pubmedAnnotatedElementsView.getArticle());
+ assertNotNull(pubmedAnnotatedElementsView.getArticle().getTitle());
+ assertTrue(pubmedAnnotatedElementsView.getElements().size()>0);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
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 2789022047..8f0dacdddf 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -1,247 +1,247 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.Color;
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.commands.ColorModelCommand;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.TextFileUtils;
-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.ColorSchema;
-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.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;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-
-public class LayoutServiceTest2 {
- Logger logger = Logger.getLogger(LayoutServiceTest2.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidPreprareTableResultForGeneric() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GenericColorSchema();
- cs.setColor(Color.CYAN);
- cs.addCompartment("BLA");
- cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
- cs.setLineWidth(3.3);
- cs.setMatches(2);
- cs.setName("UUU");
- cs.setReactionIdentifier("RE ID");
- cs.setReverseReaction(true);
- cs.addType(GenericProtein.class);
- cs.setValue(1111.1111);
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testValidPreprareTableResultForGeneVariation() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- GeneVariationColorSchema cs = new GeneVariationColorSchema();
- cs.setColor(Color.CYAN);
- cs.addCompartment("BLA");
- cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
- cs.setLineWidth(3.3);
- cs.setMatches(2);
- cs.setName("UUU");
- cs.setReactionIdentifier("RE ID");
- cs.setReverseReaction(true);
- cs.addType(GenericProtein.class);
- cs.setValue(1111.1111);
- GeneVariation gv = new GeneVariation();
- gv.setModifiedDna("C");
- gv.setContig("chr1");
- gv.setOriginalDna("T");
- gv.setPosition(12);
- gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
- gv.setReferenceGenomeVersion("hg19");
- cs.addGeneVariation(gv);
- GeneVariation gv2 = new GeneVariation();
- gv2.setModifiedDna("CC");
- gv2.setContig("chr2");
- gv2.setOriginalDna("TT");
- gv2.setPosition(124);
- gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
- gv2.setReferenceGenomeVersion("hg18");
- gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
- cs.addGeneVariation(gv2);
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyPreprareTableResultForGeneric() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GenericColorSchema();
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GeneVariationColorSchema();
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetLayoutAliasesForInvalidAlias() throws Exception {
- try {
-
- Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
-
- FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(fis).//
- async(false);
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader
- .readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
-
- ColorModelCommand command = new ColorModelCommand(model, schemas);
- command.execute();
-
- command.getModifiedElements();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSchemaWithCompartments() throws Exception {
- try {
- FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
- for (ColorSchema colorSchema : schemas) {
- for (String string : colorSchema.getCompartments()) {
- assertNotNull(string);
- assertFalse(string.isEmpty());
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.Color;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.commands.ColorModelCommand;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.GenericProtein;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+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.model.Model;
+import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
+import lcsb.mapviewer.services.utils.ColorSchemaReader;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
+import lcsb.mapviewer.services.utils.data.ColorSchemaType;
+
+public class LayoutServiceTest2 {
+ Logger logger = Logger.getLogger(LayoutServiceTest2.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidPreprareTableResultForGeneric() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GenericColorSchema();
+ cs.setColor(Color.CYAN);
+ cs.addCompartment("BLA");
+ cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+ cs.setLineWidth(3.3);
+ cs.setMatches(2);
+ cs.setName("UUU");
+ cs.setReactionIdentifier("RE ID");
+ cs.setReverseReaction(true);
+ cs.addType(GenericProtein.class);
+ cs.setValue(1111.1111);
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testValidPreprareTableResultForGeneVariation() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ GeneVariationColorSchema cs = new GeneVariationColorSchema();
+ cs.setColor(Color.CYAN);
+ cs.addCompartment("BLA");
+ cs.addIdentifierColumn(new Pair<MiriamType, String>(MiriamType.CAS, "CAS_ID"));
+ cs.setLineWidth(3.3);
+ cs.setMatches(2);
+ cs.setName("UUU");
+ cs.setReactionIdentifier("RE ID");
+ cs.setReverseReaction(true);
+ cs.addType(GenericProtein.class);
+ cs.setValue(1111.1111);
+ GeneVariation gv = new GeneVariation();
+ gv.setModifiedDna("C");
+ gv.setContig("chr1");
+ gv.setOriginalDna("T");
+ gv.setPosition(12);
+ gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+ gv.setReferenceGenomeVersion("hg19");
+ cs.addGeneVariation(gv);
+ GeneVariation gv2 = new GeneVariation();
+ gv2.setModifiedDna("CC");
+ gv2.setContig("chr2");
+ gv2.setOriginalDna("TT");
+ gv2.setPosition(124);
+ gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+ gv2.setReferenceGenomeVersion("hg18");
+ gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
+ cs.addGeneVariation(gv2);
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyPreprareTableResultForGeneric() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GenericColorSchema();
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GeneVariationColorSchema();
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetLayoutAliasesForInvalidAlias() throws Exception {
+ try {
+
+ Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
+
+ FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").//
+ directory("testDir").//
+ model(model).//
+ colorInputStream(fis).//
+ async(false);
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader
+ .readColorSchema(params.getColorInputStream(), TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
+
+ ColorModelCommand command = new ColorModelCommand(model, schemas);
+ command.execute();
+
+ command.getModifiedElements();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSchemaWithCompartments() throws Exception {
+ try {
+ FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
+ for (ColorSchema colorSchema : schemas) {
+ for (String string : colorSchema.getCompartments()) {
+ assertNotNull(string);
+ assertFalse(string.isEmpty());
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
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 5a6d651f39..f372dffd72 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LogServiceTest.java
@@ -1,134 +1,134 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.Set;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.log.GenericLog;
-import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.test.annotation.Rollback;
-
-@Rollback(true)
-public class LogServiceTest extends ServiceTestFunctions {
-
- static Logger logger = Logger.getLogger(LogServiceTest.class);
-
- private Model model;
- private Project project;
- private Set<Element> nodes;
- private Element node;
- private DataMining mc;
-
- @Before
- public void setUp() throws Exception {
- try {
- model = getModelForFile("testFiles/graph_path_example3.xml", false);
- project = new Project();
- project.addModel(model);
- projectDao.add(project);
- modelDao.add(model);
- nodes = model.getElements();
- node = nodes.iterator().next();
-
- mc = new DataMining();
- mc.setElement(node);
- missingConnectionDao.add(mc);
-
- createUser();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @After
- public void tearDown() throws Exception {
- try {
- missingConnectionDao.delete(mc);
- modelDao.delete(model);
- projectDao.delete(project);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLog1() throws Exception {
- try {
- logService.setLoggedUser(null);
- LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").object(mc);
- GenericLog log = logService.log(params);
- assertEquals(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN), log.getUser());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLog2() throws Exception {
- try {
- LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").user(user);
- GenericLog log = logService.log(params);
- logDao.delete(log);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLog3() {
- try {
- LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").user(user).object(new DataMining());
- logService.log(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- }
-
- @Test
- public void testLog4() {
- try {
- LogParams params = new LogParams().description("bla").user(user).object(mc);
- logService.log(params);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- }
-
- @Test
- public void testLog5() throws Exception {
- try {
- LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").user(user).object(mc).object(mc);
- GenericLog log = logService.log(params);
- assertNotNull(log);
- assertNotNull(log.getId());
- assertNotNull(logDao.getById(log.getId()));
- logDao.delete(log);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.Set;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+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.model.Model;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.test.annotation.Rollback;
+
+@Rollback(true)
+public class LogServiceTest extends ServiceTestFunctions {
+
+ static Logger logger = Logger.getLogger(LogServiceTest.class);
+
+ private Model model;
+ private Project project;
+ private Set<Element> nodes;
+ private Element node;
+ private DataMining mc;
+
+ @Before
+ public void setUp() throws Exception {
+ try {
+ model = getModelForFile("testFiles/graph_path_example3.xml", false);
+ project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+ modelDao.add(model);
+ nodes = model.getElements();
+ node = nodes.iterator().next();
+
+ mc = new DataMining();
+ mc.setElement(node);
+ missingConnectionDao.add(mc);
+
+ createUser();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ try {
+ missingConnectionDao.delete(mc);
+ modelDao.delete(model);
+ projectDao.delete(project);
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLog1() throws Exception {
+ try {
+ logService.setLoggedUser(null);
+ LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").object(mc);
+ GenericLog log = logService.log(params);
+ assertEquals(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN), log.getUser());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLog2() throws Exception {
+ try {
+ LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").user(user);
+ GenericLog log = logService.log(params);
+ logDao.delete(log);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLog3() {
+ try {
+ LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").user(user).object(new DataMining());
+ logService.log(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ }
+
+ @Test
+ public void testLog4() {
+ try {
+ LogParams params = new LogParams().description("bla").user(user).object(mc);
+ logService.log(params);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ }
+
+ @Test
+ public void testLog5() throws Exception {
+ try {
+ LogParams params = new LogParams().type(LogType.ADD_MISSING_CONNECTION).description("bla").user(user).object(mc).object(mc);
+ GenericLog log = logService.log(params);
+ assertNotNull(log);
+ assertNotNull(log.getId());
+ assertNotNull(logDao.getById(log.getId()));
+ logDao.delete(log);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
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 f48ace29ad..bf37237855 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -29,20 +29,20 @@ import lcsb.mapviewer.commands.CopyCommand;
import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.converter.ComplexZipConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Protein;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.map.AnnotatedObject;
-import lcsb.mapviewer.model.map.Element;
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.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
-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;
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 a677f5a753..4f1bb90793 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -18,6 +18,16 @@ import org.junit.Test;
import lcsb.mapviewer.annotation.data.Drug;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Degraded;
+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.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.Unknown;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -29,16 +39,6 @@ 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.ComplexSpecies;
-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.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;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.ISearchService.CoordinatesSearchParams;
import lcsb.mapviewer.services.search.data.FullAliasView;
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 930de2e986..e144cedee6 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/SearchResultFactoryTest.java
@@ -8,10 +8,10 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-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;
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 cea3dbadde..efe150fa18 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
@@ -21,11 +21,14 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.data.Chebi;
import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Compartment;
+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.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.agregator.Compartment;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
@@ -37,9 +40,6 @@ 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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.overlay.ChebiTreeRow;
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 be4ba23f73..5806f92d3e 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
@@ -1,101 +1,101 @@
-package lcsb.mapviewer.services.search.db.chemical;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-
-public class ChemicalServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ChemicalServiceTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * @throws Exception
- */
- @Test
- public void testgetPDChemicalByName() throws Exception {
- try {
- List<ChemicalView> result = null;
- MiriamData pdDiseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
-
- List<String> names = new ArrayList<String>();
- names.add("Dopamine");
- names.add("2-(2-furanyl)-7-(2-(4-(4-(2-methoxyethoxy)phenyl)-1-piperazinyl)ethyl)-7H-pyrazolo(4,3-e)(1,2,4)triazolo(1,5-c)pyrimidine-5-amine");
- names.add("Anti-Inflammatory Agents, Non-Steroidal");
- names.add("2-furanyl");
- names.add(null);
- result = chemicalService.getByNames(names, new DbSearchCriteria().disease(pdDiseaseID));
- assertNotNull(result);
- assertTrue(!result.isEmpty());
- assertTrue(result.size() == 3);
- names.clear();
- names.add("2-furanyl");
- result = chemicalService.getByNames(names, new DbSearchCriteria().disease(pdDiseaseID));
- assertNotNull(result);
- assertTrue(result.isEmpty());
-
- assertEquals("No warnings expected.", 0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testgetPDChemicalByName2() throws Exception {
- try {
- MiriamData pdDiseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
- String name = "Amphetamine";
- ChemicalView result = chemicalService.getByName(name, new DbSearchCriteria().disease(pdDiseaseID));
- assertNotNull(result);
- assertEquals("D000661", result.getSourceLink().getName());
-
- assertEquals("No warnings expected.", 0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchByElements4() throws Exception {
- try {
- List<Element> elements = new ArrayList<Element>();
- Rna protein = new Rna();
- protein.setName("GDNF");
- elements.add(protein);
-
- List<ChemicalView> chemicals = chemicalService.getForTargets(elements, new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
- assertNotNull(chemicals);
- assertTrue(chemicals.size() > 0);
-
- assertEquals("No warnings expected.", 0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.services.search.db.chemical;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Rna;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+
+public class ChemicalServiceTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(ChemicalServiceTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * @throws Exception
+ */
+ @Test
+ public void testgetPDChemicalByName() throws Exception {
+ try {
+ List<ChemicalView> result = null;
+ MiriamData pdDiseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
+
+ List<String> names = new ArrayList<String>();
+ names.add("Dopamine");
+ names.add("2-(2-furanyl)-7-(2-(4-(4-(2-methoxyethoxy)phenyl)-1-piperazinyl)ethyl)-7H-pyrazolo(4,3-e)(1,2,4)triazolo(1,5-c)pyrimidine-5-amine");
+ names.add("Anti-Inflammatory Agents, Non-Steroidal");
+ names.add("2-furanyl");
+ names.add(null);
+ result = chemicalService.getByNames(names, new DbSearchCriteria().disease(pdDiseaseID));
+ assertNotNull(result);
+ assertTrue(!result.isEmpty());
+ assertTrue(result.size() == 3);
+ names.clear();
+ names.add("2-furanyl");
+ result = chemicalService.getByNames(names, new DbSearchCriteria().disease(pdDiseaseID));
+ assertNotNull(result);
+ assertTrue(result.isEmpty());
+
+ assertEquals("No warnings expected.", 0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testgetPDChemicalByName2() throws Exception {
+ try {
+ MiriamData pdDiseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
+ String name = "Amphetamine";
+ ChemicalView result = chemicalService.getByName(name, new DbSearchCriteria().disease(pdDiseaseID));
+ assertNotNull(result);
+ assertEquals("D000661", result.getSourceLink().getName());
+
+ assertEquals("No warnings expected.", 0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchByElements4() throws Exception {
+ try {
+ List<Element> elements = new ArrayList<Element>();
+ Rna protein = new Rna();
+ protein.setName("GDNF");
+ elements.add(protein);
+
+ List<ChemicalView> chemicals = chemicalService.getForTargets(elements, new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+ assertNotNull(chemicals);
+ assertTrue(chemicals.size() > 0);
+
+ assertEquals("No warnings expected.", 0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
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 6c1aecbfa2..355a1dd62e 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
@@ -16,17 +16,17 @@ import lcsb.mapviewer.annotation.services.TaxonomyBackend;
import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.converter.ComplexZipConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+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.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
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.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.db.TargetView;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
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 d82ef8d9b6..d6b93643f6 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
@@ -1,155 +1,155 @@
-package lcsb.mapviewer.services.search.db.drug;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-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.Species;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.overlay.IconManager;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.search.db.TargetDetails;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.search.db.TargetViewFactory;
-import lcsb.mapviewer.services.view.AnnotationView;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
-
-public class DrugViewFactoryTest extends ServiceTestFunctions {
-
- @Autowired
- TargetViewFactory targetViewFactory;
-
- Logger logger = Logger.getLogger(DrugViewFactoryTest.class);
-
- @Autowired
- AnnotationViewFactory avFactory;
-
- @Autowired
- DrugViewFactory dvf;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGeneToOverlayList() throws Exception {
- try {
- Model model = getModelForFile("testFiles/drug_target.xml", true);
- model.setTileSize(256);
- List<Model> models = new ArrayList<>();
- models.add(model);
-
- AnnotationView annotation = avFactory.create(new MiriamData());
- annotation.setName("M");
-
- List<ElementIdentifier> overlays = dvf.geneToOverlayList(annotation, IconManager.getInstance().getEmpyIcon(), models);
- assertEquals(1, overlays.size());
-
- annotation.setName("GRIN2B");
- overlays = dvf.geneToOverlayList(annotation, IconManager.getInstance().getEmpyIcon(), models);
- assertEquals(3, overlays.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexToOverlayList() throws Exception {
- try {
- Drug drug = chemblParser.findDrug("AMANTADINE");
- Target exampleTarget = null;
- assertTrue(drug.getTargets().size() > 0);
- for (Target target : drug.getTargets()) {
- if (target.getName().equals("Glutamate [NMDA] receptor")) {
- target.setType(TargetType.COMPLEX_PROTEIN);
- exampleTarget = target;
- }
- logger.debug(target);
- }
- assertNotNull(exampleTarget);
- Model model = getModelForFile("testFiles/drug_target.xml", true);
- model.setTileSize(256);
- List<Model> models = new ArrayList<>();
- models.add(model);
- TargetView view = targetViewFactory.create(exampleTarget);
- view.setIcon(IconManager.getInstance().getEmpyIcon());
-
- List<ElementIdentifier> overlays = dvf.complexToOverlayList(view, models);
- assertEquals(2, overlays.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testgetElementInformationForResult() throws Exception {
- try {
- Drug drug = chemblParser.findDrug("AMANTADINE");
- Model model = getModelForFile("testFiles/drug_target.xml", false);
- Species species = model.getSpeciesBySpeciesId("s9");
- species.setName("M");
- Alias alias = model.getAliasesBySpeciesId(species.getElementId()).get(0);
- alias.setId(12);
- model.removeAlias(alias);
- model.addAlias(alias);
- ElementIdentifier ei = new ElementIdentifier(alias, null);
- model.setTileSize(256);
- List<Model> models = new ArrayList<>();
- models.add(model);
- DrugView view = dvf.create(drug);
- TargetDetails result = dvf.getElementInformationForResult(view.getTargetRows(), ei, model);
- assertNotNull(result);
- assertFalse(result.getDatabaseSource().equals(result.getReferences().get(0)));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateEmpty() throws Exception {
- try {
- Object object = dvf.create(null);
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateGson() throws Exception {
- try {
- DrugView object = dvf.create(null);
- assertNotNull(dvf.createGson(object));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.search.db.drug;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Species;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.overlay.IconManager;
+import lcsb.mapviewer.services.search.data.ElementIdentifier;
+import lcsb.mapviewer.services.search.db.TargetDetails;
+import lcsb.mapviewer.services.search.db.TargetView;
+import lcsb.mapviewer.services.search.db.TargetViewFactory;
+import lcsb.mapviewer.services.view.AnnotationView;
+import lcsb.mapviewer.services.view.AnnotationViewFactory;
+
+public class DrugViewFactoryTest extends ServiceTestFunctions {
+
+ @Autowired
+ TargetViewFactory targetViewFactory;
+
+ Logger logger = Logger.getLogger(DrugViewFactoryTest.class);
+
+ @Autowired
+ AnnotationViewFactory avFactory;
+
+ @Autowired
+ DrugViewFactory dvf;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGeneToOverlayList() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/drug_target.xml", true);
+ model.setTileSize(256);
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+
+ AnnotationView annotation = avFactory.create(new MiriamData());
+ annotation.setName("M");
+
+ List<ElementIdentifier> overlays = dvf.geneToOverlayList(annotation, IconManager.getInstance().getEmpyIcon(), models);
+ assertEquals(1, overlays.size());
+
+ annotation.setName("GRIN2B");
+ overlays = dvf.geneToOverlayList(annotation, IconManager.getInstance().getEmpyIcon(), models);
+ assertEquals(3, overlays.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexToOverlayList() throws Exception {
+ try {
+ Drug drug = chemblParser.findDrug("AMANTADINE");
+ Target exampleTarget = null;
+ assertTrue(drug.getTargets().size() > 0);
+ for (Target target : drug.getTargets()) {
+ if (target.getName().equals("Glutamate [NMDA] receptor")) {
+ target.setType(TargetType.COMPLEX_PROTEIN);
+ exampleTarget = target;
+ }
+ logger.debug(target);
+ }
+ assertNotNull(exampleTarget);
+ Model model = getModelForFile("testFiles/drug_target.xml", true);
+ model.setTileSize(256);
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ TargetView view = targetViewFactory.create(exampleTarget);
+ view.setIcon(IconManager.getInstance().getEmpyIcon());
+
+ List<ElementIdentifier> overlays = dvf.complexToOverlayList(view, models);
+ assertEquals(2, overlays.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testgetElementInformationForResult() throws Exception {
+ try {
+ Drug drug = chemblParser.findDrug("AMANTADINE");
+ Model model = getModelForFile("testFiles/drug_target.xml", false);
+ Species species = model.getSpeciesBySpeciesId("s9");
+ species.setName("M");
+ Alias alias = model.getAliasesBySpeciesId(species.getElementId()).get(0);
+ alias.setId(12);
+ model.removeAlias(alias);
+ model.addAlias(alias);
+ ElementIdentifier ei = new ElementIdentifier(alias, null);
+ model.setTileSize(256);
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ DrugView view = dvf.create(drug);
+ TargetDetails result = dvf.getElementInformationForResult(view.getTargetRows(), ei, model);
+ assertNotNull(result);
+ assertFalse(result.getDatabaseSource().equals(result.getReferences().get(0)));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateEmpty() throws Exception {
+ try {
+ Object object = dvf.create(null);
+ assertNotNull(object);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateGson() throws Exception {
+ try {
+ DrugView object = dvf.create(null);
+ assertNotNull(dvf.createGson(object));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
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 6c51589a57..fd9fef970f 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
@@ -1,103 +1,103 @@
-package lcsb.mapviewer.services.utils.graph;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.Collection;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MissingConnectionDaoTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(MissingConnectionDaoTest.class);
-
- private Model model;
- private Collection<Element> nodes;
-
- private Project project;
-
- @Before
- public void setUp() throws Exception {
- project = new Project();
- projectDao.add(project);
- dbUtils.setAutoFlush(false);
- model =getModelForFile("testFiles/graph_path_example.xml",false);
- project.addModel(model);
- modelDao.add((Model) model);
-
- nodes = model.getElements();
- }
-
- @After
- public void tearDown() throws Exception {
- modelDao.delete((Model) model);
- dbUtils.setAutoFlush(true);
- projectDao.delete(project);
- }
-
- @Test
- public void testGetMissingConnections() {
- try {
- Element node = nodes.iterator().next();
-
- DataMining mc = new DataMining();
- mc.setDescription("desc a");
- mc.setElement(node);
- mc.addReference(new MiriamData(MiriamType.PUBMED, "12345"));
- mc.addReference(new MiriamData(MiriamType.PUBMED, "123456"));
-
- missingConnectionDao.add(mc);
-
- DataMining mc2 = new DataMining();
- mc2.setDescription("desc ab");
- mc2.setElement(node);
- mc2.addReference(new MiriamData(MiriamType.PUBMED, "323456"));
-
- missingConnectionDao.add(mc2);
- missingConnectionDao.flush();
- missingConnectionDao.evict(mc);
- missingConnectionDao.evict(mc2);
-
- Collection<DataMining> collection = missingConnectionDao.getMissingConnectionForElement(node);
-
- assertNotNull(collection);
-
- DataMining mc3 = null;
- DataMining mc4 = null;
-
- assertEquals(2,collection.size());
-
- for (DataMining missingConnection : collection) {
- if (mc3 == null)
- mc3 = missingConnection;
- else if (mc4 == null)
- mc4 = missingConnection;
- else
- fail("Incorrect number of elemenets in collection");
- }
-
- assertTrue("invalid number of references: "+mc3.getReferences().size(),mc3.getReferences().size() == 2 || mc3.getReferences().size() == 1);
- assertTrue("invalid number of references: "+mc4.getReferences().size(),mc4.getReferences().size() == 2 || mc4.getReferences().size() == 1);
-
- missingConnectionDao.delete(mc3);
- missingConnectionDao.delete(mc4);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception occured");
- }
- }
-
-}
+package lcsb.mapviewer.services.utils.graph;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.Collection;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+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.model.Model;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MissingConnectionDaoTest extends ServiceTestFunctions {
+ static Logger logger = Logger.getLogger(MissingConnectionDaoTest.class);
+
+ private Model model;
+ private Collection<Element> nodes;
+
+ private Project project;
+
+ @Before
+ public void setUp() throws Exception {
+ project = new Project();
+ projectDao.add(project);
+ dbUtils.setAutoFlush(false);
+ model =getModelForFile("testFiles/graph_path_example.xml",false);
+ project.addModel(model);
+ modelDao.add((Model) model);
+
+ nodes = model.getElements();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ modelDao.delete((Model) model);
+ dbUtils.setAutoFlush(true);
+ projectDao.delete(project);
+ }
+
+ @Test
+ public void testGetMissingConnections() {
+ try {
+ Element node = nodes.iterator().next();
+
+ DataMining mc = new DataMining();
+ mc.setDescription("desc a");
+ mc.setElement(node);
+ mc.addReference(new MiriamData(MiriamType.PUBMED, "12345"));
+ mc.addReference(new MiriamData(MiriamType.PUBMED, "123456"));
+
+ missingConnectionDao.add(mc);
+
+ DataMining mc2 = new DataMining();
+ mc2.setDescription("desc ab");
+ mc2.setElement(node);
+ mc2.addReference(new MiriamData(MiriamType.PUBMED, "323456"));
+
+ missingConnectionDao.add(mc2);
+ missingConnectionDao.flush();
+ missingConnectionDao.evict(mc);
+ missingConnectionDao.evict(mc2);
+
+ Collection<DataMining> collection = missingConnectionDao.getMissingConnectionForElement(node);
+
+ assertNotNull(collection);
+
+ DataMining mc3 = null;
+ DataMining mc4 = null;
+
+ assertEquals(2,collection.size());
+
+ for (DataMining missingConnection : collection) {
+ if (mc3 == null)
+ mc3 = missingConnection;
+ else if (mc4 == null)
+ mc4 = missingConnection;
+ else
+ fail("Incorrect number of elemenets in collection");
+ }
+
+ assertTrue("invalid number of references: "+mc3.getReferences().size(),mc3.getReferences().size() == 2 || mc3.getReferences().size() == 1);
+ assertTrue("invalid number of references: "+mc4.getReferences().size(),mc4.getReferences().size() == 2 || mc4.getReferences().size() == 1);
+
+ missingConnectionDao.delete(mc3);
+ missingConnectionDao.delete(mc4);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception occured");
+ }
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java b/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
index 68671a2166..4e59b89d1f 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ChemicalBean.java
@@ -13,8 +13,8 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IUserService;
diff --git a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
index aedad5dce4..fc34f958f4 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/DrugBean.java
@@ -1,421 +1,421 @@
-package lcsb.mapviewer.bean;
-
-import java.awt.geom.Path2D;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.bean.ViewScoped;
-import javax.faces.event.ActionEvent;
-
-import org.apache.log4j.Logger;
-
-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.Element;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.ElementIdentifierDetails;
-import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
-import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-import lcsb.mapviewer.services.search.db.TargetDetails;
-import lcsb.mapviewer.services.search.db.drug.DrugView;
-import lcsb.mapviewer.services.search.db.drug.DrugViewFactory;
-import lcsb.mapviewer.services.search.db.drug.IDrugService;
-import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-
-/**
- * Bean used for drug interface. It allows to look for the drugs that targets
- * some proteins or to find all possible information about a drug entered by
- * user.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(name = "drugMB")
-@ViewScoped
-public class DrugBean extends AbstractMarkerManagerBean<DrugView> implements Serializable {
-
- /**
- * Name of the param passed in the request that contains name of drug to
- * search.
- */
- private static final String DRUG_NAME_PARAM = "tabView:drugForm:searchDrug";
-
- /**
- * Name of the session field that store last query.
- */
- private static final String DRUG_LAST_SEARCH_SESSION_PARAM = "DRUG_SEARCH_PARAM";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(DrugBean.class);
-
- /**
- * List of drugs suggested for vizualization (we cannot vizualize all of them,
- * because it's too much data).
- */
- private List<DrugView> suggestedDrugs = new ArrayList<DrugView>();
-
- /**
- * Polygon selected on the map. It is used to find targets for drugs. This
- * polygon is in serialized javascript format.
- */
- private String polygon = "";
-
- /**
- * Service used to query about drugs.
- *
- * @see IDrugService
- */
- @ManagedProperty(value = "#{DrugService}")
- private transient IDrugService drugService;
-
- /**
- * Factory for drug elements.
- *
- */
- @ManagedProperty(value = "#{DrugViewFactory}")
- private transient DrugViewFactory drugViewFactory;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for communication with the client side about the map currently
- * visualized.
- *
- * @see MapBean
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- /**
- * This method populates list of suggested drugs. As the input we take a
- * polygon (which should contains some proteins to target)
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void findDrugsForMapFragment(final ActionEvent actionEvent) {
- Model model = getCurrentTopModel();
- if (model == null) {
- logger.warn("Unknown model. Skipping...");
- return;
- }
- // transform serialized polygon into set of points
- CoordinationConverter cc = new CoordinationConverter(model);
- Path2D awtPolygon = cc.latLngToPolygon(polygon);
-
- // create a part of the model that contains only the elements from the
- // polygon
- SubModelCommand subModelCommand = new SubModelCommand(model, awtPolygon);
- Model partModel = subModelCommand.execute();
- suggestedDrugs.addAll(drugService.getForTargets(partModel.getElements(), new DbSearchCriteria().organisms(mapBean.getOrganism())));
- }
-
- /**
- * Empty list of suggested drugs.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void clearDrugsForMapFragment(final ActionEvent actionEvent) {
- suggestedDrugs = new ArrayList<DrugView>();
- }
-
- /**
- * This method look for the drugs.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void search(final ActionEvent actionEvent) {
-
- String searchText = getRequestParameter(DRUG_NAME_PARAM);
-
- findDrug(searchText);
- }
-
- /**
- * Look for a drug using query given in the parameter.
- *
- * @param query
- * search query
- */
- protected void findDrug(String query) {
- if (getCurrentTopModel() == null) {
- logger.warn("Unknown model. Skipping...");
- return;
- }
-
- // gather information for search engine
- String ipAddress = getClientIpAddress();
- Model model = getCurrentTopModel();
-
- clearResults();
-
- // drugs are comma separated
- List<String> names = splitQuery(query, true);
- int set = 0;
- for (String string : names) {
- DrugView drug = drugService.getByName(string, new DbSearchCriteria().ipAddress(ipAddress).model(model).organisms(mapBean.getOrganism()).colorSet(set++));
- if (drug != null) {
- addResult(drug);
- }
- }
-
- // format results
- if (getResults().size() == 0) { // if there are no results, add empty drug
- logger.debug("No results found");
- DrugView drug = drugService.createEmptyView();
- drug.setName("Not found");
- addResult(drug);
- }
-
- // send it to the client
- refreshDataInJavascript();
-
- addSessionParam(DRUG_LAST_SEARCH_SESSION_PARAM + getCurrentMapId(), query);
- }
-
- /**
- * Check privileges for advanced drug targeting view.
- *
- * @return true if user has advanced privilege view for drugs
- */
- public boolean getUserHasAdvancedView() {
- Project project = getCurrentProject();
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.DRUG_TARGETING_ADVANCED_VIEW_PROJECT, project);
- return result;
- }
-
- @Override
- public void clear() {
- addSessionParam(DRUG_LAST_SEARCH_SESSION_PARAM + getCurrentMapId(), null);
- setSuggestedDrugs(new ArrayList<DrugView>());
- setPolygon("");
- clearResults();
- refreshDataInJavascript();
- }
-
- /**
- * @return the suggestedDrugs
- * @see #suggestedDrugs
- */
- public List<DrugView> getSuggestedDrugs() {
- return suggestedDrugs;
- }
-
- /**
- * @param suggestedDrugs
- * the suggestedDrugs to set
- * @see #suggestedDrugs
- */
- public void setSuggestedDrugs(List<DrugView> suggestedDrugs) {
- this.suggestedDrugs = suggestedDrugs;
- }
-
- /**
- * @return the polygon
- * @see #polygon
- */
- public String getPolygon() {
- return polygon;
- }
-
- /**
- * @param polygon
- * the polygon to set
- * @see #polygon
- */
- public void setPolygon(String polygon) {
- this.polygon = polygon;
- }
-
- /**
- * @return the drugService
- * @see #drugService
- */
- public IDrugService getDrugService() {
- return drugService;
- }
-
- /**
- * @param drugService
- * the drugService to set
- * @see #drugService
- */
- public void setDrugService(IDrugService drugService) {
- this.drugService = drugService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- @Override
- public void init() {
- String searchVal = (String) getSessionParam(DRUG_LAST_SEARCH_SESSION_PARAM + getCurrentMapId());
- if (searchVal != null && !searchVal.isEmpty()) {
- findDrug(searchVal);
- }
-
- }
-
- @Override
- protected List<ElementIdentifier> getLightElementsForSearchResult(DrugView result) {
- return drugViewFactory.searchResultToElementIdentifier(result, getCurrentTopModel());
- }
-
- @Override
- protected ElementIdentifierDetails getElementInformationForResult(ElementIdentifier element, DrugView result) {
- return drugViewFactory.getElementInformationForResult(result.getTargetRows(), element, getCurrentTopModel());
- }
-
- @Override
- protected List<Pair<String, ElementIdentifierDetails>> getElementInformationForResult(ElementIdentifier element) {
- if (element.getType().equals(ElementIdentifierType.ALIAS.getJsName())) {
- List<Pair<String, ElementIdentifierDetails>> result = new ArrayList<>();
-
- Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
-
- Alias alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
- Element e = alias.getElement();
- List<Element> list = new ArrayList<>();
- list.add(e);
- List<DrugView> drugs = drugService.getForTargets(list, new DbSearchCriteria().model(getCurrentTopModel()).organisms(mapBean.getOrganism()));
- for (DrugView drugView : drugs) {
- TargetDetails td = drugViewFactory.getElementInformationForResult(drugView.getTargetRows(), element, getCurrentTopModel());
- if (td != null) {
- result.add(new Pair<String, ElementIdentifierDetails>(drugView.getName(), td));
- }
- }
- return result;
- } else {
- throw new InvalidArgumentException("Drugs are not supported for element: " + element.getType());
- }
- }
-
- /**
- * @return the drugViewFactory
- * @see #drugViewFactory
- */
- public DrugViewFactory getDrugViewFactory() {
- return drugViewFactory;
- }
-
- /**
- * @param drugViewFactory
- * the drugViewFactory to set
- * @see #drugViewFactory
- */
- public void setDrugViewFactory(DrugViewFactory drugViewFactory) {
- this.drugViewFactory = drugViewFactory;
- }
-
- /**
- * Returns currently browsed map.
- *
- * @return currently browsed map
- */
- private Model getCurrentTopModel() {
- return mapBean.getCurrentTopModel();
- }
-
- /**
- * Returns identifier of browsed map (if such map wasn't setup it will be
- * default identifier).
- *
- * @return identifier of browsed map
- */
- private String getCurrentMapId() {
- return mapBean.getCurrentMapId();
- }
-
- /**
- * Returns curently browsed project.
- *
- * @return curently browsed project
- */
- private Project getCurrentProject() {
- return getCurrentTopModel().getProject();
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
-}
+package lcsb.mapviewer.bean;
+
+import java.awt.geom.Path2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.faces.bean.ManagedBean;
+import javax.faces.bean.ManagedProperty;
+import javax.faces.bean.ViewScoped;
+import javax.faces.event.ActionEvent;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.SubModelCommand;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.ElementIdentifierDetails;
+import lcsb.mapviewer.services.search.data.ElementIdentifier;
+import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
+import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.TargetDetails;
+import lcsb.mapviewer.services.search.db.drug.DrugView;
+import lcsb.mapviewer.services.search.db.drug.DrugViewFactory;
+import lcsb.mapviewer.services.search.db.drug.IDrugService;
+import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
+
+/**
+ * Bean used for drug interface. It allows to look for the drugs that targets
+ * some proteins or to find all possible information about a drug entered by
+ * user.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@ManagedBean(name = "drugMB")
+@ViewScoped
+public class DrugBean extends AbstractMarkerManagerBean<DrugView> implements Serializable {
+
+ /**
+ * Name of the param passed in the request that contains name of drug to
+ * search.
+ */
+ private static final String DRUG_NAME_PARAM = "tabView:drugForm:searchDrug";
+
+ /**
+ * Name of the session field that store last query.
+ */
+ private static final String DRUG_LAST_SEARCH_SESSION_PARAM = "DRUG_SEARCH_PARAM";
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(DrugBean.class);
+
+ /**
+ * List of drugs suggested for vizualization (we cannot vizualize all of them,
+ * because it's too much data).
+ */
+ private List<DrugView> suggestedDrugs = new ArrayList<DrugView>();
+
+ /**
+ * Polygon selected on the map. It is used to find targets for drugs. This
+ * polygon is in serialized javascript format.
+ */
+ private String polygon = "";
+
+ /**
+ * Service used to query about drugs.
+ *
+ * @see IDrugService
+ */
+ @ManagedProperty(value = "#{DrugService}")
+ private transient IDrugService drugService;
+
+ /**
+ * Factory for drug elements.
+ *
+ */
+ @ManagedProperty(value = "#{DrugViewFactory}")
+ private transient DrugViewFactory drugViewFactory;
+
+ /**
+ * Service used to access information about users.
+ *
+ * @see IUserService
+ */
+ @ManagedProperty(value = "#{UserService}")
+ private transient IUserService userService;
+
+ /**
+ * Bean used for communication with the client side about the data related to
+ * users (including information about currently logged user).
+ *
+ * @see UserBean
+ */
+ @ManagedProperty(value = "#{userMB}")
+ private transient UserBean userBean;
+
+ /**
+ * Bean used for communication with the client side about the map currently
+ * visualized.
+ *
+ * @see MapBean
+ */
+ @ManagedProperty(value = "#{mapMB}")
+ private transient MapBean mapBean;
+
+ /**
+ * This method populates list of suggested drugs. As the input we take a
+ * polygon (which should contains some proteins to target)
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void findDrugsForMapFragment(final ActionEvent actionEvent) {
+ Model model = getCurrentTopModel();
+ if (model == null) {
+ logger.warn("Unknown model. Skipping...");
+ return;
+ }
+ // transform serialized polygon into set of points
+ CoordinationConverter cc = new CoordinationConverter(model);
+ Path2D awtPolygon = cc.latLngToPolygon(polygon);
+
+ // create a part of the model that contains only the elements from the
+ // polygon
+ SubModelCommand subModelCommand = new SubModelCommand(model, awtPolygon);
+ Model partModel = subModelCommand.execute();
+ suggestedDrugs.addAll(drugService.getForTargets(partModel.getElements(), new DbSearchCriteria().organisms(mapBean.getOrganism())));
+ }
+
+ /**
+ * Empty list of suggested drugs.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void clearDrugsForMapFragment(final ActionEvent actionEvent) {
+ suggestedDrugs = new ArrayList<DrugView>();
+ }
+
+ /**
+ * This method look for the drugs.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void search(final ActionEvent actionEvent) {
+
+ String searchText = getRequestParameter(DRUG_NAME_PARAM);
+
+ findDrug(searchText);
+ }
+
+ /**
+ * Look for a drug using query given in the parameter.
+ *
+ * @param query
+ * search query
+ */
+ protected void findDrug(String query) {
+ if (getCurrentTopModel() == null) {
+ logger.warn("Unknown model. Skipping...");
+ return;
+ }
+
+ // gather information for search engine
+ String ipAddress = getClientIpAddress();
+ Model model = getCurrentTopModel();
+
+ clearResults();
+
+ // drugs are comma separated
+ List<String> names = splitQuery(query, true);
+ int set = 0;
+ for (String string : names) {
+ DrugView drug = drugService.getByName(string, new DbSearchCriteria().ipAddress(ipAddress).model(model).organisms(mapBean.getOrganism()).colorSet(set++));
+ if (drug != null) {
+ addResult(drug);
+ }
+ }
+
+ // format results
+ if (getResults().size() == 0) { // if there are no results, add empty drug
+ logger.debug("No results found");
+ DrugView drug = drugService.createEmptyView();
+ drug.setName("Not found");
+ addResult(drug);
+ }
+
+ // send it to the client
+ refreshDataInJavascript();
+
+ addSessionParam(DRUG_LAST_SEARCH_SESSION_PARAM + getCurrentMapId(), query);
+ }
+
+ /**
+ * Check privileges for advanced drug targeting view.
+ *
+ * @return true if user has advanced privilege view for drugs
+ */
+ public boolean getUserHasAdvancedView() {
+ Project project = getCurrentProject();
+ User user = userBean.getLoggedUser();
+ boolean result = userService.userHasPrivilege(user, PrivilegeType.DRUG_TARGETING_ADVANCED_VIEW_PROJECT, project);
+ return result;
+ }
+
+ @Override
+ public void clear() {
+ addSessionParam(DRUG_LAST_SEARCH_SESSION_PARAM + getCurrentMapId(), null);
+ setSuggestedDrugs(new ArrayList<DrugView>());
+ setPolygon("");
+ clearResults();
+ refreshDataInJavascript();
+ }
+
+ /**
+ * @return the suggestedDrugs
+ * @see #suggestedDrugs
+ */
+ public List<DrugView> getSuggestedDrugs() {
+ return suggestedDrugs;
+ }
+
+ /**
+ * @param suggestedDrugs
+ * the suggestedDrugs to set
+ * @see #suggestedDrugs
+ */
+ public void setSuggestedDrugs(List<DrugView> suggestedDrugs) {
+ this.suggestedDrugs = suggestedDrugs;
+ }
+
+ /**
+ * @return the polygon
+ * @see #polygon
+ */
+ public String getPolygon() {
+ return polygon;
+ }
+
+ /**
+ * @param polygon
+ * the polygon to set
+ * @see #polygon
+ */
+ public void setPolygon(String polygon) {
+ this.polygon = polygon;
+ }
+
+ /**
+ * @return the drugService
+ * @see #drugService
+ */
+ public IDrugService getDrugService() {
+ return drugService;
+ }
+
+ /**
+ * @param drugService
+ * the drugService to set
+ * @see #drugService
+ */
+ public void setDrugService(IDrugService drugService) {
+ this.drugService = drugService;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the userBean
+ * @see #userBean
+ */
+ public UserBean getUserBean() {
+ return userBean;
+ }
+
+ /**
+ * @param userBean
+ * the userBean to set
+ * @see #userBean
+ */
+ public void setUserBean(UserBean userBean) {
+ this.userBean = userBean;
+ }
+
+ @Override
+ public void init() {
+ String searchVal = (String) getSessionParam(DRUG_LAST_SEARCH_SESSION_PARAM + getCurrentMapId());
+ if (searchVal != null && !searchVal.isEmpty()) {
+ findDrug(searchVal);
+ }
+
+ }
+
+ @Override
+ protected List<ElementIdentifier> getLightElementsForSearchResult(DrugView result) {
+ return drugViewFactory.searchResultToElementIdentifier(result, getCurrentTopModel());
+ }
+
+ @Override
+ protected ElementIdentifierDetails getElementInformationForResult(ElementIdentifier element, DrugView result) {
+ return drugViewFactory.getElementInformationForResult(result.getTargetRows(), element, getCurrentTopModel());
+ }
+
+ @Override
+ protected List<Pair<String, ElementIdentifierDetails>> getElementInformationForResult(ElementIdentifier element) {
+ if (element.getType().equals(ElementIdentifierType.ALIAS.getJsName())) {
+ List<Pair<String, ElementIdentifierDetails>> result = new ArrayList<>();
+
+ Model model = getCurrentTopModel().getSubmodelById(element.getModelId());
+
+ Alias alias = model.getAliasByDbId(Integer.valueOf(element.getObjectId()));
+ Element e = alias.getElement();
+ List<Element> list = new ArrayList<>();
+ list.add(e);
+ List<DrugView> drugs = drugService.getForTargets(list, new DbSearchCriteria().model(getCurrentTopModel()).organisms(mapBean.getOrganism()));
+ for (DrugView drugView : drugs) {
+ TargetDetails td = drugViewFactory.getElementInformationForResult(drugView.getTargetRows(), element, getCurrentTopModel());
+ if (td != null) {
+ result.add(new Pair<String, ElementIdentifierDetails>(drugView.getName(), td));
+ }
+ }
+ return result;
+ } else {
+ throw new InvalidArgumentException("Drugs are not supported for element: " + element.getType());
+ }
+ }
+
+ /**
+ * @return the drugViewFactory
+ * @see #drugViewFactory
+ */
+ public DrugViewFactory getDrugViewFactory() {
+ return drugViewFactory;
+ }
+
+ /**
+ * @param drugViewFactory
+ * the drugViewFactory to set
+ * @see #drugViewFactory
+ */
+ public void setDrugViewFactory(DrugViewFactory drugViewFactory) {
+ this.drugViewFactory = drugViewFactory;
+ }
+
+ /**
+ * Returns currently browsed map.
+ *
+ * @return currently browsed map
+ */
+ private Model getCurrentTopModel() {
+ return mapBean.getCurrentTopModel();
+ }
+
+ /**
+ * Returns identifier of browsed map (if such map wasn't setup it will be
+ * default identifier).
+ *
+ * @return identifier of browsed map
+ */
+ private String getCurrentMapId() {
+ return mapBean.getCurrentMapId();
+ }
+
+ /**
+ * Returns curently browsed project.
+ *
+ * @return curently browsed project
+ */
+ private Project getCurrentProject() {
+ return getCurrentTopModel().getProject();
+ }
+
+ /**
+ * @return the mapBean
+ * @see #mapBean
+ */
+ public MapBean getMapBean() {
+ return mapBean;
+ }
+
+ /**
+ * @param mapBean
+ * the mapBean to set
+ * @see #mapBean
+ */
+ public void setMapBean(MapBean mapBean) {
+ this.mapBean = mapBean;
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
index 9b185b6fee..66c334eaed 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
@@ -49,8 +49,19 @@ import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.converter.graphics.SvgImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+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.Element;
+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.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -61,17 +72,6 @@ import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
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.AntisenseRna;
-import lcsb.mapviewer.model.map.species.ComplexSpecies;
-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.Unknown;
import lcsb.mapviewer.services.interfaces.IExporterService;
import lcsb.mapviewer.services.interfaces.IExporterService.ExporterParameters;
import lcsb.mapviewer.services.interfaces.ILayoutService;
diff --git a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
index 7b94062520..83277c00b0 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/FeedbackBean.java
@@ -19,8 +19,8 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Modifier;
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java b/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
index e3e693baad..1691d560f8 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/MiRNABean.java
@@ -13,7 +13,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.converter.model.celldesigner.structure.Element;
import lcsb.mapviewer.model.map.layout.alias.Alias;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.search.ElementIdentifierDetails;
--
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