From f8f4a66f18d3dedcb61da5a5758fb03d09691870 Mon Sep 17 00:00:00 2001
From: "piotr.gawron" <piotr.gawron@uni-new>
Date: Wed, 5 Oct 2016 14:25:28 +0200
Subject: [PATCH] model javadoc added and structure refactoried
---
.../services/ModelAnnotatorTest.java | 14 +-
.../lcsb/mapviewer/run/ConsoleConverter.java | 2 +-
.../celldesigner/CellDesignerXmlParser.java | 6 +-
.../alias/ComplexAliasXmlParser.java | 2 +-
.../alias/SpeciesAliasXmlParser.java | 2 +-
.../CellDesignerXmlParserTest.java | 12 +-
.../celldesigner/ComplexParserTests.java | 4 +-
.../celldesigner/LayerXmlParserTest.java | 10 +-
.../alias/SpeciesAliasXmlParserTest.java | 4 +-
.../ReactionCollectionXmlParserTest.java | 24 +--
.../reaction/ReactionFromXmlTest.java | 8 +-
.../reaction/ReactionParserTests.java | 24 +--
.../reaction/ReactionToXmlTest.java | 8 +-
.../species/ComplexParserTest.java | 10 +-
.../SpeciesCollectionXmlParserTest.java | 4 +-
.../model/sbgnml/SbgnmlXmlParser.java | 6 +-
.../graphics/NormalImageGeneratorTest.java | 6 +-
.../graphics/PdfImageGeneratorTest.java | 2 +-
.../placefinder/AllPlaceFinderTest.java | 24 +--
.../converter/ComplexZipConverterTest.java | 22 +--
.../lcsb/mapviewer/commands/CopyCommand.java | 12 +-
.../commands/CreateHierarchyCommand.java | 4 +-
.../commands/CommandTestFunctions.java | 4 +-
.../mapviewer/commands/CopyCommandTest.java | 10 +-
.../lcsb/mapviewer/model/map/MiriamType.java | 13 +-
.../lcsb/mapviewer/model/map/model/Model.java | 12 +-
.../model/map/model/ModelFullIndexed.java | 47 +++--
.../model/map/species/AntisenseRna.java | 43 ++++-
.../map/species/AntisenseRnaComparator.java | 10 +-
.../mapviewer/model/map/species/Chemical.java | 15 ++
.../model/map/species/ChemicalComparator.java | 44 ++++-
.../mapviewer/model/map/species/Complex.java | 30 +--
.../model/map/species/ComplexComparator.java | 2 +-
.../mapviewer/model/map/species/Degraded.java | 26 ++-
.../model/map/species/DegradedComparator.java | 8 +-
.../mapviewer/model/map/species/Drug.java | 25 ++-
.../model/map/species/DrugComparator.java | 14 +-
.../mapviewer/model/map/species/Element.java | 174 ++++++++++--------
.../model/map/species/ElementComparator.java | 5 +-
.../mapviewer/model/map/species/Gene.java | 40 +++-
.../model/map/species/GeneComparator.java | 6 +
.../model/map/species/GenericProtein.java | 26 ++-
.../map/species/GenericProteinComparator.java | 6 +
.../lcsb/mapviewer/model/map/species/Ion.java | 26 ++-
.../model/map/species/IonChannelProtein.java | 26 ++-
.../species/IonChannelProteinComparator.java | 6 +
.../model/map/species/IonComparator.java | 12 +-
.../model/map/species/Phenotype.java | 25 ++-
.../map/species/PhenotypeComparator.java | 6 +
.../mapviewer/model/map/species/Protein.java | 28 ++-
.../model/map/species/ProteinComparator.java | 33 ++--
.../model/map/species/ReceptorProtein.java | 25 ++-
.../species/ReceptorProteinComparator.java | 6 +
.../lcsb/mapviewer/model/map/species/Rna.java | 42 ++++-
.../model/map/species/RnaComparator.java | 6 +
.../model/map/species/SimpleMolecule.java | 26 ++-
.../map/species/SimpleMoleculeComparator.java | 32 +---
.../mapviewer/model/map/species/Species.java | 37 ++--
.../model/map/species/SpeciesComparator.java | 117 ++++++++----
.../model/map/species/TruncatedProtein.java | 25 ++-
.../species/TruncatedProteinComparator.java | 14 +-
.../mapviewer/model/map/species/Unknown.java | 25 ++-
.../model/map/species/UnknownComparator.java | 14 +-
.../mapviewer/model/map/MiriamTypeTest.java | 19 +-
.../BottomSquareCompartmentTest.java | 12 +-
.../map/compartment/CompartmentTest.java | 33 ++--
.../LeftSquareCompartmentTest.java | 12 +-
.../map/compartment/OvalCompartmentTest.java | 15 +-
.../RightSquareCompartmentTest.java | 16 +-
.../compartment/SquareCompartmentTest.java | 11 +-
.../compartment/TopSquareCompartmentTest.java | 10 +-
...AliasSubmodelConnectionComparatorTest.java | 6 +-
.../model/map/model/ModelComparatorTest.java | 22 +--
.../model/map/model/ModelFullIndexedTest.java | 146 +++++++++++----
...ModelSubmodelConnectionComparatorTest.java | 4 +-
.../mapviewer/model/map/model/ModelTest.java | 28 +--
.../SubmodelConnectionComparatorTest.java | 4 +-
.../reaction/NodeOperatorComparatorTest.java | 8 +
.../model/map/species/AllSpeciesTests.java | 6 +
.../species/AntisenseRnaComparatorTest.java | 13 +-
.../model/map/species/AntisenseRnaTest.java | 10 +-
.../map/species/ChemicalComparatorTest.java | 84 +++++++++
.../map/species/ComplexComparatorTest.java | 38 +---
.../model/map/species/ComplexTest.java | 40 +++-
.../map/species/DegradedComparatorTest.java | 10 +-
.../model/map/species/DegradedTest.java | 64 ++++++-
.../model/map/species/DrugComparatorTest.java | 10 +-
.../mapviewer/model/map/species/DrugTest.java | 10 +-
.../map/species/ElementComparatorTest.java | 6 +-
.../model/map/species/GeneComparatorTest.java | 10 +-
.../mapviewer/model/map/species/GeneTest.java | 10 +-
.../species/GenericProteinComparatorTest.java | 84 +++++++++
.../model/map/species/GenericProteinTest.java | 10 +-
.../IonChannelProteinComparatorTest.java | 84 +++++++++
.../model/map/species/IonComparatorTest.java | 10 +-
.../mapviewer/model/map/species/IonTest.java | 10 +-
.../map/species/PhenotypeComparatorTest.java | 13 +-
.../model/map/species/PhenotypeTest.java | 34 +++-
.../map/species/ProteinComparatorTest.java | 110 ++++++-----
.../ReceptorProteinComparatorTest.java | 84 +++++++++
.../map/species/ReceptorProteinTest.java | 10 +-
.../model/map/species/RnaComparatorTest.java | 10 +-
.../mapviewer/model/map/species/RnaTest.java | 10 +-
.../species/SimpleMoleculeComparatorTest.java | 14 +-
.../model/map/species/SimpleMoleculeTest.java | 10 +-
.../map/species/SpeciesComparatorTest.java | 3 -
.../TruncatedProteinComparatorTest.java | 84 +++++++++
.../map/species/TruncatedProteinTest.java | 10 +-
.../map/species/UnknownComparatorTest.java | 10 +-
.../model/map/species/UnknownTest.java | 10 +-
.../modelutils/map/ElementUtilsTest.java | 36 ++++
.../wikipathway/XML/ModelContructor.java | 10 +-
.../wikipathway/XML/ModelToGPMLTest.java | 2 +-
.../mapviewer/persist/dao/ProjectDaoTest.java | 16 +-
.../persist/dao/map/CommentDaoTest.java | 18 +-
.../persist/dao/map/LayoutDaoTest.java | 18 +-
.../persist/dao/map/ModelDaoTest.java | 20 +-
.../dao/map/graph/DataMiningDaoTest.java | 2 +-
.../dao/map/layout/alias/AliasDaoTest.java | 16 +-
.../map/layout/alias/AntisenseRnaTest.java | 2 +-
.../persist/dao/map/layout/alias/RnaTest.java | 2 +-
.../services/impl/SearchServiceTest.java | 8 +-
.../search/data/FullAliasViewFactoryTest.java | 8 +-
.../search/db/drug/DrugViewFactoryTest.java | 2 +-
124 files changed, 1860 insertions(+), 868 deletions(-)
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java
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 b75019e872..b920636e1d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -80,8 +80,8 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
proteinAlias2.setName("PDK1");
proteinAlias2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
- model.addAlias(proteinAlias1);
- model.addAlias(proteinAlias2);
+ model.addElement(proteinAlias1);
+ model.addElement(proteinAlias2);
modelAnnotator.annotateModel(model, updater, null);
@@ -100,12 +100,12 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
Model model = new ModelFullIndexed(null);
GenericProtein species = new GenericProtein("id1");
species.setName("SNCA");
- model.addAlias(species);
+ model.addElement(species);
GenericProtein species2 = new GenericProtein("id2");
species2.setName("PDK1");
species2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
- model.addAlias(species2);
+ model.addElement(species2);
model.addReaction(new Reaction());
Map<Class<?>, List<ElementAnnotator>> annotators = new HashMap<>();
@@ -305,9 +305,9 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
model.addSubmodelConnection(new ModelSubmodelConnection(submodel2, SubmodelType.UNKNOWN));
- model.addAlias(protein);
- submodel.addAlias(protein);
- submodel2.addAlias(protein);
+ model.addElement(protein);
+ submodel.addElement(protein);
+ submodel2.addElement(protein);
final MutableDouble maxProgress = new MutableDouble(0.0);
diff --git a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
index 3a237968f4..badffff4c3 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ConsoleConverter.java
@@ -130,7 +130,7 @@ public class ConsoleConverter {
double angle = x / size * 2 * Math.PI;
alias.setX(middleX + Math.sin(angle) * inputOptions.getRadius());
alias.setY(middleY + Math.cos(angle) * inputOptions.getRadius());
- model.addAlias(alias);
+ model.addElement(alias);
x++;
}
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 cce1a06bd6..7badb62f75 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
@@ -414,7 +414,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
List<Compartment> aliases = aliasCollectionParser.parseXmlCompartmentAliasCollection(listOfComparmentAlias);
for (Element alias : aliases) {
rap.processNotes(alias);
- model.addAlias(alias);
+ model.addElement(alias);
}
}
@@ -454,7 +454,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
List<Complex> aliases = aliasCollectionParser.parseXmlComplexAliasCollection(listOfComplexSpeciesAlias);
for (Element alias : aliases) {
rap.processNotes(alias);
- model.addAlias(alias);
+ model.addElement(alias);
}
}
@@ -462,7 +462,7 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
List<Species> aliases = aliasCollectionParser.parseXmlSpeciesAliasCollection(listofSpeciesAlias);
for (Element alias : aliases) {
rap.processNotes(alias);
- model.addAlias(alias);
+ model.addElement(alias);
}
}
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 e4d207986e..57f6280526 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
@@ -140,7 +140,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
result.setState(state);
String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
if (!compartmentAliasId.isEmpty()) {
- Compartment ca = model.getCompartmentAliasByCompartmentAliasId(compartmentAliasId);
+ Compartment ca = model.getElementByElementId(compartmentAliasId);
if (ca == null) {
throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
} else {
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 29e9294458..7b2e486120 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
@@ -111,7 +111,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
result.setState(state);
String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
if (!compartmentAliasId.isEmpty()) {
- Compartment ca = model.getCompartmentAliasByCompartmentAliasId(compartmentAliasId);
+ Compartment ca = model.getElementByElementId(compartmentAliasId);
if (ca == null) {
throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
} else {
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 4f05057943..7c2638d7d4 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
@@ -453,22 +453,22 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
rap.processNotes(
"Symbol: ROS1\r\nName: c-ros oncogene 1 , receptor tyrosine kinase\r\nDescription: RecName: Full=Proto-oncogene tyrosine-protein kinase ROS; EC=2.7.10.1; AltName: Full=Proto-oncogene c-Ros; AltName: Full=Proto-oncogene c-Ros-1; AltName: Full=Receptor tyrosine kinase c-ros oncogene 1; AltName: Full=c-Ros receptor tyrosine kinase; Flags: Precursor;\r\nPrevious Symbols:\r\nSynonyms: ROS, MCF3",
speciesAlias);
- model.addAlias(speciesAlias);
+ model.addElement(speciesAlias);
GenericProtein alias = new GenericProtein("id");
alias.setName("ROS");
- model.addAlias(alias);
+ model.addElement(alias);
SimpleMolecule speciesAlias2 = new SimpleMolecule("id2");
speciesAlias2.setName("PDK1");
rap.processNotes(
"Symbol: ROS1\r\nName: c-ros oncogene 1 , receptor tyrosine kinase\r\nDescription: RecName: Full=Proto-oncogene tyrosine-protein kinase ROS; EC=2.7.10.1; AltName: Full=Proto-oncogene c-Ros; AltName: Full=Proto-oncogene c-Ros-1; AltName: Full=Receptor tyrosine kinase c-ros oncogene 1; AltName: Full=c-Ros receptor tyrosine kinase; Flags: Precursor;\r\nPrevious Symbols:\r\nSynonyms: ROS, MCF3",
speciesAlias2);
- model.addAlias(speciesAlias2);
+ model.addElement(speciesAlias2);
SimpleMolecule alias2 = new SimpleMolecule("id3");
alias2.setName("PDK1");
- model.addAlias(alias2);
+ model.addElement(alias2);
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xmlString = parser.toXml(model);
@@ -521,7 +521,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
model.setIdModel("id");
Species alias = new GenericProtein("a");
alias.setName("AA");
- model.addAlias(alias);
+ model.addElement(alias);
parser.toXml(model);
} catch (Exception e) {
@@ -806,7 +806,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
model.setHeight(100);
Gene gene = new Gene("gene_id_1");
gene.setName("geneNAME");
- model.addAlias(gene);
+ model.addElement(gene);
String xmlString = parser.toXml(model);
assertTrue(xmlString.contains("gene_id_1"));
assertTrue(xmlString.contains("geneNAME"));
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 53828971c0..dc31440d59 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
@@ -256,7 +256,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
model.setHeight(100);
GenericProtein alias = new GenericProtein("aid");
alias.setName("name & no-name");
- model.addAlias(alias);
+ model.addElement(alias);
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String string = parser.toXml(model);
@@ -286,7 +286,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
model.setHeight(100);
GenericProtein alias = new GenericProtein("aid");
alias.setName("name\rno-name");
- model.addAlias(alias);
+ model.addElement(alias);
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String string = parser.toXml(model);
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 2353bd3dc5..c653991cf3 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
@@ -148,7 +148,7 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
try {
Model model = new ModelFullIndexed(null);
GenericProtein alias = new GenericProtein("sa1");
- model.addAlias(alias);
+ model.addElement(alias);
String xmlString = readFile("testFiles/invalid/group_collection3.xml");
Node node = getNodeFromXmlString(xmlString);
@@ -409,16 +409,16 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
try {
Model model = new ModelFullIndexed(null);
Species alias = new GenericProtein("sa1035");
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("sa1036");
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("sa1037");
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("sa1038");
- model.addAlias(alias);
+ model.addElement(alias);
String string = "<celldesigner:group id=\"g74\" members=\"sa1035,sa1036,sa1037,sa1038\"/>";
Node node = getNodeFromXmlString(string);
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 90cc28dac5..d60228eb0a 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
@@ -56,7 +56,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
private Model createStubModel() {
Model model = new ModelFullIndexed(null);
- model.addAlias(new Compartment("ca1"));
+ model.addElement(new Compartment("ca1"));
return model;
}
@@ -308,7 +308,7 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
alias.setActivity(true);
elements.addElement(new CellDesignerComplexSpecies(testSpeciesId));
- model.addAlias(alias);
+ model.addElement(alias);
SpeciesAliasXmlParser parser = new SpeciesAliasXmlParser(elements, model);
String xml = parser.toXml(alias);
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 269ea1ad7b..cd73ccc96c 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
@@ -104,84 +104,84 @@ public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
sa1.setY(200.0);
sa1.setWidth(300.0);
sa1.setHeight(400.0);
- model.addAlias(sa1);
+ model.addElement(sa1);
Species sa2 = new GenericProtein("sa2");
sa2.setX(1050.0);
sa2.setY(2050.0);
sa2.setWidth(300.0);
sa2.setHeight(450.0);
- model.addAlias(sa2);
+ model.addElement(sa2);
Species sa3 = new GenericProtein("sa3");
sa3.setX(600.0);
sa3.setY(250.0);
sa3.setWidth(300.0);
sa3.setHeight(400.0);
- model.addAlias(sa3);
+ model.addElement(sa3);
Species sa4 = new GenericProtein("sa4");
sa4.setX(550.0);
sa4.setY(350.0);
sa4.setWidth(300.0);
sa4.setHeight(450.0);
- model.addAlias(sa4);
+ model.addElement(sa4);
Species sa5 = new GenericProtein("sa5");
sa5.setX(10.0);
sa5.setY(250.0);
sa5.setWidth(300.0);
sa5.setHeight(450.0);
- model.addAlias(sa5);
+ model.addElement(sa5);
Species sa6 = new GenericProtein("sa6");
sa6.setX(10.0);
sa6.setY(250.0);
sa6.setWidth(300.0);
sa6.setHeight(450.0);
- model.addAlias(sa6);
+ model.addElement(sa6);
Species sa10 = new GenericProtein("sa10");
sa10.setX(210.0);
sa10.setY(220.0);
sa10.setWidth(320.0);
sa10.setHeight(250.0);
- model.addAlias(sa10);
+ model.addElement(sa10);
Species sa11 = new GenericProtein("sa11");
sa11.setX(11.0);
sa11.setY(320.0);
sa11.setWidth(321.0);
sa11.setHeight(150.0);
- model.addAlias(sa11);
+ model.addElement(sa11);
Species sa12 = new GenericProtein("sa12");
sa12.setX(12.0);
sa12.setY(20.0);
sa12.setWidth(321.0);
sa12.setHeight(150.0);
- model.addAlias(sa12);
+ model.addElement(sa12);
Species sa13 = new GenericProtein("sa13");
sa13.setX(513.0);
sa13.setY(20.0);
sa13.setWidth(321.0);
sa13.setHeight(150.0);
- model.addAlias(sa13);
+ model.addElement(sa13);
Species sa14 = new GenericProtein("sa14");
sa14.setX(14.0);
sa14.setY(820.0);
sa14.setWidth(321.0);
sa14.setHeight(150.0);
- model.addAlias(sa14);
+ model.addElement(sa14);
Species sa15 = new GenericProtein("sa15");
sa15.setX(815.0);
sa15.setY(620.0);
sa15.setWidth(321.0);
sa15.setHeight(150.0);
- model.addAlias(sa15);
+ model.addElement(sa15);
return model;
}
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 9e568dd336..cc85c6f0e7 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
@@ -38,16 +38,16 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
parser = new ReactionXmlParser(elements);
Species alias = new GenericProtein("sa1");
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("sa2");
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("sa3");
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("sa4");
- model.addAlias(alias);
+ model.addElement(alias);
elements.addElement(new CellDesignerGenericProtein("s1"));
elements.addElement(new CellDesignerGenericProtein("s2"));
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 c9f057780d..82e37d7d14 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
@@ -1550,7 +1550,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa1.setY(200.0);
sa1.setWidth(300.0);
sa1.setHeight(400.0);
- model.addAlias(sa1);
+ model.addElement(sa1);
elements.addAlias(sa1, new CellDesignerGenericProtein("s1"));
Species sa2 = new GenericProtein("sa2");
@@ -1558,7 +1558,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa2.setY(2050.0);
sa2.setWidth(300.0);
sa2.setHeight(450.0);
- model.addAlias(sa2);
+ model.addElement(sa2);
elements.addAlias(sa2, new CellDesignerGenericProtein("s2"));
Species sa3 = new GenericProtein("sa3");
@@ -1566,7 +1566,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa3.setY(250.0);
sa3.setWidth(300.0);
sa3.setHeight(400.0);
- model.addAlias(sa3);
+ model.addElement(sa3);
elements.addAlias(sa3, new CellDesignerGenericProtein("s3"));
Species sa4 = new GenericProtein("sa4");
@@ -1574,7 +1574,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa4.setY(350.0);
sa4.setWidth(300.0);
sa4.setHeight(450.0);
- model.addAlias(sa4);
+ model.addElement(sa4);
elements.addElement(new CellDesignerGenericProtein("s4"));
Species sa5 = new GenericProtein("sa5");
@@ -1582,7 +1582,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa5.setY(250.0);
sa5.setWidth(300.0);
sa5.setHeight(450.0);
- model.addAlias(sa5);
+ model.addElement(sa5);
elements.addElement(new CellDesignerGenericProtein("s5"));
Species sa6 = new GenericProtein("sa6");
@@ -1590,7 +1590,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa6.setY(250.0);
sa6.setWidth(300.0);
sa6.setHeight(450.0);
- model.addAlias(sa6);
+ model.addElement(sa6);
elements.addElement(new CellDesignerGenericProtein("s6"));
@@ -1599,7 +1599,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa10.setY(220.0);
sa10.setWidth(320.0);
sa10.setHeight(250.0);
- model.addAlias(sa10);
+ model.addElement(sa10);
elements.addElement(new CellDesignerGenericProtein("s10"));
Species sa11 = new GenericProtein("sa11");
@@ -1607,7 +1607,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa11.setY(320.0);
sa11.setWidth(321.0);
sa11.setHeight(150.0);
- model.addAlias(sa11);
+ model.addElement(sa11);
elements.addElement(new CellDesignerGenericProtein("s11"));
Species sa12 = new GenericProtein("sa12");
@@ -1615,7 +1615,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa12.setY(20.0);
sa12.setWidth(321.0);
sa12.setHeight(150.0);
- model.addAlias(sa12);
+ model.addElement(sa12);
elements.addElement(new CellDesignerGenericProtein("s12"));
Species sa13 = new GenericProtein("sa13");
@@ -1623,7 +1623,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa13.setY(20.0);
sa13.setWidth(321.0);
sa13.setHeight(150.0);
- model.addAlias(sa13);
+ model.addElement(sa13);
elements.addElement(new CellDesignerGenericProtein("s13"));
Species sa14 = new GenericProtein("sa14");
@@ -1631,7 +1631,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa14.setY(820.0);
sa14.setWidth(321.0);
sa14.setHeight(150.0);
- model.addAlias(sa14);
+ model.addElement(sa14);
elements.addElement(new CellDesignerGenericProtein("s14"));
Species sa15 = new GenericProtein("sa15");
@@ -1639,7 +1639,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
sa15.setY(620.0);
sa15.setWidth(321.0);
sa15.setHeight(150.0);
- model.addAlias(sa15);
+ model.addElement(sa15);
elements.addElement(new CellDesignerGenericProtein("s15"));
return model;
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 09d2068026..6599085012 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
@@ -58,7 +58,7 @@ public class ReactionToXmlTest {
Model model = new ModelFullIndexed(null);
Species alias = new GenericProtein("2");
- model.addAlias(alias);
+ model.addElement(alias);
Reaction reaction = new TransportReaction();
@@ -115,7 +115,7 @@ public class ReactionToXmlTest {
Model model = new ModelFullIndexed(null);
Species alias = new GenericProtein("2");
- model.addAlias(alias);
+ model.addElement(alias);
Complex complex = new Complex("4");
complex.addAlias(alias);
@@ -123,7 +123,7 @@ public class ReactionToXmlTest {
alias.setParent(complex);
alias.setComplexAlias(complex);
- model.addAlias(complex);
+ model.addElement(complex);
Reaction reaction = new TransportReaction();
@@ -152,7 +152,7 @@ public class ReactionToXmlTest {
Model model = new ModelFullIndexed(null);
Species alias = new GenericProtein("2");
- model.addAlias(alias);
+ model.addElement(alias);
Reaction reaction = new Reaction();
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 9416efdc86..80dc4c55f2 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
@@ -170,7 +170,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
alias.setParent(ca);
- model.addAlias(alias);
+ model.addElement(alias);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
String xml = parser.toXml(alias);
@@ -195,7 +195,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
alias.setCompartmentAlias(ca);
- model.addAlias(alias);
+ model.addElement(alias);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
String xml = parser.toXml(alias);
@@ -243,7 +243,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
alias.setHeight(100);
alias.setModel(model);
- model.addAlias(alias);
+ model.addElement(alias);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
String xml = parser.toXml(alias);
@@ -268,7 +268,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
alias.setParent(ca);
- model.addAlias(alias);
+ model.addElement(alias);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
String xml = parser.toXml(alias);
@@ -291,7 +291,7 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
alias.setActivity(true);
- model.addAlias(alias);
+ model.addElement(alias);
ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
String xml = parser.toXml(alias);
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 ca6b5b5173..0357a7fdef 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
@@ -311,10 +311,10 @@ public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
species.setModel(model);
Species alias = species.createAlias("alias" + (x++));
- model.addAlias(alias);
+ model.addElement(alias);
speciesList.add(alias);
}
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
String convertedString = parser.speciesCollectionToSbmlString(speciesList);
assertNotNull(convertedString);
node = getNodeFromXmlString(convertedString);
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 14c9a29591..0383f44f69 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
@@ -645,7 +645,7 @@ public class SbgnmlXmlParser {
if (g.getCompartmentRef() != null) {
Glyph compartmentGlyph = (Glyph) g.getCompartmentRef();
- Compartment compartmentAlias = model.getCompartmentAliasByCompartmentAliasId(compartmentGlyph.getId());
+ Compartment compartmentAlias = model.getElementByElementId(compartmentGlyph.getId());
newAlias.setParent(compartmentAlias);
newAlias.setCompartmentAlias(compartmentAlias);
compartmentAlias.addElement(newAlias);
@@ -671,7 +671,7 @@ public class SbgnmlXmlParser {
}
}
- model.addAlias(newAlias);
+ model.addElement(newAlias);
}
/**
@@ -1504,6 +1504,6 @@ public class SbgnmlXmlParser {
compAlias.getX() + compAlias.getThickness() + CONTAINER_NAME_MARGIN, compAlias.getY() + compAlias.getThickness() + CONTAINER_NAME_MARGIN);
}
- model.addAlias(compAlias);
+ model.addElement(compAlias);
}
}
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 96d8113bbb..d2f9ef6899 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
@@ -90,7 +90,7 @@ public class NormalImageGeneratorTest {
alias.setY(10);
alias.setWidth(200);
alias.setHeight(50);
- model.addAlias(alias);
+ model.addElement(alias);
Species a2 = new GenericProtein("2");
a2.setName("b");
@@ -99,7 +99,7 @@ public class NormalImageGeneratorTest {
a2.setWidth(200);
a2.setHeight(50);
a2.setFontSize(30);
- model.addAlias(a2);
+ model.addElement(a2);
return model;
}
@@ -155,7 +155,7 @@ public class NormalImageGeneratorTest {
alias.setY(90);
alias.setWidth(100);
alias.setHeight(50);
- model.addAlias(alias);
+ model.addElement(alias);
return model;
}
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 a69271674f..86428c73d4 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
@@ -94,7 +94,7 @@ public class PdfImageGeneratorTest {
alias.setY(90);
alias.setWidth(100);
alias.setHeight(50);
- model.addAlias(alias);
+ model.addElement(alias);
return model;
}
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 aee2aa52a3..15dd6e4f68 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
@@ -27,7 +27,7 @@ public class AllPlaceFinderTest {
public void oneEmptyCompartments() throws InvalidXmlSchemaException, IOException {
String actual = null;
Model model = new ModelFullIndexed(null);
- model.addAlias(createCompartmentAlias(94.0, 70.0, 355.0, 173.0));
+ model.addElement(createCompartmentAlias(94.0, 70.0, 355.0, 173.0));
for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
@@ -43,8 +43,8 @@ public class AllPlaceFinderTest {
public void twoSeparatedCompartments() throws InvalidXmlSchemaException, IOException {
String actual = null;
Model model = new ModelFullIndexed(null);
- model.addAlias(createCompartmentAlias(70.0, 81.0, 229.0, 213.0));
- model.addAlias(createCompartmentAlias(332.0, 66.0, 188.0, 255.0));
+ model.addElement(createCompartmentAlias(70.0, 81.0, 229.0, 213.0));
+ model.addElement(createCompartmentAlias(332.0, 66.0, 188.0, 255.0));
String expected = "";
for (Compartment alias : model.getCompartmentsAliases()) {
@@ -60,9 +60,9 @@ public class AllPlaceFinderTest {
public void twoIntersectingCompartments() throws InvalidXmlSchemaException, IOException {
Model model = new ModelFullIndexed(null);
Compartment alias = createCompartmentAlias(87.0, 56.0, 235.0, 219.0);
- model.addAlias(alias);
+ model.addElement(alias);
Compartment alias2 = createCompartmentAlias(227.0, 17.0, 290.0, 317.0);
- model.addAlias(alias2);
+ model.addElement(alias2);
PlaceFinder pf = new PlaceFinder(model);
Rectangle2D rect = pf.getRetangle(alias2);
@@ -74,8 +74,8 @@ public class AllPlaceFinderTest {
@Test
public void oneCompartmentCompletlyOverlapSecondOne() throws InvalidXmlSchemaException, IOException {
Model model = new ModelFullIndexed(null);
- model.addAlias(createCompartmentAlias(45.0, 38.0, 174.0, 169.0));
- model.addAlias(createCompartmentAlias(118.0, 85.0, 60.0, 68.0));
+ model.addElement(createCompartmentAlias(45.0, 38.0, 174.0, 169.0));
+ model.addElement(createCompartmentAlias(118.0, 85.0, 60.0, 68.0));
double actual = 0.0;
for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
@@ -88,9 +88,9 @@ public class AllPlaceFinderTest {
@Test
public void perfectOverlapingOfThreeCompartments() throws InvalidXmlSchemaException, IOException {
Model model = new ModelFullIndexed(null);
- model.addAlias(createCompartmentAlias(226.0, 70.0, 138.0, 112.0));
- model.addAlias(createCompartmentAlias(163.0, 70.0, 138.0, 112.0));
- model.addAlias(createCompartmentAlias(88.0, 70.0, 138.0, 112.0));
+ model.addElement(createCompartmentAlias(226.0, 70.0, 138.0, 112.0));
+ model.addElement(createCompartmentAlias(163.0, 70.0, 138.0, 112.0));
+ model.addElement(createCompartmentAlias(88.0, 70.0, 138.0, 112.0));
double actual = 0.0;
Rectangle2D result = null;
for (Compartment alias : model.getCompartmentsAliases()) {
@@ -133,8 +133,8 @@ public class AllPlaceFinderTest {
@Test
public void problematic() throws InvalidXmlSchemaException, IOException {
Model model = new ModelFullIndexed(null);
- model.addAlias(createCompartmentAlias(4521.0, 0.0, 10000.0, 6000.0));
- model.addAlias(createCompartmentAlias(4828.0, 0.0, 5172.0, 6000.0));
+ model.addElement(createCompartmentAlias(4521.0, 0.0, 10000.0, 6000.0));
+ model.addElement(createCompartmentAlias(4828.0, 0.0, 5172.0, 6000.0));
double actual = 0.0;
for (Compartment alias : model.getCompartmentsAliases()) {
PlaceFinder pf = new PlaceFinder(model);
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index 62f7709fc9..cc87a72141 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -60,44 +60,44 @@ public class ComplexZipConverterTest {
Model result = new ModelFullIndexed(null);
Species sa1 = new GenericProtein("sa1");
- result.addAlias(sa1);
+ result.addElement(sa1);
Species sa2 = new GenericProtein("sa2");
- result.addAlias(sa2);
+ result.addElement(sa2);
Species sa3 = new GenericProtein("sa3");
- result.addAlias(sa3);
+ result.addElement(sa3);
Species sa4 = new Phenotype("sa4");
- result.addAlias(sa4);
+ result.addElement(sa4);
Complex ca1 = new Complex("ca1");
ca1.setName("main");
- result.addAlias(ca1);
+ result.addElement(ca1);
Species sa5 = new GenericProtein("sa5");
sa5.setName("sa1");
- result.addAlias(sa5);
+ result.addElement(sa5);
ca1.addAlias(sa5);
Species sa6 = new Phenotype("sa6");
sa6.setName("sa4");
- result.addAlias(sa6);
+ result.addElement(sa6);
ca1.addAlias(sa6);
Complex ca2 = new Complex("ca2");
ca2.setName("s1");
- result.addAlias(ca2);
+ result.addElement(ca2);
Species sa7 = new GenericProtein("sa7");
sa7.setName("sa1");
- result.addAlias(sa7);
+ result.addElement(sa7);
ca2.addAlias(sa7);
Complex ca3 = new Complex("cs3");
ca3.setName("s2");
- result.addAlias(ca3);
+ result.addElement(ca3);
Complex ca4 = new Complex("cs4");
ca4.setName("s3");
- result.addAlias(ca4);
+ result.addElement(ca4);
Reaction r1 = new TransportReaction();
r1.addReactant(new Reactant(sa5));
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 70253198c1..fbab64735f 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -178,7 +178,7 @@ public class CopyCommand extends NewModelCommand {
if (alias instanceof Compartment) {
Compartment copy = ((Compartment) alias).copy();
copy.getElements().clear();
- result.addAlias(copy);
+ result.addElement(copy);
}
}
@@ -194,15 +194,15 @@ public class CopyCommand extends NewModelCommand {
// the trick is that in addAlias also some connections are added, so
// lets clear info about parents
- result.addAlias(copy);
+ result.addElement(copy);
if (ca != null) {
- ca = result.getCompartmentAliasByCompartmentAliasId(ca.getElementId());
+ ca = result.getElementByElementId(ca.getElementId());
copy.setCompartmentAlias(ca);
}
if (parent instanceof Compartment) {
ca = (Compartment) parent;
- ca = result.getCompartmentAliasByCompartmentAliasId(ca.getElementId());
+ ca = result.getElementByElementId(ca.getElementId());
copy.setParent(ca);
}
} else if (alias instanceof Compartment) {
@@ -367,7 +367,7 @@ public class CopyCommand extends NewModelCommand {
private void updateAliasReferences(Element alias, Model model, Model originalModel) {
if (alias instanceof Compartment) {
Compartment compartmentAlias = (Compartment) alias;
- Compartment original = originalModel.getCompartmentAliasByCompartmentAliasId(alias.getElementId());
+ Compartment original = originalModel.getElementByElementId(alias.getElementId());
for (Element a : original.getElements()) {
compartmentAlias.addElement(model.getElementByElementId(a.getElementId()));
}
@@ -402,7 +402,7 @@ public class CopyCommand extends NewModelCommand {
alias.setModel(model);
if (alias.getCompartmentAlias() != null) {
- alias.setCompartmentAlias(model.getCompartmentAliasByCompartmentAliasId(alias.getCompartmentAlias().getElementId()));
+ alias.setCompartmentAlias(model.getElementByElementId(alias.getCompartmentAlias().getElementId()));
}
}
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index 98ff78e39a..14ec54cc19 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -157,7 +157,7 @@ public class CreateHierarchyCommand extends ModelCommand {
alias.setNamePoint(
new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
- model.addAlias(alias);
+ model.addElement(alias);
}
for (LayerText text : layer.getTexts()) {
PathwayCompartment alias = new PathwayCompartment("art" + (id++));
@@ -170,7 +170,7 @@ public class CreateHierarchyCommand extends ModelCommand {
alias.setNamePoint(
new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
- model.addAlias(alias);
+ model.addElement(alias);
}
}
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 685dc44f7c..0ca7374b24 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -53,11 +53,11 @@ public abstract class CommandTestFunctions {
alias.setFormerSymbols(list2);
Complex complexAlias = new Complex("complex_alias_id");
- model.addAlias(complexAlias);
+ model.addElement(complexAlias);
complexAlias.addAlias(alias);
- model.addAlias(alias);
+ model.addElement(alias);
return model;
}
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 6336703fe6..cf881e785b 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -61,7 +61,7 @@ public class CopyCommandTest extends CommandTestFunctions {
GenericProtein protein = new GenericProtein("A");
protein.setNotes(null);
- model.addAlias(protein);
+ model.addElement(protein);
Model copy = new CopyCommand(model).execute();
@@ -83,14 +83,14 @@ public class CopyCommandTest extends CommandTestFunctions {
GenericProtein protein = new GenericProtein("A");
protein.setNotes(null);
complexAlias.addAlias(protein);
- model.addAlias(protein);
- model.addAlias(complexAlias);
+ model.addElement(protein);
+ model.addElement(complexAlias);
GenericProtein alias = new GenericProtein("B");
alias.setNotes(null);
complexAlias.addAlias(alias);
- model.addAlias(alias);
+ model.addElement(alias);
Model copy = new CopyCommand(model).execute();
@@ -281,7 +281,7 @@ public class CopyCommandTest extends CommandTestFunctions {
GenericProtein alias = new GenericProtein("a_id");
alias.setName("ad");
- model.addAlias(alias);
+ model.addElement(alias);
Layer layer = new Layer();
layer.setName("layer name");
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 08822f4c56..e4d697d089 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -488,19 +488,10 @@ public enum MiriamType {
this.uris.add(string);
}
for (Class<?> clazz : classes) {
- if (AnnotatedObject.class.isAssignableFrom(clazz)) {
- this.validClass.add((Class<? extends AnnotatedObject>) clazz);
- } else {
- throw new InvalidArgumentException();
- }
+ this.validClass.add((Class<? extends AnnotatedObject>) clazz);
}
for (Class<?> clazz : requiredClasses) {
- if (AnnotatedObject.class.isAssignableFrom(clazz)) {
- this.requiredClass.add((Class<? extends AnnotatedObject>) clazz);
- } else {
- throw new InvalidArgumentException();
- }
-
+ this.requiredClass.add((Class<? extends AnnotatedObject>) clazz);
}
this.registryIdentifier = registryIdentifier;
}
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 66e27206ac..b29a5720fd 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
@@ -52,7 +52,7 @@ public interface Model {
* @param alias
* alias to add
*/
- void addAlias(Element alias);
+ void addElement(Element alias);
/**
* Returns map model version.
@@ -146,16 +146,6 @@ public interface Model {
*/
Set<Reaction> getReactions();
- /**
- * Returns compartment alias with the given alias id.
- *
- * @param id
- * compartment alias identifier ({@link Element#aliasId})
- * @return compartment alias with the given compartment alias id
- */
-
- Compartment getCompartmentAliasByCompartmentAliasId(String id);
-
/**
* @return list of compartment aliases
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 84004ea609..72eeeed647 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
@@ -114,34 +114,34 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addAlias(Element alias) {
- if (alias instanceof Species) {
- addSpeciesAlias((Species) alias);
- } else if (alias instanceof Compartment) {
- addCompartmentAlias((Compartment) alias);
+ public void addElement(Element element) {
+ if (element.getElementId() == null || element.getElementId().isEmpty()) {
+ throw new InvalidArgumentException("Element identifier cannot be empty");
+ }
+ if (element instanceof Species) {
+ addSpecies((Species) element);
+ } else if (element instanceof Compartment) {
+ addCompartmentAlias((Compartment) element);
} else {
- throw new InvalidArgumentException("Unknown type of alias: " + alias);
+ throw new InvalidArgumentException("Unknown type of element: " + element);
}
}
/**
* Adds {@link Species} to the model.
*
- * @param al
+ * @param species
* alias to add
*/
- private void addSpeciesAlias(Species al) {
- if (al.getElementId() == null || al.getElementId().isEmpty()) {
- throw new InvalidArgumentException("Alias identifier cannot be empty");
- }
- modelData.addAlias(al);
+ private void addSpecies(Species species) {
+ modelData.addAlias(species);
- Element alias2 = aliasByAliasId.get(al.getElementId());
+ Element alias2 = aliasByAliasId.get(species.getElementId());
if (alias2 == null) {
- aliasByAliasId.put(al.getElementId(), al);
- aliasByDbId.put(al.getId(), al);
+ aliasByAliasId.put(species.getElementId(), species);
+ aliasByDbId.put(species.getId(), species);
} else {
- throw new InvalidArgumentException("Alias with duplicated id: " + al.getElementId());
+ throw new InvalidArgumentException("Species with duplicated id: " + species.getElementId());
}
}
@@ -225,11 +225,6 @@ public class ModelFullIndexed implements Model {
}
}
- @Override
- public Compartment getCompartmentAliasByCompartmentAliasId(String id) {
- return (Compartment) aliasByAliasId.get(id);
- }
-
@Override
public List<Compartment> getCompartmentsAliases() {
List<Compartment> result = new ArrayList<Compartment>();
@@ -254,7 +249,7 @@ public class ModelFullIndexed implements Model {
@Override
public void addAliases(List<? extends Element> aliases) {
for (Element alias : aliases) {
- addAlias(alias);
+ addElement(alias);
}
}
@@ -770,10 +765,10 @@ public class ModelFullIndexed implements Model {
@Override
public List<Species> getSpeciesList() {
- List<Species> result = new ArrayList<Species>();
- for (Element alias : modelData.getAliases()) {
- if (alias instanceof Species) {
- result.add((Species) alias);
+ List<Species> result = new ArrayList<>();
+ for (Element element : modelData.getAliases()) {
+ if (element instanceof Species) {
+ result.add((Species) element);
}
}
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
index 386f48cd6d..779352ff3a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
@@ -15,6 +15,12 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+/**
+ * Entity representing antisense rna element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("ANTISENSE_RNA_ALIAS")
public class AntisenseRna extends Species {
@@ -22,16 +28,29 @@ public class AntisenseRna extends Species {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
+ /**
+ * List of {@link AntisenseRnaRegion regions} related to this
+ * {@link AntisenseRna}.
+ */
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "species")
@LazyCollection(LazyCollectionOption.FALSE)
- private List<AntisenseRnaRegion> regions = new ArrayList<>();
+ private List<AntisenseRnaRegion> regions = new ArrayList<>();
+ /**
+ * Empty constructor required by hibernate.
+ */
AntisenseRna() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public AntisenseRna(AntisenseRna original) {
super(original);
for (AntisenseRnaRegion region : original.getRegions()) {
@@ -39,15 +58,27 @@ public class AntisenseRna extends Species {
}
}
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public AntisenseRna(String elementId) {
+ setElementId(elementId);
+ }
+
+ /**
+ * Adds {@link AntisenseRnaRegion} to the object.
+ *
+ * @param antisenseRnaRegionAlias
+ * alement to be added
+ */
public void addRegion(AntisenseRnaRegion antisenseRnaRegionAlias) {
regions.add(antisenseRnaRegionAlias);
antisenseRnaRegionAlias.setSpecies(this);
}
- public AntisenseRna(String aliasId) {
- setElementId(aliasId);
- }
-
@Override
public AntisenseRna copy() {
if (this.getClass() == AntisenseRna.class) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
index f886d20073..e7dfa3ef10 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
@@ -11,8 +11,14 @@ import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+/**
+ * Comparator class used for comparing {@link AntisenseRna} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
-
+
/**
* Default class logger.
*/
@@ -98,7 +104,7 @@ public class AntisenseRnaComparator implements Comparator<AntisenseRna> {
if (stringSetComparator.compare(set1, set2) != 0) {
return stringSetComparator.compare(set1, set2);
}
-
+
return 0;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
index 72703817ac..bec1401d70 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
@@ -4,6 +4,12 @@ import javax.persistence.Column;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
+/**
+ * Entity representing chemical element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("CHEMICAL_ALIAS")
public abstract class Chemical extends Species {
@@ -37,9 +43,18 @@ public abstract class Chemical extends Species {
private String inChIKey;
+ /**
+ * Empty constructor required by hibernate.
+ */
Chemical() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Chemical(Chemical original) {
super(original);
smiles = original.getSmiles();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
index 4b9cba9976..c9d1bb5ff3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
@@ -5,23 +5,36 @@ import java.util.Comparator;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link Chemical} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class ChemicalComparator implements Comparator<Chemical> {
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ChemicalComparator.class);
+ private static Logger logger = Logger.getLogger(ChemicalComparator.class);
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private double epsilon;
- private IonComparator ionAliasComparator;
- private SimpleMoleculeComparator simpleMoleculeAliasComparator;
+ /**
+ * Comparator for {@link Ion} implementation of {@link Chemical}.
+ */
+ private IonComparator ionAliasComparator;
+
+ /**
+ * Comparator for {@link SimpleMolecule} implementation of {@link Chemical}.
+ */
+ private SimpleMoleculeComparator simpleMoleculeAliasComparator;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -55,9 +68,7 @@ public class ChemicalComparator implements Comparator<Chemical> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Chemical.class)) {
- return internalCompare(arg0, arg1);
- } else if (arg0.getClass().equals(Ion.class)) {
+ if (arg0.getClass().equals(Ion.class)) {
return ionAliasComparator.compare((Ion) arg0, (Ion) arg1);
} else if (arg0.getClass().equals(SimpleMolecule.class)) {
return simpleMoleculeAliasComparator.compare((SimpleMolecule) arg0, (SimpleMolecule) arg1);
@@ -87,6 +98,23 @@ public class ChemicalComparator implements Comparator<Chemical> {
if (result != 0) {
return result;
}
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getSmiles(), arg1.getSmiles()) != 0) {
+ logger.debug("Smiles different: " + arg0.getSmiles() + ", " + arg1.getSmiles());
+ return stringComparator.compare(arg0.getSmiles(), arg1.getSmiles());
+ }
+
+ if (stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey()) != 0) {
+ logger.debug("InChIKey different: " + arg0.getInChIKey() + ", " + arg1.getInChIKey());
+ return stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey());
+ }
+
+ if (stringComparator.compare(arg0.getInChI(), arg1.getInChI()) != 0) {
+ logger.debug("InChI different: " + arg0.getInChI() + ", " + arg1.getInChI());
+ return stringComparator.compare(arg0.getInChI(), arg1.getInChI());
+ }
+
return 0;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
index 3e3d0b78d6..6d63bf94fd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
@@ -17,7 +17,8 @@ import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.NotImplementedException;
/**
- * Class that represents alias of a complex in the model.
+ * Class that represents complex in the model. Complex elements contain
+ * subelements.
*
* @author Piotr Gawron
*
@@ -29,12 +30,12 @@ public class Complex extends Species {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(Complex.class);
+ private static Logger logger = Logger.getLogger(Complex.class);
/**
* List of aliases that are in this complex alias (only aliases that lies
@@ -42,15 +43,15 @@ public class Complex extends Species {
*/
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.EAGER, mappedBy = "complexAlias")
- private List<Species> aliases = new ArrayList<>();
+ private List<Species> aliases = new ArrayList<>();
/**
* State of the complex species.
*/
- private String structuralState = null;
+ private String structuralState = null;
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
Complex() {
super();
@@ -73,13 +74,13 @@ public class Complex extends Species {
}
/**
- * Constructor that creates complex alias with given alias id.
+ * Default constructor.
*
- * @param aliasId
- * identifier of the alias
+ * @param elementId
+ * uniqe (within model) element identifier
*/
- public Complex(String aliasId) {
- super(aliasId);
+ public Complex(String elementId) {
+ super(elementId);
}
/**
@@ -172,6 +173,12 @@ public class Complex extends Species {
this.structuralState = structuralState;
}
+ /**
+ * Returns all children and subchildren elements for this element. Only non
+ * {@link Complex} children will be returned.
+ *
+ * @return all children and subchildren elements for this element
+ */
public Set<Species> getAllSimpleChildren() {
Set<Species> result = new HashSet<>();
for (Species element : getAliases()) {
@@ -189,5 +196,4 @@ public class Complex extends Species {
return "Complex";
}
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
index 992a54475f..6b005eed4a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
@@ -13,7 +13,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
/**
- * This class implements comparator interface for ComplexAlias.
+ * This class implements comparator interface for {@link Complex}.
*
* @author Piotr Gawron
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
index 0fcb066a14..d030136fce 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
@@ -5,6 +5,12 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing degraded element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("DEGRADED_ALIAS")
public class Degraded extends Species {
@@ -13,15 +19,30 @@ public class Degraded extends Species {
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
Degraded() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Degraded(Degraded original) {
super(original);
}
- public Degraded(String aliasId) {
- super.setElementId(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Degraded(String elementId) {
+ super.setElementId(elementId);
}
@Override
@@ -38,5 +59,4 @@ public class Degraded extends Species {
return "Degraded";
}
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
index 7f16484bd8..ef33ffeb78 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
@@ -7,8 +7,14 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link Degraded} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class DegradedComparator implements Comparator<Degraded> {
-
+
/**
* Default class logger.
*/
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
index 82b2735f03..aec5c847fd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
@@ -5,6 +5,12 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing drug element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("DRUG_ALIAS")
public class Drug extends Species {
@@ -13,15 +19,30 @@ public class Drug extends Species {
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
Drug() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Drug(Drug original) {
super(original);
}
- public Drug(String aliasId) {
- setElementId(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Drug(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
index cc33157ba8..0f64edd06d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
@@ -7,8 +7,14 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link Drug} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class DrugComparator implements Comparator<Drug> {
-
+
/**
* Default class logger.
*/
@@ -61,9 +67,9 @@ public class DrugComparator implements Comparator<Drug> {
}
/**
- * This method compares only the fields that are defined in DrugAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * This method compares only the fields that are defined in DrugAlias class in
+ * inheritence tree. By the design it calls also comparator of the upper
+ * (SpeciesAlias) class.
*
* @param arg0
* first object to compare
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 7f165e052d..a00cdb5d9a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -48,11 +48,9 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
/**
- * Abstract class representing alias objects in the model. Aliases are objects
- * that contains graphical representation data for element (like, species,
- * compartments; but not reactions) in the map. It is possible to connect many
- * aliases to one element (they reference to one instance of the element, but
- * show them in different places on the map).
+ * Abstract class representing objects in the model. Elements are objects that
+ * contains graphical representation data for element and metainformation about
+ * element (like symbol, name, etc.).
*
* @author Piotr Gawron
*
@@ -67,42 +65,42 @@ public abstract class Element implements AnnotatedObject, Serializable {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Default font size for alias element.
*/
- private static final double DEFAULT_FONT_SIZE = 12.0;
+ private static final double DEFAULT_FONT_SIZE = 12.0;
/**
* Maximum length of the valid synonym name.
*/
- private static final int MAX_SYNONYM_LENGTH = 255;
+ private static final int MAX_SYNONYM_LENGTH = 255;
/**
* Comparator of aliases that takes into consideration size (width*height) of
* aliases.
*/
public static final Comparator<Element> SIZE_COMPARATOR = new Comparator<Element>() {
- @Override
- public int compare(Element alias1, Element alias2) {
-
- double size = alias1.getWidth() * alias1.getHeight();
- double size2 = alias2.getWidth() * alias2.getHeight();
- if (size < size2) {
- return 1;
- } else if (size > size2) {
- return -1;
- } else {
- return 0;
+ @Override
+ public int compare(Element alias1, Element alias2) {
+
+ double size = alias1.getWidth() * alias1.getHeight();
+ double size2 = alias2.getWidth() * alias2.getHeight();
+ if (size < size2) {
+ return 1;
+ } else if (size > size2) {
+ return -1;
+ } else {
+ return 0;
+ }
}
- }
- };
+ };
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(Element.class);
+ private static Logger logger = Logger.getLogger(Element.class);
/**
* Database identifier.
@@ -110,7 +108,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
@Column(name = "idDb", unique = true, nullable = false)
- private int id;
+ private int id;
/**
* This object reference to the parent alias. Parent is a ComplexAlias which
@@ -127,56 +125,56 @@ public abstract class Element implements AnnotatedObject, Serializable {
* Map model object to which alias belongs to.
*/
@ManyToOne(fetch = FetchType.LAZY)
- private ModelData model;
+ private ModelData model;
/**
* Submodel that is extension of these element alias.
*/
@ManyToOne(fetch = FetchType.LAZY, cascade = javax.persistence.CascadeType.ALL)
- private AliasSubmodelConnection submodel;
+ private AliasSubmodelConnection submodel;
/**
* CompartmentAlias where alias is located. When alias lies outside of every
* compartment then null value is assigned.
*/
@ManyToOne
- private Compartment compartmentAlias;
+ private Compartment compartmentAlias;
/**
- * Unique string identifier within one model object (usually imported
- * from external source from which map was imported).
+ * Unique string identifier within one model object (usually imported from
+ * external source from which map was imported).
*/
- private String elementId;
+ private String elementId;
/**
* X coordinate on the map where alias is located (top left corner).
*/
- private Double x;
+ private Double x;
/**
* Y coordinate on the map where alias is located (top left corner).
*/
- private Double y;
+ private Double y;
/**
* Width of the alias.
*/
- private Double width;
+ private Double width;
/**
* Height of the alias.
*/
- private Double height;
+ private Double height;
/**
* Size of the font used for description.
*/
- private Double fontSize;
+ private Double fontSize;
/**
* Color of filling.
*/
- private Color color;
+ private Color color;
/**
* From which level alias should be visible.
@@ -185,7 +183,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
* @see lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params#level
* AbstractImageGenerator.Params#level
*/
- private int visibilityLevel;
+ private int visibilityLevel;
/**
* From which level alias should be transparent.
@@ -193,45 +191,45 @@ public abstract class Element implements AnnotatedObject, Serializable {
* @see #visibilityLevel
* @see AbstractImageGenerator.Params#level
*/
- private int transparencyLevel;
+ private int transparencyLevel;
/**
* List of search indexes that describe this element.
*/
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.EAGER, mappedBy = "source", orphanRemoval = true)
- private List<SearchIndex> searchIndexes = new ArrayList<SearchIndex>();
+ private List<SearchIndex> searchIndexes = new ArrayList<SearchIndex>();
/**
* Notes describing this element.
*/
@Column(name = "notes", columnDefinition = "TEXT")
- private String notes = "";
+ private String notes = "";
/**
* Symbol of the element.
*/
- private String symbol;
+ private String symbol;
/**
* Full name of the element.
*/
- private String fullName;
+ private String fullName;
/**
* Abbreviation associated with the element.
*/
- private String abbreviation;
+ private String abbreviation;
/**
* Formula associated with the element.
*/
- private String formula;
+ private String formula;
/**
* Short name of the element.
*/
- private String name = "";
+ private String name = "";
/**
* Lists of all synonyms used for describing this element.
@@ -244,7 +242,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
@Column(name = "synonym")
@IndexColumn(name = "idx")
@Cascade({ org.hibernate.annotations.CascadeType.ALL })
- private List<String> synonyms = new ArrayList<>();
+ private List<String> synonyms = new ArrayList<>();
/**
* List of former symbols used to describe this element.
@@ -257,7 +255,7 @@ public abstract class Element implements AnnotatedObject, Serializable {
@Column(name = "symbol")
@IndexColumn(name = "idx")
@Cascade({ org.hibernate.annotations.CascadeType.ALL })
- private List<String> formerSymbols = new ArrayList<>();
+ private List<String> formerSymbols = new ArrayList<>();
/**
* Set of miriam annotations for this element.
@@ -266,49 +264,55 @@ public abstract class Element implements AnnotatedObject, Serializable {
@ManyToMany(fetch = FetchType.EAGER)
@JoinTable(name = "element_miriam", joinColumns = { @JoinColumn(name = "element_id", referencedColumnName = "idDb", nullable = false, updatable = false) },
inverseJoinColumns = { @JoinColumn(name = "miriam_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
- private Set<MiriamData> miriamData = new HashSet<>();
+ private Set<MiriamData> miriamData = new HashSet<>();
/**
- * Constructor that initialize alias with the data from the parameter alias.
+ * Constructor that creates a copy of the element given in the parameter.
*
- * @param param
- * source alias
- */
- protected Element(Element param) {
- elementId = param.getElementId();
- x = param.getX();
- y = param.getY();
- width = param.getWidth();
- height = param.getHeight();
- fontSize = param.getFontSize();
- parent = param.getParent();
- visibilityLevel = param.getVisibilityLevel();
- color = param.getColor();
- for (SearchIndex searchIndex : param.getSearchIndexes()) {
+ * @param original
+ * original object that will be used for creating copy
+ */
+ protected Element(Element original) {
+ elementId = original.getElementId();
+ x = original.getX();
+ y = original.getY();
+ width = original.getWidth();
+ height = original.getHeight();
+ fontSize = original.getFontSize();
+ parent = original.getParent();
+ visibilityLevel = original.getVisibilityLevel();
+ color = original.getColor();
+ for (SearchIndex searchIndex : original.getSearchIndexes()) {
searchIndexes.add(searchIndex.copy());
}
- if (param.getSubmodel() != null) {
- setSubmodel(param.getSubmodel().copy());
+ if (original.getSubmodel() != null) {
+ setSubmodel(original.getSubmodel().copy());
}
- this.notes = param.notes;
- this.symbol = param.symbol;
- this.fullName = param.fullName;
- this.name = param.getName();
- addSynonyms(param.getSynonyms());
- addFormerSymbols(param.getFormerSymbols());
+ this.notes = original.notes;
+ this.symbol = original.symbol;
+ this.fullName = original.fullName;
+ this.name = original.getName();
+ addSynonyms(original.getSynonyms());
+ addFormerSymbols(original.getFormerSymbols());
- addMiriamData(param.getMiriamData());
- this.abbreviation = param.getAbbreviation();
- this.formula = param.getFormula();
+ addMiriamData(original.getMiriamData());
+ this.abbreviation = original.getAbbreviation();
+ this.formula = original.getFormula();
}
+ /**
+ * Adds list of former symbol to the object.
+ *
+ * @param formerSymbols
+ * list of former symbols to add
+ */
public void addFormerSymbols(List<String> formerSymbols) {
this.formerSymbols.addAll(formerSymbols);
}
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
protected Element() {
super();
@@ -1050,15 +1054,31 @@ public abstract class Element implements AnnotatedObject, Serializable {
this.notes = notes;
}
+ /**
+ * Adds former symbol to the object.
+ *
+ * @param formerSymbol
+ * former symbol to add
+ */
public void addFormerSymbol(String formerSymbol) {
formerSymbols.add(formerSymbol);
-
}
- public void addSynonym(String string) {
- synonyms.add(string);
+ /**
+ * Adds synonym to object.
+ *
+ * @param synonym
+ * synonym to be added
+ */
+ public void addSynonym(String synonym) {
+ synonyms.add(synonym);
}
+ /**
+ * Return human readable {@link String} representing class.
+ *
+ * @return human readable {@link String} representing class
+ */
public abstract String getStringType();
}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index 72c7ed7861..0800590d1b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -19,11 +19,10 @@ import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
import lcsb.mapviewer.model.map.model.AliasSubmodelConnectionComparator;
/**
- * This class implements comparator interface for Alias. It also handles
- * comparison of subclasses of Alias class.
+ * Comparator class used for comparing {@link Element} objects.
*
* @author Piotr Gawron
- *
+ *
*/
public class ElementComparator implements Comparator<Element> {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
index da92b8f45f..db6c9cb840 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
@@ -15,6 +15,12 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+/**
+ * Entity representing gene element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("GENE_ALIAS")
public class Gene extends Species {
@@ -22,7 +28,7 @@ public class Gene extends Species {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* List of modifications for the Gene.
@@ -30,11 +36,20 @@ public class Gene extends Species {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "species", orphanRemoval = true)
@LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidue> modificationResidues = new ArrayList<>();
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
+ /**
+ * Empty constructor required by hibernate.
+ */
Gene() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Gene(Gene original) {
super(original);
for (ModificationResidue mr : original.getModificationResidues()) {
@@ -42,16 +57,28 @@ public class Gene extends Species {
}
}
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Gene(String elementId) {
+ setElementId(elementId);
+ }
+
+ /**
+ * Adds {@link ModificationResidue}.
+ *
+ * @param modificationResidue
+ * {@link ModificationResidue} to be added
+ */
public void addModificationResidue(ModificationResidue modificationResidue) {
modificationResidues.add(modificationResidue);
modificationResidue.setSpecies(this);
}
- public Gene(String aliasId) {
- setElementId(aliasId);
- }
-
@Override
public Gene copy() {
if (this.getClass() == Gene.class) {
@@ -83,5 +110,4 @@ public class Gene extends Species {
return "Gene";
}
-
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
index d67f46e73a..5ec522cc4f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
@@ -11,6 +11,12 @@ import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+/**
+ * Comparator class used for comparing {@link Gene} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class GeneComparator implements Comparator<Gene> {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
index aa919053ca..428c069554 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
@@ -5,21 +5,43 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing generic protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("GENERIC_PROTEIN_ALIAS")
public class GenericProtein extends Protein {
+
/**
*
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
GenericProtein() {
}
- public GenericProtein(String aliasId) {
- super(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public GenericProtein(String elementId) {
+ super(elementId);
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public GenericProtein(GenericProtein original) {
super(original);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
index 6b11bf5ef2..4fb7a683db 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
@@ -7,6 +7,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link GenericProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class GenericProteinComparator implements Comparator<GenericProtein> {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
index 23ab6180db..8170a7890e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
@@ -5,23 +5,45 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing ion element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("ION_ALIAS")
public class Ion extends Chemical {
+
/**
*
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
Ion() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Ion(Ion original) {
super(original);
}
- public Ion(String aliasId) {
- setElementId(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Ion(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
index 73d4ca35c9..95225bc76e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
@@ -5,23 +5,45 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing ion channel protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("ION_CHANNEL_PROTEIN_ALIAS")
public class IonChannelProtein extends Protein {
+
/**
*
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
IonChannelProtein() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public IonChannelProtein(IonChannelProtein original) {
super(original);
}
- public IonChannelProtein(String aliasId) {
- setElementId(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public IonChannelProtein(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
index 276547baee..4cd44ebde6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
@@ -7,6 +7,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link IonChannelProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class IonChannelProteinComparator implements Comparator<IonChannelProtein> {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
index e17cad0f42..cddddd1b5b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
@@ -7,6 +7,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link Ion} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class IonComparator implements Comparator<Ion> {
/**
@@ -61,9 +67,9 @@ public class IonComparator implements Comparator<Ion> {
}
/**
- * This method compares only the fields that are defined in {@link Ion}
- * class in inheritence tree. By the design it calls also comparator of the
- * upper {@link Chemical} class.
+ * This method compares only the fields that are defined in {@link Ion} class
+ * in inheritence tree. By the design it calls also comparator of the upper
+ * {@link Chemical} class.
*
* @param arg0
* first object to compare
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
index 0fd1e4ce0e..58634bdeee 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
@@ -5,6 +5,12 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing phenotype element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("PHENTOYPE_ALIAS")
public class Phenotype extends Species {
@@ -14,15 +20,30 @@ public class Phenotype extends Species {
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
Phenotype() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Phenotype(Phenotype original) {
super(original);
}
- public Phenotype(String aliasId) {
- setElementId(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Phenotype(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
index ad63c97a93..b6a01629f0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
@@ -7,6 +7,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link Phenotype} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class PhenotypeComparator implements Comparator<Phenotype> {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
index 7149cffe9d..7fadc2e18f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
@@ -14,6 +14,12 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+/**
+ * Entity representing protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("PROTEIN_ALIAS")
public abstract class Protein extends Species {
@@ -36,10 +42,19 @@ public abstract class Protein extends Species {
@LazyCollection(LazyCollectionOption.FALSE)
private List<ModificationResidue> modificationResidues = new ArrayList<>();
+ /**
+ * Empty constructor required by hibernate.
+ */
Protein() {
}
- public Protein(Protein original) {
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ protected Protein(Protein original) {
super(original);
this.structuralState = original.getStructuralState();
for (ModificationResidue mr : original.getModificationResidues()) {
@@ -47,8 +62,15 @@ public abstract class Protein extends Species {
}
}
- public Protein(String aliasId) {
- super(aliasId);
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ protected Protein(String elementId) {
+ super(elementId);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
index 158be0cb0e..7090a9316c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
@@ -7,18 +7,22 @@ import java.util.Set;
import org.apache.log4j.Logger;
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.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+/**
+ * Comparator class used for comparing {@link Protein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class ProteinComparator implements Comparator<Protein> {
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(ProteinComparator.class);
/**
@@ -26,9 +30,24 @@ public class ProteinComparator implements Comparator<Protein> {
*/
private double epsilon;
+ /**
+ * Comparator for {@link GenericProtein} implementation of {@link Protein}.
+ */
private GenericProteinComparator genericProteinAliasComparator;
+
+ /**
+ * Comparator for {@link IonChannelProtein} implementation of {@link Protein}.
+ */
private IonChannelProteinComparator ionChannelProteinAliasComparator;
+
+ /**
+ * Comparator for {@link ReceptorProtein} implementation of {@link Protein}.
+ */
private ReceptorProteinComparator receptorProteinAliasComparator;
+
+ /**
+ * Comparator for {@link TruncatedProtein} implementation of {@link Protein}.
+ */
private TruncatedProteinComparator truncatedProteinAliasComparator;
/**
@@ -65,9 +84,7 @@ public class ProteinComparator implements Comparator<Protein> {
}
if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(Protein.class)) {
- return internalCompare(arg0, arg1);
- } else if (arg0.getClass().equals(GenericProtein.class)) {
+ if (arg0.getClass().equals(GenericProtein.class)) {
return genericProteinAliasComparator.compare((GenericProtein) arg0, (GenericProtein) arg1);
} else if (arg0.getClass().equals(IonChannelProtein.class)) {
return ionChannelProteinAliasComparator.compare((IonChannelProtein) arg0, (IonChannelProtein) arg1);
@@ -103,14 +120,8 @@ public class ProteinComparator implements Comparator<Protein> {
}
StringComparator stringComparator = new StringComparator();
- IntegerComparator integerComparator = new IntegerComparator();
StringSetComparator stringSetComparator = new StringSetComparator();
- if (integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer()) != 0) {
- logger.debug("homodimer different: " + arg0.getHomodimer() + ", " + arg1.getHomodimer());
- return integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer());
- }
-
if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
logger.debug("structural state different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
index 71e5c768c2..89aa61cf12 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
@@ -5,6 +5,12 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing receptor protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("RECEPTOR_PROTEIN_ALIAS")
public class ReceptorProtein extends Protein {
@@ -13,15 +19,30 @@ public class ReceptorProtein extends Protein {
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
ReceptorProtein() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public ReceptorProtein(ReceptorProtein original) {
super(original);
}
- public ReceptorProtein(String aliasId) {
- super(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public ReceptorProtein(String elementId) {
+ super(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
index f0bc587d0e..724edc151a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
@@ -7,6 +7,12 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link ReceptorProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class ReceptorProteinComparator implements Comparator<ReceptorProtein> {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
index c738ee367e..7e3df3a906 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Rna.java
@@ -15,6 +15,12 @@ import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
+/**
+ * Entity representing rna element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("RNA_ALIAS")
public class Rna extends Species {
@@ -22,7 +28,7 @@ public class Rna extends Species {
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* List of rna regions (some rna sequences) in this object.
@@ -30,11 +36,20 @@ public class Rna extends Species {
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "species", orphanRemoval = true)
@LazyCollection(LazyCollectionOption.FALSE)
- private List<RnaRegion> regions = new ArrayList<>();
+ private List<RnaRegion> regions = new ArrayList<>();
+ /**
+ * Empty constructor required by hibernate.
+ */
Rna() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Rna(Rna original) {
super(original);
for (RnaRegion region : original.getRegions()) {
@@ -42,14 +57,26 @@ public class Rna extends Species {
}
}
- public Rna(String aliasId) {
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Rna(String elementId) {
super();
- setElementId(aliasId);
+ setElementId(elementId);
}
- public void addRegion(RnaRegion rnaRegionAlias) {
- regions.add(rnaRegionAlias);
- rnaRegionAlias.setSpecies(this);
+ /**
+ * Adds {@link RnaRegion}.
+ *
+ * @param rnaRegion
+ * object to be added
+ */
+ public void addRegion(RnaRegion rnaRegion) {
+ regions.add(rnaRegion);
+ rnaRegion.setSpecies(this);
}
@Override
@@ -78,7 +105,6 @@ public class Rna extends Species {
this.regions = regions;
}
-
@Override
public String getStringType() {
return "RNA";
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
index bf6b8bc991..1703a391c1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
@@ -11,6 +11,12 @@ import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
+/**
+ * Comparator class used for comparing {@link Rna} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class RnaComparator implements Comparator<Rna> {
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
index f14b3c55ad..37f9f9fbcb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
@@ -5,23 +5,45 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing simple molecule element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("SIMPLE_MOLECULE_ALIAS")
public class SimpleMolecule extends Chemical {
+
/**
*
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
SimpleMolecule() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public SimpleMolecule(SimpleMolecule original) {
super(original);
}
- public SimpleMolecule(String aliasId) {
- setElementId(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public SimpleMolecule(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
index e276ddd994..463b37c0b8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
@@ -5,11 +5,16 @@ import java.util.Comparator;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link SimpleMolecule} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
-
+
/**
* Default class logger.
*/
@@ -62,9 +67,9 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
}
/**
- * This method compares only the fields that are defined in SimpleMoleculeAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * This method compares only the fields that are defined in
+ * SimpleMoleculeAlias class in inheritence tree. By the design it calls also
+ * comparator of the upper (SpeciesAlias) class.
*
* @param arg0
* first object to compare
@@ -80,23 +85,6 @@ public class SimpleMoleculeComparator implements Comparator<SimpleMolecule> {
return result;
}
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getSmiles(), arg1.getSmiles()) != 0) {
- logger.debug("Smiles different: " + arg0.getSmiles() + ", " + arg1.getSmiles());
- return stringComparator.compare(arg0.getSmiles(), arg1.getSmiles());
- }
-
- if (stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey()) != 0) {
- logger.debug("InChIKey different: " + arg0.getInChIKey() + ", " + arg1.getInChIKey());
- return stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey());
- }
-
- if (stringComparator.compare(arg0.getInChI(), arg1.getInChI()) != 0) {
- logger.debug("InChI different: " + arg0.getInChI() + ", " + arg1.getInChI());
- return stringComparator.compare(arg0.getInChI(), arg1.getInChI());
- }
-
return 0;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index 37eb0ce5fc..712f212bd2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -134,9 +134,9 @@ public abstract class Species extends Element {
}
/**
- * Default constructor.
+ * Empty constructor required by hibernate.
*/
- public Species() {
+ Species() {
super();
activity = false;
lineWidth = 1.0;
@@ -147,26 +147,26 @@ public abstract class Species extends Element {
* Constructor that initializes data with the information given in the
* parameter.
*
- * @param alias
+ * @param original
* object from which data will be initialized
*/
- public Species(Species alias) {
- super(alias);
- activity = alias.getActivity();
- lineWidth = alias.getLineWidth();
- state = alias.getState();
+ protected Species(Species original) {
+ super(original);
+ activity = original.getActivity();
+ lineWidth = original.getLineWidth();
+ state = original.getState();
- complexAlias = alias.getComplexAlias();
- aliasStateLabel = alias.getAliasStateLabel();
- aliasStatePrefix = alias.getAliasStatePrefix();
+ complexAlias = original.getComplexAlias();
+ aliasStateLabel = original.getAliasStateLabel();
+ aliasStatePrefix = original.getAliasStatePrefix();
- initialAmount = alias.getInitialAmount();
- charge = alias.getCharge();
- initialConcentration = alias.getInitialConcentration();
- onlySubstanceUnits = alias.getOnlySubstanceUnits();
- homodimer = alias.getHomodimer();
- positionToCompartment = alias.getPositionToCompartment();
- hypothetical = alias.getHypothetical();
+ initialAmount = original.getInitialAmount();
+ charge = original.getCharge();
+ initialConcentration = original.getInitialConcentration();
+ onlySubstanceUnits = original.getOnlySubstanceUnits();
+ homodimer = original.getHomodimer();
+ positionToCompartment = original.getPositionToCompartment();
+ hypothetical = original.getHypothetical();
// don't copy reaction nodes
}
@@ -290,6 +290,7 @@ public abstract class Species extends Element {
this.aliasStateLabel = aliasStateLabel;
}
+ @Override
public abstract Species copy();
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
index 4ce6963c78..678e18507d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
@@ -12,33 +12,72 @@ import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
/**
- * This class implements comparator interface for SpeciesAlias. It also handles
- * comparison of subclasses of SpeciesAlias class.
+ * Comparator class used for comparing {@link Species} objects.
*
* @author Piotr Gawron
- *
+ *
*/
public class SpeciesComparator implements Comparator<Species> {
+
/**
* Default class logger.
*/
- private Logger logger = Logger.getLogger(SpeciesComparator.class);
-
- private AntisenseRnaComparator antisenseRnaAliasComparator;
- private ChemicalComparator chemicalAliasComparator;
- private ComplexComparator complexAliasComparator;
- private DegradedComparator degradedAliasComparator;
- private DrugComparator drugAliasComparator;
- private GeneComparator geneAliasComparator;
- private PhenotypeComparator phenotypeAliasComparator;
- private ProteinComparator proteinAliasComparator;
- private RnaComparator rnaAliasComparator;
- private UnknownComparator unknownAliasComparator;
+ private Logger logger = Logger.getLogger(SpeciesComparator.class);
+
+ /**
+ * Comparator for {@link AntisenseRna} implementation of {@link Species}.
+ */
+ private AntisenseRnaComparator antisenseRnaComparator;
+
+ /**
+ * Comparator for {@link Chemical} implementation of {@link Species}.
+ */
+ private ChemicalComparator chemicalComparator;
+
+ /**
+ * Comparator for {@link Complex} implementation of {@link Species}.
+ */
+ private ComplexComparator complexComparator;
+
+ /**
+ * Comparator for {@link Degraded} implementation of {@link Species}.
+ */
+ private DegradedComparator degradedComparator;
+
+ /**
+ * Comparator for {@link Drug} implementation of {@link Species}.
+ */
+ private DrugComparator drugComparator;
+
+ /**
+ * Comparator for {@link Gene} implementation of {@link Species}.
+ */
+ private GeneComparator geneComparator;
+
+ /**
+ * Comparator for {@link Phenotype} implementation of {@link Species}.
+ */
+ private PhenotypeComparator phenotypeComparator;
+
+ /**
+ * Comparator for {@link Protein} implementation of {@link Species}.
+ */
+ private ProteinComparator proteinComparator;
+
+ /**
+ * Comparator for {@link Rna} implementation of {@link Species}.
+ */
+ private RnaComparator rnaComparator;
+
+ /**
+ * Comparator for {@link Unknown} implementation of {@link Species}.
+ */
+ private UnknownComparator unknownComparator;
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
@@ -48,16 +87,16 @@ public class SpeciesComparator implements Comparator<Species> {
*/
public SpeciesComparator(double epsilon) {
this.epsilon = epsilon;
- antisenseRnaAliasComparator = new AntisenseRnaComparator(epsilon);
- chemicalAliasComparator = new ChemicalComparator(epsilon);
- complexAliasComparator = new ComplexComparator(epsilon);
- degradedAliasComparator = new DegradedComparator(epsilon);
- drugAliasComparator = new DrugComparator(epsilon);
- geneAliasComparator = new GeneComparator(epsilon);
- phenotypeAliasComparator = new PhenotypeComparator(epsilon);
- proteinAliasComparator = new ProteinComparator(epsilon);
- rnaAliasComparator = new RnaComparator(epsilon);
- unknownAliasComparator = new UnknownComparator(epsilon);
+ antisenseRnaComparator = new AntisenseRnaComparator(epsilon);
+ chemicalComparator = new ChemicalComparator(epsilon);
+ complexComparator = new ComplexComparator(epsilon);
+ degradedComparator = new DegradedComparator(epsilon);
+ drugComparator = new DrugComparator(epsilon);
+ geneComparator = new GeneComparator(epsilon);
+ phenotypeComparator = new PhenotypeComparator(epsilon);
+ proteinComparator = new ProteinComparator(epsilon);
+ rnaComparator = new RnaComparator(epsilon);
+ unknownComparator = new UnknownComparator(epsilon);
}
/**
@@ -81,25 +120,25 @@ public class SpeciesComparator implements Comparator<Species> {
if (arg0.getClass().equals(arg1.getClass())) {
if (arg0.getClass().equals(AntisenseRna.class)) {
- return antisenseRnaAliasComparator.compare((AntisenseRna) arg0, (AntisenseRna) arg1);
+ return antisenseRnaComparator.compare((AntisenseRna) arg0, (AntisenseRna) arg1);
} else if (arg0 instanceof Chemical) {
- return chemicalAliasComparator.compare((Chemical) arg0, (Chemical) arg1);
+ return chemicalComparator.compare((Chemical) arg0, (Chemical) arg1);
} else if (arg0.getClass().equals(Complex.class)) {
- return complexAliasComparator.compare((Complex) arg0, (Complex) arg1);
+ return complexComparator.compare((Complex) arg0, (Complex) arg1);
} else if (arg0.getClass().equals(Degraded.class)) {
- return degradedAliasComparator.compare((Degraded) arg0, (Degraded) arg1);
+ return degradedComparator.compare((Degraded) arg0, (Degraded) arg1);
} else if (arg0.getClass().equals(Drug.class)) {
- return drugAliasComparator.compare((Drug) arg0, (Drug) arg1);
+ return drugComparator.compare((Drug) arg0, (Drug) arg1);
} else if (arg0.getClass().equals(Gene.class)) {
- return geneAliasComparator.compare((Gene) arg0, (Gene) arg1);
+ return geneComparator.compare((Gene) arg0, (Gene) arg1);
} else if (arg0.getClass().equals(Phenotype.class)) {
- return phenotypeAliasComparator.compare((Phenotype) arg0, (Phenotype) arg1);
+ return phenotypeComparator.compare((Phenotype) arg0, (Phenotype) arg1);
} else if (arg0 instanceof Protein) {
- return proteinAliasComparator.compare((Protein) arg0, (Protein) arg1);
+ return proteinComparator.compare((Protein) arg0, (Protein) arg1);
} else if (arg0.getClass().equals(Rna.class)) {
- return rnaAliasComparator.compare((Rna) arg0, (Rna) arg1);
+ return rnaComparator.compare((Rna) arg0, (Rna) arg1);
} else if (arg0.getClass().equals(Unknown.class)) {
- return unknownAliasComparator.compare((Unknown) arg0, (Unknown) arg1);
+ return unknownComparator.compare((Unknown) arg0, (Unknown) arg1);
} else {
throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
}
@@ -109,9 +148,9 @@ public class SpeciesComparator implements Comparator<Species> {
}
/**
- * This method compares only the fields that are defined in
- * {@link Species} class in inheritence tree. By the design it calls also
- * comparator of the upper ({@link Element}) class.
+ * This method compares only the fields that are defined in {@link Species}
+ * class in inheritence tree. By the design it calls also comparator of the
+ * upper ({@link Element}) class.
*
* @param arg0
* first object to compare
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
index 58a3d8c52a..2d487478b4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
@@ -5,6 +5,12 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing truncated protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("TRUNCATED_PROTEIN_ALIAS")
public class TruncatedProtein extends Protein {
@@ -13,15 +19,30 @@ public class TruncatedProtein extends Protein {
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
TruncatedProtein() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public TruncatedProtein(TruncatedProtein original) {
super(original);
}
- public TruncatedProtein(String aliasId) {
- super(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public TruncatedProtein(String elementId) {
+ super(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
index a8918abee6..39493f31f0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
@@ -7,8 +7,14 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link TruncatedProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class TruncatedProteinComparator implements Comparator<TruncatedProtein> {
-
+
/**
* Default class logger.
*/
@@ -61,9 +67,9 @@ public class TruncatedProteinComparator implements Comparator<TruncatedProtein>
}
/**
- * This method compares only the fields that are defined in TruncatedProteinAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * This method compares only the fields that are defined in
+ * TruncatedProteinAlias class in inheritence tree. By the design it calls
+ * also comparator of the upper (SpeciesAlias) class.
*
* @param arg0
* first object to compare
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
index 389c116073..d475d6de9d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
@@ -5,6 +5,12 @@ import javax.persistence.Entity;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Entity representing unknown element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
@Entity
@DiscriminatorValue("UNKNOWN_ALIAS")
public class Unknown extends Species {
@@ -14,15 +20,30 @@ public class Unknown extends Species {
*/
private static final long serialVersionUID = 1L;
+ /**
+ * Empty constructor required by hibernate.
+ */
Unknown() {
}
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
public Unknown(Unknown original) {
super(original);
}
- public Unknown(String aliasId) {
- setElementId(aliasId);
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Unknown(String elementId) {
+ setElementId(elementId);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
index b0654cd439..96aea95884 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
@@ -7,8 +7,14 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.NotImplementedException;
+/**
+ * Comparator class used for comparing {@link Unknown} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
public class UnknownComparator implements Comparator<Unknown> {
-
+
/**
* Default class logger.
*/
@@ -61,9 +67,9 @@ public class UnknownComparator implements Comparator<Unknown> {
}
/**
- * This method compares only the fields that are defined in UnknownAlias
- * class in inheritence tree. By the design it calls also comparator of the
- * upper (SpeciesAlias) class.
+ * This method compares only the fields that are defined in UnknownAlias class
+ * in inheritence tree. By the design it calls also comparator of the upper
+ * (SpeciesAlias) class.
*
* @param arg0
* first object to compare
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
index 92fed4f8dd..ec19ddedcb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
@@ -65,6 +65,7 @@ public class MiriamTypeTest {
}
}
+
@Test
public void testGetMiriamDataFromInvalidIdentifier2() {
try {
@@ -91,7 +92,7 @@ public class MiriamTypeTest {
public void testGetMiriamByUri1() throws Exception {
try {
MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384:SF5");
- assertTrue(new MiriamData(MiriamType.PANTHER,"PTHR19384:SF5").equals(md));
+ assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -102,7 +103,7 @@ public class MiriamTypeTest {
public void testGetMiriamByUri2() throws Exception {
try {
MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384%3ASF5");
- assertTrue(new MiriamData(MiriamType.PANTHER,"PTHR19384:SF5").equals(md));
+ assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -113,7 +114,19 @@ public class MiriamTypeTest {
public void testGetMiriamByUri3() throws Exception {
try {
MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family%3APTHR19384%3ASF5");
- assertTrue(new MiriamData(MiriamType.PANTHER,"PTHR19384:SF5").equals(md));
+ assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamByInvalidUri() throws Exception {
+ try {
+ MiriamType.getMiriamByUri("invalid_uri");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
index 34e53d6e94..cfcd1f7b1a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
@@ -7,10 +7,9 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -73,13 +72,8 @@ public class BottomSquareCompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new BottomSquareCompartment() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ BottomSquareCompartment compartment = Mockito.spy(BottomSquareCompartment.class);
+ compartment.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
index 4fb5698713..179cb23a91 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
@@ -14,16 +14,16 @@ import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
@@ -154,12 +154,12 @@ public class CompartmentTest {
private Model createCrossModel() {
Model model = new ModelFullIndexed(null);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
- model.addAlias(createSpeciesAlias(3264.8333333333335, 7517.75, 86.0, 46.0, "sa1115"));
- model.addAlias(createSpeciesAlias(3267.6666666666665, 7438.75, 80.0, 40.0, "sa1117"));
- model.addAlias(createSpeciesAlias(3261.6666666666665, 7600.75, 92.0, 52.0, "sa1119"));
- model.addAlias(createSpeciesAlias(3203.666666666667, 7687.75, 98.0, 58.0, "sa1121"));
+ model.addElement(createSpeciesAlias(3264.8333333333335, 7517.75, 86.0, 46.0, "sa1115"));
+ model.addElement(createSpeciesAlias(3267.6666666666665, 7438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpeciesAlias(3261.6666666666665, 7600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpeciesAlias(3203.666666666667, 7687.75, 98.0, 58.0, "sa1121"));
Species alias = createSpeciesAlias(7817.714285714286, 11287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(8224.964285714286, 11241.392857142859, 80.0, 40.0, "sa1419");
@@ -169,11 +169,11 @@ public class CompartmentTest {
alias.setParent(alias3);
alias2.setParent(alias3);
- model.addAlias(alias);
- model.addAlias(alias2);
- model.addAlias(alias3);
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
- model.addAlias(createCompartmentAlias(1380.0, 416.0, 15893.0, 10866.0, "ca1"));
+ model.addElement(createCompartmentAlias(1380.0, 416.0, 15893.0, 10866.0, "ca1"));
return model;
}
@@ -285,7 +285,7 @@ public class CompartmentTest {
compartment.setElements(elements);
assertEquals(elements, compartment.getElements());
-
+
assertNotNull(compartment.getStringType());
} catch (Exception e) {
@@ -381,13 +381,8 @@ public class CompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new Compartment() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ Compartment compartment = Mockito.spy(Compartment.class);
+ compartment.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
index be0eae8f0a..4b61f698f6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
@@ -7,10 +7,9 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -73,13 +72,8 @@ public class LeftSquareCompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new LeftSquareCompartment() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ LeftSquareCompartment compartment = Mockito.spy(LeftSquareCompartment.class);
+ compartment.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java
index 7034f15507..e4f7886231 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java
@@ -7,9 +7,9 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.OvalCompartment;
public class OvalCompartmentTest {
@@ -30,7 +30,7 @@ public class OvalCompartmentTest {
throw e;
}
}
-
+
@Test
public void testConstructor() {
try {
@@ -58,13 +58,8 @@ public class OvalCompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new OvalCompartment() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ OvalCompartment compartment = Mockito.spy(OvalCompartment.class);
+ compartment.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
@@ -72,5 +67,5 @@ public class OvalCompartmentTest {
throw e;
}
}
-
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
index 4d303ceeec..1135e99739 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
@@ -8,10 +8,9 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -34,7 +33,6 @@ public class RightSquareCompartmentTest {
throw e;
}
}
-
@Test
public void testConstructor1() {
@@ -77,7 +75,7 @@ public class RightSquareCompartmentTest {
try {
RightSquareCompartment alias = new RightSquareCompartment();
alias.setPoint("10", "10");
- assertTrue(alias.getWidth()<0);
+ assertTrue(alias.getWidth() < 0);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -87,13 +85,8 @@ public class RightSquareCompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new RightSquareCompartment() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ RightSquareCompartment compartment = Mockito.spy(RightSquareCompartment.class);
+ compartment.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
@@ -102,5 +95,4 @@ public class RightSquareCompartmentTest {
}
}
-
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java
index 643499af11..ec25e462c6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/SquareCompartmentTest.java
@@ -7,9 +7,9 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
public class SquareCompartmentTest {
@@ -58,13 +58,8 @@ public class SquareCompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new SquareCompartment() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ SquareCompartment compartment = Mockito.spy(SquareCompartment.class);
+ compartment.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
index 40aba67fbe..244fa59044 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -74,13 +75,8 @@ public class TopSquareCompartmentTest {
@Test
public void testInvalidCopy() {
try {
- new TopSquareCompartment() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ TopSquareCompartment compartment = Mockito.spy(TopSquareCompartment.class);
+ compartment.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
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 6d28272b8a..56b498f591 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
@@ -96,13 +96,13 @@ public class AliasSubmodelConnectionComparatorTest {
model.setNotes("Some description");
GenericProtein protein = new GenericProtein("A");
protein.setName("ad");
- model.addAlias(protein);
+ model.addElement(protein);
GenericProtein alias = new GenericProtein("a_id");
alias.setName("ad");
- model.addAlias(alias);
+ model.addElement(alias);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
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 47c0b2969a..e698bf4ad6 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
@@ -86,13 +86,13 @@ public class ModelComparatorTest {
Compartment alias = new PathwayCompartment("1");
Compartment alias2 = new PathwayCompartment("12");
- model1.addAlias(alias);
- model1.addAlias(alias2);
+ model1.addElement(alias);
+ model1.addElement(alias2);
alias = new PathwayCompartment("1");
alias2 = new PathwayCompartment("12");
- model2.addAlias(alias);
- model2.addAlias(alias2);
+ model2.addElement(alias);
+ model2.addElement(alias2);
alias2.setElementId("1");
assertTrue(comparator.compare(model1, model2) != 0);
@@ -143,9 +143,9 @@ public class ModelComparatorTest {
Species mockAlias = Mockito.mock(Species.class);
when(mockAlias.getElementId()).thenReturn("1");
- model1.addAlias(mockAlias);
+ model1.addElement(mockAlias);
- model2.addAlias(mockAlias);
+ model2.addElement(mockAlias);
try {
comparator.compare(model1, model2);
@@ -190,7 +190,7 @@ public class ModelComparatorTest {
GenericProtein alias = new GenericProtein("SAd");
- model1.addAlias(alias);
+ model1.addElement(alias);
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -206,7 +206,7 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.addAlias(new Compartment("unk_id"));
+ model1.addElement(new Compartment("unk_id"));
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -238,7 +238,7 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.addAlias(new GenericProtein("ASdas"));
+ model1.addElement(new GenericProtein("ASdas"));
assertTrue(comparator.compare(model1, model2) != 0);
assertTrue(comparator.compare(model2, model1) != 0);
@@ -385,9 +385,9 @@ public class ModelComparatorTest {
GenericProtein alias = new GenericProtein("a_id");
alias.setName("ad");
- model.addAlias(alias);
+ model.addElement(alias);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
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 d192167efd..ca457e1bc4 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
@@ -38,8 +38,8 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.User;
@@ -66,12 +66,12 @@ public class ModelFullIndexedTest {
Element compartmentAlias = new Compartment("aaa");
Element compartmentAlias3 = new Compartment("aaa3");
Element compartmentAlias2 = new PathwayCompartment("aaa2");
- model.addAlias(proteinAlias);
- model.addAlias(proteinAlias2);
- model.addAlias(proteinAlias3);
- model.addAlias(compartmentAlias);
- model.addAlias(compartmentAlias2);
- model.addAlias(compartmentAlias3);
+ model.addElement(proteinAlias);
+ model.addElement(proteinAlias2);
+ model.addElement(proteinAlias3);
+ model.addElement(compartmentAlias);
+ model.addElement(compartmentAlias2);
+ model.addElement(compartmentAlias3);
Reaction reaction = new TransportReaction();
reaction.addReactant(new Reactant(proteinAlias));
@@ -98,6 +98,55 @@ public class ModelFullIndexedTest {
}
}
+ @Test
+ public void testGetByName() {
+ try {
+ String name1 = "1a";
+ String name2 = "2a";
+ String unknownName = "unk";
+ ModelFullIndexed model = new ModelFullIndexed(null);
+ Species protein = new GenericProtein("id1");
+ protein.setName(name1);
+ Species protein2 = new GenericProtein("id2");
+ protein2.setName(name2);
+
+ model.addElement(protein);
+ model.addElement(protein2);
+
+ List<Element> elements = model.getElementsByName(name1);
+ List<Element> unkElements = model.getElementsByName(unknownName);
+
+ assertEquals(1, elements.size());
+ assertEquals(0, unkElements.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSpeciesList() {
+ try {
+ ModelFullIndexed model = new ModelFullIndexed(null);
+ Species protein = new GenericProtein("id1");
+ Species protein2 = new GenericProtein("id2");
+
+ model.addElement(protein);
+ model.addElement(protein2);
+ model.addElement(new Compartment("compId"));
+
+
+ List<Species> speciesList = model.getSpeciesList();
+
+ assertEquals(2, speciesList.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testConstructor2() {
try {
@@ -118,7 +167,7 @@ public class ModelFullIndexedTest {
try {
Element alias = Mockito.mock(Element.class);
ModelFullIndexed model = new ModelFullIndexed(null);
- model.addAlias(alias);
+ model.addElement(alias);
new ModelFullIndexed(model.getModelData());
@@ -138,9 +187,9 @@ public class ModelFullIndexedTest {
Complex alias = new Complex("1");
- model.addAlias(alias);
+ model.addElement(alias);
try {
- model.addAlias(alias);
+ model.addElement(alias);
fail("Exception expected");
} catch (InvalidArgumentException e) {
}
@@ -170,7 +219,7 @@ public class ModelFullIndexedTest {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
Complex alias = new Complex("1");
@@ -178,9 +227,9 @@ public class ModelFullIndexedTest {
proteinAlias.setElementId("zz");
proteinAlias.setParent(alias);
- model.addAlias(alias);
+ model.addElement(alias);
- model.addAlias(proteinAlias);
+ model.addElement(proteinAlias);
assertEquals(3, model.getAliases().size());
@@ -196,7 +245,7 @@ public class ModelFullIndexedTest {
ModelFullIndexed model = new ModelFullIndexed(null);
Compartment compAlias = new Compartment("default");
- model.addAlias(compAlias);
+ model.addElement(compAlias);
Complex alias = new Complex("1");
alias.setParent(compAlias);
@@ -205,9 +254,9 @@ public class ModelFullIndexedTest {
proteinAlias.setElementId("zz");
proteinAlias.setParent(alias);
- model.addAlias(alias);
+ model.addElement(alias);
- model.addAlias(proteinAlias);
+ model.addElement(proteinAlias);
assertEquals(3, model.getAliases().size());
@@ -226,7 +275,7 @@ public class ModelFullIndexedTest {
Species alias = new GenericProtein("asd");
alias.setElementId("id");
- model.addAlias(alias);
+ model.addElement(alias);
assertNotNull(model.getElementByElementId("id"));
@@ -244,9 +293,9 @@ public class ModelFullIndexedTest {
Compartment alias = new Compartment("1");
assertEquals(0, model.getCompartmentsAliases().size());
- model.addAlias(alias);
+ model.addElement(alias);
assertEquals(1, model.getCompartmentsAliases().size());
- model.addAlias(alias);
+ model.addElement(alias);
fail("Exception expected");
} catch (InvalidArgumentException e) {
@@ -298,7 +347,7 @@ public class ModelFullIndexedTest {
Element alias = new GenericProtein("1");
alias.setId(aliasId);
assertNull(model.getAliasByDbId(aliasId));
- model.addAlias(alias);
+ model.addElement(alias);
assertEquals(alias, model.getAliasByDbId(aliasId));
} catch (Exception e) {
@@ -314,15 +363,15 @@ public class ModelFullIndexedTest {
Compartment alias = new Compartment("a1");
alias.setWidth(12);
alias.setHeight(12);
- model.addAlias(alias);
+ model.addElement(alias);
alias = new Compartment("a2");
alias.setWidth(14);
alias.setHeight(14);
- model.addAlias(alias);
+ model.addElement(alias);
alias = new Compartment("a3");
alias.setWidth(13);
alias.setHeight(13);
- model.addAlias(alias);
+ model.addElement(alias);
List<Compartment> aliases = model.getSortedCompartmentsAliases();
assertEquals(196.0, aliases.get(0).getSize(), Configuration.EPSILON);
@@ -342,12 +391,12 @@ public class ModelFullIndexedTest {
Compartment alias = new Compartment("a1");
alias.setWidth(12);
alias.setHeight(12);
- model.addAlias(alias);
+ model.addElement(alias);
alias = new Compartment("a2");
alias.setWidth(14);
alias.setHeight(14);
- model.addAlias(alias);
+ model.addElement(alias);
assertEquals(2, model.getAliases().size());
model.removeAlias(alias);
@@ -399,20 +448,49 @@ public class ModelFullIndexedTest {
}
@Test
- public void testRemoveCompartmentAlias() {
+ public void testAddInvalidElement() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
+ Element element = Mockito.spy(Element.class);
+ element.setElementId("id");
+ model.addElement(element);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidElement2() {
+ try {
+ ModelFullIndexed model = new ModelFullIndexed(null);
+ GenericProtein protein = new GenericProtein((String) null);
+ model.addElement(protein);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Compartment parentAlias = new Compartment("parent_id");
+ @Test
+ public void testRemoveCompartment() {
+ try {
+ ModelFullIndexed model = new ModelFullIndexed(null);
- Compartment alias = new Compartment("child_id");
- alias.setParent(parentAlias);
+ Compartment parent = new Compartment("parent_id");
+
+ Compartment compartment = new Compartment("child_id");
+ compartment.setParent(parent);
- model.addAlias(alias);
+ model.addElement(compartment);
assertEquals(1, model.getAliases().size());
- model.removeAlias(alias);
+ model.removeAlias(compartment);
assertEquals(0, model.getAliases().size());
} catch (Exception e) {
@@ -425,7 +503,7 @@ public class ModelFullIndexedTest {
public void testRemoveComplexAlias() {
try {
ModelFullIndexed model = new ModelFullIndexed(null);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
Complex parentAlias = new Complex("a");
@@ -436,7 +514,7 @@ public class ModelFullIndexedTest {
alias.setCompartmentAlias(new Compartment("comp_alias"));
alias.setComplexAlias(new Complex("d"));
- model.addAlias(alias);
+ model.addElement(alias);
assertEquals(2, model.getAliases().size());
@@ -826,7 +904,7 @@ public class ModelFullIndexedTest {
reaction.setIdReaction(reactionId);
model.addReaction(reaction);
Species alias = new GenericProtein("2");
- model.addAlias(alias);
+ model.addElement(alias);
Collection<AnnotatedObject> obj = model.getAnnotatedObjects();
assertEquals(2, obj.size());
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 fe5dcd2ee1..39759fa416 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
@@ -88,9 +88,9 @@ public class ModelSubmodelConnectionComparatorTest {
Species alias = new GenericProtein("a_id");
alias.setName("ad");
- model.addAlias(alias);
+ model.addElement(alias);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
index 120e2ecc90..2325cd8ab9 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
@@ -51,7 +51,7 @@ public class ModelTest {
@Test
public void testAddAlias() {
try {
- model.addAlias(alias);
+ model.addElement(alias);
Element sAlias = model.getElementByElementId(alias.getElementId());
assertNotNull(sAlias);
sAlias = model.getElementByElementId(alias.getElementId() + "blbla");
@@ -68,7 +68,7 @@ public class ModelTest {
try {
Set<Element> aliases = model.getAliases();
assertEquals(0, aliases.size());
- model.addAlias(alias);
+ model.addElement(alias);
assertEquals(1, aliases.size());
Element sAlias = model.getElementByElementId(alias.getElementId());
@@ -79,7 +79,7 @@ public class ModelTest {
sAlias = model.getElementByElementId(cAlias.getElementId());
assertNull(sAlias);
- model.addAlias(cAlias);
+ model.addElement(cAlias);
assertEquals(2, aliases.size());
sAlias = model.getElementByElementId(cAlias.getElementId());
assertNotNull(sAlias);
@@ -155,26 +155,26 @@ public class ModelTest {
Species proteinAlias = new GenericProtein("sa1");
proteinAlias.setName("s1");
- model.addAlias(proteinAlias);
+ model.addElement(proteinAlias);
Species proteinAlias2 = new GenericProtein("sa2");
proteinAlias2.setName("s1");
- model.addAlias(proteinAlias2);
+ model.addElement(proteinAlias2);
Species proteinAlias3 = new GenericProtein("sa3");
proteinAlias3.setName("s1");
- model.addAlias(proteinAlias3);
+ model.addElement(proteinAlias3);
Species proteinAlias4 = new GenericProtein("sa4");
proteinAlias4.setName("s5");
proteinAlias4.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEMBL_TARGET, "CHEMBL12345"));
- model.addAlias(proteinAlias4);
+ model.addElement(proteinAlias4);
Compartment compartmentAlias = new Compartment("cca");
compartmentAlias.setName("c1");
compartmentAlias.addMiriamData(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEBI, "CHEBI:12"));
- model.addAlias(compartmentAlias);
+ model.addElement(compartmentAlias);
return model;
}
@@ -187,32 +187,32 @@ public class ModelTest {
Species alias = new GenericProtein("2");
alias.setWidth(100);
alias.setHeight(100);
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("3");
alias.setWidth(10);
alias.setHeight(10);
- model.addAlias(alias);
+ model.addElement(alias);
alias = new GenericProtein("4");
alias.setWidth(200);
alias.setHeight(100);
- model.addAlias(alias);
+ model.addElement(alias);
Compartment cAlias = new Compartment("5");
cAlias.setWidth(10);
cAlias.setHeight(20);
- model.addAlias(cAlias);
+ model.addElement(cAlias);
cAlias = new Compartment("6");
cAlias.setWidth(100);
cAlias.setHeight(200);
- model.addAlias(cAlias);
+ model.addElement(cAlias);
cAlias = new Compartment("7");
cAlias.setWidth(20);
cAlias.setHeight(30);
- model.addAlias(cAlias);
+ model.addElement(cAlias);
List<Element> sortedAliases = model.getAliasesSortedBySize();
if (sortedAliases.size() > 0) {
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 858fc735fe..2351aa6a17 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
@@ -168,9 +168,9 @@ public class SubmodelConnectionComparatorTest {
Species alias = new GenericProtein("a_id");
alias.setName("ad");
alias.setElementId("a_id");
- model.addAlias(alias);
+ model.addElement(alias);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
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 752671aace..208cf3e900 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
@@ -81,6 +81,14 @@ public class NodeOperatorComparatorTest {
operator1 = createNodeOperator();
operator2 = createNodeOperator();
+ Product product= (Product) operator1.getOutputs().get(0);
+ product.setAlias(new GenericProtein("id666"));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
reactant = (Reactant) operator1.getInputs().get(0);
reactant.getAlias().setName("bla");
assertTrue(comparator.compare(operator1, operator2) != 0);
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
index e788f45443..7d9ef9c87c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
@@ -10,6 +10,7 @@ import lcsb.mapviewer.model.map.species.field.AllFieldTests;
@SuiteClasses({ AllFieldTests.class, //
AntisenseRnaComparatorTest.class, //
AntisenseRnaTest.class, //
+ ChemicalComparatorTest.class, //
ComplexComparatorTest.class, //
ComplexTest.class, //
DegradedComparatorTest.class, //
@@ -19,8 +20,11 @@ import lcsb.mapviewer.model.map.species.field.AllFieldTests;
ElementComparatorTest.class, //
ElementTest.class, //
GeneComparatorTest.class, //
+ GenericProteinComparatorTest.class, //
+ GenericProteinTest.class, //
GeneTest.class, //
IonChannelProteinTest.class, //
+ IonChannelProteinComparatorTest.class, //
IonComparatorTest.class, //
IonTest.class, //
PhenotypeComparatorTest.class, //
@@ -28,6 +32,7 @@ import lcsb.mapviewer.model.map.species.field.AllFieldTests;
ProteinComparatorTest.class, //
ProteinTest.class, //
ReceptorProteinTest.class, //
+ ReceptorProteinComparatorTest.class, //
RnaComparatorTest.class, //
RnaTest.class, //
SimpleMoleculeComparatorTest.class, //
@@ -35,6 +40,7 @@ import lcsb.mapviewer.model.map.species.field.AllFieldTests;
SpeciesComparatorTest.class, //
SpeciesTest.class, //
TruncatedProteinTest.class, //
+ TruncatedProteinComparatorTest.class, //
UnknownComparatorTest.class, //
UnknownTest.class, //
})
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
index 6668697f82..09242c6506 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
@@ -66,9 +67,7 @@ public class AntisenseRnaComparatorTest {
unknown.setName("n");
assertTrue(comparator.compare(unknown, aRna2) != 0);
- assertTrue(comparator.compare(unknown, new AntisenseRna() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(unknown, Mockito.mock(AntisenseRna.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -91,12 +90,8 @@ public class AntisenseRnaComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends AntisenseRna {
- private static final long serialVersionUID = 1L;
- }
- Tmp object = new Tmp();
-
- comparator.compare(object, object);
+ AntisenseRna element = Mockito.mock(AntisenseRna.class);
+ comparator.compare(element, element);
fail("Exception expected");
} catch (NotImplementedException e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
index 797200f2ec..a6c6ec3bfb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaTest.java
@@ -11,6 +11,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
@@ -79,13 +80,8 @@ public class AntisenseRnaTest {
@Test
public void testInvalidCopy() {
try {
- new AntisenseRna() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ AntisenseRna element = Mockito.spy(AntisenseRna.class);
+ element.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
new file mode 100644
index 0000000000..b024670527
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
@@ -0,0 +1,84 @@
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ChemicalComparatorTest {
+
+ ChemicalComparator comparator = new ChemicalComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Chemical drug1 = createChemical();
+ Chemical drug2 = createChemical();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Chemical drug2 = createChemical();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Chemical drug = createChemical();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(Chemical.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Chemical createChemical() {
+ Chemical result = new Ion();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Chemical object = Mockito.mock(Chemical.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
index 487cc2f5bb..295600e2ca 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
@@ -115,10 +115,6 @@ public class ComplexComparatorTest {
assertTrue(comparator.compare(alias1, alias2) != 0);
assertTrue(comparator.compare(alias2, alias1) != 0);
- assertTrue(comparator.compare(alias2, new Complex() {
- private static final long serialVersionUID = 1L;
- }) != 0);
-
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -152,14 +148,9 @@ public class ComplexComparatorTest {
@Test
public void testInvalid3() {
try {
- class Tmp extends Complex {
- private static final long serialVersionUID = 1L;
- }
- ;
- Tmp alias1 = new Tmp();
- Tmp alias2 = new Tmp();
+ Complex invalidComplex = Mockito.mock(Complex.class);
- comparator.compare(alias1, alias2);
+ comparator.compare(invalidComplex, invalidComplex);
fail("Exception expected");
} catch (NotImplementedException e) {
@@ -214,23 +205,6 @@ public class ComplexComparatorTest {
}
}
- @Test
- public void testInvalidComp() throws Exception {
- try {
- class Tmp extends Complex {
- private static final long serialVersionUID = 1L;
- }
-
- comparator.compare(new Tmp(), new Tmp());
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
@Test
public void testInvalidComp2() throws Exception {
try {
@@ -324,13 +298,7 @@ public class ComplexComparatorTest {
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
- assertTrue(comparator.compare(new Complex(), new Complex() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(new Complex(), Mockito.mock(Complex.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
index ba80d63614..34a28408e0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
@@ -8,11 +8,9 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
public class ComplexTest {
@@ -122,15 +120,37 @@ public class ComplexTest {
}
@Test
- public void testInvalidCopy() {
+ public void testGetters() {
try {
- new Complex() {
+ Complex original = new Complex();
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ @Test
+ public void testGetAllSimpleChildren() {
+ try {
+ Complex child = new Complex();
+ child.addAlias(new GenericProtein("id2"));
+ Complex original = new Complex();
+ original.addAlias(child);
+ original.addAlias(new Complex());
+ original.addAlias(new GenericProtein("id"));
+ assertEquals(2, original.getAllSimpleChildren().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Complex object = Mockito.spy(Complex.class);
+ object.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
index fcd2c76542..9256b2a65a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -60,9 +61,7 @@ public class DegradedComparatorTest {
degraded.setName("n");
assertTrue(comparator.compare(degraded, degraded1) != 0);
- assertTrue(comparator.compare(degraded, new Degraded() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(degraded, Mockito.mock(Degraded.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
fail("Unknowne exception occurred");
@@ -78,10 +77,7 @@ public class DegradedComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Degraded {
- private static final long serialVersionUID = 1L;
- }
- Tmp object = new Tmp();
+ Degraded object = Mockito.mock(Degraded.class);
comparator.compare(object, object);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
index 7936da6c48..b41fdde8f4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
@@ -1,17 +1,17 @@
package lcsb.mapviewer.model.map.species;
-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.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
-public class DegradedTest {
+import lcsb.mapviewer.common.exception.NotImplementedException;
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+public class DegradedTest {
@Before
public void setUp() throws Exception {
@@ -22,11 +22,55 @@ public class DegradedTest {
}
@Test
- public void testConstructor() {
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Degraded());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Degraded degraded = new Degraded("");
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Degraded degraded = new Degraded(new Degraded());
+ assertNotNull(degraded.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Degraded degraded = new Degraded().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
try {
- String id = "id";
- Degraded degraded = new Degraded(id);
- assertEquals(id, degraded.getElementId());
+ Degraded object = Mockito.spy(Degraded.class);
+ object.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/DrugComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
index 058e18c95e..f0568d1dec 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -51,9 +52,7 @@ public class DrugComparatorTest {
drug.setName("n");
assertTrue(comparator.compare(drug, drug2) != 0);
- assertTrue(comparator.compare(drug, new Drug() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(drug, Mockito.mock(Drug.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -69,10 +68,7 @@ public class DrugComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Drug {
- private static final long serialVersionUID = 1L;
- }
- Tmp object = new Tmp();
+ Drug object = Mockito.mock(Drug.class);
comparator.compare(object, object);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
index cad4f1a371..bb1dd2c8b5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -66,13 +67,8 @@ public class DrugTest {
@Test
public void testInvalidCopy() {
try {
- new Drug() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ Drug drug = Mockito.spy(Drug.class);
+ drug.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
index a9225cc0a5..43cbdec5fc 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
@@ -134,13 +134,13 @@ public class ElementComparatorTest {
model.setNotes("Some description");
GenericProtein protein = new GenericProtein("A");
protein.setName("ad");
- model.addAlias(protein);
+ model.addElement(protein);
Protein alias = new GenericProtein("a_id");
alias.setName("ad");
- model.addAlias(alias);
+ model.addElement(alias);
- model.addAlias(new Compartment("default"));
+ model.addElement(new Compartment("default"));
Layer layer = new Layer();
layer.setName("layer name");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
index 6f2653df93..5d41302f56 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@@ -66,9 +67,7 @@ public class GeneComparatorTest {
gene.setName("n");
assertTrue(comparator.compare(gene, gene2) != 0);
- assertTrue(comparator.compare(gene, new Gene() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(gene, Mockito.mock(Gene.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -95,10 +94,7 @@ public class GeneComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Gene {
- private static final long serialVersionUID = 1L;
- }
- Tmp object = new Tmp();
+ Gene object = Mockito.mock(Gene.class);
comparator.compare(object, object);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
index d5fad50721..ec7c48dcd1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
@@ -11,6 +11,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@@ -76,13 +77,8 @@ public class GeneTest {
@Test
public void testInvalidCopy() {
try {
- new Gene() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ Gene gene = Mockito.spy(Gene.class);
+ gene.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java
new file mode 100644
index 0000000000..08c34c0b73
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java
@@ -0,0 +1,84 @@
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class GenericProteinComparatorTest {
+
+ GenericProteinComparator comparator = new GenericProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ GenericProtein drug1 = createGenericProtein();
+ GenericProtein drug2 = createGenericProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ GenericProtein drug2 = createGenericProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ GenericProtein drug = createGenericProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(GenericProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public GenericProtein createGenericProtein() {
+ GenericProtein result = new GenericProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ GenericProtein object = Mockito.mock(GenericProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
index 53aa91c095..213f7baefc 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -55,13 +56,8 @@ public class GenericProteinTest {
@Test
public void testCopy2() {
try {
- new GenericProtein() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ GenericProtein protein = Mockito.spy(GenericProtein.class);
+ protein.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java
new file mode 100644
index 0000000000..b1aae7f059
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java
@@ -0,0 +1,84 @@
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class IonChannelProteinComparatorTest {
+
+ IonChannelProteinComparator comparator = new IonChannelProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ IonChannelProtein drug1 = createIonChannelProtein();
+ IonChannelProtein drug2 = createIonChannelProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ IonChannelProtein drug2 = createIonChannelProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ IonChannelProtein drug = createIonChannelProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(IonChannelProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public IonChannelProtein createIonChannelProtein() {
+ IonChannelProtein result = new IonChannelProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ IonChannelProtein object = Mockito.mock(IonChannelProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
index a9e5691708..8163f74c76 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -51,9 +52,7 @@ public class IonComparatorTest {
ion.setName("n");
assertTrue(comparator.compare(ion, ion2) != 0);
- assertTrue(comparator.compare(ion, new Ion() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(ion, Mockito.mock(Ion.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -68,10 +67,7 @@ public class IonComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Ion {
- private static final long serialVersionUID = 1L;
- }
- Tmp object = new Tmp();
+ Ion object = Mockito.mock(Ion.class);
comparator.compare(object, object);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
index c109339377..dd3a5ace78 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -66,13 +67,8 @@ public class IonTest {
@Test
public void testInvalidCopy() {
try {
- new Ion() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ Ion ion = Mockito.spy(Ion.class);
+ ion.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
index 55b6357c7e..8d0db8a144 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -42,13 +43,9 @@ public class PhenotypeComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Phenotype {
- private static final long serialVersionUID = 1L;
- }
- Tmp phenotype1 = new Tmp();
- Tmp phenotype2 = new Tmp();
+ Phenotype phenotype1 = Mockito.mock(Phenotype.class);
- comparator.compare(phenotype1, phenotype2);
+ comparator.compare(phenotype1, phenotype1);
fail("Exception expected");
} catch (NotImplementedException e) {
@@ -67,9 +64,7 @@ public class PhenotypeComparatorTest {
assertTrue(comparator.compare(phenotype2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- assertTrue(comparator.compare(phenotype2, new Phenotype() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(phenotype2, Mockito.mock(Phenotype.class)) != 0);
Phenotype phenotype = createPhenotype();
phenotype2 = createPhenotype();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
index fd370eb7e4..5342df9a7d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.model.map.species;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
@@ -7,6 +8,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -42,6 +44,29 @@ public class PhenotypeTest {
}
}
+ @Test
+ public void testConstructor2() {
+ try {
+ String id = "idd";
+ Phenotype copy = new Phenotype(id);
+ assertEquals(id, copy.getElementId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Phenotype copy = new Phenotype("id");
+ assertNotNull(copy.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testCopy() {
try {
@@ -56,13 +81,8 @@ public class PhenotypeTest {
@Test
public void testInvalidCopy() {
try {
- new Phenotype() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ Phenotype phenotype = Mockito.spy(Phenotype.class);
+ phenotype.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
index a96555a5a4..177a924e83 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
@@ -7,7 +7,9 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
+import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -26,60 +28,86 @@ public class ProteinComparatorTest {
@Test
public void testEquals() {
try {
- GenericProtein aRna1 = createProtein();
- GenericProtein aRna2 = createProtein();
+ GenericProtein protein1 = createProtein();
+ GenericProtein protein2 = createProtein();
- assertEquals(0, comparator.compare(aRna1, aRna1));
+ assertEquals(0, comparator.compare(protein1, protein1));
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
+ assertEquals(0, comparator.compare(protein1, protein2));
+ assertEquals(0, comparator.compare(protein2, protein1));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ assertEquals(0, comparator.compare(new TruncatedProtein(), new TruncatedProtein()));
+ assertEquals(0, comparator.compare(new ReceptorProtein(), new ReceptorProtein()));
+ assertEquals(0, comparator.compare(new IonChannelProtein(), new IonChannelProtein()));
} catch (Exception e) {
e.printStackTrace();
- fail("Unknowne exception occurred");
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownProteinImplementations() {
+ try {
+ Protein protein1 = Mockito.mock(Protein.class);
+ assertEquals(0, comparator.compare(protein1, protein1));
+
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
}
}
@Test
public void testDifferent() {
try {
- GenericProtein aRna1 = createProtein();
- GenericProtein aRna2 = createProtein();
- aRna1.getModificationResidues().get(0).setName("bla");
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createProtein();
- aRna2 = createProtein();
- aRna1.getModificationResidues().clear();
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createProtein();
- aRna2 = createProtein();
- assertTrue(comparator.compare(null, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, null) != 0);
+ GenericProtein protein1 = createProtein();
+ GenericProtein protein2 = createProtein();
+ assertTrue(comparator.compare(null, protein2) != 0);
+ assertTrue(comparator.compare(protein2, null) != 0);
+
+ protein1.getModificationResidues().get(0).setName("bla");
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.getModificationResidues().clear();
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ assertTrue(comparator.compare(null, protein2) != 0);
+ assertTrue(comparator.compare(protein2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- assertTrue(comparator.compare(aRna2, new GenericProtein()) != 0);
-
- aRna1 = createProtein();
- aRna2 = createProtein();
- aRna1.setName("a");
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createProtein();
- aRna2 = createProtein();
- aRna1.setStructuralState("a");
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createProtein();
- aRna2 = createProtein();
- aRna1.setHomodimer(1);
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
+ assertTrue(comparator.compare(protein2, new GenericProtein()) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.setName("a");
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.setStructuralState("a");
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ protein1 = createProtein();
+ protein2 = createProtein();
+ protein1.setHomodimer(1);
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+
+ assertTrue(comparator.compare(new GenericProtein(), new TruncatedProtein()) != 0);
} catch (Exception e) {
e.printStackTrace();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java
new file mode 100644
index 0000000000..29c5801d47
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java
@@ -0,0 +1,84 @@
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ReceptorProteinComparatorTest {
+
+ ReceptorProteinComparator comparator = new ReceptorProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ ReceptorProtein drug1 = createReceptorProtein();
+ ReceptorProtein drug2 = createReceptorProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ ReceptorProtein drug2 = createReceptorProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ ReceptorProtein drug = createReceptorProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(ReceptorProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public ReceptorProtein createReceptorProtein() {
+ ReceptorProtein result = new ReceptorProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ ReceptorProtein object = Mockito.mock(ReceptorProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
index 8d94528dbc..7b8a84dab4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -55,13 +56,8 @@ public class ReceptorProteinTest {
@Test
public void testCopy2() {
try {
- new ReceptorProtein() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ ReceptorProtein protein = Mockito.spy(ReceptorProtein.class);
+ protein.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
index e86a6cf44c..3ead55dee7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -66,9 +67,7 @@ public class RnaComparatorTest {
rna.setName("n");
assertTrue(comparator.compare(rna, aRna2) != 0);
- assertTrue(comparator.compare(rna, new Rna() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(rna, Mockito.mock(Rna.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -93,10 +92,7 @@ public class RnaComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Rna {
- private static final long serialVersionUID = 1L;
- }
- Tmp object = new Tmp();
+ Rna object = Mockito.mock(Rna.class);
comparator.compare(object, object);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
index 9bee28a121..6cde518d7d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaTest.java
@@ -12,6 +12,7 @@ import org.apache.log4j.Logger;
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.field.RnaRegion;
@@ -91,13 +92,8 @@ public class RnaTest {
@Test
public void testInvalidCopy() {
try {
- new Rna() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ Rna object = Mockito.spy(Rna.class);
+ object.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
index fc05700b63..b696a4286f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -66,9 +67,7 @@ public class SimpleMoleculeComparatorTest {
assertTrue(comparator.compare(simpleMolecule2, null) != 0);
assertTrue(comparator.compare(null, null) == 0);
- assertTrue(comparator.compare(simpleMolecule1, new SimpleMolecule() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(simpleMolecule1, Mockito.mock(SimpleMolecule.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -79,13 +78,8 @@ public class SimpleMoleculeComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends SimpleMolecule {
- private static final long serialVersionUID = 1L;
- }
- ;
- Tmp simpleMolecule1 = new Tmp();
- Tmp simpleMolecule2 = new Tmp();
- comparator.compare(simpleMolecule1, simpleMolecule2);
+ SimpleMolecule simpleMolecule1 = Mockito.mock(SimpleMolecule.class);
+ comparator.compare(simpleMolecule1, simpleMolecule1);
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
index a2e3158d89..65d2709d38 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -66,13 +67,8 @@ public class SimpleMoleculeTest {
@Test
public void testInvalidCopy() {
try {
- new SimpleMolecule() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ SimpleMolecule simpleMolecule = Mockito.spy(SimpleMolecule.class);
+ simpleMolecule.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
index cc774a095d..acbe0f722f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
@@ -11,7 +11,6 @@ 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.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
@@ -20,7 +19,6 @@ import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
public class SpeciesComparatorTest {
-
SpeciesComparator comparator = new SpeciesComparator();
@Before
@@ -147,7 +145,6 @@ public class SpeciesComparatorTest {
}
}
-
@Test
public void testException() {
try {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java
new file mode 100644
index 0000000000..8c81b8f89f
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java
@@ -0,0 +1,84 @@
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class TruncatedProteinComparatorTest {
+
+ TruncatedProteinComparator comparator = new TruncatedProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ TruncatedProtein drug1 = createTruncatedProtein();
+ TruncatedProtein drug2 = createTruncatedProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ TruncatedProtein drug2 = createTruncatedProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ TruncatedProtein drug = createTruncatedProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(TruncatedProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public TruncatedProtein createTruncatedProtein() {
+ TruncatedProtein result = new TruncatedProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ TruncatedProtein object = Mockito.mock(TruncatedProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
index 3a00d4471f..1150dc7a2d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -55,13 +56,8 @@ public class TruncatedProteinTest {
@Test
public void testCopy2() {
try {
- new TruncatedProtein() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ TruncatedProtein protein = Mockito.spy(TruncatedProtein.class);
+ protein.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
index a1e0a71553..fbc4809cd9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
@@ -7,6 +7,7 @@ import static org.junit.Assert.fail;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -51,9 +52,7 @@ public class UnknownComparatorTest {
unknown.setName("n");
assertTrue(comparator.compare(unknown, unknown2) != 0);
- assertTrue(comparator.compare(unknown, new Unknown() {
- private static final long serialVersionUID = 1L;
- }) != 0);
+ assertTrue(comparator.compare(unknown, Mockito.mock(Unknown.class)) != 0);
} catch (Exception e) {
e.printStackTrace();
@@ -69,10 +68,7 @@ public class UnknownComparatorTest {
@Test
public void testInvalid() {
try {
- class Tmp extends Unknown {
- private static final long serialVersionUID = 1L;
- }
- Tmp object = new Tmp();
+ Unknown object = Mockito.mock(Unknown.class);
comparator.compare(object, object);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
index ce6a2a0a88..5dc8c9566d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
@@ -7,6 +7,7 @@ import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -66,13 +67,8 @@ public class UnknownTest {
@Test
public void testInvalidCopy() {
try {
- new Unknown() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
+ Unknown object = Mockito.spy(Unknown.class);
+ object.copy();
fail("Exception expected");
} catch (NotImplementedException e) {
} catch (Exception 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 949c2fb8e5..41ef01ea86 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
@@ -5,6 +5,7 @@ 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;
import java.util.LinkedList;
import java.util.List;
@@ -14,11 +15,15 @@ import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.IonChannelProtein;
import lcsb.mapviewer.model.map.species.Protein;
@@ -74,6 +79,37 @@ public class ElementUtilsTest {
}
}
+ @Test
+ public void testGetTag2() throws Exception {
+ try {
+ ElementUtils elementUtils = new ElementUtils();
+
+ GenericProtein protein = new GenericProtein("id");
+
+ assertNotNull(elementUtils.getElementTag(protein, new Object()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTagForInvalidElement() throws Exception {
+ try {
+ ElementUtils elementUtils = new ElementUtils();
+
+ AnnotatedObject element = Mockito.mock(AnnotatedObject.class);
+ assertNotNull(elementUtils.getElementTag(element));
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
protected void print(ClassTreeNode top, int indent) {
if (indent > 10) {
throw new InvalidArgumentException();
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 826bcee04c..40d498bf84 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -312,7 +312,7 @@ public class ModelContructor {
alias.setColor(DEFAULT_COMPLEX_ALIAS_COLOR);
data.id2alias.put(group.getGraphId(), alias);
- model.addAlias(alias);
+ model.addElement(alias);
}
}
@@ -334,7 +334,7 @@ public class ModelContructor {
Element alias = updateAlias(dataNode, species);
data.id2alias.put(dataNode.getGraphId(), alias);
- model.addAlias(alias);
+ model.addElement(alias);
}
for (Label label : graph.getLabels()) {
if (label.isTreatAsNode()) {
@@ -344,7 +344,7 @@ public class ModelContructor {
Element alias = updateAlias(label, species);
data.id2alias.put(label.getGraphId(), alias);
- model.addAlias(alias);
+ model.addElement(alias);
} else {
LayerText text = createText(label);
data.layer.addLayerText(text);
@@ -358,7 +358,7 @@ public class ModelContructor {
Element alias = updateAlias(shape, species);
data.id2alias.put(shape.getGraphId(), alias);
- model.addAlias(alias);
+ model.addElement(alias);
} else {
if (!shape.isCompartment()) {
@@ -372,7 +372,7 @@ public class ModelContructor {
} else {
Compartment compartment = new Compartment(shape.getGraphId());
Element cmpAl = updateAlias(shape, compartment);
- model.addAlias(cmpAl);
+ model.addElement(cmpAl);
}
}
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
index b69a4bb8b7..2331550164 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
@@ -72,7 +72,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
alias.setX(1);
alias.setY(1);
- model.addAlias(alias);
+ model.addElement(alias);
String xml = parser.getGPML(model);
assertNotNull(xml);
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 b7e079d5b2..ba1eb26bf8 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -171,10 +171,10 @@ public class ProjectDaoTest extends PersistTestFunctions {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- model.addAlias(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
- model.addAlias(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
- model.addAlias(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
- model.addAlias(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
+ model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
+ model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
@@ -184,11 +184,11 @@ public class ProjectDaoTest extends PersistTestFunctions {
alias.setParent(alias3);
alias2.setParent(alias3);
- model.addAlias(alias);
- model.addAlias(alias2);
- model.addAlias(alias3);
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
- model.addAlias(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
+ model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
model.setWidth(2000);
model.setHeight(2000);
return model;
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 4b8a46b053..856380cd3f 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
@@ -103,13 +103,13 @@ public class CommentDaoTest extends PersistTestFunctions {
Model model = new ModelFullIndexed(null);
GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
@@ -119,12 +119,12 @@ public class CommentDaoTest extends PersistTestFunctions {
alias.setParent(alias3);
alias2.setParent(alias3);
- model.addAlias(alias);
- model.addAlias(alias2);
- model.addAlias(alias3);
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addAlias(cAlias);
+ model.addElement(cAlias);
model.setWidth(2000);
model.setHeight(2000);
@@ -142,7 +142,7 @@ public class CommentDaoTest extends PersistTestFunctions {
model.addReaction(reaction);
alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addAlias(alias);
+ model.addElement(alias);
ModificationResidue mr = new ModificationResidue();
mr.setName("mr");
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 f752760343..0e48ff8d14 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
@@ -150,13 +150,13 @@ public class LayoutDaoTest extends PersistTestFunctions {
Model model = new ModelFullIndexed(null);
Species alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
@@ -166,12 +166,12 @@ public class LayoutDaoTest extends PersistTestFunctions {
alias.setParent(alias3);
alias2.setParent(alias3);
- model.addAlias(alias);
- model.addAlias(alias2);
- model.addAlias(alias3);
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addAlias(cAlias);
+ model.addElement(cAlias);
model.setWidth(2000);
model.setHeight(2000);
@@ -189,7 +189,7 @@ public class LayoutDaoTest extends PersistTestFunctions {
model.addReaction(reaction);
Protein protein = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addAlias(protein);
+ model.addElement(protein);
ModificationResidue mr = new ModificationResidue();
mr.setName("mr");
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 a5126a28a6..b7cd79ee28 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
@@ -115,7 +115,7 @@ public class ModelDaoTest extends PersistTestFunctions {
test = false;
for (Element alias : model.getAliases()) {
if (alias instanceof Compartment) {
- assertNotNull(fullModel.getCompartmentAliasByCompartmentAliasId(alias.getElementId()));
+ assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
test = true;
}
}
@@ -330,13 +330,13 @@ public class ModelDaoTest extends PersistTestFunctions {
Model model = new ModelFullIndexed(null);
GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addAlias(alias);
+ model.addElement(alias);
alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
@@ -346,12 +346,12 @@ public class ModelDaoTest extends PersistTestFunctions {
alias.setParent(alias3);
alias2.setParent(alias3);
- model.addAlias(alias);
- model.addAlias(alias2);
- model.addAlias(alias3);
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addAlias(cAlias);
+ model.addElement(cAlias);
model.setWidth(2000);
model.setHeight(2000);
@@ -369,7 +369,7 @@ public class ModelDaoTest extends PersistTestFunctions {
model.addReaction(reaction);
alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addAlias(alias);
+ model.addElement(alias);
ModificationResidue mr = new ModificationResidue();
mr.setName("mr");
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 352746c1d4..edc89b4ba9 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
@@ -42,7 +42,7 @@ public class DataMiningDaoTest extends PersistTestFunctions {
project.setProjectId(projectId);
Model model = new ModelFullIndexed(null);
Element alias = new GenericProtein("some_el_id");
- model.addAlias(alias);
+ model.addElement(alias);
project.addModel(model);
projectDao.add(project);
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 c754a4adc7..a0d5a976a2 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
@@ -71,10 +71,10 @@ public class AliasDaoTest extends PersistTestFunctions {
private Model createModel() {
Model model = new ModelFullIndexed(null);
- model.addAlias(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
- model.addAlias(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
- model.addAlias(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
- model.addAlias(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
+ model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
+ model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
@@ -84,11 +84,11 @@ public class AliasDaoTest extends PersistTestFunctions {
alias.setParent(alias3);
alias2.setParent(alias3);
- model.addAlias(alias);
- model.addAlias(alias2);
- model.addAlias(alias3);
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
- model.addAlias(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
+ model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
model.setWidth(2000);
model.setHeight(2000);
return model;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
index 8f8121b864..4faae67b56 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
@@ -80,7 +80,7 @@ public class AntisenseRnaTest extends PersistTestFunctions {
alias.setY(2);
alias.setWidth(10);
alias.setHeight(20);
- model.addAlias(alias);
+ model.addElement(alias);
return model;
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
index b275d90736..723b4dd75c 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
@@ -79,7 +79,7 @@ public class RnaTest extends PersistTestFunctions {
alias.setY(2);
alias.setWidth(10);
alias.setHeight(20);
- model.addAlias(alias);
+ model.addElement(alias);
return model;
}
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 de566229ae..cbe8096960 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -279,11 +279,11 @@ public class SearchServiceTest extends ServiceTestFunctions {
proteinAlias.getSynonyms().add("PROT synonym");
proteinAlias.getSynonyms().add("another synonym");
proteinAlias.setFullName("Protein common name");
- model.addAlias(proteinAlias);
+ model.addElement(proteinAlias);
SimpleMolecule alias = new SimpleMolecule("a2");
alias.setName("Molecule2");
- model.addAlias(alias);
+ model.addElement(alias);
int oldVal = Configuration.getAutocompleteSize();
Configuration.setAutocompleteSize(5);
@@ -325,11 +325,11 @@ public class SearchServiceTest extends ServiceTestFunctions {
GenericProtein proteinAlias = new GenericProtein("a1");
proteinAlias.setName("PROT identifier");
proteinAlias.setNotes("Synonyms: PROT synonym, another synonym\nName: Protein common name");
- model.addAlias(proteinAlias);
+ model.addElement(proteinAlias);
SimpleMolecule alias = new SimpleMolecule("a2");
alias.setName("Molecule2");
- model.addAlias(alias);
+ model.addElement(alias);
List<String> list = searchService.getAutocompleteList(model, "PROT identifier");
assertNotNull(list);
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 45445bb354..538ec5894c 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
@@ -76,14 +76,14 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
alias.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.WIKIPEDIA, "144352"));
alias.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "43345"));
- model.addAlias(alias);
+ model.addElement(alias);
alias2 = new GenericProtein("AL2");
alias2.setName("blablabla2");
alias2.setX(100.0);
alias2.setY(120.0);
- model.addAlias(alias2);
+ model.addElement(alias2);
midPoint = new Point2D.Double(30, 100);
@@ -104,7 +104,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
alias3.setX(200.0);
alias3.setY(120.0);
- model.addAlias(alias3);
+ model.addElement(alias3);
reaction = new NegativeInfluenceReaction(reaction);
reaction.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "cc"));
@@ -116,7 +116,7 @@ public class FullAliasViewFactoryTest extends ServiceTestFunctions {
compartmentAlias.setY(10);
compartmentAlias.setWidth(10);
compartmentAlias.setHeight(10);
- model.addAlias(compartmentAlias);
+ model.addElement(compartmentAlias);
}
@After
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 3e3e73c0fd..14bcf86a90 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
@@ -113,7 +113,7 @@ public class DrugViewFactoryTest extends ServiceTestFunctions {
alias.setName("M");
alias.setId(12);
model.removeAlias(alias);
- model.addAlias(alias);
+ model.addElement(alias);
ElementIdentifier ei = new ElementIdentifier(alias, null);
model.setTileSize(256);
List<Model> models = new ArrayList<>();
--
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