From 24e9d06d245b661cd89f6839496f5a033a505275 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 2 Jan 2019 15:52:03 +0100
Subject: [PATCH] adding modification residues is class dependent (there is no
possibil;ity to add invalid residue type)
---
.../structure/CellDesignerAntisenseRna.java | 18 +++++++++--
.../structure/CellDesignerGene.java | 22 +++++++++++--
.../structure/CellDesignerProtein.java | 18 ++++++++---
.../structure/CellDesignerRna.java | 20 +++++++++---
.../structure/SpeciesStateTest.java | 4 +--
.../model/sbgnml/SbgnmlXmlParser.java | 2 +-
.../model/sbgnml/SbgnmlXmlParserTest2.java | 2 +-
.../element/species/SpeciesConverterTest.java | 2 +-
.../model/sbml/SbmlExporterTest.java | 31 +++++++++++++++++++
.../model/map/species/AntisenseRna.java | 23 +++++++++++---
.../mapviewer/model/map/species/Gene.java | 22 ++++++++++++-
.../mapviewer/model/map/species/Protein.java | 14 +++++++--
.../lcsb/mapviewer/model/map/species/Rna.java | 23 +++++++++++---
.../field/AbstractSiteModification.java | 4 +++
.../species/field/ModificationResidue.java | 4 +++
.../model/map/species/field/Residue.java | 4 +++
.../species/AntisenseRnaComparatorTest.java | 2 +-
.../model/map/species/AntisenseRnaTest.java | 2 +-
.../model/map/species/GeneComparatorTest.java | 12 +++----
.../mapviewer/model/map/species/GeneTest.java | 2 +-
.../map/species/ProteinComparatorTest.java | 2 +-
.../model/map/species/RnaComparatorTest.java | 2 +-
.../mapviewer/model/map/species/RnaTest.java | 2 +-
.../wikipathway/XML/ModelContructor.java | 4 +--
.../persist/dao/map/CommentDaoTest.java | 4 +--
.../persist/dao/map/LayoutDaoTest.java | 2 +-
.../persist/dao/map/ModelDaoTest.java | 2 +-
.../dao/map/layout/alias/AliasDaoTest2.java | 6 ++--
.../map/layout/alias/AntisenseRnaTest.java | 2 +-
.../persist/dao/map/layout/alias/RnaTest.java | 2 +-
.../elements/ElementRestImplTest.java | 6 ++--
31 files changed, 210 insertions(+), 55 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
index 9ad77efd72..1e2809aa35 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
@@ -5,10 +5,15 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
/**
* Class representing CellDesigner {@link AntisenseRna}.
@@ -140,9 +145,18 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
}
@Override
- public void updateModelElementAfterLayoutAdded(Species element) {
+ public void updateModelElementAfterLayoutAdded(AntisenseRna antisenseRna) {
for (CellDesignerModificationResidue region : regions) {
- ((AntisenseRna) element).addRegion(region.createModificationResidue(element));
+ ModificationResidue mr = region.createModificationResidue(antisenseRna);
+ if (mr instanceof CodingRegion) {
+ antisenseRna.addCodingRegion((CodingRegion) mr);
+ } else if (mr instanceof ModificationSite) {
+ antisenseRna.addModificationSite((ModificationSite) mr);
+ } else if (mr instanceof ProteinBindingDomain) {
+ antisenseRna.addProteinBindingDomain((ProteinBindingDomain) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
index 247887c598..cd8e8ee223 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
@@ -3,10 +3,16 @@ package lcsb.mapviewer.converter.model.celldesigner.structure;
import java.util.ArrayList;
import java.util.List;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
/**
* Class representing CellDesigner {@link Gene}.
@@ -113,10 +119,20 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
}
@Override
- public void updateModelElementAfterLayoutAdded(Species element) {
+ public void updateModelElementAfterLayoutAdded(Gene gene) {
for (CellDesignerModificationResidue region : modificationResidues) {
- ((Gene) element).addModificationResidue(region.createModificationResidue(element));
+ ModificationResidue mr = region.createModificationResidue(gene);
+ if (mr instanceof CodingRegion) {
+ gene.addCodingRegion((CodingRegion) mr);
+ } else if (mr instanceof ModificationSite) {
+ gene.addModificationSite((ModificationSite) mr);
+ } else if (mr instanceof RegulatoryRegion) {
+ gene.addRegulatoryRegion((RegulatoryRegion) mr);
+ } else if (mr instanceof TranscriptionSite) {
+ gene.addTranscriptionSite((TranscriptionSite) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
}
}
-
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index 9fa15ca0df..d82a2060b3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -5,10 +5,13 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
/**
* Class representing CellDesigner {@link Protein} object.
@@ -150,9 +153,16 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
}
@Override
- public void updateModelElementAfterLayoutAdded(Species element) {
- for (CellDesignerModificationResidue mr : modificationResidues) {
- ((Protein) element).addModificationResidue(mr.createModificationResidue(element));
+ public void updateModelElementAfterLayoutAdded(Protein element) {
+ for (CellDesignerModificationResidue region : modificationResidues) {
+ ModificationResidue mr = region.createModificationResidue(element);
+ if (mr instanceof Residue) {
+ element.addResidue((Residue) mr);
+ } else if (mr instanceof BindingRegion) {
+ element.addBindingRegion((BindingRegion) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index 64e121ad9a..1e2406c374 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -5,10 +5,14 @@ import java.util.List;
import org.apache.log4j.Logger;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
/**
* Class representing CellDesigner {@link Rna}.
@@ -139,10 +143,18 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
}
@Override
- public void updateModelElementAfterLayoutAdded(Species element) {
+ public void updateModelElementAfterLayoutAdded(Rna rna) {
for (CellDesignerModificationResidue region : regions) {
- Rna rna = (Rna) element;
- rna.addRegion(region.createModificationResidue(rna));
+ ModificationResidue mr = region.createModificationResidue(rna);
+ if (mr instanceof CodingRegion) {
+ rna.addCodingRegion((CodingRegion) mr);
+ } else if (mr instanceof ModificationSite) {
+ rna.addModificationSite((ModificationSite) mr);
+ } else if (mr instanceof ProteinBindingDomain) {
+ rna.addProteinBindingDomain((ProteinBindingDomain) mr);
+ } else {
+ throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
+ }
}
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
index 5e24aa5ddb..1c6e9ca880 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
@@ -56,7 +56,7 @@ public class SpeciesStateTest {
rna.setHeight(10);
CodingRegion mr = new CodingRegion();
mr.setPosition(new Point2D.Double(10, 40));
- rna.addRegion(mr);
+ rna.addCodingRegion(mr);
SpeciesState state = new SpeciesState(rna);
assertEquals(1, state.getModifications().size());
}
@@ -68,7 +68,7 @@ public class SpeciesStateTest {
gene.setHeight(10);
ModificationSite mr = new ModificationSite();
mr.setPosition(new Point2D.Double(10, 40));
- gene.addModificationResidue(mr);
+ gene.addModificationSite(mr);
SpeciesState state = new SpeciesState(gene);
assertEquals(1, state.getModifications().size());
}
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 7c6c5e53d5..3be28e7f95 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
@@ -831,7 +831,7 @@ public class SbgnmlXmlParser {
mr.setPosition(new Point2D.Double(x, y));
- protein.addModificationResidue(mr);
+ protein.addResidue(mr);
}
/**
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
index fd00fea41c..e14f56980f 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
@@ -33,7 +33,7 @@ public class SbgnmlXmlParserTest2 {
Residue mr = new Residue();
Point2D position = new Point2D.Double(100, 20);
mr.setPosition(position);
- protein.addModificationResidue(mr);
+ protein.addResidue(mr);
parser.adjustModificationCoordinates(protein);
assertTrue(mr.getPosition().distance(position) > Configuration.EPSILON);
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index 9b1ec5616f..d44d12eefa 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -197,7 +197,7 @@ public class SpeciesConverterTest {
bindingRegion.setPosition(new Point2D.Double(10, 10));
bindingRegion.setWidth(100.0);
bindingRegion.setHeight(10.0);
- protein.addModificationResidue(bindingRegion);
+ protein.addBindingRegion(bindingRegion);
ProteinConverter converter = Mockito.spy(new ProteinConverter(colorExtractor));
converter.drawModification(bindingRegion, graphics, false);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 1ae127b723..cffe83e934 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -50,7 +50,9 @@ import lcsb.mapviewer.model.map.species.IonChannelProtein;
import lcsb.mapviewer.model.map.species.ReceptorProtein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+import lcsb.mapviewer.model.map.species.field.Residue;
public class SbmlExporterTest {
Logger logger = Logger.getLogger(SbmlExporterTest.class);
@@ -606,4 +608,33 @@ public class SbmlExporterTest {
speciesExtension.getListOfSpeciesFeatures().size() > 0);
}
+ @Test
+ public void testExportResidue() throws Exception {
+ Model model = createEmptyModel();
+ GenericProtein element = new GenericProtein("id");
+ element.setName("test name");
+ element.setX(10);
+ element.setWidth(10);
+ element.setY(10);
+ element.setHeight(10);
+ Residue mr = new Residue("x1");
+ mr.setName("217U");
+ mr.setState(ModificationState.PHOSPHORYLATED);
+ element.addResidue(mr);
+ mr = new Residue("Y");
+ mr.setName("218");
+ mr.setState(ModificationState.PHOSPHORYLATED);
+ element.addResidue(mr);
+ mr = new Residue("Z");
+ mr.setName("219");
+ mr.setState(ModificationState.UBIQUITINATED);
+ element.addResidue(mr);
+ model.addElement(element);
+ Model deserializedModel = getModelAfterSerializing(model);
+
+ GenericProtein protein = deserializedModel.getElementByElementId("id");
+ assertEquals("Residues weren't exported/imported properly", 3, protein.getModificationResidues().size());
+
+ }
+
}
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 bf985706d3..416802d7db 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
@@ -13,7 +13,10 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
/**
* Entity representing antisense rna element on the map.
@@ -38,7 +41,7 @@ public class AntisenseRna extends Species {
@OneToMany(mappedBy = "species")
@LazyCollection(LazyCollectionOption.FALSE)
private List<ModificationResidue> regions = new ArrayList<>();
-
+
/**
* Empty constructor required by hibernate.
*/
@@ -54,7 +57,7 @@ public class AntisenseRna extends Species {
public AntisenseRna(AntisenseRna original) {
super(original);
for (ModificationResidue region : original.getRegions()) {
- addRegion(region.copy());
+ addModificationResidue(region.copy());
}
}
@@ -74,11 +77,23 @@ public class AntisenseRna extends Species {
* @param antisenseRnaRegion
* region to be added
*/
- public void addRegion(ModificationResidue antisenseRnaRegion) {
+ private void addModificationResidue(ModificationResidue antisenseRnaRegion) {
regions.add(antisenseRnaRegion);
antisenseRnaRegion.setSpecies(this);
}
-
+
+ public void addCodingRegion(CodingRegion codingRegion) {
+ this.addModificationResidue(codingRegion);
+ }
+
+ public void addProteinBindingDomain(ProteinBindingDomain codingRegion) {
+ this.addModificationResidue(codingRegion);
+ }
+
+ public void addModificationSite(ModificationSite codingRegion) {
+ this.addModificationResidue(codingRegion);
+ }
+
@Override
public AntisenseRna copy() {
if (this.getClass() == AntisenseRna.class) {
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 183c684ef1..9c87b44c78 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
@@ -13,7 +13,11 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
/**
* Entity representing gene element on the map.
@@ -73,12 +77,28 @@ public class Gene extends Species {
* @param modificationResidue
* {@link ModificationResidue} to be added
*/
- public void addModificationResidue(ModificationResidue modificationResidue) {
+ private void addModificationResidue(ModificationResidue modificationResidue) {
modificationResidues.add(modificationResidue);
modificationResidue.setSpecies(this);
}
+ public void addCodingRegion(CodingRegion codingRegion) {
+ this.addModificationResidue(codingRegion);
+ }
+
+ public void addModificationSite(ModificationSite modificationSite) {
+ this.addModificationResidue(modificationSite);
+ }
+
+ public void addRegulatoryRegion(RegulatoryRegion regulatoryRegion) {
+ this.addModificationResidue(regulatoryRegion);
+ }
+
+ public void addTranscriptionSite(TranscriptionSite transcriptionSite) {
+ this.addModificationResidue(transcriptionSite);
+ }
+
@Override
public Gene copy() {
if (this.getClass() == Gene.class) {
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 829ca43483..9a52c46031 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
@@ -12,7 +12,9 @@ import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
/**
* Entity representing protein element on the map.
@@ -41,7 +43,7 @@ public abstract class Protein extends Species {
@OneToMany(mappedBy = "species", orphanRemoval = true)
@LazyCollection(LazyCollectionOption.FALSE)
private List<ModificationResidue> modificationResidues = new ArrayList<>();
-
+
/**
* Empty constructor required by hibernate.
*/
@@ -78,11 +80,19 @@ public abstract class Protein extends Species {
* @param modificationResidue
* modification to add
*/
- public void addModificationResidue(ModificationResidue modificationResidue) {
+ private void addModificationResidue(ModificationResidue modificationResidue) {
modificationResidues.add(modificationResidue);
modificationResidue.setSpecies(this);
}
+ public void addBindingRegion(BindingRegion bindingRegion) {
+ this.addModificationResidue(bindingRegion);
+ }
+
+ public void addResidue(Residue residue) {
+ this.addModificationResidue(residue);
+ }
+
/**
* @return the modificationResidues
* @see #modificationResidues
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 b9d6f9233f..cbaedd90b4 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
@@ -13,7 +13,10 @@ import org.hibernate.annotations.LazyCollection;
import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
/**
* Entity representing rna element on the map.
@@ -53,7 +56,7 @@ public class Rna extends Species {
public Rna(Rna original) {
super(original);
for (ModificationResidue region : original.getRegions()) {
- addRegion(region.copy());
+ addModificationResidue(region.copy());
}
}
@@ -74,9 +77,21 @@ public class Rna extends Species {
* @param rnaRegion
* object to be added
*/
- public void addRegion(ModificationResidue rnaRegion) {
- regions.add(rnaRegion);
- rnaRegion.setSpecies(this);
+ private void addModificationResidue(ModificationResidue antisenseRnaRegion) {
+ regions.add(antisenseRnaRegion);
+ antisenseRnaRegion.setSpecies(this);
+ }
+
+ public void addCodingRegion(CodingRegion codingRegion) {
+ this.addModificationResidue(codingRegion);
+ }
+
+ public void addProteinBindingDomain(ProteinBindingDomain codingRegion) {
+ this.addModificationResidue(codingRegion);
+ }
+
+ public void addModificationSite(ModificationSite codingRegion) {
+ this.addModificationResidue(codingRegion);
}
@Override
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
index e1b7030a96..86ef4c8d19 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
@@ -31,6 +31,10 @@ public abstract class AbstractSiteModification extends ModificationResidue {
this.state = mr.getState();
}
+ public AbstractSiteModification(String modificationId) {
+ super(modificationId);
+ }
+
public ModificationState getState() {
return state;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
index 6d76f71c98..4225d31fb3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
@@ -92,6 +92,10 @@ public abstract class ModificationResidue implements Serializable {
this.position = mr.position;
}
+ public ModificationResidue(String modificationId) {
+ this.idModificationResidue = modificationId;
+ }
+
/**
* @return the idModificationResidue
* @see #id
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
index d93cc8956d..c20e0606fb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
@@ -29,6 +29,10 @@ public class Residue extends AbstractSiteModification {
super(residue);
}
+ public Residue(String modificationId) {
+ super(modificationId);
+ }
+
/**
* Creates copy of the object.
*
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 3df395f239..858bc750ba 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
@@ -79,7 +79,7 @@ public class AntisenseRnaComparatorTest {
AntisenseRna result = new AntisenseRna();
CodingRegion region1 = new CodingRegion();
- result.addRegion(region1);
+ result.addCodingRegion(region1);
region1.setIdModificationResidue("a");
region1.setName("name");
region1.setPosition(new Point2D.Double(0, 1));
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 f52284cd4f..102da4683c 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
@@ -41,7 +41,7 @@ public class AntisenseRnaTest {
public void testConstructor1() {
try {
AntisenseRna original = new AntisenseRna();
- original.addRegion(new CodingRegion());
+ original.addCodingRegion(new CodingRegion());
AntisenseRna aRna = new AntisenseRna(original);
assertNotNull(aRna);
} catch (Exception e) {
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 e255b76e32..7b7d6d4869 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
@@ -82,13 +82,13 @@ public class GeneComparatorTest {
Gene result = new Gene();
result.setHypothetical(true);
- AbstractSiteModification residue = new ModificationSite();
- result.addModificationResidue(residue);
+ ModificationSite modificationSite = new ModificationSite();
+ result.addModificationSite(modificationSite);
- residue.setIdModificationResidue("a");
- residue.setName("name");
- residue.setPosition(new Point2D.Double(10, 20));
- residue.setState(ModificationState.ACETYLATED);
+ modificationSite.setIdModificationResidue("a");
+ modificationSite.setName("name");
+ modificationSite.setPosition(new Point2D.Double(10, 20));
+ modificationSite.setState(ModificationState.ACETYLATED);
return result;
}
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 5dd200337e..f79e6affe7 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
@@ -41,7 +41,7 @@ public class GeneTest {
public void testConstructor1() {
try {
Gene original = new Gene();
- original.addModificationResidue(new ModificationSite());
+ original.addModificationSite(new ModificationSite());
Gene gene = new Gene(original);
assertNotNull(gene);
} 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 e07e6d0e81..e0cdc967ea 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
@@ -126,7 +126,7 @@ public class ProteinComparatorTest {
result.setHypothetical(true);
Residue residue = new Residue();
- result.addModificationResidue(residue);
+ result.addResidue(residue);
residue.setIdModificationResidue("a");
residue.setName("name");
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 819c28ea1d..f99156d913 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
@@ -81,7 +81,7 @@ public class RnaComparatorTest {
result.setHypothetical(true);
CodingRegion region1 = new CodingRegion();
- result.addRegion(region1);
+ result.addCodingRegion(region1);
region1.setIdModificationResidue("a");
region1.setPosition(new Point2D.Double(0, 10));
region1.setWidth(2.0);
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 948f46dcb1..f36d79d001 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
@@ -54,7 +54,7 @@ public class RnaTest {
public void testConstructor() {
try {
Rna rna = new Rna("d");
- rna.addRegion(new CodingRegion());
+ rna.addCodingRegion(new CodingRegion());
Rna rna2 = new Rna(rna);
assertEquals(rna.getRegions().size(), rna2.getRegions().size());
} catch (Exception e) {
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index f340ba5f5b..83d5009859 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -390,10 +390,10 @@ public class ModelContructor {
if (species instanceof Protein) {
mr = new Residue();
- ((Protein) species).addModificationResidue(mr);
+ ((Protein) species).addResidue((Residue) mr);
} else if (species instanceof Gene) {
mr = new ModificationSite();
- ((Gene) species).addModificationResidue(mr);
+ ((Gene) species).addModificationSite((ModificationSite) mr);
} else {
logger.warn(
state.getWarningPrefix() + "state for " + species.getClass().getSimpleName() + " is not supported.");
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 e00f0b9d3a..f44acde754 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
@@ -145,9 +145,9 @@ public class CommentDaoTest extends PersistTestFunctions {
alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
model.addElement(alias);
- ModificationResidue mr = new Residue();
+ Residue mr = new Residue();
mr.setName("mr");
- alias.addModificationResidue(mr);
+ alias.addResidue(mr);
alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
return model;
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 406af68352..d896472061 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
@@ -195,7 +195,7 @@ public class LayoutDaoTest extends PersistTestFunctions {
Residue mr = new Residue();
mr.setName("mr");
- protein.addModificationResidue(mr);
+ protein.addResidue(mr);
protein.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
return model;
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 719167ffff..400af2be98 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
@@ -424,7 +424,7 @@ public class ModelDaoTest extends PersistTestFunctions {
Residue mr = new Residue();
mr.setName("mr");
mr.setPosition(new Point2D.Double(10, 20));
- alias.addModificationResidue(mr);
+ alias.addResidue(mr);
alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
return model;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
index abab8f1ff1..08cfd58ce8 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
@@ -108,7 +108,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
mr.setPosition(new Point2D.Double(10, 20));
mr.setName("name");
mr.setState(ModificationState.GLYCOSYLATED);
- protein.addModificationResidue(mr);
+ protein.addResidue(mr);
elementDao.add(protein);
@@ -143,7 +143,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
ModificationSite mr = new ModificationSite();
mr.setName("name");
mr.setState(ModificationState.DONT_CARE);
- sp.addRegion(mr);
+ sp.addModificationSite(mr);
elementDao.add(sp);
elementDao.evict(sp);
@@ -177,7 +177,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
AntisenseRna sp = new AntisenseRna(testIdAlias);
ModificationSite mr = new ModificationSite();
mr.setName("name");
- sp.addRegion(mr);
+ sp.addModificationSite(mr);
elementDao.add(sp);
elementDao.evict(sp);
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 44bb7dcec7..1b67cca4e9 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
@@ -75,7 +75,7 @@ public class AntisenseRnaTest extends PersistTestFunctions {
Model model = new ModelFullIndexed(null);
AntisenseRna alias = new AntisenseRna("As");
- alias.addRegion(new CodingRegion());
+ alias.addCodingRegion(new CodingRegion());
alias.setX(1);
alias.setY(2);
alias.setWidth(10);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
index 4eea1e67a9..d0392f51a0 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
@@ -74,7 +74,7 @@ public class RnaTest extends PersistTestFunctions {
Model model = new ModelFullIndexed(null);
Rna alias = new Rna("As");
- alias.addRegion(new CodingRegion());
+ alias.addCodingRegion(new CodingRegion());
alias.setX(1);
alias.setY(2);
alias.setWidth(10);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index 61b7458f8e..c9701d3a83 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -117,7 +117,7 @@ public class ElementRestImplTest extends RestTestFunctions {
Residue mr = new Residue();
mr.setState(ModificationState.ACETYLATED);
mr.setName("S250");
- protein.addModificationResidue(mr);
+ protein.addResidue(mr);
protein.setStructuralState(state);
Map<String, Object> result = _elementsRestImpl.getOthersForElement(protein);
assertNotNull(result.get("modifications"));
@@ -139,7 +139,7 @@ public class ElementRestImplTest extends RestTestFunctions {
ModificationSite mr = new ModificationSite();
mr.setState(ModificationState.ACETYLATED);
mr.setName("S250");
- rna.addRegion(mr);
+ rna.addModificationSite(mr);
rna.setState(state);
Map<String, Object> result = _elementsRestImpl.getOthersForElement(rna);
assertNotNull(result.get("modifications"));
@@ -160,7 +160,7 @@ public class ElementRestImplTest extends RestTestFunctions {
AntisenseRna antisenseRna = new AntisenseRna("s1");
ModificationSite mr = new ModificationSite();
mr.setName("S250");
- antisenseRna.addRegion(mr);
+ antisenseRna.addModificationSite(mr);
antisenseRna.setState(state);
Map<String, Object> result = _elementsRestImpl.getOthersForElement(antisenseRna);
assertNotNull(result.get("modifications"));
--
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