From 24efbac9f77dc16654bd1bebe17c1505c662b148 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 15:38:27 +0100
Subject: [PATCH] export of modification residues in aliases contains info
about alias reference id
---
.../sbml/species/SbmlSpeciesExporter.java | 14 ++-
.../model/sbml/species/SbmlSpeciesParser.java | 30 +++--
.../cd_for_multi/modification_in_aliases.xml | 109 ++++++++++++++++++
3 files changed, 141 insertions(+), 12 deletions(-)
create mode 100644 converter-sbml/testFiles/cd_for_multi/modification_in_aliases.xml
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index a3c6131fb7..cb70338973 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -13,7 +13,9 @@ import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.Dimensions;
+import org.sbml.jsbml.ext.layout.GeneralGlyph;
import org.sbml.jsbml.ext.layout.Point;
+import org.sbml.jsbml.ext.layout.ReferenceGlyph;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
@@ -453,14 +455,15 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
if (isExtensionEnabled(SbmlExtension.MULTI)) {
if (element instanceof SpeciesWithModificationResidue) {
for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
- org.sbml.jsbml.Species sbmlSpecies = getSbmlModel().getSpecies(speciesGlyph.getReference());
- createModificationGlyph(mr, sbmlSpecies);
+ createModificationGlyph(mr, speciesGlyph);
}
}
}
}
- private void createModificationGlyph(ModificationResidue mr, org.sbml.jsbml.Species sbmlSpecies) {
+ private void createModificationGlyph(ModificationResidue mr, AbstractReferenceGlyph speciesGlyph) {
+ org.sbml.jsbml.Species sbmlSpecies = getSbmlModel().getSpecies(speciesGlyph.getReference());
+
MultiSpeciesPlugin speciesExtension = (MultiSpeciesPlugin) sbmlSpecies.getExtension("multi");
SpeciesFeature feature = null;
String featureTypeId = MultiPackageNamingUtils.getModificationFeatureId(mr);
@@ -477,8 +480,11 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
- AbstractReferenceGlyph modificationGlyph = getLayout().createGeneralGlyph("modification_" + (idCounter++),
+ GeneralGlyph modificationGlyph = getLayout().createGeneralGlyph("modification_" + (idCounter++),
modificationFeatureValue.getId());
+ ReferenceGlyph referenceGlyph = new ReferenceGlyph("modification_reference_" + (idCounter++));
+ referenceGlyph.setReference(speciesGlyph.getId());
+ modificationGlyph.addReferenceGlyph(referenceGlyph);
double width, height;
if (mr instanceof AbstractRegionModification) {
width = ((AbstractRegionModification) mr).getWidth();
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index de9ba5546d..468348e344 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -12,6 +12,7 @@ import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.CompartmentGlyph;
import org.sbml.jsbml.ext.layout.GeneralGlyph;
import org.sbml.jsbml.ext.layout.GraphicalObject;
+import org.sbml.jsbml.ext.layout.ReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
@@ -366,14 +367,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
private void assignModificationResiduesLayout(Element element) {
if (element instanceof SpeciesWithModificationResidue) {
for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
- GeneralGlyph residueGlyph = null;
- for (GraphicalObject graphicalObject : getLayout().getListOfAdditionalGraphicalObjects()) {
- if (graphicalObject instanceof GeneralGlyph) {
- if (((GeneralGlyph) graphicalObject).getReference().equals(mr.getIdModificationResidue())) {
- residueGlyph = (GeneralGlyph) graphicalObject;
- }
- }
- }
+ GeneralGlyph residueGlyph = getResidueGlyphForModification(mr);
if (residueGlyph != null) {
if (residueGlyph.getBoundingBox() == null || residueGlyph.getBoundingBox().getDimensions() == null) {
logger.warn(new ElementUtils().getElementTag(mr) + "Layout doesn't contain coordinates");
@@ -394,6 +388,26 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
+ private GeneralGlyph getResidueGlyphForModification(ModificationResidue mr) {
+ GeneralGlyph residueGlyph = null;
+ for (GraphicalObject graphicalObject : getLayout().getListOfAdditionalGraphicalObjects()) {
+ if (graphicalObject instanceof GeneralGlyph) {
+ if (((GeneralGlyph) graphicalObject).getReference().equals(mr.getIdModificationResidue())) {
+ if (((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().size() > 0) {
+ // find a reference to the alias in layout, so we know it's the proper value
+ ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
+ if (referenceGlyph.getReference().equals(mr.getSpecies().getElementId())) {
+ residueGlyph = (GeneralGlyph) graphicalObject;
+ }
+ } else {
+ residueGlyph = (GeneralGlyph) graphicalObject;
+ }
+ }
+ }
+ }
+ return residueGlyph;
+ }
+
private void assignCompartment(Element element, String compartmentId) {
Compartment compartment = getMinervaModel().getElementByElementId(compartmentId);
if (compartment == null && getLayout() != null) {
diff --git a/converter-sbml/testFiles/cd_for_multi/modification_in_aliases.xml b/converter-sbml/testFiles/cd_for_multi/modification_in_aliases.xml
new file mode 100644
index 0000000000..b2b1a3cf81
--- /dev/null
+++ b/converter-sbml/testFiles/cd_for_multi/modification_in_aliases.xml
@@ -0,0 +1,109 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="120.0" y="168.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa3" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="267.0" y="165.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC">
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" id="rs1" side="none"/>
+</celldesigner:listOfModificationResidues>
+</celldesigner:protein>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
--
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