From e1bf8b039f987dd9ad25bdce33c069798a3491f9 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 2 Jan 2019 12:54:21 +0100
Subject: [PATCH] export with MULTI property separates species wth different
structural state
---
.../converter/model/sbml/SbmlExporter.java | 1 -
.../sbml/species/SbmlSpeciesExporter.java | 15 +++++++-
.../sbml/species/SbmlSpeciesExporterTest.java | 36 ++++++++++++++-----
3 files changed, 42 insertions(+), 10 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 247453556b..9897735de5 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -189,7 +189,6 @@ public class SbmlExporter {
private Map<Class<?>, MultiSpeciesType> speciesTypeByClass = new HashMap<>();
- @SuppressWarnings("unchecked")
protected MultiModelPlugin createSbmlMultiPlugin(Model result) {
MultiModelPlugin multiPlugin = new MultiModelPlugin(result);
result.addExtension("multi", multiPlugin);
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 dd6773fba2..04e566a37f 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
@@ -159,7 +159,20 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
if (element.getComplex() != null) {
complexName = element.getComplex().getName();
}
- return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n" + complexName;
+ String multiDistinguisher = null;
+
+ if (isExtensionEnabled(SbmlExtension.MULTI)) {
+ String structuralState = null;
+ if (element instanceof Protein) {
+ structuralState = ((Protein) element).getStructuralState();
+ } else if (element instanceof Complex) {
+ structuralState = ((Complex) element).getStructuralState();
+ }
+ multiDistinguisher = structuralState;
+ }
+ String result =element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n" + complexName
+ + "\n" + multiDistinguisher;
+ return result;
}
protected LocalStyle createStyle(Species element) {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
index 36b459def4..918231660e 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
@@ -1,13 +1,14 @@
package lcsb.mapviewer.converter.model.sbml.species;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
import java.util.Arrays;
+import java.util.Collection;
import org.apache.log4j.Logger;
import org.junit.Test;
import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.ext.layout.Layout;
import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
@@ -18,15 +19,14 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
public class SbmlSpeciesExporterTest {
Logger logger = Logger.getLogger(SbmlSpeciesExporterTest.class);
- SbmlCompartmentExporter compartmentExporter;
-
org.sbml.jsbml.Model sbmlModel;
- Layout sbmlLayout;
@Test
public void testOneElementWithTwoAliases() throws InconsistentModelException {
@@ -68,19 +68,39 @@ public class SbmlSpeciesExporterTest {
}
private SbmlSpeciesExporter createExporter(Model model) throws InconsistentModelException {
+ return createExporter(model, Arrays.asList(new SbmlExtension[] { SbmlExtension.RENDER, SbmlExtension.LAYOUT }));
+ }
+
+ private SbmlSpeciesExporter createExporter(Model model, Collection<SbmlExtension> sbmlExtensions)
+ throws InconsistentModelException {
SBMLDocument doc = new SBMLDocument(3, 1);
sbmlModel = doc.createModel(model.getIdModel());
SbmlExporter sbmlExporter = new SbmlExporter();
- sbmlLayout = sbmlExporter.createSbmlLayout(model, sbmlModel);
+ sbmlExporter.createSbmlLayout(model, sbmlModel);
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(sbmlModel, model,
Arrays.asList(SbmlExtension.values()));
compartmentExporter.exportElements();
- SbmlSpeciesExporter result = new SbmlSpeciesExporter(sbmlModel, model,
- Arrays.asList(new SbmlExtension[] { SbmlExtension.RENDER, SbmlExtension.LAYOUT }),
- compartmentExporter);
+
+ SbmlSpeciesExporter result = new SbmlSpeciesExporter(sbmlModel, model, sbmlExtensions, compartmentExporter);
return result;
}
+ @Test
+ public void testIdsOfSpeciesWithStructuralStates() throws InconsistentModelException {
+ Species protein1 = new GenericProtein("sa1");
+ protein1.setName("SNCA");
+ Protein protein2 = new GenericProtein("sa2");
+ protein2.setName("SNCA");
+ protein2.setStructuralState("X");
+ Model model = new ModelFullIndexed(null);
+ model.addElement(protein1);
+ model.addElement(protein2);
+
+ SbmlSpeciesExporter exporter = createExporter(model, Arrays.asList(SbmlExtension.values()));
+
+ assertFalse(exporter.getSbmlIdKey(protein1).equals(exporter.getSbmlIdKey(protein2)));
+ }
+
}
--
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