From 23a161c895257f4a06357c6f46f9c3f99b4a9ed6 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 21 Dec 2017 17:38:05 +0100
Subject: [PATCH] simple export of reaction layout
---
.../model/sbml/SbmlBioEntityExporter.java | 2 +-
.../model/sbml/SbmlReactionExporter.java | 85 +++++++++++++++++--
.../model/sbml/SbmlExporterTest.java | 43 ++++++++++
3 files changed, 121 insertions(+), 9 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
index 4e9d5a26ab..97f1c528a8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -57,7 +57,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
public abstract S createSbmlElement(T element) throws InconsistentModelException;
protected S getSbmlElement(T element, String compartmentName) throws InconsistentModelException {
- String mapKey = element.getName() + "\n" + compartmentName;
+ String mapKey = element.getClass().getSimpleName() + "\n" + element.getElementId() + "\n" + compartmentName;
if (sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
S sbmlElement = createSbmlElement(element);
sbmlElement.setName(element.getName());
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
index e6be4a1c1e..de7951c7cb 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
@@ -1,17 +1,30 @@
package lcsb.mapviewer.converter.model.sbml;
+import java.awt.geom.Line2D;
import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
import org.apache.log4j.Logger;
+import org.sbml.jsbml.SimpleSpeciesReference;
import org.sbml.jsbml.Species;
+import org.sbml.jsbml.SpeciesReference;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.Curve;
import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LineSegment;
+import org.sbml.jsbml.ext.layout.Point;
+import org.sbml.jsbml.ext.layout.ReactionGlyph;
+import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
+import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sbml.jsbml.Reaction> {
Logger logger = Logger.getLogger(SbmlReactionExporter.class);
@@ -23,29 +36,36 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
this.speciesExporter = speciesExporter;
}
+ Map<ReactionNode, SimpleSpeciesReference> speciesReferenceByReactionNode = new HashMap<>();
+
@Override
public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
+ logger.debug(reaction);
org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (getNextId()));
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
- result.createProduct(sbmlSymbol);
+ SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
+ speciesReferenceByReactionNode.put(product, speciesReference);
}
for (Reactant reactant : reaction.getReactants()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(reactant.getElement().getElementId());
- result.createReactant(sbmlSymbol);
+ SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
+ logger.debug(reactant);
+ speciesReferenceByReactionNode.put(reactant, speciesReference);
}
for (Modifier modifier : reaction.getModifiers()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(modifier.getElement().getElementId());
- result.createModifier(sbmlSymbol);
+ SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
+ speciesReferenceByReactionNode.put(modifier, speciesReference);
}
return result;
}
@Override
protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
-// AbstractReferenceGlyph speciesGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
-// return speciesGlyph;
- return null;
+ ReactionGlyph reactionGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
+
+ return reactionGlyph;
}
@Override
@@ -54,9 +74,58 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
@Override
- protected void assignLayoutToGlyph(Reaction element, AbstractReferenceGlyph compartmentGlyph) {
- // TODO Auto-generated method stub
+ protected void assignLayoutToGlyph(Reaction reaction, AbstractReferenceGlyph compartmentGlyph) {
+ logger.debug(reaction);
+ ReactionGlyph reactionGlyph = (ReactionGlyph) compartmentGlyph;
+ boolean firstReactant = true;
+ for (Reactant reactant : reaction.getReactants()) {
+ SpeciesReferenceGlyph reactantGlyph = createNodeGlyph(reactionGlyph, reactant);
+ if (firstReactant) {
+ reactantGlyph.setRole(SpeciesReferenceRole.SUBSTRATE);
+ } else {
+ reactantGlyph.setRole(SpeciesReferenceRole.SIDESUBSTRATE);
+ }
+ firstReactant = false;
+ }
+ boolean firstProduct = true;
+ for (Product product : reaction.getProducts()) {
+ SpeciesReferenceGlyph productGlyph = createNodeGlyph(reactionGlyph, product);
+ if (firstProduct) {
+ productGlyph.setRole(SpeciesReferenceRole.PRODUCT);
+ } else {
+ productGlyph.setRole(SpeciesReferenceRole.SIDEPRODUCT);
+ }
+ firstProduct = false;
+ }
+ for (Modifier modifier : reaction.getModifiers()) {
+ SpeciesReferenceGlyph modifierGlyph = createNodeGlyph(reactionGlyph, modifier);
+ if (modifier instanceof Inhibition) {
+ modifierGlyph.setRole(SpeciesReferenceRole.INHIBITOR);
+ } else {
+ modifierGlyph.setRole(SpeciesReferenceRole.MODIFIER);
+ }
+ }
+
+ }
+ private SpeciesReferenceGlyph createNodeGlyph(ReactionGlyph reactionGlyph, ReactionNode node) {
+ SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
+ reactantGlyph.setSpeciesGlyph(speciesExporter.sbmlGlyphByElementId.get(node.getElement().getElementId()).getId());
+ reactantGlyph.setCurve(createCurve(node));
+ logger.debug(node);
+ reactantGlyph.setSpeciesReference(speciesReferenceByReactionNode.get(node));
+ return reactantGlyph;
+ }
+
+ private Curve createCurve(ReactionNode reactant) {
+ Curve curve = new Curve();
+ for (Line2D line : reactant.getLine().getLines()) {
+ LineSegment segment = new LineSegment();
+ segment.setStart(new Point(line.getX1(), line.getY1()));
+ segment.setEnd(new Point(line.getX2(), line.getY2()));
+ curve.addCurveSegment(segment);
+ }
+ return curve;
}
}
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 32345a0b66..54d333f7fc 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
@@ -6,6 +6,7 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.awt.Desktop;
+import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.nio.file.Files;
@@ -13,15 +14,21 @@ import java.nio.file.Files;
import org.apache.log4j.Logger;
import org.junit.Test;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.model.graphics.PolylineData;
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.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class SbmlExporterTest {
@@ -152,4 +159,40 @@ public class SbmlExporterTest {
assertNotNull(deserializedModel);
}
+ @Test
+ public void testExportReactionWithLayout() throws Exception {
+ Model model = new ModelFullIndexed(null);
+ GenericProtein p1 = new GenericProtein("s1");
+ p1.setWidth(100);
+ p1.setHeight(20);
+ p1.setX(10);
+ p1.setY(10);
+ model.addElement(p1);
+ GenericProtein p2 = new GenericProtein("s2");
+ p2.setWidth(100);
+ p2.setHeight(20);
+ p2.setX(10);
+ p2.setY(50);
+ model.addElement(p2);
+ Reaction reaction = new StateTransitionReaction();
+ Reactant reactant = new Reactant(p1);
+ Product product = new Product(p2);
+ PolylineData reactantLine = new PolylineData();
+ reactantLine.addPoint(new Point2D.Double(50, 20));
+ reactantLine.addPoint(new Point2D.Double(50, 30));
+ reactant.setLine(reactantLine);
+ PolylineData productLine = new PolylineData();
+ productLine.addPoint(new Point2D.Double(50, 40));
+ productLine.addPoint(new Point2D.Double(50, 60));
+ product.setLine(productLine);
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+ model.addReaction(reaction);
+ Model deserializedModel = getModelAfterSerializing(model);
+ Reaction deserializedReaction = deserializedModel.getReactions().iterator().next();
+ assertEquals(reactantLine.length(), deserializedReaction.getReactants().get(0).getLine().length(), Configuration.EPSILON);
+ assertEquals(productLine.length(), deserializedReaction.getProducts().get(0).getLine().length(), Configuration.EPSILON);
+
+ }
+
}
--
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