From 18b64eb61e3f58098dbfdd54d6401882b1000dab Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 9 Oct 2018 15:06:10 +0200
Subject: [PATCH] reaction line color is export/imported properly
---
.../model/sbml/SbmlBioEntityParser.java | 4 +-
.../sbml/reaction/SbmlReactionExporter.java | 6 ++
.../sbml/reaction/SbmlReactionParser.java | 85 ++++++++++++-------
.../model/sbml/SbmlExporterTest.java | 13 +++
4 files changed, 77 insertions(+), 31 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index b87599f0e2..f7ce691c21 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -100,7 +100,7 @@ public class SbmlBioEntityParser extends XmlParser {
* object role identifier
* @return {@link LocalStyle} from the layout data
*/
- LocalStyle getStyleForRole(String objectRole) {
+ protected LocalStyle getStyleForRole(String objectRole) {
RenderLayoutPlugin renderPlugin = (RenderLayoutPlugin) layout.getExtension("render");
for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
for (LocalStyle style : lri.getListOfLocalStyles()) {
@@ -112,7 +112,7 @@ public class SbmlBioEntityParser extends XmlParser {
return null;
}
- Color getColorByColorDefinition(String fill) {
+ protected Color getColorByColorDefinition(String fill) {
RenderLayoutPlugin renderPlugin = (RenderLayoutPlugin) layout.getExtension("render");
for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
if (lri.getColorDefinition(fill) != null) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index da286cb62b..d84408a695 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -245,6 +245,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
}
+ LocalStyle style = createStyle(reaction);
+ ColorDefinition color = getColorDefinition(reaction.getReactants().get(0).getLine().getColor());
+ style.getGroup().setFill(color.getId());
+
+ assignStyleToGlyph(reactionGlyph, style);
+
}
private void addOperatorLineToGlyph(ReactionGlyph reactantGlyph, NodeOperator operator, boolean reverse) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index add9c0916d..2fba4974ab 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
+import java.awt.Color;
import java.awt.geom.Point2D;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
@@ -22,6 +23,9 @@ import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.RenderConstants;
+import org.sbml.jsbml.ext.render.RenderGraphicalObjectPlugin;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -41,6 +45,7 @@ import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.modifier.Trigger;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
@@ -56,8 +61,6 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlReactionParser extends SbmlBioEntityParser {
Logger logger = Logger.getLogger(SbmlReactionParser.class);
- Layout layout;
-
lcsb.mapviewer.model.map.model.Model minervaModel;
ElementUtils eu = new ElementUtils();
@@ -108,33 +111,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
SpeciesGlyph speciesGlyph = layout.getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
ReactionNode minervaNode = null;
- Class<? extends ReactionNode> nodeClass = null;
- if (speciesRefernceGlyph.getRole() != null) {
- switch (speciesRefernceGlyph.getRole()) {
- case ACTIVATOR:
- nodeClass = Trigger.class;
- break;
- case INHIBITOR:
- nodeClass = Inhibition.class;
- break;
- case PRODUCT:
- nodeClass = Product.class;
- break;
- case SIDEPRODUCT:
- nodeClass = Product.class;
- break;
- case SIDESUBSTRATE:
- nodeClass = Reactant.class;
- break;
- case SUBSTRATE:
- nodeClass = Reactant.class;
- break;
- case UNDEFINED:
- case MODIFIER:
- nodeClass = null;
- break;
- }
- }
+ Class<? extends ReactionNode> nodeClass = getReactionNodeClass(speciesRefernceGlyph);
if (reactionWithLayout.isReversible() && (nodeClass == Reactant.class || nodeClass == Product.class)) {
nodeClass = null;
@@ -233,6 +210,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
operator.setLine(line);
reactionWithLayout.addNode(operator);
}
+ assignColorToReaction(glyph, reactionWithLayout);
+
minervaModel.addReaction(reactionWithLayout);
} catch (InvalidArgumentException e) {
throw new InvalidInputDataExecption(e);
@@ -255,6 +234,54 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
+ private Class<? extends ReactionNode> getReactionNodeClass(SpeciesReferenceGlyph speciesRefernceGlyph) {
+ Class<? extends ReactionNode> nodeClass = null;
+ if (speciesRefernceGlyph.getRole() != null) {
+ switch (speciesRefernceGlyph.getRole()) {
+ case ACTIVATOR:
+ nodeClass = Trigger.class;
+ break;
+ case INHIBITOR:
+ nodeClass = Inhibition.class;
+ break;
+ case PRODUCT:
+ nodeClass = Product.class;
+ break;
+ case SIDEPRODUCT:
+ nodeClass = Product.class;
+ break;
+ case SIDESUBSTRATE:
+ nodeClass = Reactant.class;
+ break;
+ case SUBSTRATE:
+ nodeClass = Reactant.class;
+ break;
+ case UNDEFINED:
+ case MODIFIER:
+ nodeClass = null;
+ break;
+ }
+ }
+ return nodeClass;
+ }
+
+ private void assignColorToReaction(ReactionGlyph glyph, Reaction reactionWithLayout)
+ throws InvalidInputDataExecption {
+ RenderGraphicalObjectPlugin rgop = (RenderGraphicalObjectPlugin) glyph.getExtension(RenderConstants.shortLabel);
+ if (rgop != null) {
+ LocalStyle style = getStyleForRole(rgop.getObjectRole());
+ if (style == null) {
+ throw new InvalidInputDataExecption("Style " + rgop.getObjectRole() + " is not defined");
+ }
+ if (style.getGroup().getFill() != null) {
+ Color color = getColorByColorDefinition(style.getGroup().getFill());
+ for (AbstractNode node : reactionWithLayout.getNodes()) {
+ node.getLine().setColor(color);
+ }
+ }
+ }
+ }
+
private PolylineData getLineFromReferenceGlyph(SpeciesReferenceGlyph speciesRefernceGlyph) {
PolylineData line = null;
for (CurveSegment segment : speciesRefernceGlyph.getCurve().getListOfCurveSegments()) {
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 abe75da28a..df98e6f93a 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
@@ -26,6 +26,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -285,4 +286,16 @@ public class SbmlExporterTest {
assertEquals(0, comparator.compare(model, model2));
}
+ @Test
+ public void testReactionColorParsing() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
+ for (Reaction element : model.getReactions()) {
+ for (AbstractNode node: element.getNodes()) {
+ node.getLine().setColor(Color.BLUE);
+ }
+ }
+ Model model2 = getModelAfterSerializing(model);
+ assertEquals(0, comparator.compare(model, model2));
+ }
+
}
--
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