From 7f88dcd670899b2dcc26b700257c532ea05ecd06 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 24 Nov 2017 16:57:28 +0100
Subject: [PATCH] operators for reaction added
---
.../model/sbml/SbmlReactionParser.java | 107 +++++++++++++++++-
.../converter/model/sbml/SbmlParserTest.java | 15 ++-
2 files changed, 117 insertions(+), 5 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
index bec76e8dcd..2acf38c9ff 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
import java.awt.geom.Point2D;
+import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
@@ -23,15 +24,24 @@ import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.util.NotImplementedException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
+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.AndOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
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.SplitOperator;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -84,9 +94,40 @@ public class SbmlReactionParser {
for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
SpeciesGlyph speciesGlyph = layout.getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
ReactionNode minervaNode = null;
+ Class<? extends ReactionNode> nodeClass = null;
+ switch (speciesRefernceGlyph.getRole()) {
+ case ACTIVATOR:
+ nodeClass = Trigger.class;
+ break;
+ case INHIBITOR:
+ nodeClass = Inhibition.class;
+ break;
+ case MODIFIER:
+ nodeClass = Modulation.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:
+ nodeClass = null;
+ break;
+ }
for (ReactionNode node : reactionWithLayout.getReactionNodes()) {
if (node.getElement().getElementId().equals(speciesGlyph.getSpecies())) {
- minervaNode = node;
+ if (nodeClass == null) {
+ minervaNode = node;
+ } else if (node.getClass().isAssignableFrom(nodeClass)) {
+ minervaNode = node;
+ }
}
}
if (minervaNode == null) {
@@ -109,22 +150,80 @@ public class SbmlReactionParser {
line.addPoint(end);
}
}
+ if (minervaNode instanceof Reactant) {
+ line = line.reverse();
+ }
+ if (minervaNode instanceof Product) {
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.FULL);
+ line.setEndAtd(atd);
+ } else if (minervaNode instanceof Modifier) {
+ for (ModifierType mt : ModifierType.values()) {
+ if (mt.getClazz().equals(nodeClass)) {
+ line.setEndAtd(mt.getAtd());
+ line.setType(mt.getLineType());
+ }
+ }
+ }
minervaNode.setLine(line);
minervaNode.setElement(minervaElement);
+ if (nodeClass != minervaNode.getClass()) {
+ reactionWithLayout.removeModifier((Modifier) minervaNode);
+
+ try {
+ ReactionNode newNode = nodeClass.getConstructor().newInstance();
+ newNode.setElement(minervaElement);
+ newNode.setLine(line);
+ reactionWithLayout.addNode(newNode);
+ } catch (InstantiationException | IllegalAccessException | IllegalArgumentException
+ | InvocationTargetException | NoSuchMethodException | SecurityException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+ }
+ if (reactionWithLayout.getReactants().size()>1 && reactionWithLayout.getProducts().size()>0) {
+ PolylineData line = new PolylineData();
+ Point2D p1 = reactionWithLayout.getReactants().get(0).getLine().getEndPoint();
+ Point2D p2 = reactionWithLayout.getProducts().get(0).getLine().getBeginPoint();
+ Point2D center = new Point2D.Double((p1.getX()+p2.getX())/2, (p1.getY()+p2.getY())/2);
+ line.addPoint(p1);
+ line.addPoint(center);
+ NodeOperator operator = new AndOperator();
+ operator.addInputs(reactionWithLayout.getReactants());
+ operator.setLine(line);
+ reactionWithLayout.addNode(operator);
}
+ if (reactionWithLayout.getReactants().size()>0 && reactionWithLayout.getProducts().size()>1) {
+ PolylineData line = new PolylineData();
+ Point2D p1 = reactionWithLayout.getReactants().get(0).getLine().getEndPoint();
+ Point2D p2 = reactionWithLayout.getProducts().get(0).getLine().getBeginPoint();
+ Point2D center = new Point2D.Double((p1.getX()+p2.getX())/2, (p1.getY()+p2.getY())/2);
+ line.addPoint(p2);
+ line.addPoint(center);
+ NodeOperator operator = new SplitOperator();
+ operator.addOutputs(reactionWithLayout.getProducts());
+ operator.setLine(line);
+ reactionWithLayout.addNode(operator);
+ }
+
+ logger.debug(glyph.getCurve().getListOfCurveSegments().get(0));
try {
minervaModel.addReaction(new StateTransitionReaction(reactionWithLayout));
} catch (InvalidArgumentException e) {
throw new InvalidInputDataExecption(e);
}
}
+ Set<Reaction> elementsToRemove = new HashSet<>();
for (Reaction reaction : elements) {
if (!used.contains(reaction)) {
logger.warn("Layout doesn't contain information about Element: " + reaction.getIdReaction());
} else {
- minervaModel.removeReaction(reaction);
+ elementsToRemove.add(reaction);
}
}
+ for (Reaction reaction : elementsToRemove) {
+ minervaModel.removeReaction(reaction);
+ }
}
protected Reaction parse(org.sbml.jsbml.Reaction sbmlReaction, Model sbmlModel) throws InvalidInputDataExecption {
@@ -144,7 +243,7 @@ public class SbmlReactionParser {
for (ModifierSpeciesReference modifier : sbmlReaction.getListOfModifiers()) {
Species element = minervaModel.getElementByElementId(modifier.getSpecies());
- reaction.addModifier(new Catalysis(element));
+ reaction.addModifier(new Modifier(element));
}
return reaction;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index 6673591d17..260e80486d 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -5,7 +5,9 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
+import java.awt.Desktop;
import java.awt.Point;
+import java.io.File;
import java.io.FileNotFoundException;
import org.apache.log4j.Logger;
@@ -13,6 +15,9 @@ import org.junit.Test;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -94,7 +99,7 @@ public class SbmlParserTest {
}
@Test
- public void testParseReaction() throws FileNotFoundException, InvalidInputDataExecption {
+ public void testParseReaction() throws Exception {
Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/Complete_Example.xml"));
assertNotNull(model);
assertEquals(1, model.getReactions().size());
@@ -103,6 +108,14 @@ public class SbmlParserTest {
assertNotNull(node.getLine());
assertTrue(node.getLine().length() > 0);
}
+// assertEquals(2, reaction.getOperators().size());
+
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
+ .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
+ NormalImageGenerator nig = new PngImageGenerator(params);
+ nig.saveToFile("tmp.png");
+ Desktop.getDesktop().open(new File("tmp.png"));
+
}
}
--
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