From eb97d7f5b8e48008693c7a033823028cc3febb33 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 14 Nov 2018 11:06:26 +0100
Subject: [PATCH] export of reaction contains information about arrow types and
line types
---
.../converter/model/sbml/SbmlParser.java | 7 +-
.../sbml/reaction/SBOTermReactionType.java | 20 +-
.../sbml/reaction/SbmlReactionExporter.java | 22 ++-
.../sbml/reaction/SbmlReactionParser.java | 119 ++++++++++--
.../sbml/GenericSbmlToXmlParserTest.java | 3 +-
.../reaction/AllSbmlReactionParserTests.java | 3 +-
.../reaction/SbmlReactionExportArrowType.java | 183 ++++++++++++++++++
7 files changed, 336 insertions(+), 21 deletions(-)
create mode 100644 converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 84188fea07..2b97fc6adf 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -40,7 +40,9 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -98,6 +100,7 @@ public class SbmlParser implements IConverter {
speciesParser.mergeLayout(model.getSpeciesList(), layout, sbmlModel);
reactionParser.mergeLayout(model.getReactions(), layout, sbmlModel);
}
+
reactionParser.validateReactions(model.getReactions());
if (sbmlModel.getConstraintCount() > 0) {
@@ -228,7 +231,9 @@ public class SbmlParser implements IConverter {
if (node.getLine() == null) {
return false;
} else if (node.getLine().length() == 0) {
- return false;
+ if (!(node instanceof NodeOperator) || !(reaction instanceof BooleanLogicGateReaction)) {
+ return false;
+ }
}
}
return true;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
index 1461e078d0..dcc34214e6 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
@@ -6,10 +6,15 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
+import lcsb.mapviewer.model.map.reaction.type.CatalysisReaction;
import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.InhibitionReaction;
import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
+import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction;
import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
@@ -18,7 +23,10 @@ import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction;
@@ -27,24 +35,32 @@ import lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
public enum SBOTermReactionType {
+ BOOLEAN_LOGIC_GATE(BooleanLogicGateReaction.class, new String[] { "SBO:0000547" }),
+ CATALYSIS(CatalysisReaction.class, new String[] { "SBO:0000013" }),
DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }),
HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }),
+ INHIBITION(InhibitionReaction.class, new String[] { "SBO:0000537" }),
KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }),
+ MODULATION(ModulationReaction.class, new String[] { "SBO:0000594" }),
NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }),
+ PHYSICAL_STIMULATION(PhysicalStimulationReaction.class, new String[] { "SBO:0000459" }),
POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }),
REDUCED_MODULATION(ReducedModulationReaction.class, new String[] { "SBO:0000632" }),
REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000411" }),
- REDUCED_TRIGGER(ReducedTriggerReaction.class, new String[] { "SBO:0000461" }),
+ REDUCED_TRIGGER(ReducedTriggerReaction.class, new String[] { "SBO:0000533" }),
STATE_TRANSITION(StateTransitionReaction.class, new String[] { "SBO:0000176" }),
TRANSCRIPTION(TranscriptionReaction.class, new String[] { "SBO:0000183" }),
TRANSLATION(TranslationReaction.class, new String[] { "SBO:0000184" }),
TRANSPORT(TransportReaction.class, new String[] { "SBO:0000185" }),
+ TRIGGER(TriggerReaction.class, new String[] { "SBO:0000461" }),
TRUNCATION(TruncationReaction.class, new String[] { "SBO:0000178" }),
+ UNKNOWN_CATALYSIS(UnknownCatalysisReaction.class, new String[] { "SBO:0000462" }),
+ UNKNOWN_INHIBITION(UnknownInhibitionReaction.class, new String[] { "SBO:0000536" }),
UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, new String[] { "SBO:0000169" }),
UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000172" }),
UNKNOWN_REDUCED_MODULATION(UnknownReducedModulationReaction.class, new String[] { "SBO:0000631" }),
UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class, new String[] { "SBO:0000170" }),
- UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, new String[] { "SBO:0000533" }),
+ UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, new String[] { "SBO:0000534" }),
UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }),
;
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 8143019170..5594f48fab 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
@@ -24,7 +24,9 @@ import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
import org.sbml.jsbml.ext.render.ColorDefinition;
+import org.sbml.jsbml.ext.render.LocalRenderInformation;
import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.RenderGroup;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.Configuration;
@@ -243,15 +245,31 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
} else {
modifierGlyph.setRole(SpeciesReferenceRole.MODIFIER);
}
+ LocalStyle style = createStyleForModifier(modifier);
+ assignStyleToGlyph(modifierGlyph, style);
}
-
+
LocalStyle style = createStyle(reaction);
ColorDefinition color = getColorDefinition(reaction.getReactants().get(0).getLine().getColor());
style.getGroup().setStrokeWidth(reaction.getReactants().get(0).getLine().getWidth());
style.getGroup().setFill(color.getId());
+ style.getGroup().setStroke(reaction.getReactants().get(0).getLine().getType().name());
+ style.getGroup().setEndHead(reaction.getProducts().get(0).getLine().getEndAtd().getArrowType().name());
assignStyleToGlyph(reactionGlyph, style);
-
+
+ }
+
+ private LocalStyle createStyleForModifier(Modifier modifier) {
+ LocalRenderInformation renderInformation = new LocalRenderInformation();
+ LocalStyle style = new LocalStyle();
+ style.getRoleList()
+ .add("style_" + modifier.getReaction().getElementId() + "_modifier_" + modifier.getElement().getElementId());
+ style.setGroup(new RenderGroup());
+ renderInformation.addLocalStyle(style);
+ getRenderPlugin().addLocalRenderInformation(renderInformation);
+ style.getGroup().setStroke(modifier.getLine().getType().name());
+ return 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 78f4e55e4d..0b001e485d 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
@@ -26,6 +26,7 @@ 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.sbml.jsbml.ext.render.RenderGroup;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -39,6 +40,7 @@ import lcsb.mapviewer.converter.model.sbml.SbmlParameterParser;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
@@ -48,6 +50,7 @@ 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.AssociationOperator;
+import lcsb.mapviewer.model.map.reaction.DissociationOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -55,7 +58,10 @@ 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.TruncationOperator;
+import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -107,6 +113,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
used.add(source);
try {
+ Map<ReactionNode, SpeciesReferenceGlyph> glyphByNode = new HashMap<>();
Reaction reactionWithLayout = source.copy();
// getId doesn't have to be unique, therefore we concatenate with reaction
reactionWithLayout.setIdReaction(glyph.getReaction() + "__" + glyph.getId());
@@ -135,6 +142,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
throw new InvalidInputDataExecption(
"Cannot find reaction node for layouted reaction: " + speciesGlyph.getSpecies() + ", " + glyph.getId());
}
+ glyphByNode.put(minervaNode, speciesRefernceGlyph);
Element minervaElement = minervaModel.getElementByElementId(speciesGlyph.getId());
if (minervaElement == null) {
throw new InvalidInputDataExecption("Cannot find layouted reaction node for layouted reaction: "
@@ -190,19 +198,18 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
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);
+ NodeOperator operator = createOutputOperator(reactionWithLayout);
reactionWithLayout.addNode(operator);
}
assignRenderDataToReaction(glyph, reactionWithLayout);
+ for (Modifier modifier : reactionWithLayout.getModifiers()) {
+ SpeciesReferenceGlyph speciesGlyph = glyphByNode.get(modifier);
+ if (speciesGlyph != null) {
+ assignRenderDataToModifier(speciesGlyph, modifier);
+ }
+ }
+
minervaModel.addReaction(reactionWithLayout);
} catch (InvalidArgumentException e) {
throw new InvalidInputDataExecption(e);
@@ -225,6 +232,67 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
+ private void assignRenderDataToModifier(SpeciesReferenceGlyph glyph, ReactionNode modifier)
+ 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");
+ }
+ applyStyleToReactionNode(modifier, style);
+ }
+ }
+
+ private void applyStyleToReactionNode(ReactionNode modifier, LocalStyle style) {
+ RenderGroup group = style.getGroup();
+ if (group.isSetFill()) {
+ Color color = getColorByColorDefinition(group.getFill());
+ modifier.getLine().setColor(color);
+ }
+ if (group.isSetStrokeWidth()) {
+ modifier.getLine().setWidth(group.getStrokeWidth());
+ }
+ if (group.isSetStroke()) {
+ try {
+ LineType type = LineType.valueOf(group.getStroke());
+ modifier.getLine().setType(type);
+ } catch (Exception e) {
+ logger.warn(new ElementUtils().getElementTag(modifier.getReaction()) + "Problematic line type: "
+ + group.getStroke(), e);
+ }
+ }
+ if (group.isSetEndHead()) {
+ try {
+ ArrowType type = ArrowType.valueOf(group.getEndHead());
+ modifier.getLine().getEndAtd().setArrowType(type);
+ } catch (Exception e) {
+ logger.warn(new ElementUtils().getElementTag(modifier.getReaction()) + "Problematic arrow type: "
+ + group.getStroke(), e);
+ }
+ }
+ }
+
+ private NodeOperator createOutputOperator(Reaction reactionWithLayout) {
+ 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;
+ if (reactionWithLayout instanceof TruncationReaction) {
+ operator = new TruncationOperator();
+ } else if (reactionWithLayout instanceof DissociationReaction) {
+ operator = new DissociationOperator();
+ } else {
+ operator = new SplitOperator();
+ }
+ operator.addOutputs(reactionWithLayout.getProducts());
+ operator.setLine(line);
+ return operator;
+ }
+
private NodeOperator createInputOperator(Reaction reactionWithLayout) {
PolylineData line = new PolylineData();
Point2D p1 = reactionWithLayout.getReactants().get(0).getLine().getEndPoint();
@@ -232,7 +300,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
Point2D center = new Point2D.Double((p1.getX() + p2.getX()) / 2, (p1.getY() + p2.getY()) / 2);
line.addPoint(p1);
line.addPoint(center);
- NodeOperator operator ;
+ NodeOperator operator;
if (reactionWithLayout instanceof HeterodimerAssociationReaction) {
operator = new AssociationOperator();
} else {
@@ -287,15 +355,38 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
public void applyStyleToReaction(Reaction reactionWithLayout, LocalStyle style) {
- if (style.getGroup().getFill() != null) {
- Color color = getColorByColorDefinition(style.getGroup().getFill());
+ RenderGroup group = style.getGroup();
+ if (group.getFill() != null) {
+ Color color = getColorByColorDefinition(group.getFill());
for (AbstractNode node : reactionWithLayout.getNodes()) {
node.getLine().setColor(color);
}
}
- if (style.getGroup().getStrokeWidth() != null) {
+ if (group.isSetStrokeWidth()) {
for (AbstractNode node : reactionWithLayout.getNodes()) {
- node.getLine().setWidth(style.getGroup().getStrokeWidth());
+ node.getLine().setWidth(group.getStrokeWidth());
+ }
+ }
+ if (group.isSetStroke()) {
+ try {
+ LineType type = LineType.valueOf(group.getStroke());
+ for (AbstractNode node : reactionWithLayout.getNodes()) {
+ node.getLine().setType(type);
+ }
+ } catch (Exception e) {
+ logger.warn(new ElementUtils().getElementTag(reactionWithLayout) + "Problematic line type: "
+ + group.getStroke(), e);
+ }
+ }
+ if (group.isSetEndHead()) {
+ try {
+ ArrowType type = ArrowType.valueOf(group.getEndHead());
+ for (Product node : reactionWithLayout.getProducts()) {
+ node.getLine().getEndAtd().setArrowType(type);
+ }
+ } catch (Exception e) {
+ logger.warn(new ElementUtils().getElementTag(reactionWithLayout) + "Problematic arrow type: "
+ + group.getStroke(), e);
}
}
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index 10843990e9..f9e8649a5a 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -22,6 +22,7 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
@RunWith(Parameterized.class)
public class GenericSbmlToXmlParserTest {
@@ -65,7 +66,7 @@ public class GenericSbmlToXmlParserTest {
+ filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
String xmlFilePath = pathWithouExtension.concat(".xml");
converter.exportModelToFile(model, xmlFilePath);
-
+
Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
model2.setName(null);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
index d6e54657fa..b6b6039b1f 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java
@@ -5,7 +5,8 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ SbmlReactionExporterTest.class,
+@SuiteClasses({ SbmlReactionExportArrowType.class,
+ SbmlReactionExporterTest.class,
SbmlReactionParserTest.class
})
public class AllSbmlReactionParserTests {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
new file mode 100644
index 0000000000..99be077087
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
@@ -0,0 +1,183 @@
+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
+import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
+import lcsb.mapviewer.converter.model.sbml.SbmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.AssociationOperator;
+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.ReactionComparator;
+import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.TruncationOperator;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+@RunWith(Parameterized.class)
+public class SbmlReactionExportArrowType {
+
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlReactionExportArrowType.class);
+
+ SbmlParser parser = new SbmlParser();
+ SbmlExporter exporter = new SbmlExporter();
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws Exception {
+ Collection<Object[]> data = new ArrayList<>();
+ ElementUtils eu = new ElementUtils();
+ for (Class<?> clazz : eu.getAvailableReactionSubclasses()) {
+ Model modelAfterSerialization = createModelForReactionType(clazz);
+
+ data.add(new Object[] { clazz.getSimpleName(), modelAfterSerialization });
+ }
+ return data;
+ }
+
+ private static Model createModelForReactionType(Class<?> clazz) throws InstantiationException, IllegalAccessException,
+ InvocationTargetException, NoSuchMethodException, InconsistentModelException, InvalidInputDataExecption {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(1000);
+ model.setHeight(1000);
+ Ion ion = new Ion("x1");
+ ion.setName("ion 1");
+ ion.setWidth(100);
+ ion.setHeight(100);
+ ion.setX(200);
+ ion.setY(50);
+ model.addElement(ion);
+
+ Ion ion2 = new Ion("x2");
+ ion2.setName("ion 1");
+ ion2.setWidth(100);
+ ion2.setHeight(100);
+ ion2.setX(200);
+ ion2.setY(250);
+ model.addElement(ion2);
+
+ Ion ion3 = new Ion("x3");
+ ion3.setName("ion 1");
+ ion3.setWidth(100);
+ ion3.setHeight(100);
+ ion3.setX(400);
+ ion3.setY(450);
+ model.addElement(ion3);
+
+ Reaction reaction = (Reaction) clazz.getConstructor().newInstance();
+ reaction.addReactant(createReactant(ion));
+ Product product = createProduct(ion2);
+ reaction.addProduct(product);
+ if (SimpleReactionInterface.class.isAssignableFrom(clazz)) {
+ } else if (TwoReactantReactionInterface.class.isAssignableFrom(clazz)) {
+ reaction.addReactant(createReactant(ion3));
+ NodeOperator operator;
+ if (HeterodimerAssociationReaction.class.isAssignableFrom(clazz)) {
+ operator = new AssociationOperator();
+ } else {
+ operator = new AndOperator();
+ ReactionLineData lineData = ReactionLineData.TRIGGER;
+ product.getLine().getEndAtd().setArrowLineType(lineData.getLineType());
+ product.getLine().getEndAtd().setArrowType(lineData.getProductArrowType());
+ product.getLine().setType(lineData.getLineType());
+ }
+ operator.addInputs(reaction.getReactants());
+ operator.setLine(new PolylineData(new Point2D.Double(100, 100), new Point2D.Double(100, 200)));
+ reaction.addNode(operator);
+ } else if (TwoProductReactionInterface.class.isAssignableFrom(clazz)) {
+ reaction.addProduct(createProduct(ion3));
+ NodeOperator operator = new SplitOperator();
+ if (TruncationReaction.class.isAssignableFrom(clazz)) {
+ operator = new TruncationOperator();
+ }
+ operator.addOutputs(reaction.getProducts());
+ operator.setLine(new PolylineData(new Point2D.Double(10, 10), new Point2D.Double(10, 20)));
+ reaction.addNode(operator);
+ } else {
+ throw new NotImplementedException();
+ }
+ model.addReaction(reaction);
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+ String xmlString = cellDesignerXmlParser.toXml(model);
+ Model modelAfterSerialization = cellDesignerXmlParser
+ .createModel(new ConverterParams().inputStream(new ByteArrayInputStream(xmlString.getBytes())));
+ return modelAfterSerialization;
+ }
+
+ private static Reactant createReactant(Ion ion) {
+ Reactant result = new Reactant(ion);
+ Point2D point = ion.getCenter();
+ point.setLocation(point.getX() + 300, point.getY());
+ result.setLine(new PolylineData(ion.getCenter(), point));
+ return result;
+ }
+
+ private static Product createProduct(Ion ion) {
+ Product result = new Product(ion);
+ Point2D point = ion.getCenter();
+ point.setLocation(point.getX() + 300, point.getY());
+ result.setLine(new PolylineData(ion.getCenter(), point));
+ return result;
+ }
+
+ Model modelToBeTested;
+
+ public SbmlReactionExportArrowType(String name, Model model) {
+ modelToBeTested = model;
+ }
+
+ @Test
+ public void test() throws Exception {
+ try {
+ Model modelAfterSerialization = getModelAfterSerializing(modelToBeTested);
+
+ ReactionComparator reactionComparator = new ReactionComparator();
+
+ Reaction originalReaction = modelToBeTested.getReactions().iterator().next();
+ Reaction afterSerializationReaction = modelAfterSerialization.getReactions().iterator().next();
+
+ afterSerializationReaction.setIdReaction(originalReaction.getIdReaction());
+ assertEquals(0, reactionComparator.compare(originalReaction, afterSerializationReaction));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModelAfterSerializing(Model originalModel) throws Exception {
+ String xml = exporter.toXml(originalModel);
+ ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
+ Model result = parser.createModel(new ConverterParams().inputStream(stream));
+ return result;
+ }
+
+}
--
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