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 50be3be76dcbce74732f82ac78e28606678c5b36..3a633ce4f7101f43ca7c18838751294dcaa62b39 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
@@ -89,125 +89,124 @@ public class SbmlReactionParser {
throw new InvalidInputDataExecption("Layout contains invalid Species id: " + glyph.getReaction());
}
used.add(source);
- Reaction reactionWithLayout = source.copy();
- reactionWithLayout.setIdReaction(glyph.getId());
- 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())) {
- if (nodeClass == null) {
- minervaNode = node;
- } else if (node.getClass().isAssignableFrom(nodeClass)) {
- minervaNode = node;
+ try {
+ Reaction reactionWithLayout = source.copy();
+ reactionWithLayout.setIdReaction(glyph.getId());
+ 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())) {
+ if (nodeClass == null) {
+ minervaNode = node;
+ } else if (node.getClass().isAssignableFrom(nodeClass)) {
+ minervaNode = node;
+ }
}
}
- }
- if (minervaNode == null) {
- throw new InvalidInputDataExecption(
- "Cannot find reaction node for layouted reaction: " + speciesGlyph.getSpecies() + ", " + glyph.getId());
- }
- Element minervaElement = minervaModel.getElementByElementId(speciesGlyph.getId());
- if (minervaElement == null) {
- throw new InvalidInputDataExecption("Cannot find layouted reaction node for layouted reaction: "
- + speciesGlyph.getId() + ", " + glyph.getId());
- }
+ if (minervaNode == null) {
+ throw new InvalidInputDataExecption(
+ "Cannot find reaction node for layouted reaction: " + speciesGlyph.getSpecies() + ", " + glyph.getId());
+ }
+ Element minervaElement = minervaModel.getElementByElementId(speciesGlyph.getId());
+ if (minervaElement == null) {
+ throw new InvalidInputDataExecption("Cannot find layouted reaction node for layouted reaction: "
+ + speciesGlyph.getId() + ", " + glyph.getId());
+ }
- PolylineData line = null;
- for (CurveSegment segment : speciesRefernceGlyph.getCurve().getListOfCurveSegments()) {
- Point2D start = new Point2D.Double(segment.getStart().getX(), segment.getStart().getY());
- Point2D end = new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY());
- if (line == null) {
- line = new PolylineData(start, end);
- } else {
- line.addPoint(end);
+ PolylineData line = null;
+ for (CurveSegment segment : speciesRefernceGlyph.getCurve().getListOfCurveSegments()) {
+ Point2D start = new Point2D.Double(segment.getStart().getX(), segment.getStart().getY());
+ Point2D end = new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY());
+ if (line == null) {
+ line = new PolylineData(start, end);
+ } else {
+ 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());
+ 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);
+ 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);
+ 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 {
+ 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);
+ }
+
minervaModel.addReaction(new StateTransitionReaction(reactionWithLayout));
} catch (InvalidArgumentException e) {
throw new InvalidInputDataExecption(e);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..5841758afbbd099cba792497ba0c14f26707c199
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -0,0 +1,11 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ GenericSbmlParserTest.class, SbmlPareserForInvalidReactionTest.class, SbmlParserTest.class })
+public class AllSbmlConverterTests {
+
+}
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 dfa7b80ef15b547b23f48cb5740db0c3a855ca85..21c3124f6213a06978d1eaa91abfabddc2bb322c 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
@@ -5,9 +5,7 @@ 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;
@@ -15,9 +13,6 @@ 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;
@@ -110,32 +105,34 @@ public class SbmlParserTest {
}
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"));
+ // 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"));
}
@Test
public void testReactionWithoutLayout() throws Exception {
- Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/Complete_Example_level2.xml"));
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/layoutExample/Complete_Example_level2.xml"));
assertNotNull(model);
assertEquals(1, model.getReactions().size());
Reaction reaction = model.getReactions().iterator().next();
for (ReactionNode node : reaction.getReactionNodes()) {
- logger.debug(node.getClass()+","+node.getElement());
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"));
+ // 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"));
}