From d5e5d5090e98771049ff13e77708eacb2945d8aa Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 9 Jan 2018 16:15:28 +0100
Subject: [PATCH] export of reaction layout added
---
.../model/sbml/SbmlReactionExporter.java | 25 +-
.../model/sbml/SbmlExporterTest.java | 8 -
.../graphics/PolylineDataComparator.java | 232 +++++++++---------
.../map/reaction/AbstractNodeComparator.java | 6 +-
4 files changed, 141 insertions(+), 130 deletions(-)
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 82f63a0e25..f91be25fbd 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
@@ -3,6 +3,7 @@ package lcsb.mapviewer.converter.model.sbml;
import java.awt.geom.Line2D;
import java.util.Collection;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
@@ -18,6 +19,7 @@ import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -41,12 +43,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
@Override
public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
String reactionId = getReactionId(reaction);
- logger.debug(reactionId);
org.sbml.jsbml.Reaction result = super.sbmlElementByElementId.get(reactionId);
if (result != null) {
return result;
}
result = sbmlModel.createReaction(reactionId);
+ result.setReversible(reaction.isReversible());
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
@@ -79,7 +81,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
if (separatorIndex > 0) {
glyphId = glyphId.substring(separatorIndex + 2);
}
- logger.debug(glyphId);
ReactionGlyph reactionGlyph;
try {
// handle case when input data cannot doesn't come from SBML parser and contains
@@ -135,18 +136,24 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
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));
+ reactantGlyph.setCurve(createCurve(node, node instanceof Reactant));
reactantGlyph.setSpeciesReference(speciesReferenceByReactionNode.get(node));
return reactantGlyph;
}
- private Curve createCurve(ReactionNode reactant) {
+ private Curve createCurve(ReactionNode reactant, boolean reverse) {
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);
+ List<Line2D> lines = reactant.getLine().getLines();
+ if (reverse) {
+ lines = reactant.getLine().reverse().getLines();
+ }
+ for (Line2D line : lines) {
+ if (line.getP1().distance(line.getP2())>Configuration.EPSILON) {
+ 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 cde6d4d78d..ade2723f7b 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
@@ -231,14 +231,6 @@ public class SbmlExporterTest {
Model model2 = converter.createModel(new ConverterParams().filename("tmp.xml"));
model2.setName(null);
-
- for (Reaction r: model.getReactions()) {
- logger.debug(r.getIdReaction());
- }
- logger.debug("---");
- for (Reaction r: model2.getReactions()) {
- logger.debug(r.getIdReaction());
- }
assertNotNull(model2);
ModelComparator comparator = new ModelComparator(1.0);
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
index 2be249dcdc..d06b841c16 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
@@ -17,115 +17,127 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
*
*/
public class PolylineDataComparator implements Comparator<PolylineData> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PolylineDataComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public PolylineDataComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public PolylineDataComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(PolylineData arg0, PolylineData arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.getClass().equals(arg1.getClass())) {
- if (arg0.getClass().equals(PolylineData.class)) {
- return internalCompare(arg0, arg1);
- } else {
- throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
- }
- } else {
- return -1;
- }
- }
-
- /**
- * This method compares only the fields that are defined in
- * {@link PolylineData} class in inheritence tree.
- *
- * @param arg0
- * first object to compare
- * @param arg1
- * second object to compare
- * @return if all fields are qual then returns 0. If they are different then
- * -1/1 is returned.
- */
- private int internalCompare(PolylineData arg0, PolylineData arg1) {
- IntegerComparator integerComparator = new IntegerComparator();
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
-
- if (integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size()) != 0) {
- logger.debug("Lines have different size: " + arg0.getPoints().size() + ", " + arg1.getPoints().size());
- return integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size());
- }
- // TODO this should be fixed
- // for (int i = 0; i < arg0.getPoints().size(); i++) {
- // if
- // (doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
- // 0.0) != 0) {
- // logger.debug("Lines have different points: " + arg0.getPoints().get(i) +
- // ", " + arg1.getPoints().get(i));
- // return
- // doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
- // 0.0);
- // }
- // }
-
- if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
- logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
- return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
- }
-
- if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
- logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
- return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
- }
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
- logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
- return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
- }
-
- if (arg0.getType().compareTo(arg1.getType()) != 0) {
- logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
- return arg0.getType().compareTo(arg1.getType());
- }
-
- return 0;
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PolylineDataComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public PolylineDataComparator(double epsilon) {
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public PolylineDataComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public int compare(PolylineData arg0, PolylineData arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (arg0.getClass().equals(arg1.getClass())) {
+ if (arg0.getClass().equals(PolylineData.class)) {
+ return internalCompare(arg0, arg1);
+ } else {
+ throw new NotImplementedException("Don't know how to compare classes: " + arg0.getClass());
+ }
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * This method compares only the fields that are defined in {@link PolylineData}
+ * class in inheritance tree.
+ *
+ * @param arg0
+ * first object to compare
+ * @param arg1
+ * second object to compare
+ * @return if all fields are equal then returns 0. If they are different then
+ * -1/1 is returned.
+ */
+ private int internalCompare(PolylineData arg0, PolylineData arg1) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
+
+ int different1=0;
+ int different2=0;
+ for (int i=1;i<arg0.getPoints().size();i++) {
+ if (arg0.getPoints().get(i).distance(arg0.getPoints().get(i-1))>Configuration.EPSILON) {
+ different1++;
+ }
+ }
+ for (int i=1;i<arg1.getPoints().size();i++) {
+ if (arg1.getPoints().get(i).distance(arg1.getPoints().get(i-1))>Configuration.EPSILON) {
+ different2++;
+ }
+ }
+ if (integerComparator.compare(different1, different2) != 0) {
+ logger.debug("Lines have different size: " + different1 + ", " + different2);
+ return integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size());
+ }
+ // TODO this should be fixed
+ // for (int i = 0; i < arg0.getPoints().size(); i++) {
+ // if
+ // (doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
+ // 0.0) != 0) {
+ // logger.debug("Lines have different points: " + arg0.getPoints().get(i) +
+ // ", " + arg1.getPoints().get(i));
+ // return
+ // doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
+ // 0.0);
+ // }
+ // }
+
+ if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
+ logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
+ return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
+ }
+
+ if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
+ logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
+ return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
+ }
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
+ logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
+ return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
+ }
+
+ if (arg0.getType().compareTo(arg1.getType()) != 0) {
+ logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
+ return arg0.getType().compareTo(arg1.getType());
+ }
+
+ return 0;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
index 47b9fee26e..20305f8d3d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
@@ -58,7 +58,7 @@ public class AbstractNodeComparator implements Comparator<AbstractNode> {
// now check class types
if (arg0.getClass().equals(arg1.getClass())) {
- // and call comparator of apropriate subclass
+ // and call comparator of appropriate subclass
if (arg0 instanceof NodeOperator) {
NodeOperatorComparator nodeOperatorComparator = new NodeOperatorComparator(epsilon);
return nodeOperatorComparator.compare((NodeOperator) arg0, (NodeOperator) arg1);
@@ -75,13 +75,13 @@ public class AbstractNodeComparator implements Comparator<AbstractNode> {
/**
* This method compares only the fields that are defined in AbstractNode class
- * in inheritence tree. By the design it is called by subclass comparator.
+ * in inheritance tree. By the design it is called by subclass comparator.
*
* @param arg0
* first object to compare
* @param arg1
* second object to compare
- * @return if all fields are qual then returns 0. If they are different then
+ * @return if all fields are equal then returns 0. If they are different then
* -1/1 is returned.
*/
protected int internalCompare(AbstractNode arg0, AbstractNode arg1) {
--
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