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 675593c468f9965859d0f7983c466e38eb0121dc..f0cb9f2087f964378a9f39010d99a904640f5b87 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
@@ -18,8 +18,11 @@ import org.sbml.jsbml.LocalParameter;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ModifierSpeciesReference;
import org.sbml.jsbml.SpeciesReference;
+import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.Curve;
import org.sbml.jsbml.ext.layout.CurveSegment;
+import org.sbml.jsbml.ext.layout.LineSegment;
+import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
@@ -274,8 +277,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
private NodeOperator createOutputOperator(Reaction reactionWithLayout, ReactionGlyph reactionGlyph) {
PolylineData line = new PolylineData();
- Curve curve = reactionGlyph.getCurve();
-
+ Curve curve = extractCurve(reactionGlyph, reactionWithLayout);
+
int min = 0;
if (reactionWithLayout.getReactants().size() > 1) {
// with operator in the output we need to leave something for the operator
@@ -305,7 +308,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
private NodeOperator createInputOperator(Reaction reactionWithLayout, ReactionGlyph reactionGlyph) {
PolylineData line = new PolylineData();
- Curve curve = reactionGlyph.getCurve();
+ Curve curve = extractCurve(reactionGlyph, reactionWithLayout);
int max = curve.getCurveSegmentCount();
if (reactionWithLayout.getProducts().size() > 1) {
@@ -319,7 +322,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
line.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
- if (line.getPoints().size()==0) {
+ if (line.getPoints().size() == 0) {
Point2D point = reactionWithLayout.getReactants().get(0).getLine().getEndPoint();
line.addPoint(new Point2D.Double(point.getX(), point.getY()));
line.addPoint(new Point2D.Double(point.getX(), point.getY()));
@@ -336,6 +339,33 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
return operator;
}
+ /**
+ * Returns {@link Curve} associated to {@link ReactionGlyph}. If curve doesn't
+ * exist then method will try to create it from {@link BoundingBox} (due to SBML
+ * specification).
+ *
+ * @param reactionGlyph
+ * @return
+ */
+ private Curve extractCurve(ReactionGlyph reactionGlyph, Reaction reaction) {
+ Curve curve = reactionGlyph.getCurve();
+ if (curve == null) {
+ curve = new Curve(getSbmlModel().getLevel(), getSbmlModel().getVersion());
+ BoundingBox box = reactionGlyph.getBoundingBox();
+ if (box != null && box.getDimensions() != null && box.getPosition() != null) {
+ LineSegment curveSegment = new LineSegment(getSbmlModel().getLevel(), getSbmlModel().getVersion());
+ curveSegment.setStart(new Point(box.getPosition()));
+ curveSegment.setEnd(new Point(box.getPosition().getX() + box.getDimensions().getWidth(),
+ box.getPosition().getY() + box.getDimensions().getHeight()));
+ curve.addCurveSegment(curveSegment);
+ } else {
+ logger.warn(new ElementUtils().getElementTag(reaction) + " invalid curve line for reaction (node: "
+ + reactionGlyph.getId() + ")");
+ }
+ }
+ return curve;
+ }
+
private Class<? extends ReactionNode> getReactionNodeClass(SpeciesReferenceGlyph speciesRefernceGlyph) {
Class<? extends ReactionNode> nodeClass = null;
if (speciesRefernceGlyph.getRole() != null) {
diff --git a/converter-sbml/testFiles/layoutExample/no_curve_in_reaction.xml b/converter-sbml/testFiles/layoutExample/no_curve_in_reaction.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bfee8d12f3b8811f884db9cbb82d5ba7321b1495
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/no_curve_in_reaction.xml
@@ -0,0 +1,166 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" version="1" layout:required="false">
+ <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
+ <listOfUnitDefinitions>
+ <unitDefinition id="per_second">
+ <listOfUnits>
+ <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+ </listOfUnits>
+ </unitDefinition>
+ </listOfUnitDefinitions>
+ <listOfCompartments>
+ <compartment id="default" constant="false"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species sboTerm="SBO:0000252" id="species_3" name="s4" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000247" id="species_5" name="s6" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000244" id="species_0" name="s7" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000297" id="species_1" name="s1" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ <species sboTerm="SBO:0000247" id="species_6" name="s5" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction sboTerm="SBO:0000176" id="re1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="species_1" constant="false"/>
+ <speciesReference species="species_6" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="species_3" constant="false"/>
+ <speciesReference species="species_5" constant="false"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="species_0"/>
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <layout:layout layout:id="predicted_layout">
+ <layout:dimensions layout:width="592" layout:height="352"/>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="sg_sa3" layout:species="species_3">
+ <layout:boundingBox layout:id="bb_sg_sa3">
+ <layout:position layout:x="461" layout:y="293"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="sg_sa5" layout:species="species_5">
+ <layout:boundingBox layout:id="bb_sg_sa5">
+ <layout:position layout:x="452" layout:y="186"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="sg_sa6" layout:species="species_0">
+ <layout:boundingBox layout:id="bb_sg_sa6">
+ <layout:position layout:x="355" layout:y="61"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="sg_csa1" layout:species="species_1">
+ <layout:boundingBox layout:id="bb_sg_csa1">
+ <layout:position layout:x="109" layout:y="207"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="sg_sa4" layout:species="species_6">
+ <layout:boundingBox layout:id="bb_sg_sa4">
+ <layout:position layout:x="233" layout:y="63"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="rg_re1_0" layout:reaction="re1">
+ <layout:boundingBox>
+ <layout:position layout:x="0" layout:y="0"/>
+ <layout:dimensions layout:width="0" layout:height="0"/>
+ </layout:boundingBox>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="srg_sa6" layout:speciesGlyph="sg_sa6" layout:role="inhibitor">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="395" layout:y="81"/>
+ <layout:end layout:x="352" layout:y="260"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="srg_sa3" layout:speciesGlyph="sg_sa3" layout:role="product">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="352" layout:y="260"/>
+ <layout:end layout:x="501" layout:y="313"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="srg_sa5" layout:speciesGlyph="sg_sa5" layout:role="sideproduct">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="352" layout:y="260"/>
+ <layout:end layout:x="492" layout:y="206"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="srg_csa1" layout:speciesGlyph="sg_csa1" layout:role="substrate">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="352" layout:y="260"/>
+ <layout:end layout:x="149" layout:y="227"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="srg_sa4" layout:speciesGlyph="sg_sa4" layout:role="sidesubstrate">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+ <layout:start layout:x="352" layout:y="260"/>
+ <layout:end layout:x="273" layout:y="83"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:id="tg_sa3" layout:originOfText="sg_sa3" layout:graphicalObject="sg_sa3">
+ <layout:boundingBox layout:id="bb_tg_sa3">
+ <layout:position layout:x="461" layout:y="293"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="tg_sa5" layout:originOfText="sg_sa5" layout:graphicalObject="sg_sa5">
+ <layout:boundingBox layout:id="bb_tg_sa5">
+ <layout:position layout:x="452" layout:y="186"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="tg_sa6" layout:originOfText="sg_sa6" layout:graphicalObject="sg_sa6">
+ <layout:boundingBox layout:id="bb_tg_sa6">
+ <layout:position layout:x="355" layout:y="61"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="tg_csa1" layout:originOfText="sg_csa1" layout:graphicalObject="sg_csa1">
+ <layout:boundingBox layout:id="bb_tg_csa1">
+ <layout:position layout:x="109" layout:y="207"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="tg_sa4" layout:originOfText="sg_sa4" layout:graphicalObject="sg_sa4">
+ <layout:boundingBox layout:id="bb_tg_sa4">
+ <layout:position layout:x="233" layout:y="63"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ </model>
+</sbml>