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Commit 0e7449a4 authored by Piotr Gawron's avatar Piotr Gawron
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when reaction line was short (1 segment) and there was need for operator in... 

when reaction line was short (1 segment) and there was need for operator in product/reactant side the layout was regenerated
parent 2e142293
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
View file @ 0e7449a4
......@@ -31,6 +31,7 @@ import org.sbml.jsbml.ext.render.RenderGroup;
import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
......@@ -117,8 +118,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
Reaction reactionWithLayout = source.copy();
// getId doesn't have to be unique, therefore we concatenate with reaction
reactionWithLayout.setIdReaction(glyph.getReaction() + "__" + glyph.getId());
//z index
// z index
if (glyph.getBoundingBox() != null && glyph.getBoundingBox().getPosition() != null
&& glyph.getBoundingBox().getPosition().isSetZ()) {
reactionWithLayout.setZ((int) glyph.getBoundingBox().getPosition().getZ());
......@@ -281,23 +282,6 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
private NodeOperator createOutputOperator(Reaction reactionWithLayout, ReactionGlyph reactionGlyph) {
PolylineData line = new PolylineData();
Curve curve = extractCurve(reactionGlyph, reactionWithLayout);
// 1 is for the process in the center
int min = 1;
if (reactionWithLayout.getReactants().size() > 1) {
// with operator in the output we need to leave something for the operator
min++;
}
for (int i = min; i < curve.getCurveSegmentCount(); i++) {
CurveSegment segment = curve.getCurveSegment(i);
if (line.getPoints().size() == 0) {
line.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
}
line.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
NodeOperator operator;
if (reactionWithLayout instanceof TruncationReaction) {
operator = new TruncationOperator();
......@@ -306,34 +290,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
} else {
operator = new SplitOperator();
}
PolylineData line = extractCurve(reactionGlyph, reactionWithLayout, operator.getClass());
operator.addOutputs(reactionWithLayout.getProducts());
operator.setLine(line.reverse());
return operator;
}
private NodeOperator createInputOperator(Reaction reactionWithLayout, ReactionGlyph reactionGlyph) {
PolylineData line = new PolylineData();
Curve curve = extractCurve(reactionGlyph, reactionWithLayout);
// -1 is for the process in the center
int max = curve.getCurveSegmentCount() - 1;
if (reactionWithLayout.getProducts().size() > 1) {
// with operator in the output we need to leave something for the operator
max--;
}
for (int i = 0; i < max; i++) {
CurveSegment segment = curve.getCurveSegment(i);
if (line.getPoints().size() == 0) {
line.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
}
line.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
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()));
}
NodeOperator operator;
if (reactionWithLayout instanceof HeterodimerAssociationReaction) {
......@@ -341,6 +305,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
} else {
operator = new AndOperator();
}
PolylineData line = extractCurve(reactionGlyph, reactionWithLayout, operator.getClass());
operator.addInputs(reactionWithLayout.getReactants());
operator.setLine(line);
return operator;
......@@ -352,9 +317,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
* specification).
*
* @param reactionGlyph
* @param operator
* class of {@link NodeOperator} that requires the line (this line can
* be separated into 3 different segments - reactant, center, product
* parts)
* @return
*/
private Curve extractCurve(ReactionGlyph reactionGlyph, Reaction reaction) {
private PolylineData extractCurve(ReactionGlyph reactionGlyph, Reaction reaction,
Class<? extends NodeOperator> operator) {
Curve curve = reactionGlyph.getCurve();
if (curve == null) {
curve = new Curve(getSbmlModel().getLevel(), getSbmlModel().getVersion());
......@@ -370,7 +340,85 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
+ reactionGlyph.getId() + ")");
}
}
return curve;
if (curve.getCurveSegmentCount() == 0) {
return new PolylineData();
}
int requiredLines = 1;
if (reaction.getReactants().size() > 1) {
requiredLines++;
}
if (reaction.getProducts().size() > 1) {
requiredLines++;
}
int existingLines = curve.getCurveSegmentCount();
int reactantBreak;
int productBreak;
if (requiredLines == 3) {
reactantBreak = (existingLines - 1) / 2;
} else if (requiredLines == 2 && reaction.getReactants().size() > 1) {
reactantBreak = existingLines - 1;
} else if (requiredLines == 2 && reaction.getProducts().size() > 1) {
reactantBreak = 0;
} else {
throw new InvalidArgumentException(
new ElementUtils().getElementTag(reaction) + "Reaction has no products and reactants");
}
productBreak = reactantBreak + 1;
PolylineData result = new PolylineData();
if (operator == TruncationOperator.class ||
operator == DissociationOperator.class ||
operator == SplitOperator.class) {
// Product operator
if (existingLines >= requiredLines) {
CurveSegment segment = curve.getCurveSegment(productBreak);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
for (int i = productBreak; i < curve.getCurveSegmentCount(); i++) {
segment = curve.getCurveSegment(i);
result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
} else if (existingLines == 1) {
CurveSegment segment = curve.getCurveSegment(0);
double startX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) * (requiredLines-1) / requiredLines;
double startY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) * (requiredLines-1) / requiredLines;
result.addPoint(new Point2D.Double(startX, startY));
result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
} else {
CurveSegment segment = curve.getCurveSegment(1);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
} else if (operator == AssociationOperator.class || operator == AndOperator.class) {
// Reactant operator
if (existingLines >= requiredLines) {
CurveSegment segment = curve.getCurveSegment(0);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
for (int i = 0; i < reactantBreak; i++) {
segment = curve.getCurveSegment(i);
result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
}
} else if (existingLines == 1) {
CurveSegment segment = curve.getCurveSegment(0);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
double endX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) / requiredLines;
double endY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) / requiredLines;
result.addPoint(new Point2D.Double(endX, endY));
} else {
CurveSegment segment = curve.getCurveSegment(0);
result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
double endX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) / 2;
double endY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) / 2;
result.addPoint(new Point2D.Double(endX, endY));
}
} else {
throw new InvalidArgumentException("Unknown operator class: " + operator);
}
return result;
}
private Class<? extends ReactionNode> getReactionNodeClass(SpeciesReferenceGlyph speciesRefernceGlyph) {
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
View file @ 0e7449a4
......@@ -17,11 +17,13 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
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.species.Element;
......@@ -188,12 +190,6 @@ public class SbmlParserTest {
assertEquals(1, model.getCompartments().iterator().next().getMiriamData().size());
}
@Test(expected = InvalidInputDataExecption.class)
public void testInvalidReactionLayout() throws Exception {
parser.createModel(
new ConverterParams().filename("testFiles/invalidReaction/reaction_with_missing_part_of_layout.xml"));
}
@Test
public void testEmpyModel() throws Exception {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/empty.xml"));
......@@ -259,4 +255,19 @@ public class SbmlParserTest {
assertNotNull("Creation date is not defined", model.getCreationDate());
}
@Test
public void testParseProblematicLayout() throws Exception {
try {
Model model = parser
.createModel(new ConverterParams().filename("testFiles/small/problematic_layout.xml"));
Reaction reaction = model.getReactions().iterator().next();
Reactant reactant = reaction.getReactants().get(0);
assertEquals("Reactant line should start at position 120, 40", 0,
reactant.getLine().getBeginPoint().distance(120, 40), Configuration.EPSILON);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
converter-sbml/testFiles/small/problematic_layout.xml 0 → 100644
View file @ 0e7449a4
<?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_1" name="s2" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species sboTerm="SBO:0000252" id="species_0" name="s1" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species sboTerm="SBO:0000252" id="species_2" name="s3" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfReactions>
<reaction sboTerm="SBO:0000176" id="re3" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="species_1" constant="false"/>
<speciesReference species="species_0" constant="false"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="species_2" constant="false"/>
</listOfProducts>
</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="564" layout:height="217"/>
<layout:listOfCompartmentGlyphs>
<layout:compartmentGlyph layout:id="cg_default" layout:compartment="default">
<layout:boundingBox layout:id="bb_cg_default">
<layout:position layout:x="0" layout:y="0"/>
<layout:dimensions layout:width="484" layout:height="177"/>
</layout:boundingBox>
</layout:compartmentGlyph>
</layout:listOfCompartmentGlyphs>
<layout:listOfSpeciesGlyphs>
<layout:speciesGlyph layout:id="sg_re3_0_sa2" layout:species="species_1">
<layout:boundingBox layout:id="bb_sg_re3_0_sa2">
<layout:position layout:x="40" layout:y="20"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="sg_re3_0_sa1" layout:species="species_0">
<layout:boundingBox layout:id="bb_sg_re3_0_sa1">
<layout:position layout:x="46" layout:y="117"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="sg_re3_0_sa3" layout:species="species_2">
<layout:boundingBox layout:id="bb_sg_re3_0_sa3">
<layout:position layout:x="364" layout:y="96"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:speciesGlyph>
</layout:listOfSpeciesGlyphs>
<layout:listOfReactionGlyphs>
<layout:reactionGlyph layout:id="rg_re3_0" layout:reaction="re3">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="209.6" layout:y="70.4"/>
<layout:end layout:x="242" layout:y="78"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
<layout:listOfSpeciesReferenceGlyphs>
<layout:speciesReferenceGlyph layout:id="srg_re3_0_sa2_SUBSTRATE_1" layout:speciesGlyph="sg_re3_0_sa2">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="209.6" layout:y="70.4"/>
<layout:end layout:x="120" layout:y="40"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
<layout:speciesReferenceGlyph layout:id="srg_re3_0_sa1_SIDESUBSTRATE_1" layout:speciesGlyph="sg_re3_0_sa1">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="209.6" layout:y="70.4"/>
<layout:end layout:x="126" layout:y="137"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
<layout:speciesReferenceGlyph layout:id="srg_re3_0_sa3_PRODUCT_1" layout:speciesGlyph="sg_re3_0_sa3">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="242" layout:y="78"/>
<layout:end layout:x="364" layout:y="116"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
</layout:listOfSpeciesReferenceGlyphs>
</layout:reactionGlyph>
</layout:listOfReactionGlyphs>
<layout:listOfTextGlyphs>
<layout:textGlyph layout:id="tg_re3_0_sa2" layout:originOfText="sg_re3_0_sa2" layout:graphicalObject="sg_re3_0_sa2">
<layout:boundingBox layout:id="bb_tg_re3_0_sa2">
<layout:position layout:x="40" layout:y="20"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="tg_re3_0_sa1" layout:originOfText="sg_re3_0_sa1" layout:graphicalObject="sg_re3_0_sa1">
<layout:boundingBox layout:id="bb_tg_re3_0_sa1">
<layout:position layout:x="46" layout:y="117"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="tg_re3_0_sa3" layout:originOfText="sg_re3_0_sa3" layout:graphicalObject="sg_re3_0_sa3">
<layout:boundingBox layout:id="bb_tg_re3_0_sa3">
<layout:position layout:x="364" layout:y="96"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
</layout:listOfTextGlyphs>
</layout:layout>
</layout:listOfLayouts>
</model>
</sbml>
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