diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
index 2f06de27b17abbeb88ad01bbe0543a0ba359c362..3125c6585a97b3531fc6039344a622db4fe65b23 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
@@ -9,6 +9,7 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -17,6 +18,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* Parser used for extracting collections of reaction from CellDesigner xml.
@@ -26,88 +28,92 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
*/
public class ReactionCollectionXmlParser extends XmlParser {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionCollectionXmlParser.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionCollectionXmlParser.class.getName());
- /**
- * Model for which parsing (or transformation to xml) is being done.
- */
- private Model model = null;
+ /**
+ * Model for which parsing (or transformation to xml) is being done.
+ */
+ private Model model = null;
- /**
- * Object used for parsing single reaction.
- */
- private ReactionXmlParser xmlStructureFactory;
+ /**
+ * Object used for parsing single reaction.
+ */
+ private ReactionXmlParser xmlStructureFactory;
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param sbgn
- * should sbgn standard be used
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @param model
- * model that is parsed/transformed into xml
- */
- public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn) {
- this.model = model;
- xmlStructureFactory = new ReactionXmlParser(elements, sbgn);
- }
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param sbgn
+ * should sbgn standard be used
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @param model
+ * model that is parsed/transformed into xml
+ */
+ public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn) {
+ this.model = model;
+ xmlStructureFactory = new ReactionXmlParser(elements, sbgn);
+ }
- /**
- * Parse CellDesigner xml node with set of reactions into list of
- * {@link Reaction}.
- *
- * @param reactionsNode
- * xml node
- * @return list of reaction taken from xml node
- * @throws CellDesignerParserException
- * thrown when there is a problem with xml node
- * @throws InvalidXmlSchemaException
- * thrown when reactionsNode is invalid xml
- */
- public List<Reaction> parseXmlReactionCollection(Node reactionsNode) throws CellDesignerParserException, InvalidXmlSchemaException {
- List<Reaction> result = new ArrayList<Reaction>();
- NodeList nodes = reactionsNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("reaction")) {
- Reaction reaction = xmlStructureFactory.getReaction(node, model);
- result.add(reaction);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of model/listOfReactions: " + node.getNodeName());
- }
- }
- }
+ /**
+ * Parse CellDesigner xml node with set of reactions into list of
+ * {@link Reaction}.
+ *
+ * @param reactionsNode
+ * xml node
+ * @return list of reaction taken from xml node
+ * @throws CellDesignerParserException
+ * thrown when there is a problem with xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when reactionsNode is invalid xml
+ */
+ public List<Reaction> parseXmlReactionCollection(Node reactionsNode)
+ throws CellDesignerParserException, InvalidXmlSchemaException {
+ List<Reaction> result = new ArrayList<Reaction>();
+ NodeList nodes = reactionsNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("reaction")) {
+ Reaction reaction = xmlStructureFactory.getReaction(node, model);
+ result.add(reaction);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of model/listOfReactions: " + node.getNodeName());
+ }
+ }
+ }
- return result;
- }
+ return result;
+ }
- /**
- * Transforms set of reactions into CellDesigner xml string.
- *
- * @param collection
- * set of reactions
- * @return CellDesigner xml string representing set of reactions
- * @throws ConverterException
- */
- public String reactionCollectionToXmlString(Collection<Reaction> collection) throws InconsistentModelException {
- String result = "";
- result += "<listOfReactions>\n";
- for (Reaction reaction : collection) {
- try {
- result += xmlStructureFactory.toXml(reaction);
- } catch (SelfReactionException e) {
- logger.warn("Reaction omitted: " + e.getMessage());
- }
- }
- result += "</listOfReactions>\n";
- return result;
- }
+ /**
+ * Transforms set of reactions into CellDesigner xml string.
+ *
+ * @param collection
+ * set of reactions
+ * @return CellDesigner xml string representing set of reactions
+ * @throws ConverterException
+ */
+ public String reactionCollectionToXmlString(Collection<Reaction> collection) throws InconsistentModelException {
+ String result = "";
+ result += "<listOfReactions>\n";
+ for (Reaction reaction : collection) {
+ try {
+ result += xmlStructureFactory.toXml(reaction);
+ } catch (InvalidArgumentException e) {
+ throw new InconsistentModelException(
+ new ElementUtils().getElementTag(reaction) + "Problem with exporting reaction", e);
+ } catch (SelfReactionException e) {
+ logger.warn("Reaction omitted: " + e.getMessage());
+ }
+ }
+ result += "</listOfReactions>\n";
+ return result;
+ }
}
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 05889cd4ff94cab9cbf1ebecdcd9c47234cca9b8..488a9f8b896b10da6c3698cb75ecbd4dfca507a7 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
@@ -1,7 +1,6 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
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 749de4d4cf47559cc9fedb40f769e74033260b31..675593c468f9965859d0f7983c466e38eb0121dc 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
@@ -319,6 +319,11 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
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) {
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 8144beb26ab92392654e69bd2c9c0310f9cc3255..8397387884e3d26a5621edd3ed662c967a01f4da 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
@@ -675,4 +675,18 @@ public class SbmlExporterTest {
}
+ @Test
+ public void testExportImportBooleanGate() throws Exception {
+ Model originalModel = new CellDesignerXmlParser()
+ .createModel(new ConverterParams().filename("testFiles/cell_designer_problems/boolean_logic_gate.xml"));
+ Model model = getModelAfterSerializing(originalModel);
+
+ new CellDesignerXmlParser().toXml(model);
+ List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
+ List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
+
+ ListComparator<Line2D> comparator = new ListComparator<>(new LineComparator(Configuration.EPSILON));
+ assertEquals(0, comparator.compare(lines1, lines2));
+
+ }
}
diff --git a/converter-sbml/testFiles/cell_designer_problems/boolean_logic_gate.xml b/converter-sbml/testFiles/cell_designer_problems/boolean_logic_gate.xml
new file mode 100644
index 0000000000000000000000000000000000000000..af4d6c8f71fdcd7ea8e68d4e9fa9f1a971ea9564
--- /dev/null
+++ b/converter-sbml/testFiles/cell_designer_problems/boolean_logic_gate.xml
@@ -0,0 +1,224 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="190.0" y="44.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="184.0" y="183.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="414.0" y="113.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+<celldesigner:protein id="pr3" name="s3" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00008" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>BOOLEAN_LOGIC_GATE</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1"/>
+<celldesigner:baseReactant species="s2" alias="sa2"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct"/>
+<celldesigner:editPoints>297.6666666666667,136.66666666666666</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+<celldesigner:listOfGateMember>
+<celldesigner:GateMember type="BOOLEAN_LOGIC_GATE_AND" aliases="sa1,sa2" modificationType="REDUCED_TRIGGER" targetLineIndex="-1,-1" editPoints="297.6666666666667,136.66666666666666">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:GateMember>
+<celldesigner:GateMember type="REDUCED_TRIGGER" aliases="sa1">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:GateMember>
+<celldesigner:GateMember type="REDUCED_TRIGGER" aliases="sa2">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:GateMember>
+</celldesigner:listOfGateMember>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>