diff --git a/CHANGELOG b/CHANGELOG
index 4013acd70eb001a0a50e49cec21e94e751ed808e..018af25c4a97d3e9299c6b4b7753accf4e8c95ac 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -18,6 +18,8 @@ minerva (14.0.0~beta.0) unstable; urgency=low
* Bug fix: curator couldn't update data overlay in some situations (#905)
* Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome",
"Edit Project", "Edit User" (#881)
+ * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
+ properly (#907)
* Bug fix: user with modify access to the project can edit it in admin panel
(#901)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index 8fdfaeaf5963219877a0230a7c6a1c24affd7c75..942ecfe62f3b50d0eed7fb4209dc69dfae5e2390 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -409,6 +409,9 @@ public class ReactionFromXml {
}
applyStylingToLine(line, result.getLine());
+ if (booleanLogicGateType!=null) {
+ assignColorFromGateMembers(result, gateMembers);
+ }
if (reactantsLinkNode != null) {
parseReactantLinks(result, reactantsLinkNode, model);
}
@@ -906,10 +909,10 @@ public class ReactionFromXml {
PolylineData line = new PolylineData();
line.addPoint(pointTransformation.copyPoint(product.getLine().getBeginPoint()));
- Point2D secondPoint = pointTransformation.getPointOnLine(product.getLine().getPoints().get(1),
- product.getLine().getPoints().get(0), 0.4);
- Point2D thirdPoint = pointTransformation.getPointOnLine(product.getLine().getPoints().get(1),
- product.getLine().getPoints().get(0), 0.6);
+ Point2D secondPoint = pointTransformation.getPointOnLine(product.getLine().getPoints().get(0),
+ product.getLine().getPoints().get(1), 0.4);
+ Point2D thirdPoint = pointTransformation.getPointOnLine(product.getLine().getPoints().get(0),
+ product.getLine().getPoints().get(1), 0.6);
line.addPoint(pointTransformation.copyPoint(secondPoint));
operator.setLine(line);
@@ -927,6 +930,37 @@ public class ReactionFromXml {
}
}
+ private void assignColorFromGateMembers(Reaction result, Node gateMembers) {
+ int elementIndex = 0;
+ for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
+ Node child = gateMembers.getChildNodes().item(i);
+ if (child.getNodeType() == Node.ELEMENT_NODE) {
+ if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
+ Node lineNode = XmlParser.getNode("celldesigner:line", child);
+ if (lineNode != null) {
+ LineProperties line = getLineProperties(lineNode);
+ Set<PolylineData> polylines = new HashSet<>();
+ if (elementIndex == 0) {
+ if (result.getOperators().size() > 0) {
+ polylines.add(result.getOperators().get(result.getOperators().size() - 1).getLine());
+ polylines.add(result.getLine());
+ }
+ } else {
+ if (result.getReactants().size() >= elementIndex) {
+ polylines.add(result.getReactants().get(elementIndex - 1).getLine());
+ }
+ }
+ for (PolylineData polyline: polylines) {
+ polyline.setColor(line.getColor());
+ polyline.setWidth(line.getWidth());
+ }
+ }
+ elementIndex++;
+ }
+ }
+ }
+ }
+
/**
* Creates lines for reaction that belongs to
* {@link TwoProductReactionInterface}.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index fe18a84c3046b2ef514d135d473ec84378c2831e..543b16a5bd33771872fa62f07070c3b89683153e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -492,7 +492,7 @@ public class ReactionToXml {
sb.append(getListOfModificationsXmlStringForReaction(reaction));
sb.append(getListOfGateMembersXmlStringForReaction(reaction));
- sb.append(getLineXmlStringForLines(reaction.getReactants().get(0).getLine()));
+ sb.append(getLineXmlStringForLines(reaction.getLine()));
XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
sb.append("</celldesigner:extension>\n");
@@ -584,6 +584,7 @@ public class ReactionToXml {
}
result.append("</celldesigner:listOfLineDirection>\n");
result.append("</celldesigner:connectScheme>\n");
+ result.append(getLineXmlStringForLines(operator.getLine()));
result.append("</celldesigner:GateMember>\n");
@@ -684,11 +685,7 @@ public class ReactionToXml {
sb.append(getConnectSchemeXmlStringForLines(new PolylineData[] { reactant.getLine() }));
sb.append(getEditPointsXmlStringForLine(new PolylineData[] { reactant.getLine() }, 0));
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + reactant.getLine().getWidth() + "\" ");
- sb.append("color=\"" + XmlParser.colorToString(reactant.getLine().getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
+ sb.append(getLineXmlStringForLines(reactant.getLine()));
sb.append("</celldesigner:reactantLink>\n");
return sb.toString();
}
@@ -715,13 +712,8 @@ public class ReactionToXml {
sb.append(getConnectSchemeXmlStringForLines(lines));
- // TODO
sb.append(getEditPointsXmlStringForLine(lines, 0));
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + product.getLine().getWidth() + "\" ");
- sb.append("color=\"" + XmlParser.colorToString(product.getLine().getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
+ sb.append(getLineXmlStringForLines(product.getLine()));
sb.append("</celldesigner:productLink>\n");
return sb.toString();
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
index dd45ccc521e788b58910614b20718933bc9b8cc7..6bb3b60a34f27cc8dfb46fbc741086b7b8d69c68 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
@@ -1,7 +1,8 @@
package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-import java.awt.*;
+import java.awt.Color;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.model.graphics.PolylineData;
/**
@@ -99,4 +100,9 @@ public class LineProperties {
this.type = type;
}
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + " w=" + width + "; c=" + new ColorParser().colorToHtml(color) + "]";
+ }
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 0716583693194aa8307fe0a56ab8cdec00a338a6..09b54e687f8cf68ca0ca4dd471b79b10f6b95fe2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -759,4 +759,32 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
assertEquals(0, new ModelComparator().compare(model, model2));
}
+ @Test
+ public void testParseBooleanReactionWithColors() throws Exception {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/reactions/boolean-colors.xml"));
+
+ Reaction r1 = model.getReactionByReactionId("re1");
+ Set<Color> colors = new HashSet<>();
+ for (AbstractNode node : r1.getNodes()) {
+ colors.add(node.getLine().getColor());
+ }
+ assertEquals("Three different colors were used to draw the reaction", 3, colors.size());
+ assertFalse("Black wasn't used in reaction coloring", colors.contains(Color.BLACK));
+ }
+
+ @Test
+ public void testExportBooleanReactioWithColors() throws Exception {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/reactions/boolean-colors.xml"));
+
+ model.setName(null);
+ assertNotNull(model);
+ String str = parser.model2String(model);
+ Model model2 = parser.createModel(
+ new ConverterParams().inputStream(new ByteArrayInputStream(str.getBytes(StandardCharsets.UTF_8))));
+ assertEquals(0, new ModelComparator().compare(model, model2));
+ }
+
+
}
diff --git a/converter-CellDesigner/testFiles/reactions/boolean-colors.xml b/converter-CellDesigner/testFiles/reactions/boolean-colors.xml
new file mode 100644
index 0000000000000000000000000000000000000000..23a16b92ed511048ee95d816b9a1eea92fd66995
--- /dev/null
+++ b/converter-CellDesigner/testFiles/reactions/boolean-colors.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="86.0" y="110.0" 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="91.0" y="220.0" 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="371.0" y="157.0" 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="s2" alias="sa2"/>
+<celldesigner:baseReactant species="s1" alias="sa1"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct"/>
+<celldesigner:editPoints>264.66666666666663,177.0</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ffff00ff"/>
+<celldesigner:listOfGateMember>
+<celldesigner:GateMember type="BOOLEAN_LOGIC_GATE_AND" aliases="sa2,sa1" modificationType="REDUCED_TRIGGER" targetLineIndex="-1,-1" editPoints="264.66666666666663,177.0">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ffff00ff"/>
+</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="ff00cc33"/>
+</celldesigner:GateMember>
+<celldesigner:GateMember type="REDUCED_TRIGGER" aliases="sa1" targetLineIndex="-1,0">
+<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="ffff9999"/>
+</celldesigner:GateMember>
+</celldesigner:listOfGateMember>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</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>
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
index e5785c8222c11297e494e44e4032a0d5c8f8a534..925e6e2566904679644adde76b72cf9c0bc497a4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
@@ -117,6 +117,8 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
* where the rectangle should be drawn
*/
protected void drawRectangleData(final PolylineData line, final ReactionRect insideType, final Graphics2D graphics) {
+ Color color = graphics.getColor();
+ graphics.setColor(line.getColor());
Point2D startPoint = line.getPoints().get(line.getPoints().size() / 2 - 1);
Point2D endPoint = line.getPoints().get(line.getPoints().size() / 2);
@@ -125,11 +127,11 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
0.5 - RECT_SIZE / (2 * startPoint.distance(endPoint)));
Point2D rectEndPoint = pointTransformation.getPointOnLine(startPoint, endPoint,
0.5 + RECT_SIZE / (2 * startPoint.distance(endPoint)));
- PolylineData preRectangleLine = new PolylineData();
+ PolylineData preRectangleLine = line.getSubline(0, 0);
preRectangleLine.addPoint(startPoint);
preRectangleLine.addPoint(rectStartPoint);
- PolylineData postRectangleLine = new PolylineData();
+ PolylineData postRectangleLine = line.getSubline(0, 0);
postRectangleLine.addPoint(rectEndPoint);
postRectangleLine.addPoint(endPoint);
@@ -171,10 +173,9 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
// rectangle)
graphics.rotate(angle, pointX, pointY);
// fill rectangle
- Color color = graphics.getColor();
graphics.setColor(Color.white);
graphics.fill(rect);
- graphics.setColor(color);
+ graphics.setColor(line.getColor());
// draw rectangle border
graphics.draw(rect);
@@ -203,12 +204,12 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
}
+ graphics.setColor(color);
}
@Override
protected void drawImpl(final Reaction reaction, final Graphics2D graphics, final ConverterParams params) {
Color color = graphics.getColor();
- graphics.setColor(reaction.getReactants().get(0).getLine().getColor());
// first reactants
for (Reactant reactant : reaction.getReactants()) {
if (isVisible(reactant, params)) {
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 08b779a2dff81a5ec1bff34557ab7f8fe198dfe5..145e36e21ba025019f5d521ee7215783aa88f87d 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
@@ -2,13 +2,12 @@ package lcsb.mapviewer.converter.model.sbml;
import static org.junit.Assert.*;
-import java.awt.*;
+import java.awt.Color;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
import java.lang.reflect.Modifier;
import java.util.*;
-import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -22,6 +21,8 @@ import lcsb.mapviewer.common.comparator.LineComparator;
import lcsb.mapviewer.common.comparator.ListComparator;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.graphics.PolylineDataComparator;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.model.map.reaction.*;
@@ -572,11 +573,17 @@ public class SbmlExporterTest extends SbmlTestFunctions {
.createModel(new ConverterParams().filename("testFiles/cell_designer_problems/boolean_logic_gate.xml"));
Model model = getModelAfterSerializing(originalModel);
- new CellDesignerXmlParser().model2String(model);
- List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
- List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
+ List<PolylineData> lines1 = new ArrayList<>();
+ List<PolylineData> lines2 = new ArrayList<>();
- ListComparator<Line2D> comparator = new ListComparator<>(new LineComparator(Configuration.EPSILON));
+ for (ReactionNode node : originalModel.getReactions().iterator().next().getReactionNodes()) {
+ lines1.add(node.getLine());
+ }
+ for (ReactionNode node : model.getReactions().iterator().next().getReactionNodes()) {
+ lines2.add(node.getLine());
+ }
+
+ ListComparator<PolylineData> comparator = new ListComparator<>(new PolylineDataComparator(Configuration.EPSILON));
assertEquals(0, comparator.compare(lines1, lines2));
}