From 67255046d48967e37ee55f76c8170e4e8e95b4bb Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 18 Sep 2019 16:39:55 +0200
Subject: [PATCH] export of reaction properly align lines that are not attached
to elements
---
CHANGELOG | 2 +
.../celldesigner/reaction/ReactionToXml.java | 10 ++++
.../CellDesignerTestFunctions.java | 2 +-
.../CellDesignerXmlParserTest.java | 51 +++++++++++++++++++
.../reaction/ReactionToXmlTest.java | 32 +++++++++---
5 files changed, 90 insertions(+), 7 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index fe39b62248..81656787ed 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -19,6 +19,8 @@ minerva (14.0.0~beta.2) unstable; urgency=low
* Bug fix: hide glyphs tab when necessary (#949)
* Bug fix: user with write access but without can_create_privileges cannot
create data overlay (#939)
+ * Bug fix: export to CD could misalign reaction lines that were imported from
+ format that didn't require reaction line to be attached to the species (#933)
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 16 Sep 2019 21:00:00 +0200
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 543b16a5bd..c871cbb767 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
@@ -963,6 +963,7 @@ public class ReactionToXml {
String getEditPointsXmlStringForSimpleReaction(Reaction reaction) {
Product product = reaction.getProducts().get(0);
Reactant reactant = reaction.getReactants().get(0);
+
List<Point2D> points = new ArrayList<>();
for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
points.add(reactant.getLine().getPoints().get(i));
@@ -986,9 +987,18 @@ public class ReactionToXml {
}
PolylineData pd = new PolylineData(points);
+ pd.setPoint(0, getAnchorPoint(reactant.getElement(), reactant.getLine().getBeginPoint()));
+ pd.setPoint(pd.getPoints().size() - 1, getAnchorPoint(product.getElement(), productLine.getEndPoint()));
return getEditPointsXmlStringForLine(new PolylineData[] { pd }, centerPosition);
}
+ private Point2D getAnchorPoint(Element element, Point2D originalPoint) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, sbgn);
+
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(element, originalPoint);
+ return converter.getPointCoordinates(element, anchor);
+ }
+
/**
* Creates valid xml node with connectScheme for the reaction.
*
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
index 790087f132..d55b3d967e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
@@ -230,7 +230,7 @@ public abstract class CellDesignerTestFunctions {
throws InconsistentModelException, UnsupportedEncodingException, InvalidInputDataExecption {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
String xmlString = parser.model2String(model);
- logger.debug(xmlString);
+// logger.debug(xmlString);
InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
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 63e4b455a0..be028cc32e 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
@@ -799,5 +799,56 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
assertEquals("Whole reaction should use the same reaction type", 1, reactionTypes.size());
}
+ @Test
+ public void testExportReactoinWithLinesNotAttachedToSpecies() throws Exception {
+ Model model = new ModelFullIndexed(null);
+ model.setIdModel("as");
+ model.setWidth(1000);
+ model.setHeight(1000);
+
+ Species protein = new SimpleMolecule("id1");
+ protein.setX(383);
+ protein.setY(584);
+ protein.setWidth(140);
+ protein.setHeight(60);
+ model.addElement(protein);
+
+ Species protein2 = new SimpleMolecule("id2");
+ protein2.setX(351);
+ protein2.setY(697);
+ protein2.setWidth(100);
+ protein2.setHeight(60);
+ model.addElement(protein2);
+
+ Reaction reaction = new StateTransitionReaction();
+ reaction.setIdReaction("re1");
+ reaction.setLine(new PolylineData(new Point2D.Double(401.0, 673.0), new Point2D.Double(401.0, 673.0)));
+
+ Reactant reactant = new Reactant(protein);
+ reactant.setLine(new PolylineData(Arrays.asList(
+ new Point2D.Double(420.0, 644.0),
+ new Point2D.Double(420.0, 654.0),
+ new Point2D.Double(401.0, 654.0),
+ new Point2D.Double(401.0, 665.0))));
+ reaction.addReactant(reactant);
+ model.addReaction(reaction);
+
+ Product product = new Product(protein2);
+ product.setLine(new PolylineData(new Point2D.Double(401.0, 673.0), new Point2D.Double(401.0, 697.0)));
+ reaction.addProduct(product);
+
+ Model model2 = serializeModel(model);
+
+ Reaction reaction2 = model2.getReactionByReactionId("re1");
+
+ Reactant newReactant = reaction2.getReactants().get(0);
+
+ // center part of the line shouldn't change - edges should be aligned to touch
+ // species
+ assertEquals(0, newReactant.getLine().getPoints().get(1).distance(reactant.getLine().getPoints().get(1)),
+ Configuration.EPSILON);
+ assertEquals(0, newReactant.getLine().getPoints().get(2).distance(reactant.getLine().getPoints().get(2)),
+ Configuration.EPSILON);
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
index 3b13bce3e6..a1fddefcdb 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
@@ -47,6 +47,9 @@ public class ReactionToXmlTest extends CellDesignerTestFunctions {
Model model = new ModelFullIndexed(null);
Species protein1 = new GenericProtein("2");
Species protein2 = new GenericProtein("3");
+ protein2.setX(100);
+ protein2.setY(100);
+ Species protein3 = new GenericProtein("4");
model.addElement(protein1);
model.addElement(protein2);
@@ -61,10 +64,10 @@ public class ReactionToXmlTest extends CellDesignerTestFunctions {
reaction.addReactant(reactant);
reaction.addProduct(product);
- Modifier modifier = new Catalysis(protein1);
+ Modifier modifier = new Catalysis(protein3);
modifier.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(30, 0)));
- Modifier modifier2 = new Catalysis(protein1);
+ Modifier modifier2 = new Catalysis(protein3);
List<Point2D> points = new ArrayList<>();
points.add(new Point2D.Double(0, 0));
points.add(new Point2D.Double(30, 30));
@@ -101,6 +104,7 @@ public class ReactionToXmlTest extends CellDesignerTestFunctions {
Model model = new ModelFullIndexed(null);
Species protein1 = new GenericProtein("2");
+ protein1.setX(100);
Species protein2 = new GenericProtein("3");
model.addElement(protein1);
@@ -249,10 +253,18 @@ public class ReactionToXmlTest extends CellDesignerTestFunctions {
@Test
public void testGetEditPointsXmlStringForSimpleReaction() {
Reaction r = new TriggerReaction();
- Product product = new Product();
+ Species productSpecies = new GenericProtein("id1");
+ productSpecies.setX(20);
+ productSpecies.setY(20);
+ productSpecies.setWidth(20);
+ productSpecies.setHeight(20);
+ Product product = new Product(productSpecies);
PolylineData productLine = new PolylineData(new Point2D.Double(10, 10), new Point2D.Double(20, 20));
product.setLine(productLine);
- Reactant reactant = new Reactant();
+ Species reactantSpecies = new GenericProtein("id1");
+ reactantSpecies.setWidth(10);
+ reactantSpecies.setHeight(10);
+ Reactant reactant = new Reactant(reactantSpecies);
PolylineData reactantLine = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
reactant.setLine(reactantLine);
r.addProduct(product);
@@ -264,10 +276,18 @@ public class ReactionToXmlTest extends CellDesignerTestFunctions {
@Test
public void testGetEditPointsXmlStringForSimpleReactionWhenNotImportedFromCD() {
Reaction r = new TriggerReaction();
- Product product = new Product();
+ Species productSpecies = new GenericProtein("id1");
+ productSpecies.setX(20);
+ productSpecies.setY(20);
+ productSpecies.setWidth(20);
+ productSpecies.setHeight(20);
+ Product product = new Product(productSpecies);
PolylineData productLine = new PolylineData(new Point2D.Double(10, 10), new Point2D.Double(20, 10));
product.setLine(productLine);
- Reactant reactant = new Reactant();
+ Species reactantSpecies = new GenericProtein("id1");
+ reactantSpecies.setWidth(10);
+ reactantSpecies.setHeight(10);
+ Reactant reactant = new Reactant(reactantSpecies);
PolylineData reactantLine = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
reactant.setLine(reactantLine);
r.addProduct(product);
--
GitLab