export of reaction properly align lines that are not attached to elements

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
 

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.
    * 

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));

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);
+  }
 
 }

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);