end point for additional reactants is computed based on the new data model

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java

 package lcsb.mapviewer.converter.model.celldesigner.reaction;
 
-import java.awt.geom.Line2D;
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -11,7 +10,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 
@@ -1157,6 +1157,11 @@ public class ReactionFromXml {
     reactant.setLine(reactantLine);
     product.setLine(productLine);
 
+    PolylineData reactionLine = new PolylineData();
+    reactionLine.addPoint(reactantLine.getEndPoint());
+    reactionLine.addPoint(productLine.getBeginPoint());
+    reaction.setLine(reactionLine);
+
     ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
     reactantLine.setType(rld.getLineType());
     productLine.setType(rld.getLineType());
@@ -1310,14 +1315,7 @@ public class ReactionFromXml {
     ArrowTypeData atd = new ArrowTypeData();
     atd.setArrowType(ArrowType.NONE);
 
-    Point2D endPoint;
-
-    Line2D centerLine = reaction.getCenterLine();
-
-    double dx = centerLine.getX2() - centerLine.getX1();
-    double dy = centerLine.getY2() - centerLine.getY1();
-    double coef = REACTANT_END_RATIO;
-    endPoint = new Point2D.Double(centerLine.getX1() + dx * coef, centerLine.getY1() + dy * coef);
+    Point2D endPoint = getPointForAdditionalNode(reaction, REACTANT_END_RATIO);
 
     PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(additionalPoint, endPoint, points);
 
@@ -1329,6 +1327,45 @@ public class ReactionFromXml {
     return result;
   }
 
+  /**
+   * Returns end point for additional reactants/products.
+   * 
+   * @param reaction
+   *          reaction for which we need to compute end point
+   * @param coef
+   *          coefficient determining location of the reactant product end point.
+   *          It should be one of hard-coded values: {@link #REACTANT_END_RATIO},
+   *          {@link #PRODUCT_START_RATIO}.
+   * @return
+   */
+  private Point2D getPointForAdditionalNode(Reaction reaction, double coef) {
+    Point2D endPoint;
+
+    // central line points
+    Point2D p1 = reaction.getReactants().get(0).getLine().getPoints()
+        .get(reaction.getReactants().get(0).getLine().getPoints().size() - 2);
+    Point2D p2 = reaction.getProducts().get(0).getLine().getPoints().get(1);
+
+    Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
+    Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
+    for (NodeOperator operator : reaction.getOperators()) {
+      toExclude.addAll(operator.getInputs());
+      if (operator.isReactantOperator()) {
+        toInclude.add(operator);
+        // if we have operator in input then central line changes
+        p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+      }
+      if (operator.isProductOperator()) {
+        // if we have operator in output then central line changes
+        p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+      }
+    }
+    double dx = p2.getX() - p1.getX();
+    double dy = p2.getY() - p1.getY();
+    endPoint = new Point2D.Double(p1.getX() + dx * coef, p1.getY() + dy * coef);
+    return endPoint;
+  }
+
   /**
    * Parses xml node with productLink nodes and creates products in the reaction.
    * 
@@ -1413,32 +1450,7 @@ public class ReactionFromXml {
     ArrowTypeData atd = new ArrowTypeData();
     atd.setArrowType(ArrowType.NONE);
 
-    Point2D endPoint;
-
-    // central line points
-    Point2D p1 = reaction.getReactants().get(0).getLine().getPoints()
-        .get(reaction.getReactants().get(0).getLine().getPoints().size() - 2);
-    Point2D p2 = reaction.getProducts().get(0).getLine().getPoints().get(1);
-
-    Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
-    Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
-    for (NodeOperator operator : reaction.getOperators()) {
-      toExclude.addAll(operator.getInputs());
-      if (operator.isReactantOperator()) {
-        toInclude.add(operator);
-        // if we have operator in input then central line changes
-        p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
-      }
-      if (operator.isProductOperator()) {
-        // if we have operator in output then central line changes
-        p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
-      }
-    }
-
-    double dx = p2.getX() - p1.getX();
-    double dy = p2.getY() - p1.getY();
-    double coef = PRODUCT_START_RATIO;
-    endPoint = new Point2D.Double(p1.getX() + dx * coef, p1.getY() + dy * coef);
+    Point2D endPoint = getPointForAdditionalNode(reaction, PRODUCT_START_RATIO);
 
     PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(endPoint, additionalPoint, points);
     additionalPoint = reactantConverter.getAnchorPointCoordinates(element, anchor, polyline.reverse());

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java

@@ -29,6 +29,7 @@ import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
 import lcsb.mapviewer.model.map.reaction.AndOperator;
 import lcsb.mapviewer.model.map.reaction.AssociationOperator;
 import lcsb.mapviewer.model.map.reaction.DissociationOperator;
@@ -161,28 +162,6 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     }
   }
 
-  @Test
-  public void testCenterLineInSimpleReaction() throws Exception {
-    Model model;
-    try {
-      model = getModelForFile("testFiles/reactions/transition.xml");
-      assertEquals(1, model.getReactions().size());
-      Reaction reaction = model.getReactions().iterator().next();
-      Reactant reactant = reaction.getReactants().get(0);
-
-      Product product = reaction.getProducts().get(0);
-
-      // center of the line should be different than edge points of
-      // reactant/product description
-      assertFalse(reaction.getCenterLine().getP1().distance(reactant.getLine().getEndPoint()) < 1e-6);
-      assertFalse(reaction.getCenterLine().getP2().distance(product.getLine().getBeginPoint()) < 1e-6);
-
-    } catch (Exception e) {
-      e.printStackTrace();
-      throw e;
-    }
-  }
-
   @Test
   public void testTransition2() throws Exception {
     Model model;
@@ -1374,7 +1353,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
 
       List<Line2D> lines1 = reaction1.getLines();
       List<Line2D> lines2 = reaction2.getLines();
-
+      
       for (int i = 0; i < lines1.size(); i++) {
         assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
         assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
@@ -1383,7 +1362,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
       }
       assertEquals(reaction1.getClass(), reaction2.getClass());
     } catch (Exception e) {
-      logger.error(e.getMessage(), e);
+      e.printStackTrace();
       throw e;
     }
   }
@@ -1824,7 +1803,7 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
     try {
       model = getModelForFile("testFiles/problematic/reaction_drawing_problem.xml");
       Reaction reaction = model.getReactionByReactionId("re1");
-      assertEquals(0, reaction.getCenterPoint().distance(new Point2D.Double(258.5, 145.0)), EPSILON);
+      assertNotNull(reaction.getLine());
     } catch (Exception e) {
       e.printStackTrace();
       throw e;