when providing automatic layout set center line properly

model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java

@@ -240,16 +240,21 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
     Element productElement = reaction.getProducts().get(0).getElement();
     Element reactantElement = reaction.getReactants().get(0).getElement();
 
-    Point2D middle = getMiddlePoint(productElement.getCenter(), reactantElement.getCenter());
+    Point2D centerLineStart = getMiddlePoint(reactantElement.getCenter(), productElement.getCenter(), 0.4);
+    Point2D centerLineEnd = getMiddlePoint(reactantElement.getCenter(), productElement.getCenter(), 0.6);
+    Point2D middle = getMiddlePoint(reactantElement.getCenter(), productElement.getCenter(), 0.5);
 
     // for self reactions
     if (productElement.equals(reactantElement)) {
-      middle.setLocation(middle.getX(), middle.getY() + 50);
+      centerLineStart.setLocation(centerLineStart.getX(), centerLineStart.getY() + 50);
+      centerLineEnd.setLocation(centerLineStart.getX(), centerLineEnd.getY() + 50);
     }
 
-    modifyProducts(reaction, middle);
-    modifyReactants(reaction, middle);
+    modifyReactants(reaction, centerLineStart);
+    modifyProducts(reaction, centerLineEnd);
     modifyModifiers(reaction, middle);
+    
+    reaction.setLine(new PolylineData(centerLineStart, centerLineEnd));
 
     if (super.isAddReactionPrefixes()) {
       super.getModel().removeReaction(reaction);
@@ -258,7 +263,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
     }
   }
 
-  private Point2D.Double getMiddlePoint(Point2D middle, Point2D productPoint) {
+  private Point2D.Double getMiddlePoint(Point2D middle, Point2D productPoint, double coef) {
     return new Point2D.Double((productPoint.getX() + middle.getX()) / 2, (productPoint.getY() + middle.getY()) / 2);
   }
 
@@ -271,7 +276,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
         operator = new AndOperator();
       }
       Point2D productPoint = reaction.getReactants().get(0).getElement().getCenter();
-      Point2D operatorPoint = getMiddlePoint(middle, productPoint);
+      Point2D operatorPoint = getMiddlePoint(middle, productPoint, 0.5);
       operator.setLine(new PolylineData(operatorPoint, middle));
       reaction.addNode(operator);
       middle = operatorPoint;
@@ -310,7 +315,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
         operator = new SplitOperator();
       }
       Point2D productPoint = reaction.getProducts().get(0).getElement().getCenter();
-      Point2D operatorPoint = getMiddlePoint(middle, productPoint);
+      Point2D operatorPoint = getMiddlePoint(middle, productPoint, 0.5);
       operator.setLine(new PolylineData(operatorPoint, middle));
       reaction.addNode(operator);
       middle = operatorPoint;

model-command/src/test/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommandTest.java

@@ -16,6 +16,7 @@ import java.util.Set;
 
 import org.junit.Test;
 
+import lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.geometry.DoubleDimension;
 import lcsb.mapviewer.model.map.BioEntity;
@@ -23,6 +24,10 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.GenericProtein;
@@ -375,4 +380,35 @@ public class ApplySimpleLayoutModelCommandTest {
         Math.abs(rect.getMaxX() - resultPoint.getX()) < Configuration.EPSILON);
   }
 
+  @Test
+  public void testApplyLayoutForReaction() throws CommandExecutionException {
+    try {
+      Model model = new ModelFullIndexed(null);
+      Protein protein = createProtein();
+      model.addElement(protein);
+      Protein protein2 = createProtein();
+      model.addElement(protein2);
+
+      Reaction reaction = createReaction(protein, protein2);
+      model.addReaction(reaction);
+
+      ApplySimpleLayoutModelCommand layoutModelCommand = new ApplySimpleLayoutModelCommand(model);
+      layoutModelCommand.execute();
+      assertNotNull("Reactant doesn't have line", reaction.getReactants().get(0).getLine());
+      assertNotNull("Product doesn't have line", reaction.getProducts().get(0).getLine());
+      assertNotNull("Reaction doesn't have line", reaction.getLine());
+    } catch (CommandExecutionException e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  private Reaction createReaction(Protein protein, Protein protein2) {
+    Reaction reaction = new TransportReaction();
+    reaction.addReactant(new Reactant(protein));
+    reaction.addProduct(new Product(protein2));
+    return reaction;
+  }
+
 }