when creating layout for self reaction create a line that is not empty

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

@@ -12,7 +12,8 @@ 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 lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.common.Configuration;
@@ -58,7 +59,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
   private static final int SPECIES_WIDTH = 90;
   private static final int SPECIES_HEIGHT = 30;
   private static final double COMPLEX_PADDING = 5;
-  
+
   private PointTransformation pt = new PointTransformation();
 
   public ApplySimpleLayoutModelCommand(Model model, Collection<BioEntity> bioEntities, Double minX, Double minY,
@@ -247,17 +248,23 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
     Point2D centerLineEnd = pt.getPointOnLine(reactantElement.getCenter(), productElement.getCenter(), 0.6);
     Point2D middle = pt.getPointOnLine(reactantElement.getCenter(), productElement.getCenter(), 0.5);
 
+    PolylineData centerLine = new PolylineData();
     // for self reactions
-    if (productElement.equals(reactantElement)) {
+    if (centerLineStart.equals(centerLineEnd)) {
+      centerLine.addPoint(pt.copyPoint(centerLineStart));
       centerLineStart.setLocation(centerLineStart.getX(), centerLineStart.getY() + 50);
+      centerLine.addPoint(pt.copyPoint(centerLineStart));
+      centerLine.addPoint(pt.copyPoint(centerLineEnd));
       centerLineEnd.setLocation(centerLineStart.getX(), centerLineEnd.getY() + 50);
+    } else {
+      centerLine.addPoint(pt.copyPoint(centerLineStart));
+      centerLine.addPoint(pt.copyPoint(centerLineEnd));
     }
+    reaction.setLine(centerLine);
 
     modifyReactants(reaction, centerLineStart);
     modifyProducts(reaction, centerLineEnd);
     modifyModifiers(reaction, middle);
-    
-    reaction.setLine(new PolylineData(centerLineStart, centerLineEnd));
 
     if (super.isAddReactionPrefixes()) {
       super.getModel().removeReaction(reaction);
@@ -284,7 +291,6 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
       PolylineData line = new PolylineData();
       line.addPoint(reactant.getElement().getCenter());
       line.addPoint(middle);
-      line.addPoint(middle);
       if (reaction.isReversible()) {
         line.getBeginAtd().setArrowType(ArrowType.FULL);
       }