import from wikipathways provides center line

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java

@@ -20,8 +20,10 @@ import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
 import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
@@ -123,6 +125,8 @@ public class ModelContructor {
    */
   private BiopaxParser biopaxParser = new BiopaxParser();
 
+  private PointTransformation pt = new PointTransformation();
+
   /**
    * List of {@link Shape#shape shapes} that are not supported to be part of a
    * {@link Complex complex}.
@@ -767,6 +771,8 @@ public class ModelContructor {
       }
     }
 
+    createReactionCenterLine(reaction);
+
     ModifierTypeUtils mtu = new ModifierTypeUtils();
     for (Modifier m : reaction.getModifiers()) {
       m.getLine().setEndPoint(m.getLine().getPoints().get(m.getLine().getPoints().size() - 2));
@@ -776,6 +782,32 @@ public class ModelContructor {
     return reaction;
   }
 
+  private void createReactionCenterLine(Reaction reaction) {
+    AbstractNode input = reaction.getReactants().get(0);
+    AbstractNode output = reaction.getProducts().get(0);
+
+    for (NodeOperator operator : reaction.getOperators()) {
+      if (operator.isReactantOperator()) {
+        input = operator;
+      } else if (operator.isProductOperator()) {
+        output = operator;
+      }
+    }
+    PolylineData line = new PolylineData();
+
+    input.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+    line.addPoint(pt.copyPoint(input.getLine().getEndPoint()));
+
+    if (output instanceof NodeOperator) {
+      output.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+      line.addPoint(pt.copyPoint(output.getLine().getEndPoint()));
+    } else {
+      output.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+      line.addPoint(pt.copyPoint(output.getLine().getBeginPoint()));
+    }
+    reaction.setLine(line);
+  }
+
   /**
    * Creates {@link Reactant} from gpml edge.
    *