code: private void connectArcToPort(SbgnPDNode lPort, Port vPort)
      {
          //Iterate over the edges of l level port
          for  (Object e: (lPort.getEdges()))
          {
              //Ignore rigid edges
              if(((LEdge)e).type.equals("rigid edge"))
                  continue;
  
              //Determine the if vPort is source or target
              Arc arc = idToArcs.get(((LEdge)e).label);
              if( lPort.label.equals(((LEdge)e).getSource().label ))
              {
                  arc.setSource(vPort);
              }
              else if ( lPort.label.equals(((LEdge)e).getTarget().label ) )
              {
                  arc.setTarget(vPort);
              }
          }
      }
docs: This method connects the existing arcs to the newly created
  ports which are created by ChiLay and SBGNPD Layout.
  @param lPort l level port object.
  @param vPort v level port object.