code: private void removePortsFromArcs(List<Arc> arcs)
      {
          for(Arc arc: arcs )
          {
              // If source is port, first clear port indicators else retrieve it from hashmaps
              if (arc.getSource() instanceof Port )
              {
                  Glyph source = portIDToOwnerGlyph.get(((Port)arc.getSource()).getId());
                  arc.setSource(source);
              }
  
              // If target is port, first clear port indicators else retrieve it from hashmaps
              if (arc.getTarget() instanceof Port)
              {
                  Glyph target = portIDToOwnerGlyph.get(((Port)arc.getTarget()).getId());
                  arc.setTarget(target);
              }
          }
      }
docs: This method replaces ports of arc objects with their owners.
  @param arcs Arc list of SBGN model