public Component getListCellRendererComponent(
     JList list, Object value, int index, boolean isSelected, boolean hasFocus) {
   Component comp =
       super.getListCellRendererComponent(list, value, index, isSelected, hasFocus());
   if (!(value instanceof GKInstance)) return comp;
   String text = null;
   GKInstance instance = (GKInstance) value;
   text = instance.getDisplayName();
   if (text == null || (text != null && text.length() == 0)) {
     text = instance.getExtendedDisplayName();
   }
   String type = (String) typeMap.get(instance);
   if (type == DELETE_IN_DB_KEY) setIcon(deleteInDBIcon);
   else if (type == DELETE_KEY) setIcon(deleteIcon);
   else if (type == NEW_KEY) setIcon(newInstanceIcon);
   else if (type == NEW_CHANGE_IN_DB_KEY) setIcon(dbChangeIcon);
   else if (type == NEW_CHANGE_IN_LOCAL_KEY) setIcon(newChangeIcon);
   else if (type == CONFLICT_CHANGE_KEY || type == LOCAL_HAS_MORE_IE_KEY) setIcon(conflictIcon);
   else setIcon(icon);
   if (text == null) {
     text = "";
     setIcon(null);
   }
   setText(text);
   if (text.length() > 0) setToolTipText(text);
   else setToolTipText(null);
   return comp;
 }
 /**
  * Overlay a single disease reaction onto a normal reaction.
  *
  * @param normalReaction
  * @param diseaseReaction
  * @param overlaidObjects
  */
 private void overlayDiseaseReaction(HyperEdge normalReaction, GKInstance diseaseReaction)
     throws Exception {
   // Make a copy of the HyperEdge for future process that is related to Vertex and JSON generation
   HyperEdge reactionCopy = normalReaction.shallowCopy();
   reactionCopy.setReactomeId(diseaseReaction.getDBID());
   reactionCopy.setDisplayName(diseaseReaction.getDisplayName());
   reactionCopy.setLineColor(DefaultRenderConstants.DEFAULT_DISEASE_BACKGROUND);
   displayedObject.addComponent(reactionCopy);
   overlaidObjects.add(reactionCopy);
   // Want to handle inputs, outputs and catalysts since regulators can
   // be ignored
   List<Node> nodes = new ArrayList<Node>();
   nodes.addAll(normalReaction.getInputNodes());
   nodes.addAll(normalReaction.getOutputNodes());
   nodes.addAll(normalReaction.getHelperNodes());
   // List objects not listed in the disease reaction as crossed objects
   Set<GKInstance> participants = InstanceUtilities.getReactionParticipants(diseaseReaction);
   Set<Long> diseaseIds = new HashSet<Long>();
   for (GKInstance participant : participants) {
     diseaseIds.add(participant.getDBID());
     if (participant.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasMember)) {
       List<GKInstance> list = participant.getAttributeValuesList(ReactomeJavaConstants.hasMember);
       if (list != null && list.size() > 0) {
         for (GKInstance inst : list) diseaseIds.add(inst.getDBID());
       }
     }
     if (participant.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasCandidate)) {
       List<GKInstance> list =
           participant.getAttributeValuesList(ReactomeJavaConstants.hasCandidate);
       if (list != null && list.size() > 0) {
         for (GKInstance inst : list) diseaseIds.add(inst.getDBID());
       }
     }
   }
   Set<GKInstance> lofInstances = new HashSet<GKInstance>();
   Map<Node, GKInstance> normalToDiseaseEntity =
       mapMutatedToNormalNodes(diseaseReaction, normalReaction, nodes, lofInstances);
   for (Node node : nodes) {
     if (!diseaseIds.contains(node.getReactomeId())) {
       // Check if it should be mapped to a normal entity
       GKInstance diseaseEntity = normalToDiseaseEntity.get(node);
       if (diseaseEntity == null) crossedObjects.add(node); // Just crossed out
       else {
         Node diseaseNode =
             replaceNormalNode(node, diseaseEntity, contains(diseaseEntity, lofInstances));
         if (diseaseNode == null) continue; // Just in case
         // Re-link to diseaseNode
         ConnectInfo connectInfo = reactionCopy.getConnectInfo();
         List<?> widgets = connectInfo.getConnectWidgets();
         for (Object obj : widgets) {
           ConnectWidget widget = (ConnectWidget) obj;
           if (widget.getConnectedNode() == node) widget.replaceConnectedNode(diseaseNode);
         }
       }
     } else overlaidObjects.add(node);
   }
 }
 private boolean isLOFEntity(GKInstance ef) throws Exception {
   GKInstance pe = (GKInstance) ef.getAttributeValue(ReactomeJavaConstants.physicalEntity);
   if (pe == null) return false;
   GKInstance functionalStatus =
       (GKInstance) ef.getAttributeValue(ReactomeJavaConstants.functionalStatus);
   if (functionalStatus != null) {
     String fsName = functionalStatus.getDisplayName();
     if (fsName.contains("loss_of_function") || fsName.contains("decreased_")) return true;
   }
   return false;
 }
 private void convertReactomeToGPML(GKInstance pathway, String outputFileName) throws Exception {
   Long dbID = pathway.getDBID();
   System.out.println("converting pathway #" + dbID + " " + pathway.getDisplayName() + "...");
   Document doc = r2gConverter.convertPathway(pathway);
   XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
   outputter.output(doc, new FileOutputStream(outputFileName));
   /*
   // Test loading using JDOM and validation
   SAXBuilder builder = new SAXBuilder(true);
   builder.setFeature("http://apache.org/xml/features/validation/schema", true);
   builder.setProperty("http://apache.org/xml/properties/schema/external-schemaLocation",
                       "http://genmapp.org/GPML/2008a http://svn.bigcat.unimaas.nl/pathvisio/trunk/GPML2008a.xsd");
   doc = builder.build(new File(outputFileName));
   */
 }
 private Node replaceNormalNode(
     Node normalNode, GKInstance diseaseEntity, Boolean needDashedBorder) {
   Node diseaseNode = normalToDiseaseNode.get(normalNode);
   if (diseaseNode != null) return diseaseNode;
   try {
     // If a node exists already, it should use
     for (Renderable r : diseaseComps) {
       if (diseaseEntity.getDBID().equals(r.getReactomeId()) && r instanceof Node) {
         // This is rather arbitrary: if two nodes are very close,
         // use the existing one.
         int dx = Math.abs(r.getPosition().x - normalNode.getPosition().x);
         int dy = Math.abs(r.getPosition().y - normalNode.getPosition().y);
         if (dx < 10 && dy < 10) {
           // We don't need to create a new Node if it exists already
           normalToDiseaseNode.put(normalNode, (Node) r);
           overlaidObjects.add(r); // Add it to overlaid object to cover edges
           return (Node) r;
         }
       }
     }
     diseaseNode = normalNode.getClass().newInstance();
     RenderUtility.copyRenderInfo(normalNode, diseaseNode);
     // The following should NOT be called since NodeAttachment is
     // related to disease entity only.
     // TODO: Need to support this. Currently it is not supported!!! See example
     // in PI3/AKT cancer pathway.
     // diseaseNode.setNodeAttachmentsLocally(node.getNodeAttachments());
     diseaseNode.setDisplayName(diseaseEntity.getDisplayName());
     diseaseNode.setReactomeId(diseaseEntity.getDBID());
     diseaseNode.invalidateBounds();
     diseaseNode.setRenderer(normalNode.getRenderer());
     diseaseNode.setLineColor(DefaultRenderConstants.DEFAULT_DISEASE_BACKGROUND);
     diseaseNode.setNeedDashedBorder(needDashedBorder);
     RenderUtility.hideCompartmentInNodeName(diseaseNode);
     overlaidObjects.add(diseaseNode);
     displayedObject.addComponent(diseaseNode);
     normalToDiseaseNode.put(normalNode, diseaseNode);
     return diseaseNode;
   } catch (Exception e) {
     e.printStackTrace();
   }
   return null;
 }
  private void showComparison() {
    // Find the instance that can be used for comparision. This instance
    // should be chosen from changedList or localHasUnexpInstance
    GKInstance instance = null;
    if (changedList != null) { // Check changedList first
      List selection = changedList.getSelection();
      if (selection.size() > 0) instance = (GKInstance) selection.get(0);
    }
    if (instance == null && localHasMoreIEList != null) {
      List selection = localHasMoreIEList.getSelection();
      if (selection.size() > 0) instance = (GKInstance) selection.get(0);
    }
    if (instance == null) return;
    final InstanceComparisonPane comparisonPane = new InstanceComparisonPane();
    // Fine tune comparison pane for making comparisons with
    // database
    comparisonPane.setSaveDialogHideUnusedButtons(true);
    comparisonPane.setSaveDialogSaveAsNewBtnFirst(false);
    comparisonPane.setSaveDialogSaveAsNewBtnTitle(
        "Create new local instance and put merge into that");
    comparisonPane.setSaveDialogReplaceFirstBtnTitle(
        "Overwrite existing instance with merge (recommended)");
    comparisonPane.setCloseAfterSaving(true);
    try {
      String clsName = instance.getSchemClass().getName();
      Long instanceId = instance.getDBID();
      final GKInstance localCopy = fileAdaptor.fetchInstance(clsName, instanceId);
      dbAdaptor.setUseCache(false);
      // final GKInstance dbCopy = dbAdaptor.fetchInstance(clsName, instanceId);
      // The class type might be changed locally or remotely. So not clsName should be used
      // to fetch database instance. Otherwise, null exception will be thrown. The same thing
      // is done also in creating synchronization result.
      final GKInstance dbCopy = dbAdaptor.fetchInstance(instanceId);
      dbAdaptor.setUseCache(true);
      comparisonPane.setInstances(localCopy, dbCopy);
      String title =
          "Comparing Instances \""
              + instance.getDisplayName()
              + "\" in the local and DB repositories";
      JDialog parentDialog = (JDialog) SwingUtilities.getAncestorOfClass(JDialog.class, centerPane);
      final JDialog dialog = new JDialog(parentDialog, title);
      // Try to update the list automatically
      dialog.addWindowListener(
          new WindowAdapter() {
            public void windowClosed(WindowEvent e) {
              handleMergeResult(localCopy, dbCopy, comparisonPane);
              // To prevent double calling. It is called again when parentDialog is closed.
              dialog.removeWindowListener(this);
            }
          });
      dialog.getContentPane().add(comparisonPane, BorderLayout.CENTER);
      dialog.setModal(true);
      dialog.setSize(800, 600);
      GKApplicationUtilities.center(dialog);
      dialog.setVisible(true);

      // Update synchronization dialog panels depending on user
      // choice.
      if (comparisonPane.getSaveMergeOption() == InstanceComparisonPane.SAVE_AS_NEW) {
        GKInstance merged = comparisonPane.getMerged();

        if (newList == null) {
          List list = new ArrayList();
          list.add(merged);
          newList = initInstanceListPane(list, "Instances created locally: " + list.size());
        } else newList.addInstance(merged);
      } else if (comparisonPane.getSaveMergeOption() == InstanceComparisonPane.OVERWRITE_FIRST) {
        dbAdaptor.setUseCache(false);
        GKInstance remoteCopy = dbAdaptor.fetchInstance(instance.getDBID());
        dbAdaptor.setUseCache(true);
        if (remoteCopy != null) {
          InstanceComparer comparer = new InstanceComparer();
          int reply = comparer.compare(instance, remoteCopy);
          if (reply == InstanceComparer.LOCAL_HAS_MORE_IE) {
            if (localHasMoreIEList == null) {
              List list = new ArrayList();
              list.add(instance);
              localHasMoreIEList =
                  initInstanceListPane(
                      list, "Local instances having unexpected InstanceEdits: " + list.size());
            } else localHasMoreIEList.addInstance(instance);
          } else if (reply == InstanceComparer.IS_IDENTICAL) {
            // Merge has made local and database copies
            // identical - don't need to check in anymore
            changedList.deleteInstance(instance);
          } else if (reply != InstanceComparer.NEW_CHANGE_IN_LOCAL) {
            // Merge has produced a conflict
            typeMap.put(mapCompareResultToString(reply), instance);
          } else
            // The user should now be allowed to commit this
            // instance, because it will now have changed.
            commitToDBAction.setEnabled(true);

          JOptionPane.showMessageDialog(
              parentDialog,
              "Merge successful, you will need to check the merged instance into the database.\n\n",
              "Merge OK",
              JOptionPane.INFORMATION_MESSAGE);
        }
      }

    } catch (Exception e1) {
      System.err.println("Synchronization.createDisplayMapPane(): " + e1);
      e1.printStackTrace();
      JOptionPane.showMessageDialog(
          this,
          "Error in comparing: " + instance.toString(),
          "Error in Comparing",
          JOptionPane.ERROR_MESSAGE);
    }
  }
 /**
  * A simple helper method to get a file name for gpml output.
  *
  * @param pathway
  * @return
  */
 private String getFileName(GKInstance pathway) {
   return pathway.getDisplayName().replaceAll("[^0-9A-Za-z()_-]+", " ") + ".gpml";
 }