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";
}