@Override
public void addInstance(GKInstance instance) {
SchemaClass cls = instance.getSchemClass();
if (!cls.isa(ReactomeJavaConstants.PhysicalEntity) || cls.isa(ReactomeJavaConstants.Complex))
return; // Only display non-complex PE in this class.
DefaultMutableTreeNode clsNode = getClassNode(cls);
DefaultMutableTreeNode instanceNode = new DefaultMutableTreeNode(instance);
insertInstanceNodeAlphabetically(clsNode, instanceNode);
}
/**
* This method is used to dump all human pathway diagrams into a specified directory.
*
* @param dir
* @throws Exception
*/
public void dumpHumanPathwayDiagrams(File dir) throws Exception {
Collection<?> diagrams = adaptor.fetchInstancesByClass(ReactomeJavaConstants.PathwayDiagram);
SchemaClass cls = adaptor.fetchSchema().getClassByName(ReactomeJavaConstants.PathwayDiagram);
SchemaAttribute att = cls.getAttribute(ReactomeJavaConstants.representedPathway);
adaptor.loadInstanceAttributeValues(diagrams, att);
// Group all human pathways
for (Iterator<?> it = diagrams.iterator(); it.hasNext(); ) {
GKInstance diagram = (GKInstance) it.next();
GKInstance pathway =
(GKInstance) diagram.getAttributeValue(ReactomeJavaConstants.representedPathway);
GKInstance species = (GKInstance) pathway.getAttributeValue(ReactomeJavaConstants.species);
if (species == null) continue;
if (species.getDBID().equals(48887L)) {
String fileName = getFileName(pathway);
File file = new File(dir, fileName);
convertReactomeToGPML(pathway, file.getAbsolutePath());
}
}
}
/**
* A helper method to create a TreeNode and insert it under the root for the specified SchemaClass
* object.
*
* @param cls
* @return
*/
private DefaultMutableTreeNode createClassNode(SchemaClass cls) {
SchemaClass displayedCls = getDisplayedPESubclass(cls);
DefaultMutableTreeNode clsNode = new DefaultMutableTreeNode(displayedCls);
// Need to insert to the root
DefaultTreeModel model = (DefaultTreeModel) tree.getModel();
DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot();
// Find where it should be inserted
int index = 0;
if (root.getChildCount() > 0) {
for (int i = 0; i < root.getChildCount(); i++) {
DefaultMutableTreeNode node = (DefaultMutableTreeNode) root.getChildAt(i);
SchemaClass nodeCls = (SchemaClass) node.getUserObject();
if (nodeCls.getName().compareTo(displayedCls.getName()) > 0) {
index = i;
break;
}
}
}
model.insertNodeInto(clsNode, root, index);
return clsNode;
}
private SchemaClass getDisplayedPESubclass(SchemaClass cls) {
SchemaClass displayedCls = cls;
// Only the first level of PE is displayed. Need to map it to one of
// these subclasses
XMLFileAdaptor fileAdaptor = PersistenceManager.getManager().getActiveFileAdaptor();
GKSchemaClass pe =
(GKSchemaClass)
fileAdaptor.getSchema().getClassByName(ReactomeJavaConstants.PhysicalEntity);
for (Iterator it = pe.getSubClasses().iterator(); it.hasNext(); ) {
GKSchemaClass sub = (GKSchemaClass) it.next();
if (cls.isa(sub)) {
displayedCls = sub;
break;
}
}
return displayedCls;
}