@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);
}
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;
}