private void populateParentChildMap(Map<String, SOTerm> soTerms, String parentSOTermName) {
String parentClsName = TypeUtil.javaiseClassName(parentSOTermName);
ClassDescriptor cd = model.getClassDescriptorByName(parentClsName);
if (cd == null) {
LOG.error("couldn't find class in model:" + parentClsName);
return;
}
Class<?> parentClass = cd.getType();
// all collections for gene
Map<String, Class<?>> childCollections = model.getCollectionsForClass(parentClass);
Set<CollectionHolder> children = new HashSet<CollectionHolder>();
// for each collection, see if this is a child class
for (Map.Entry<String, Class<?>> entry : childCollections.entrySet()) {
String childCollectionName = entry.getKey();
String childClassName = entry.getValue().getSimpleName();
// TODO use same method as in the oboparser
// is this a child collection? e.g. transcript
SOTerm soterm = soTerms.get(childClassName.toLowerCase());
if (soterm == null) {
// for testing
continue;
}
// is gene in transcript parents collection
for (OntologyTerm parent : soterm.getParents()) {
if (parent.getName().equals(parentSOTermName)) {
CollectionHolder h = new CollectionHolder(childClassName, childCollectionName);
children.add(h);
}
}
}
if (children.size() > 0) {
parentToChildren.put(parentSOTermName, children);
}
}
