@Override
public void mapClass(
OWLIndividual bpInstance,
BioPAXFactory bpFactory,
XMLFileAdaptor fileAdaptor,
Map<OWLIndividual, GKInstance> bpToRInstancesMap)
throws Exception {
RDFSClass cls = bpInstance.getRDFType();
if (cls != bpFactory.getpathwayClass()) return; // this method will work for pathway only
GKInstance instance = fileAdaptor.createNewInstance(ReactomeJavaConstants.Pathway);
bpToRInstancesMap.put(bpInstance, instance);
}
private void getPathwayComponents(
OWLIndividual bpInstance,
BioPAXFactory bpFactory,
GKInstance rPathway,
Map<OWLIndividual, GKInstance> bpToRInstanceMap)
throws Exception {
OWLProperty prop = bpFactory.getOWLProperty(BioPAXJavaConstants.PATHWAY_COMPONENTS);
Collection bpComponents = bpInstance.getPropertyValues(prop);
if (bpComponents == null || bpComponents.size() == 0) return;
OWLIndividual bpComp;
RDFSClass bpCompType;
GKInstance rComp;
// Used to check value
// Try to make it work for the new schema (6/13/07 - wgm)
SchemaAttribute hasComponentAtt = null;
if (rPathway.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasComponent))
hasComponentAtt = rPathway.getSchemClass().getAttribute(ReactomeJavaConstants.hasComponent);
else if (rPathway.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasEvent))
hasComponentAtt = rPathway.getSchemClass().getAttribute(ReactomeJavaConstants.hasEvent);
if (hasComponentAtt == null) return;
// Do a sort based on NEXT_STEP
for (Iterator it = bpComponents.iterator(); it.hasNext(); ) {
Object obj = it.next();
if (!(obj instanceof OWLIndividual)) {
System.out.println(obj + " is not an OWLIndividual object!");
throw new IllegalStateException(
"Object in the pathway component list is not an OWLIndividual object: " + obj);
}
bpComp = (OWLIndividual) obj;
bpCompType = bpComp.getRDFType();
if (bpCompType == bpFactory.getpathwayStepClass()) {
// Grep the wrapped interaction or pathway instances
prop = bpFactory.getOWLProperty(BioPAXJavaConstants.STEP_INTERACTIONS);
Collection stepInteractions = bpComp.getPropertyValues(prop);
if (stepInteractions == null || stepInteractions.size() == 0) continue;
for (Iterator it1 = stepInteractions.iterator(); it1.hasNext(); ) {
OWLIndividual stepInteraction = (OWLIndividual) it1.next();
if (stepInteraction.getRDFType() != bpFactory.getcontrolClass()) {
rComp = bpToRInstanceMap.get(stepInteraction);
// Some control Individuals are listed under PATHWAY_COMPONENT. However,
// they should not be a value in hasComponent
if (rComp != null && hasComponentAtt.isValidValue(rComp))
rPathway.addAttributeValue(hasComponentAtt, rComp);
}
}
} else if (bpCompType != bpFactory.getcontrolClass()
&& !bpCompType.isSubclassOf(bpFactory.getcontrolClass())) {
// Another two types should be: Interaction and Pathway. But should exclude
// control class. Control class is attached to Reaction in Reactome
rComp = bpToRInstanceMap.get(bpComp);
if (rComp != null) rPathway.addAttributeValue(hasComponentAtt, rComp);
}
}
}