/**
* 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);
}
}
/**
* Map mutated nodes in a disease reaction to displayed nodes in a normal reaction. The mapping is
* based on sharing of referenceEntity. This may not be reliable!
*
* @param diseaseReaction
* @param nodes
* @throws InvalidAttributeException
* @throws Exception @TODO: add a new attribute normalEntity in the PhysicalEntity class.
*/
private Map<Node, GKInstance> mapMutatedToNormalNodes(
GKInstance diseaseReaction,
HyperEdge normalReaction,
List<Node> nodes,
Set<GKInstance> lofInstances)
throws InvalidAttributeException, Exception {
List<GKInstance> efs =
diseaseReaction.getAttributeValuesList(ReactomeJavaConstants.entityFunctionalStatus);
// Map mutated entities to normal entities via ReferenceGeneProduct
Map<Node, GKInstance> normalToDiseaseEntity = new HashMap<Node, GKInstance>();
if (efs == null) return normalToDiseaseEntity;
for (GKInstance ef : efs) {
GKInstance pe = (GKInstance) ef.getAttributeValue(ReactomeJavaConstants.physicalEntity);
if (pe != null) {
Set<GKInstance> refEntities = getReferenceEntity(pe);
// want to find the matched node
for (Node node : nodes) {
if (node.getReactomeId() == null) continue;
GKInstance nodeInst = adaptor.fetchInstance(node.getReactomeId());
Set<GKInstance> nodeRefEntities = getReferenceEntity(nodeInst);
nodeRefEntities.retainAll(refEntities);
if (nodeRefEntities.size() > 0) {
normalToDiseaseEntity.put(node, pe);
if (isLOFEntity(ef)) {
lofInstances.add(pe);
}
break;
}
}
}
}
// TODO: May have to consider stoichiometries too!!!
// In gain of functions, some inputs or outputs may not be used by normal reactions.
// This method will do its best to map these reaction participants
Collection<GKInstance> mapped = normalToDiseaseEntity.values();
// First check inputs
List<GKInstance> diseaseInputs =
diseaseReaction.getAttributeValuesList(ReactomeJavaConstants.input);
List<Node> normalNodes = normalReaction.getInputNodes();
randomlyMapDiseaseNodesToNormalNodes(normalToDiseaseEntity, mapped, diseaseInputs, normalNodes);
// Check outputs
List<GKInstance> diseaseOutputs =
diseaseReaction.getAttributeValuesList(ReactomeJavaConstants.output);
normalNodes = normalReaction.getOutputNodes();
randomlyMapDiseaseNodesToNormalNodes(
normalToDiseaseEntity, mapped, diseaseOutputs, normalNodes);
// Check helpers
GKInstance ca =
(GKInstance) diseaseReaction.getAttributeValue(ReactomeJavaConstants.catalystActivity);
if (ca != null) {
List<GKInstance> catalysts = ca.getAttributeValuesList(ReactomeJavaConstants.physicalEntity);
normalNodes = normalReaction.getHelperNodes();
randomlyMapDiseaseNodesToNormalNodes(normalToDiseaseEntity, mapped, catalysts, normalNodes);
}
return normalToDiseaseEntity;
}