private boolean isDiseaseObject(Renderable r, Set<Long> diseaseIds) {
if (r instanceof FlowLine) {
FlowLine fl = (FlowLine) r;
return isFlowLineRelatedToSet(fl, diseaseIds);
}
// Assume normal objects only: this is a very strong assumption
if (r.getReactomeId() == null) return false;
// A PE may be represented multiple times in a pathway diagram. Some of them
// are linked to normal reactions, and some linked to disease reactions.
// Have to check these cases.
if (r instanceof HyperEdge) return diseaseIds.contains(r.getReactomeId());
if (r instanceof Node) {
Node node = (Node) r;
List<HyperEdge> edges = node.getConnectedReactions();
boolean isDisease = false;
for (HyperEdge edge : edges) {
if (edge instanceof FlowLine) {
isDisease = isFlowLineRelatedToSet((FlowLine) edge, diseaseIds);
} else if (edge.getReactomeId() != null && diseaseIds.contains(edge.getReactomeId())) {
isDisease = true;
}
if (isDisease) return true;
}
}
return false;
}
private boolean isNormalObject(Renderable r, Set<Long> normalIds) {
if (r instanceof HyperEdge) {
if (r instanceof FlowLine) return isFlowLineRelatedToSet((FlowLine) r, normalIds);
// Most likely the following statements should not be reached. But place
// here just in case.
if (r.getReactomeId() == null) return true;
if (normalIds.contains(r.getReactomeId())) return true;
} else if (r instanceof Node) {
if (r instanceof ProcessNode) return true; // Should be used only for normal pathway.
if (r.getReactomeId() == null) return true;
// Check if it is linked to another disease entities
Node node = (Node) r;
List<HyperEdge> edges = node.getConnectedReactions();
boolean isNormal = false;
for (HyperEdge edge : edges) {
if (edge instanceof FlowLine) isNormal = isFlowLineRelatedToSet((FlowLine) edge, normalIds);
if (isNormal) return true;
if (edge.getReactomeId() != null && normalIds.contains(edge.getReactomeId())) return true;
// Some special cases that use links
if (!(edge instanceof EntitySetAndEntitySetLink)
&& !(edge instanceof EntitySetAndMemberLink)
&& edge.getReactomeId() == null) return true;
}
}
return false;
}
/**
* 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;
}
/**
* 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);
}
}
private void drawComponents(
Graphics g, List<Renderable> comps, Rectangle clip, boolean drawEdgeFirst) {
List<HyperEdge> edges = new ArrayList<HyperEdge>();
for (Renderable obj : comps) {
if (obj instanceof HyperEdge) edges.add((HyperEdge) obj);
}
if (drawEdgeFirst) {
// Draw HyperEdges
for (HyperEdge reaction : edges) {
// Have to validate connect nodes first in case empty bounds
List<Node> nodes = reaction.getConnectedNodes();
for (Node node : nodes) node.validateBounds(g);
reaction.validateConnectInfo();
if (clip.intersects(reaction.getBounds())) reaction.render(g);
}
}
// Draw complexes now
drawComplexes(comps, clip, g);
for (Renderable obj : comps) {
if (obj instanceof RenderableCompartment
|| obj instanceof RenderableComplex
|| obj instanceof RenderablePathway) continue; // Escape it. It should be drawn earlier.
if (obj instanceof Node) {
Node node = (Node) obj;
if (getHidePrivateNote() && (node instanceof Note) && ((Note) node).isPrivate()) continue;
node.validateBounds(g);
if (clip.intersects(node.getBounds())) node.render(g);
}
}
if (!drawEdgeFirst) {
// Draw HyperEdges
for (HyperEdge reaction : edges) {
reaction.validateConnectInfo();
if (clip.intersects(reaction.getBounds())) reaction.render(g);
}
}
}