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;
}