/**
* 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);
}
}
protected void validateConnectWidget(ConnectWidget widget) {
Point point = widget.getPoint();
if (widget.getRole() == HyperEdge.INPUT) {
// Should have fixed position
Point p = getLinkPoint();
point.x = p.x + 1;
point.y = p.y;
return;
}
// Always in the north
Rectangle bounds = getBounds();
int fixedY = bounds.y + RenderableGene.GENE_SYMBOL_WIDTH / 2 - 2;
if (point.y != fixedY) point.y = fixedY;
double ratio = widget.getLinkRatio();
// Don't let x goes out of the bounds
if (ratio > 0.0) {
point.x = (int) (bounds.x + bounds.width * ratio);
} else if (point.x < bounds.x) point.x = bounds.x;
else if (point.x > bounds.x + bounds.width) point.x = bounds.x + bounds.width;
}