/**
* Get a user connection infos
*
* @param userName the user
* @return the ConnectInfo
*/
public ConnectInfo getConnectInfo(String userName) {
for (int i = 0; i < this.connections.size(); i++) {
ConnectInfo ci = (ConnectInfo) this.connections.get(i);
if (ci.getName().equals(userName)) return ci;
}
return null;
}
/**
* 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);
}
}
/**
* Get the complete ConnectInfo
*
* @param ConnectInfo the user
* @return the complete ConnectInfo
*/
private ConnectInfo getCompleteConnectInfo(ConnectInfo ci) {
Iterator i = this.connections.iterator();
while (i.hasNext()) {
ConnectInfo tmp = (ConnectInfo) i.next();
if (ci.getName().equals(tmp.getName())) return tmp;
}
return ci;
}
/**
* Remove a ConnectionInfo
*
* @param user the user name
*/
private void removeConnectInfo(String user) {
for (int i = 0; i < this.connections.size(); i++) {
ConnectInfo ci = (ConnectInfo) this.connections.get(i);
if (ci.getName().equals(user)) {
this.connections.remove(ci);
break;
}
}
sendUserList();
}
/**
* Check if a user is already known
*
* @param ConnectInfo the user
* @return true or false
*/
private boolean isAlreadyKnown(ConnectInfo ci) {
boolean result = false;
Iterator i = this.connections.iterator();
while (i.hasNext() && !result) {
ConnectInfo tmp = (ConnectInfo) i.next();
result = ci.getName().equals(tmp.getName());
}
return result;
}
/**
* Remove a ConnectionInfo
*
* @param ci the connect info
*/
private void removeConnectInfo(ConnectInfo ci) {
removeConnectInfo(ci.getName());
}