@Override
public Collection<CyNode> getNeighbours(CyNode node) {
Collection<CyNode> neighbours = new HashSet<CyNode>();
CyNetwork network = getProxied();
int nodeIndex = node.getRootGraphIndex();
for (int index : network.getAdjacentEdgeIndicesArray(nodeIndex, true, true, true)) {
CyEdge edge = (CyEdge) network.getEdge(index);
CyNode other = (CyNode) edge.getSource();
if (other.getRootGraphIndex() == nodeIndex) {
other = (CyNode) edge.getTarget();
if (other.getRootGraphIndex() == nodeIndex) {
continue;
}
}
neighbours.add((CyNode) other);
}
return neighbours;
}
public gpClique[] creategpClique() {
gpClique[] gps = new gpClique[2];
gps[0] = new gpClique();
gps[1] = new gpClique();
Iterator<Edge> edgeIt = nw.edgesIterator();
CyAttributes edgeAtt = Cytoscape.getEdgeAttributes();
ArrayList largeALNodes = new ArrayList();
ArrayList targetALNodes = new ArrayList();
ArrayList matchALNodes = new ArrayList();
while (edgeIt.hasNext()) {
Edge edge = edgeIt.next();
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p2")) {
largeALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
largeALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
continue; // go directly next step
}
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p1")) {
targetALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
targetALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
continue;
}
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("pd")) {
matchALNodes.add(
new Integer(
nw.getEdgeSourceIndex(
edge
.getRootGraphIndex()))); // the matched node(containing "-") of target
// network
matchALNodes.add(
new Integer(
nw.getEdgeTargetIndex(
edge
.getRootGraphIndex()))); // the matched node(containing "-") of large
// network
continue;
}
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "File Format error!");
return null;
}
Iterator matchALNIt = matchALNodes.iterator();
CyNode node;
Integer it;
while (matchALNIt.hasNext()) {
it = (Integer) matchALNIt.next();
node =
Cytoscape.getCyNode(
nw.getNode(it.intValue()).getIdentifier().substring(1),
true); // get node according to its identifier
matchNodes.add(node);
if (!targetALNodes.contains(
node.getRootGraphIndex())) // matched node,but not a node of network
{
nw.addNode(node);
targetALNodes.add(node.getRootGraphIndex()); // add to network
}
it = (Integer) matchALNIt.next();
node =
Cytoscape.getCyNode(
nw.getNode(it.intValue()).getIdentifier().substring(1),
true); // get node according to its identifier
matchNodes.add(node);
if (!largeALNodes.contains(node.getRootGraphIndex())) {
nw.addNode(node);
largeALNodes.add(node.getRootGraphIndex());
}
}
gps[0].setgpNodes(largeALNodes);
gps[1].setgpNodes(targetALNodes);
return gps;
}