/** Add any nodes that are above the neighbor threshold to our cluster */
public NodeCluster doFilter(List<CyNode> nodeList, Map<NodeCluster, List<CyNode>> addedNodeMap) {
Set<CyNode> clusterNodes = new HashSet<CyNode>(nodeList);
List<CyNode> newNodeList = new ArrayList<CyNode>();
newNodeList.addAll(nodeList);
List<CyNode> nodesToAdd = new ArrayList<CyNode>();
for (CyNode node : nodeList) {
for (CyNode neighbor : network.getNeighborList(node, CyEdge.Type.ANY)) {
if (clusterNodes.contains(neighbor)) continue;
double adjacency = getAdjacency(neighbor, clusterNodes);
if (adjacency > context.threshold) {
// Add this node to our list
nodesToAdd.add(neighbor);
}
}
}
newNodeList.addAll(nodesToAdd);
if (newNodeList.size() > 1) {
NodeCluster newNodeCluster = new NodeCluster(newNodeList);
if (nodesToAdd.size() > 0) addedNodeMap.put(newNodeCluster, nodesToAdd);
return newNodeCluster;
}
return null;
}
/** Will fail if it doesn't find the specified interaction. */
protected void findInteraction(
CyNetwork net, String source, String target, String interaction, int count) {
for (CyNode n : net.getNodeList()) {
String sname = net.getRow(n).get(CyNetwork.NAME, String.class);
assertNotNull("Source name is NULL", sname);
if (source.equals(sname)) {
List<CyNode> neigh = net.getNeighborList(n, CyEdge.Type.ANY);
assertEquals("wrong number of neighbors", count, neigh.size());
for (CyNode nn : neigh) {
String tname = net.getRow(nn).get(CyNetwork.NAME, String.class);
assertNotNull("Target name is NULL", tname);
if (tname.equals(target)) {
List<CyEdge> con = net.getConnectingEdgeList(n, nn, CyEdge.Type.ANY);
assertTrue("Connecting edge list is empty", con.size() > 0);
for (CyEdge e : con) {
String inter = net.getRow(e).get(CyEdge.INTERACTION, String.class);
assertNotNull("Edge interaction is NULL", inter);
if (inter.equals(interaction)) {
return;
}
}
}
}
}
}
fail("couldn't find interaction: " + source + " " + interaction + " " + target);
}