private void insertScores(List<NodeCluster> clusters, PageRank<PRNode, PREdge> pageRank) {
for (PRNode node : graph.getVertices()) {
node.setPRScore(pageRank.getVertexScore(node));
for (NodeCluster cluster : clusters) {
if (cluster.getNodeScores().containsKey(node.getCyNode().getSUID())) {
cluster.addScoreToAvg(pageRank.getVertexScore(node));
}
}
}
}
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing MCL cluster");
this.monitor = monitor;
if (network == null) network = clusterManager.getNetwork();
context.setNetwork(network);
NodeCluster.init();
DistanceMatrix matrix = context.edgeAttributeHandler.getMatrix();
if (matrix == null) {
monitor.showMessage(
TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
return;
}
// Update our tunable results
clusterAttributeName = context.getClusterAttribute();
createGroups = context.advancedAttributes.createGroups;
if (canceled) return;
// Cluster the nodes
runMCL =
new RunMCL(
matrix,
context.inflation_parameter,
context.iterations,
context.clusteringThresh,
context.maxResidual,
context.maxThreads,
monitor);
runMCL.setDebug(debug);
if (canceled) return;
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
// results = runMCL.run(monitor);
List<NodeCluster> clusters = runMCL.run(network, monitor);
if (clusters == null) return; // Canceled?
monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
// Remove any leftover groups from previous runs
removeGroups(network, GROUP_ATTRIBUTE);
monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
params = new ArrayList<String>();
context.edgeAttributeHandler.setParams(params);
List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
results = new AbstractClusterResults(network, nodeClusters);
monitor.showMessage(TaskMonitor.Level.INFO, "MCL results:\n" + results);
if (context.vizProperties.showUI) {
monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
insertTasksAfterCurrentTask(
new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges));
}
}