Examples with ConnectedComponent edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.datastructure.ConnectedComponent used on opensource projects

Example 21 with ConnectedComponent

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.datastructure.ConnectedComponent in project clusterMaker2 by RBVI.

the class ConnectedComponent method reductionicf.

public static FixedParameterTreeNode reductionicf(FixedParameterTreeNode fptnNew, double maxK, ConnectedComponent cc) {
    for (int i = 0; i < fptnNew.size; i++) {
        for (int j = i + 1; j < fptnNew.size; j++) {
            float sumIcf = calculateCostsForSetForbidden(fptnNew, i, j);
            if (sumIcf + fptnNew.costs > maxK) {
                float costsForMerging = calculateCostsForMerging(fptnNew, i, j);
                FixedParameterTreeNode fptnNew2 = mergeNodes(fptnNew, i, j, costsForMerging, cc);
                fptnNew2 = reductionicf(fptnNew2, maxK, cc);
                return fptnNew2;
            }
        }
    }
    return fptnNew;
}

Example 22 with ConnectedComponent

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.datastructure.ConnectedComponent in project clusterMaker2 by RBVI.

the class ConnectedComponentsCluster method run.

public void run(TaskMonitor monitor) {
    monitor.setTitle("Performing ConnectedComponents cluster");
    this.monitor = monitor;
    if (network == null)
        network = clusterManager.getNetwork();
    // Make sure to update the context
    context.setNetwork(network);
    NodeCluster.init();
    CyMatrix 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;
    Map<Integer, List<CyNode>> components = MatrixUtils.findConnectedComponents(matrix);
    // Create the NodeClusters
    Map<Integer, NodeCluster> clusterMap = new HashMap<Integer, NodeCluster>();
    for (Integer cluster : components.keySet()) {
        clusterMap.put(cluster, new NodeCluster(components.get(cluster)));
    }
    // Now get the sorted cluster map
    int clusterNumber = 1;
    HashMap<NodeCluster, NodeCluster> cMap = new HashMap<NodeCluster, NodeCluster>();
    for (NodeCluster cluster : NodeCluster.sortMap(clusterMap)) {
        if (cMap.containsKey(cluster))
            continue;
        cMap.put(cluster, cluster);
        cluster.setClusterNumber(clusterNumber);
        clusterNumber++;
    }
    List<NodeCluster> clusters = new ArrayList<NodeCluster>(cMap.keySet());
    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, clusters);
    monitor.showMessage(TaskMonitor.Level.INFO, "ConnectedComponent results:\n" + results);
    if (context.vizProperties.showUI) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges, !context.edgeAttributeHandler.selectedOnly));
    }
}