Examples with ClusterResults edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterResults used on opensource projects

Example 1 with ClusterResults

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterResults in project clusterMaker2 by RBVI.

the class ResultsPanelTask method getClusters.

public List<NodeCluster> getClusters() {
    List<NodeCluster> clusters = new ArrayList<NodeCluster>();
    // List<List<CyNode>> clusterList = new ArrayList<List<CyNode>>();
    /*
		System.out.println(network.NAME);
		System.out.println(CyNetwork.LOCAL_ATTRS);
		System.out.println(ClusterManager.CLUSTER_ATTRIBUTE);
		*/
    clusterAttribute = network.getRow(network, CyNetwork.LOCAL_ATTRS).get(ClusterManager.CLUSTER_ATTRIBUTE, String.class);
    // Create a temporary cluster map
    Map<Integer, ArrayList<CyNode>> clusterMap = new HashMap<Integer, ArrayList<CyNode>>();
    for (CyNode node : (List<CyNode>) network.getNodeList()) {
        // For each node -- see if it's in a cluster.  If so, add it to our map
        if (ModelUtils.hasAttribute(network, node, clusterAttribute)) {
            Integer cluster = network.getRow(node).get(clusterAttribute, Integer.class);
            if (!clusterMap.containsKey(cluster))
                clusterMap.put(cluster, new ArrayList<CyNode>());
            clusterMap.get(cluster).add(node);
        }
    }
    // See if this algorithm provided it's own scores
    List<Double> scores = null;
    if (network.getDefaultNetworkTable().getColumn(clusterAttribute + "_Scores") != null) {
        scores = network.getRow(network, CyNetwork.LOCAL_ATTRS).getList(clusterAttribute + "_Scores", Double.class);
    }
    for (int clustNum : clusterMap.keySet()) {
        NodeCluster cluster = new NodeCluster(clusterMap.get(clustNum));
        cluster.setClusterNumber(clustNum);
        if (scores != null)
            cluster.setClusterScore(scores.get(clustNum - 1));
        clusters.add(cluster);
    }
    // calculating the scores for each cluster
    clusterResults = new AbstractClusterResults(network, clusters);
    List<Double> modularityList;
    if (scores == null) {
        modularityList = clusterResults.getModularityList();
    } else {
        modularityList = scores;
    }
    for (int i = 0; i < clusters.size(); i++) {
        clusters.get(i).setClusterScore(modularityList.get(i));
    }
    return clusters;
}

Example 2 with ClusterResults

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterResults in project clusterMaker2 by RBVI.

the class AbstractNetworkFilter method run.

public void run(TaskMonitor monitor) {
    monitor.setTitle("Filtering using " + getName());
    this.monitor = monitor;
    if (network == null)
        network = clusterManager.getNetwork();
    clusterAttributeName = getClusterAttributeName();
    // get the cluster list
    List<NodeCluster> clusterList = AbstractNetworkClusterer.getNodeClusters(network, getClusterAttribute());
    List<NodeCluster> newClusterList = new ArrayList<NodeCluster>();
    Map<NodeCluster, List<CyNode>> addedNodeMap = new HashMap<NodeCluster, List<CyNode>>();
    // Iterate over clusters and build a new clusterList
    for (NodeCluster nodeList : clusterList) {
        NodeCluster newCluster = doFilter(nodeList, addedNodeMap);
        if (newCluster != null && newCluster.size() > 0)
            newClusterList.add(newCluster);
    }
    // Fixup our clusters
    if (addedNodeMap.size() > 0) {
        // until this stabelized...
        for (NodeCluster addedCluster : addedNodeMap.keySet()) {
            for (NodeCluster cluster : newClusterList) {
                if (cluster.equals(addedCluster))
                    continue;
                removeNodes(cluster, addedNodeMap.get(addedCluster));
            }
        }
    }
    monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
    // Remove any leftover groups from previous runs
    removeGroups(network, groupAttribute);
    monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
    List<List<CyNode>> nodeClusters = createGroups(network, newClusterList, groupAttribute);
    results = new AbstractClusterResults(network, clusterList);
    ClusterResults results2 = new AbstractClusterResults(network, newClusterList);
    monitor.showMessage(TaskMonitor.Level.INFO, "Done.  Results:\n\nBefore Filter:\n" + results + "\n\nAfter Filter:\n" + results2);
    if (showUI()) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, restoreEdges(), false));
    }
}