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

Example 16 with ClusterManager

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

the class BiMine method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    List<String> nodeAttributeList = context.attributeList.getNodeAttributeList();
    String edgeAttribute = context.attributeList.getEdgeAttribute();
    clusterAttributeName = "BiMine_Bicluster";
    if (network.getRow(network, CyNetwork.LOCAL_ATTRS).getTable().getColumn(ClusterManager.CLUSTER_ATTRIBUTE) == null) {
        network.getRow(network, CyNetwork.LOCAL_ATTRS).getTable().createColumn(ClusterManager.CLUSTER_ATTRIBUTE, String.class, false);
    }
    network.getRow(network, CyNetwork.LOCAL_ATTRS).set(ClusterManager.CLUSTER_ATTRIBUTE, clusterAttributeName);
    if (nodeAttributeList == null && edgeAttribute == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must select either one edge column or two or more node columns");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() > 0 && edgeAttribute != null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't have both node and edge columns selected");
        return;
    }
    if (context.selectedOnly && CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true).size() < 3) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must have at least three nodes to cluster");
        return;
    }
    createGroups = context.createGroups;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        // To make debugging easier, sort the attribute list
        Collections.sort(nodeAttributeList);
    }
    // Get our attributes we're going to use for the cluster
    String[] attributeArray;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        attributeArray = new String[nodeAttributeList.size()];
        int i = 0;
        for (String attr : nodeAttributeList) {
            attributeArray[i++] = "node." + attr;
        }
    } else {
        attributeArray = new String[1];
        attributeArray[0] = "edge." + edgeAttribute;
    }
    monitor.setStatusMessage("Initializing");
    resetAttributes(network, SHORTNAME);
    // Create a new clusterer
    RunBiMine algorithm = new RunBiMine(network, attributeArray, monitor, context);
    String resultsString = "BiMine results:";
    // Cluster the nodes
    monitor.setStatusMessage("Clustering nodes");
    Integer[] rowOrder = algorithm.cluster(false);
    CyMatrix biclusterMatrix = algorithm.getBiclusterMatrix();
    int[] clusters = new int[biclusterMatrix.nRows()];
    createGroups(network, biclusterMatrix, 1, clusters, "bimine");
    updateAttributes(network, SHORTNAME, rowOrder, attributeArray, getAttributeList(), algorithm.getBiclusterMatrix());
    createBiclusterTable(algorithm.getClusterNodes(), algorithm.getClusterAttrs());
    // System.out.println(resultsString);
    if (context.showUI) {
        insertTasksAfterCurrentTask(new BiclusterView(clusterManager));
    }
}

Example 17 with ClusterManager

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

the class FeatureVectorCluster method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    List<String> nodeAttributeList = context.nodeAttributeList.getSelectedValues();
    // Sanity check all of our settings
    if (nodeAttributeList == null || nodeAttributeList.size() == 0) {
        if (monitor != null) {
            monitor.showMessage(TaskMonitor.Level.ERROR, "Error: no attribute list selected");
        }
        return;
    }
    String[] attributeArray = new String[nodeAttributeList.size()];
    int index = 0;
    for (String attr : nodeAttributeList) {
        attributeArray[index++] = "node." + attr;
    }
    // To make debugging easier, sort the attribute array
    Arrays.sort(attributeArray);
    if (monitor != null) {
        monitor.setProgress(0.0);
        monitor.setStatusMessage("Initializaing");
    }
    // Create the matrix
    // Matrix matrix = new Matrix(network, attributeArray, false, context.ignoreMissing, context.selectedOnly);
    CyMatrix matrix = CyMatrixFactory.makeSmallMatrix(network, attributeArray, false, context.ignoreMissing, context.selectedOnly, false);
    if (monitor != null) {
        monitor.setProgress(0.1);
        monitor.setStatusMessage("Calculating edge distances");
        if (canceled)
            return;
    }
    // Handle special cases
    if (context.zeroMissing)
        matrix.setMissingToZero();
    int nNodes = matrix.nRows();
    // For each node, get the distance to all other nodes
    double maxdistance = Double.MIN_VALUE;
    double mindistance = Double.MAX_VALUE;
    double[][] distanceMatrix = new double[nNodes][nNodes];
    for (int i = 0; i < nNodes; i++) {
        for (int j = i + 1; j < nNodes; j++) {
            double distance = context.metric.getSelectedValue().getMetric(matrix, matrix, i, j);
            maxdistance = Math.max(maxdistance, distance);
            mindistance = Math.min(mindistance, distance);
            distanceMatrix[i][j] = distance;
        }
        if (canceled)
            return;
        monitor.setProgress((double) i / ((double) nNodes * 4));
    }
    monitor.setStatusMessage("Min distance = " + mindistance + ", max distance = " + maxdistance);
    monitor.setStatusMessage("Assigning values to edges");
    List<CyEdge> edgeList = new ArrayList<CyEdge>();
    double scale = maxdistance - mindistance;
    CyNetwork newNet = null;
    if (context.createNewNetwork) {
        newNet = ModelUtils.createChildNetwork(clusterManager, network, network.getNodeList(), null, "--clustered");
    }
    for (int i = 0; i < nNodes; i++) {
        for (int j = i + 1; j < nNodes; j++) {
            // time = System.currentTimeMillis();
            // This scales the distances to be between 0.0 and 1.0
            double distance = (distanceMatrix[i][j] - mindistance) / scale;
            if (context.createNewNetwork == true && distance > context.edgeCutoff && context.edgeCutoff != 0.0)
                continue;
            CyNode source = (CyNode) ModelUtils.getNetworkObjectWithName(network, matrix.getRowLabel(i), CyNode.class);
            CyNode target = (CyNode) ModelUtils.getNetworkObjectWithName(network, matrix.getRowLabel(j), CyNode.class);
            // time = System.currentTimeMillis();
            if (context.createNewNetwork == true) {
                CyEdge edge = newNet.addEdge(source, target, false);
                ModelUtils.createAndSet(newNet, edge, context.edgeAttribute, distance, Double.class, null);
                edgeList.add(edge);
            } else {
                List<CyEdge> connectingEdges = network.getConnectingEdgeList(source, target, CyEdge.Type.ANY);
                // time = System.currentTimeMillis();
                if (connectingEdges == null || connectingEdges.size() == 0)
                    continue;
                CyEdge edge = connectingEdges.get(0);
                ModelUtils.createAndSet(network, edge, context.edgeAttribute, distance, Double.class, null);
            }
        }
        if (canceled)
            return;
        monitor.setProgress(25.0 + (75.0 * (double) i / (double) nNodes) / 100.0);
    }
    System.out.println("Network created -- creating view");
    // If we're supposed to, create the new network
    if (context.createNewNetwork) {
        VisualStyle style = ViewUtils.getCurrentVisualStyle(clusterManager);
        CyNetworkView view = ViewUtils.createView(clusterManager, newNet, false);
        ViewUtils.doLayout(clusterManager, view, monitor, "force-directed");
        ViewUtils.setVisualStyle(clusterManager, view, style);
        ViewUtils.registerView(clusterManager, view);
    }
    /*
		System.out.println("Created "+newEdges+" edges");
		System.out.println("Edge creation time: "+edgeCreateTime+"ms");
		System.out.println("Network add time: "+networkAddTime+"ms");
		System.out.println("Edge fetch time: "+edgeFetchTime+"ms");
		System.out.println("Node fetch time: "+nodeFetchTime+"ms");
		System.out.println("Set attribute time: "+setAttributeTime+"ms");
		*/
    monitor.setStatusMessage("Complete");
}

Example 18 with ClusterManager

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

the class MCODECluster method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    updateSettings();
    if (network == null)
        network = clusterManager.getNetwork();
    context.setNetwork(network);
    NodeCluster.init();
    if (currentParamsCopy.getScope().equals(MCODEParameterSet.SELECTION)) {
        List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
        currentParamsCopy.setSelectedNodes(selectedNodes);
    }
    MCODECurrentParameters.getInstance().setParams(currentParamsCopy, "MCODE Result", ModelUtils.getNetworkName(network));
    runMCODE = new RunMCODE(RESCORE, 1, network, monitor);
    List<NodeCluster> clusters = runMCODE.run(monitor);
    if (canceled) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Canceled by user");
        return;
    }
    monitor.showMessage(TaskMonitor.Level.INFO, "Found " + clusters.size() + " clusters");
    if (clusters == null || clusters.size() == 0) {
        monitor.showMessage(TaskMonitor.Level.WARN, "Didn't find any clusters!");
        return;
    }
    // Now, sort our list of clusters by score
    clusters = NodeCluster.rankListByScore(clusters);
    List<Double> scoreList = NodeCluster.getScoreList(clusters);
    clusterAttributeName = context.getClusterAttribute();
    createGroups = context.advancedAttributes.createGroups;
    monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
    // Remove any leftover groups from previous runs
    removeGroups(network, GROUP_ATTRIBUTE);
    monitor.setStatusMessage("Creating groups");
    List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
    results = new AbstractClusterResults(network, clusters);
    monitor.setStatusMessage("Done.  MCODE results:\n" + results);
    if (context.vizProperties.showUI) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges, !currentParamsCopy.getScope().equals(MCODEParameterSet.SELECTION)));
    }
}

Example 19 with ClusterManager

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

the class GLayCluster method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing community clustering (GLay)");
    createGroups = context.advancedAttributes.createGroups;
    clusterAttributeName = context.getClusterAttribute();
    if (network == null)
        network = clusterManager.getNetwork();
    // Make sure to update the context
    context.setNetwork(network);
    NodeCluster.init();
    GSimpleGraphData simpleGraph = new GSimpleGraphData(network, context.selectedOnly, context.undirectedEdges);
    fa = new FastGreedyAlgorithm();
    // fa.partition(simpleGraph);
    fa.execute(simpleGraph, monitor);
    NumberFormat nf = NumberFormat.getInstance();
    String modularityString = nf.format(fa.getModularity());
    List<NodeCluster> clusterList = new ArrayList<NodeCluster>();
    for (int cluster = 0; cluster < fa.getClusterNumber(); cluster++) {
        clusterList.add(new NodeCluster());
    }
    int[] membership = fa.getMembership();
    for (int index = 0; index < simpleGraph.graphIndices.length; index++) {
        int cluster = membership[index];
        clusterList.get(cluster).add(simpleGraph.graphIndices[index]);
    }
    monitor.showMessage(TaskMonitor.Level.INFO, "Found " + clusterList.size() + " clusters");
    // Remove any leftover groups from previous runs
    removeGroups(network, GROUP_ATTRIBUTE);
    monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
    List<List<CyNode>> nodeClusters = createGroups(network, clusterList, GROUP_ATTRIBUTE);
    results = new AbstractClusterResults(network, clusterList);
    monitor.showMessage(TaskMonitor.Level.INFO, "Done.  Community Clustering results:\n" + results);
    if (context.vizProperties.showUI) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges, !context.selectedOnly));
    }
}

Example 20 with ClusterManager

use of edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterManager 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));
    }
}