Examples with BiclusterView edu.ucsf.rbvi.clusterMaker2.internal.ui.BiclusterView used on opensource projects

Example 1 with BiclusterView

use of edu.ucsf.rbvi.clusterMaker2.internal.ui.BiclusterView in project clusterMaker2 by RBVI.

the class BicFinder 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 = "BicFinder_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
    RunBicFinder algorithm = new RunBicFinder(network, attributeArray, monitor, context);
    String resultsString = "BicFinder results:";
    // Cluster the nodes
    monitor.setStatusMessage("Clustering nodes");
    Integer[] rowOrder = algorithm.cluster(false);
    CyMatrix biclusterMatrix = algorithm.getBiclusterMatrix();
    int[] clusters = new int[biclusterMatrix.nRows()];
    createBiclusterGroups(algorithm.getClusterNodes());
    // createGroups(network,biclusterMatrix,1, clusters, "bicfinder");
    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 2 with BiclusterView

use of edu.ucsf.rbvi.clusterMaker2.internal.ui.BiclusterView in project clusterMaker2 by RBVI.

the class ChengChurch 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 = "CnC_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
    RunChengChurch algorithm = new RunChengChurch(network, attributeArray, monitor, context);
    String resultsString = "ChengChurch results:";
    // Cluster the nodes
    monitor.setStatusMessage("Clustering nodes");
    Integer[] rowOrder = algorithm.cluster(false);
    CyMatrix biclusterMatrix = algorithm.getBiclusterMatrix();
    createGroups(network, biclusterMatrix, context.nClusters, algorithm.getRowClustersArray(), SHORTNAME);
    updateAttributes(network, SHORTNAME, rowOrder, attributeArray, getAttributeList(), algorithm.getBiclusterMatrix());
    // Build our attribute clustesrs
    List<String> arrayList = buildClusterHeaders(algorithm.getColClustersArray(), algorithm.getBiclusterMatrix(), true);
    ModelUtils.createAndSetLocal(network, network, ClusterManager.CLUSTER_ATTR_ATTRIBUTE, arrayList, List.class, String.class);
    updateParams(network, context.getParams());
    // System.out.println(resultsString);
    if (context.showUI) {
        insertTasksAfterCurrentTask(new BiclusterView(clusterManager));
    }
}

Example 3 with BiclusterView

use of edu.ucsf.rbvi.clusterMaker2.internal.ui.BiclusterView 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));
    }
}