Examples with PRNode edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode used on opensource projects

Example 1 with PRNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.

the class HyperlinkInducedTopicSearch method addNodes.

private void addNodes() {
    for (CyNode node : nodeList) {
        PRNode prNode = new PRNode(node);
        graph.addVertex(prNode);
        idToNode.put(node.getSUID(), prNode);
    }
}

Example 2 with PRNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.

the class HyperlinkInducedTopicSearch method run.

@Override
public void run(TaskMonitor taskMonitor) {
    taskMonitor.setProgress(0.0);
    taskMonitor.setTitle("Hyperlink-Induced Topic Search ranking of clusters");
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Fetching clusters...");
    taskMonitor.setProgress(0.1);
    clusters = ClusterUtils.fetchClusters(network);
    taskMonitor.setProgress(0.5);
    initVariables();
    clusters.forEach(NodeCluster::initNodeScores);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Setting node scores in clusters");
    addNodes();
    taskMonitor.setProgress(0.6);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Setting edge scores in clusters");
    addEdges();
    taskMonitor.setProgress(0.7);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Performing HITS algorithm");
    HITS<PRNode, PREdge> hyperlinkInducedTopicSearchPriors = performHITS(graph);
    taskMonitor.setProgress(0.8);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Setting cluster scores");
    insertScores(clusters, graph, hyperlinkInducedTopicSearchPriors);
    taskMonitor.setProgress(0.9);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Insert cluster information in tables");
    ClusterUtils.insertResultsInColumns(network, clusters, SHORTNAME);
    results = new AbstractClusterResults(network, clusters);
    taskMonitor.setProgress(1.0);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Done...");
}

Example 3 with PRNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.

the class PR method run.

@Override
public void run(TaskMonitor taskMonitor) {
    taskMonitor.setProgress(0.0);
    taskMonitor.setTitle("PRWP with Priors ranking of clusters");
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Fetching clusters...");
    taskMonitor.setProgress(0.1);
    List<NodeCluster> clusters = ClusterUtils.fetchClusters(network);
    taskMonitor.setProgress(0.5);
    initVariables();
    clusters.forEach(NodeCluster::initNodeScores);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Setting node scores in clusters");
    addNodes();
    taskMonitor.setProgress(0.6);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Setting edge scores in clusters");
    addEdges();
    taskMonitor.setProgress(0.7);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Calculating PageRank scores");
    PageRank<PRNode, PREdge> pageRank = performPageRank();
    taskMonitor.setProgress(0.8);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Inserting scores into clusters");
    insertScores(clusters, pageRank);
    taskMonitor.setProgress(0.9);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Insert cluster information in tables");
    ClusterUtils.insertResultsInColumns(network, clusters, SHORTNAME);
    results = new AbstractClusterResults(network, clusters);
    taskMonitor.setProgress(1.0);
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Done...");
}

Example 4 with PRNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.

the class PRWP method addNodes.

private void addNodes() {
    for (CyNode node : nodeList) {
        PRNode prNode = new PRNode(node);
        insertNodeScore(prNode, nodeTable, nodeAttributes);
        graph.addVertex(prNode);
        idToNode.put(node.getSUID(), prNode);
    }
}

Example 5 with PRNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.

the class PRWP method addEdges.

private void addEdges() {
    for (CyEdge edge : edgeList) {
        PRNode sourceNode = idToNode.get(edge.getSource().getSUID());
        PRNode targetNode = idToNode.get(edge.getTarget().getSUID());
        PREdge prEdge = new PREdge(edge);
        insertEdgeScore(prEdge, edgeTable, edgeAttributes);
        graph.addEdge(prEdge, new Pair<>(sourceNode, targetNode), EdgeType.DIRECTED);
    }
}