use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.
the class PRWP 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");
PageRankWithPriors<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...");
}
use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.
the class HyperlinkInducedTopicSearch 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);
graph.addEdge(prEdge, new Pair<>(sourceNode, targetNode), EdgeType.DIRECTED);
}
}
use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.
the class PR 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);
}
}
use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.units.PRNode in project clusterMaker2 by RBVI.
the class PR method addNodes.
private void addNodes() {
for (CyNode node : nodeList) {
PRNode prNode = new PRNode(node);
graph.addVertex(prNode);
idToNode.put(node.getSUID(), prNode);
}
}
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