@Override
public void run(TaskMonitor taskMonitor) throws Exception {
if (network == null) network = appMgr.getCurrentNetwork();
views = new ArrayList<CyNetworkView>(viewMgr.getNetworkViews(network));
taskMonitor.showMessage(
TaskMonitor.Level.INFO, "Views for network " + DataUtils.getNetworkTitle(network));
for (CyNetworkView view : views) {
taskMonitor.showMessage(TaskMonitor.Level.INFO, " " + view);
return;
}
}
@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);
taskMonitor.setProgress(1.0);
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Done...");
}
@Override
public void run(TaskMonitor tm) throws Exception {
tm.setTitle("Loading network from table");
tm.setProgress(0.0);
tm.setStatusMessage("Loading network...");
Workbook workbook = null;
// Load Spreadsheet data for preview.
if (fileType != null
&& (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
|| fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension()))
&& workbook == null) {
try {
workbook = WorkbookFactory.create(is);
} catch (InvalidFormatException e) {
throw new IllegalArgumentException(
"Could not read Excel file. Maybe the file is broken?", e);
} finally {
if (is != null) is.close();
}
}
try {
if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
|| this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
String networkName = ntmp.getName();
if (networkName == null) networkName = workbook.getSheetName(0);
final Sheet sheet = workbook.getSheet(networkName);
reader =
new ExcelNetworkSheetReader(
networkName, sheet, ntmp, nMap, rootNetwork, serviceRegistrar);
} else {
reader = new NetworkTableReader(inputName, is, ntmp, nMap, rootNetwork, serviceRegistrar);
}
} catch (Exception ioe) {
tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
return;
}
loadNetwork(tm);
tm.setProgress(1.0);
}
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing MCL cluster");
this.monitor = monitor;
if (network == null) network = clusterManager.getNetwork();
context.setNetwork(network);
NodeCluster.init();
DistanceMatrix 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;
// Cluster the nodes
runMCL =
new RunMCL(
matrix,
context.inflation_parameter,
context.iterations,
context.clusteringThresh,
context.maxResidual,
context.maxThreads,
monitor);
runMCL.setDebug(debug);
if (canceled) return;
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
// results = runMCL.run(monitor);
List<NodeCluster> clusters = runMCL.run(network, monitor);
if (clusters == null) return; // Canceled?
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, nodeClusters);
monitor.showMessage(TaskMonitor.Level.INFO, "MCL results:\n" + results);
if (context.vizProperties.showUI) {
monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
insertTasksAfterCurrentTask(
new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges));
}
}
