use of edu.ucsf.rbvi.clusterMaker2.internal.ui.NewNetworkView in project clusterMaker2 by RBVI.
the class Fuzzifier method run.
/**
* The method run creates an instance of the RunFuzzifier and creates the fuzzy clusters
* by calling the fuzzifier algorithm.
* Also creates fuzzy groups and the Fuzzy Cluster Table
*
* @param Task Monitor
*/
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing Fuzzifier clustering");
this.monitor = monitor;
if (network == null)
network = clusterManager.getNetwork();
super.network = network;
this.Clusters = getClusters();
this.cNumber = Clusters.size();
// Make sure to update the context
context.setNetwork(network);
Long networkID = network.getSUID();
CyTable nodeAttributes = network.getDefaultNodeTable();
CyMatrix distanceMatrix = context.edgeAttributeHandler.getMatrix();
if (distanceMatrix == null) {
monitor.showMessage(TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
return;
}
// Update our tunable results
clusterAttributeName = context.getClusterAttribute();
runFuzzifier = new RunFuzzifier(Clusters, distanceMatrix, cNumber, context.membershipThreshold.getValue(), context.maxThreads, monitor);
runFuzzifier.setDebug(debug);
if (canceled)
return;
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
List<FuzzyNodeCluster> FuzzyClusters = runFuzzifier.run(network, monitor);
// Canceled?
if (FuzzyClusters == null)
return;
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 = createFuzzyGroups(network, FuzzyClusters, GROUP_ATTRIBUTE);
results = new AbstractClusterResults(network, FuzzyClusters);
monitor.showMessage(TaskMonitor.Level.INFO, "Done. Fuzzifier 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));
} else {
monitor.showMessage(TaskMonitor.Level.INFO, "Done. Fizzifier results:\n" + results);
}
System.out.println("Creating fuzzy table");
createFuzzyTable(FuzzyClusters);
System.out.println("Done");
}
use of edu.ucsf.rbvi.clusterMaker2.internal.ui.NewNetworkView in project clusterMaker2 by RBVI.
the class SCPSCluster method run.
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing SCPS 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;
// Cluster the nodes
runSCPS = new RunSCPS(matrix, context.epsilon, context.clusters, context.iterations, monitor);
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
List<NodeCluster> clusterList = runSCPS.run(network, monitor);
// Canceled?
if (clusterList == null)
return;
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, clusterList, GROUP_ATTRIBUTE);
results = new AbstractClusterResults(network, clusterList);
monitor.showMessage(TaskMonitor.Level.INFO, "Done. SCPS 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));
}
}
use of edu.ucsf.rbvi.clusterMaker2.internal.ui.NewNetworkView in project clusterMaker2 by RBVI.
the class TransClustCluster method run.
/**
* Perform the actual clustering. For TransClust, there are really
* two steps:
* 1) Assign all of the connected components
* 2) Do the TransClust clustering.
*
* There is also an optional approach called evolutionary parameter
* tuning, which takes a lot longer and is probably less relevant for
* the Cytoscape integration.
*
* @param monitor the TaskMonitor to use
*/
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing Transitivity clustering");
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;
}
updateSettings();
runTransClust = new RunTransClust(matrix, context.edgeAttributeHandler.edgeCutOff.getValue(), monitor);
if (canceled)
return;
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
createGroups = context.advancedAttributes.createGroups;
// Cluster the nodes
List<NodeCluster> clusters = runTransClust.run(monitor, network);
// Canceled?
if (clusters == null)
return;
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.setStatusMessage("Done. TransClust 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));
}
}
use of edu.ucsf.rbvi.clusterMaker2.internal.ui.NewNetworkView in project clusterMaker2 by RBVI.
the class APCluster method run.
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing AP 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;
// Cluster the nodes
runAP = new RunAP(matrix, context.lambda, context.preference, context.rNumber, monitor, debug);
if (canceled)
return;
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
List<NodeCluster> clusters = runAP.run(network, monitor);
// Canceled?
if (clusters == null)
return;
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);
setParams(params);
List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
results = new AbstractClusterResults(network, clusters);
monitor.showMessage(TaskMonitor.Level.INFO, "Done. AP 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));
}
}
use of edu.ucsf.rbvi.clusterMaker2.internal.ui.NewNetworkView in project clusterMaker2 by RBVI.
the class MCLCluster method run.
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing MCL cluster");
this.monitor = monitor;
if (network == null)
network = clusterManager.getNetwork();
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;
// Cluster the nodes
runMCL = new RunMCL(matrix, context.inflation_parameter, context.iterations, context.clusteringThresh, context.maxResidual, context.maxThreads, context.forceDecliningResidual, monitor);
runMCL.setDebug(false);
if (canceled)
return;
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
// results = runMCL.run(monitor);
List<NodeCluster> clusters = runMCL.run(network, monitor);
// Canceled?
if (clusters == null)
return;
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, "MCL 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));
}
}
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