use of org.baderlab.csplugins.enrichmentmap.model.PostAnalysisParameters.UniverseType in project EnrichmentMapApp by BaderLab.
the class PAKnownSignatureCommandTask method run.
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
if (gmtFile == null || !gmtFile.canRead())
throw new IllegalArgumentException("Signature GMT file name not valid");
CyNetwork selectedNetwork;
CyNetworkView selectedView;
if (network == null) {
selectedNetwork = applicationManager.getCurrentNetwork();
selectedView = applicationManager.getCurrentNetworkView();
if (selectedNetwork == null || selectedView == null) {
throw new IllegalArgumentException("Current network not available.");
}
} else {
selectedNetwork = network;
Collection<CyNetworkView> networkViews = networkViewManager.getNetworkViews(network);
if (networkViews == null || networkViews.isEmpty()) {
throw new IllegalArgumentException("No network view for: " + network);
}
selectedView = networkViews.iterator().next();
}
EnrichmentMap map = emManager.getEnrichmentMap(selectedNetwork.getSUID());
if (map == null)
throw new IllegalArgumentException("Network is not an Enrichment Map.");
loadGeneSets(map);
PostAnalysisFilterType filter = PostAnalysisFilterType.valueOf(filterType.getSelectedValue());
UniverseType universe = UniverseType.valueOf(hypergeomUniverseType.getSelectedValue());
PostAnalysisParameters.Builder builder = new PostAnalysisParameters.Builder();
builder.setAttributePrefix(map.getParams().getAttributePrefix());
builder.setSignatureGMTFileName(gmtFile.getAbsolutePath());
builder.setLoadedGMTGeneSets(signatureGenesets);
builder.addSelectedGeneSetNames(selectedGenesetNames);
builder.setUniverseType(universe);
builder.setUserDefinedUniverseSize(userDefinedUniverseSize);
builder.setRankTestParameters(new PostAnalysisFilterParameters(filter, cutoff));
builder.setName(name);
if (isBatch()) {
// run in batch mode
builder.setDataSetName(null);
} else {
if (map.getDataSet(dataSetName) == null) {
throw new IllegalArgumentException("Data set name not valid: '" + dataSetName + "'");
}
builder.setDataSetName(dataSetName);
}
// Mann-Whitney requires ranks
if (filter.isMannWhitney()) {
processMannWhitneyArgs(map, builder);
}
TaskFactory taskFactory = taskFactoryFactory.create(selectedView, builder.build());
TaskIterator taskIterator = new TaskIterator();
taskIterator.append(taskFactory.createTaskIterator());
Task updatePanelTask = new AbstractTask() {
@Override
public void run(TaskMonitor taskMonitor) {
controlPanelMediatorProvider.get().updateDataSetList(selectedView);
selectedView.updateView();
}
};
taskIterator.append(updatePanelTask);
insertTasksAfterCurrentTask(taskIterator);
}
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