Examples with TaskMonitor org.cytoscape.work.TaskMonitor used on opensource projects

Example 6 with TaskMonitor

use of org.cytoscape.work.TaskMonitor in project EnrichmentMapApp by BaderLab.

the class MasterDetailDialogPage method finish.

@Override
public void finish() {
    if (!validateInput())
        return;
    String prefix = legacySupport.getNextAttributePrefix();
    SimilarityMetric similarityMetric = cutoffPanel.getSimilarityMetric();
    double pvalue = cutoffPanel.getPValue();
    double qvalue = cutoffPanel.getQValue();
    NESFilter nesFilter = cutoffPanel.getNESFilter();
    double cutoff = cutoffPanel.getCutoff();
    double combined = cutoffPanel.getCombinedConstant();
    Optional<Integer> minExperiments = cutoffPanel.getMinimumExperiments();
    EMCreationParameters params = new EMCreationParameters(prefix, pvalue, qvalue, nesFilter, minExperiments, similarityMetric, cutoff, combined);
    params.setCreateDistinctEdges(distinctEdgesCheckbox.isSelected());
    List<DataSetParameters> dataSets = dataSetListModel.toList().stream().map(DataSetListItem::getDetailPanel).map(DetailPanel::createDataSetParameters).filter(x -> x != null).collect(Collectors.toList());
    // Overwrite all the expression files if the common file has been provided
    String exprPath = commonPanel.getExpressionFile();
    if (!isNullOrEmpty(exprPath)) {
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setExpressionFileName(exprPath);
        }
    }
    // Overwrite all the gmt files if a common file has been provided
    String gmtPath = commonPanel.getGmtFile();
    if (!isNullOrEmpty(gmtPath)) {
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setGMTFileName(gmtPath);
        }
    }
    CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(params, dataSets);
    TaskIterator tasks = taskFactory.createTaskIterator();
    // Close this dialog after the progress dialog finishes normally
    tasks.append(new AbstractTask() {

        public void run(TaskMonitor taskMonitor) {
            callback.close();
        }
    });
    dialogTaskManager.execute(tasks);
}

Example 7 with TaskMonitor

use of org.cytoscape.work.TaskMonitor 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);
}