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Example 1 with AbstractTask

use of org.cytoscape.work.AbstractTask 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);
}
Also used : Color(java.awt.Color) CreateEnrichmentMapTaskFactory(org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory) UIManager(javax.swing.UIManager) Inject(com.google.inject.Inject) IterableListModel(org.baderlab.csplugins.enrichmentmap.view.util.IterableListModel) Border(javax.swing.border.Border) IconManager(org.cytoscape.util.swing.IconManager) FileBrowser(org.baderlab.csplugins.enrichmentmap.view.util.FileBrowser) Map(java.util.Map) FinishStatus(org.cytoscape.work.FinishStatus) BorderLayout(java.awt.BorderLayout) JFrame(javax.swing.JFrame) ResolverTask(org.baderlab.csplugins.enrichmentmap.resolver.ResolverTask) EMCreationParameters(org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters) LegacySupport(org.baderlab.csplugins.enrichmentmap.model.LegacySupport) BorderFactory(javax.swing.BorderFactory) Component(java.awt.Component) Collectors(java.util.stream.Collectors) List(java.util.List) Stream(java.util.stream.Stream) Alignment(javax.swing.GroupLayout.Alignment) MessageType(org.baderlab.csplugins.enrichmentmap.view.creation.ErrorMessageDialog.MessageType) SwingUtil(org.baderlab.csplugins.enrichmentmap.view.util.SwingUtil) JCheckBox(javax.swing.JCheckBox) Optional(java.util.Optional) TaskObserver(org.cytoscape.work.TaskObserver) JPanel(javax.swing.JPanel) ObservableTask(org.cytoscape.work.ObservableTask) ListSelectionModel(javax.swing.ListSelectionModel) CardDialogPage(org.baderlab.csplugins.enrichmentmap.view.util.CardDialogPage) CardLayout(java.awt.CardLayout) JSplitPane(javax.swing.JSplitPane) DataSetFiles(org.baderlab.csplugins.enrichmentmap.model.DataSetFiles) AbstractTask(org.cytoscape.work.AbstractTask) Strings.isNullOrEmpty(com.google.common.base.Strings.isNullOrEmpty) Function(java.util.function.Function) SimilarityMetric(org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.SimilarityMetric) TaskIterator(org.cytoscape.work.TaskIterator) ArrayList(java.util.ArrayList) NESFilter(org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter) DataSetParameters(org.baderlab.csplugins.enrichmentmap.resolver.DataSetParameters) TaskMonitor(org.cytoscape.work.TaskMonitor) FlowLayout(java.awt.FlowLayout) Method(org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method) JButton(javax.swing.JButton) Iterator(java.util.Iterator) CardDialogCallback(org.baderlab.csplugins.enrichmentmap.view.util.CardDialogCallback) JList(javax.swing.JList) JOptionPane(javax.swing.JOptionPane) File(java.io.File) DialogTaskManager(org.cytoscape.work.swing.DialogTaskManager) JScrollPane(javax.swing.JScrollPane) LayoutStyle(javax.swing.LayoutStyle) ListCellRenderer(javax.swing.ListCellRenderer) Provider(com.google.inject.Provider) JLabel(javax.swing.JLabel) GroupLayout(javax.swing.GroupLayout) ListModel(javax.swing.ListModel) EMCreationParameters(org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters) AbstractTask(org.cytoscape.work.AbstractTask) SimilarityMetric(org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters.SimilarityMetric) NESFilter(org.baderlab.csplugins.enrichmentmap.model.EnrichmentResultFilterParams.NESFilter) CreateEnrichmentMapTaskFactory(org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory) TaskIterator(org.cytoscape.work.TaskIterator) TaskMonitor(org.cytoscape.work.TaskMonitor) DataSetParameters(org.baderlab.csplugins.enrichmentmap.resolver.DataSetParameters)

Example 2 with AbstractTask

use of org.cytoscape.work.AbstractTask 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);
}
Also used : Task(org.cytoscape.work.Task) AbstractTask(org.cytoscape.work.AbstractTask) UniverseType(org.baderlab.csplugins.enrichmentmap.model.PostAnalysisParameters.UniverseType) AbstractTask(org.cytoscape.work.AbstractTask) PostAnalysisFilterType(org.baderlab.csplugins.enrichmentmap.model.PostAnalysisFilterType) PostAnalysisFilterParameters(org.baderlab.csplugins.enrichmentmap.model.PostAnalysisFilterParameters) CyNetwork(org.cytoscape.model.CyNetwork) EnrichmentMap(org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap) PostAnalysisParameters(org.baderlab.csplugins.enrichmentmap.model.PostAnalysisParameters) TaskIterator(org.cytoscape.work.TaskIterator) TaskMonitor(org.cytoscape.work.TaskMonitor) CreateDiseaseSignatureTaskFactory(org.baderlab.csplugins.enrichmentmap.task.postanalysis.CreateDiseaseSignatureTaskFactory) TaskFactory(org.cytoscape.work.TaskFactory) CyNetworkView(org.cytoscape.view.model.CyNetworkView)

Example 3 with AbstractTask

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

the class CreateDiseaseSignatureTaskFactory method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    // Make sure that the minimum information is set in the current set of parameters
    EnrichmentMap map = emManager.getEnrichmentMap(netView.getModel().getSUID());
    StringBuilder errorBuilder = new StringBuilder();
    checkMinimalRequirements(errorBuilder, params);
    if (params.getRankTestParameters().getType().isMannWhitney() && map.getAllRanks().isEmpty())
        errorBuilder.append("Mann-Whitney requires ranks. \n");
    this.errors = errorBuilder.toString();
    if (errors.isEmpty()) {
        ControlPanelMediator controlPanelMediator = controlPanelMediatorProvider.get();
        EMStyleOptions options = controlPanelMediator.createStyleOptions(netView);
        CyCustomGraphics2<?> chart = controlPanelMediator.createChart(options);
        List<EMDataSet> dataSetList = getDataSets(map);
        TaskIterator tasks = new TaskIterator();
        tasks.append(signatureTaskFactory.create(params, map, dataSetList));
        tasks.append(applyStyleTaskFactory.create(options, chart, false));
        return tasks;
    } else {
        // MKTODO not entirely sure what to do in this case, just return an empty iterator I guess...
        return new TaskIterator(new AbstractTask() {

            @Override
            public void run(TaskMonitor taskMonitor) throws Exception {
                throw new RuntimeException(errors);
            }
        });
    }
}
Also used : EMStyleOptions(org.baderlab.csplugins.enrichmentmap.style.EMStyleOptions) AbstractTask(org.cytoscape.work.AbstractTask) EnrichmentMap(org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap) ControlPanelMediator(org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator) TaskIterator(org.cytoscape.work.TaskIterator) TaskMonitor(org.cytoscape.work.TaskMonitor) EMDataSet(org.baderlab.csplugins.enrichmentmap.model.EMDataSet)

Example 4 with AbstractTask

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

the class DetermineEnrichmentResultFileReader method getParsers.

/**
	 * Parse Enrichment results file
	 */
public TaskIterator getParsers() {
    String enrichmentsFileName1 = dataset.getEnrichments().getFilename1();
    String enrichmentsFileName2 = dataset.getEnrichments().getFilename2();
    TaskIterator parserTasks = new TaskIterator();
    try {
        if (!Strings.isNullOrEmpty(enrichmentsFileName1)) {
            AbstractTask current = readFile(enrichmentsFileName1);
            if (current instanceof ParseGREATEnrichmentResults)
                parserTasks.append(new GREATWhichPvalueQuestionTask(dataset.getMap()));
            parserTasks.append(current);
        }
        if (!Strings.isNullOrEmpty(enrichmentsFileName2)) {
            parserTasks.append(readFile(enrichmentsFileName2));
        }
        //If both of the enrichment files are null then we want to default to building a gmt file only build
        if (Strings.isNullOrEmpty(enrichmentsFileName1) && Strings.isNullOrEmpty(enrichmentsFileName2)) {
            parserTasks.append(new CreateGMTEnrichmentMapTask(dataset));
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
    return parserTasks;
}
Also used : TaskIterator(org.cytoscape.work.TaskIterator) AbstractTask(org.cytoscape.work.AbstractTask) CreateGMTEnrichmentMapTask(org.baderlab.csplugins.enrichmentmap.task.CreateGMTEnrichmentMapTask) IOException(java.io.IOException)

Aggregations

AbstractTask (org.cytoscape.work.AbstractTask)4 TaskIterator (org.cytoscape.work.TaskIterator)4 TaskMonitor (org.cytoscape.work.TaskMonitor)3 EnrichmentMap (org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap)2 Strings.isNullOrEmpty (com.google.common.base.Strings.isNullOrEmpty)1 Inject (com.google.inject.Inject)1 Provider (com.google.inject.Provider)1 BorderLayout (java.awt.BorderLayout)1 CardLayout (java.awt.CardLayout)1 Color (java.awt.Color)1 Component (java.awt.Component)1 FlowLayout (java.awt.FlowLayout)1 File (java.io.File)1 IOException (java.io.IOException)1 ArrayList (java.util.ArrayList)1 Iterator (java.util.Iterator)1 List (java.util.List)1 Map (java.util.Map)1 Optional (java.util.Optional)1 Function (java.util.function.Function)1