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

Example 16 with TaskIterator

use of org.cytoscape.work.TaskIterator 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 17 with TaskIterator

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

the class MasterDetailDialogPage method scan.

private void scan() {
    Optional<File> rootFolder = fileBrowser.browseForRootFolder(jframeProvider.get());
    if (rootFolder.isPresent()) {
        scanButton.setEnabled(false);
        ResolverTask task = new ResolverTask(rootFolder.get());
        dialogTaskManager.execute(new TaskIterator(task), new TaskObserver() {

            @Override
            public void taskFinished(ObservableTask task) {
                @SuppressWarnings("unchecked") List<DataSetParameters> datasets = task.getResults(List.class);
                if (!datasets.isEmpty()) {
                    datasets.forEach(MasterDetailDialogPage.this::addDataSetToList);
                    dataSetList.setSelectedValue(datasets.get(0), true);
                }
            }

            @Override
            public void allFinished(FinishStatus finishStatus) {
                scanButton.setEnabled(true);
                updateButtonEnablement();
            }
        });
    }
}

Example 18 with TaskIterator

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

the class AddRanksDialog method loadRanksAndClose.

private void loadRanksAndClose() {
    String rankFileName = ranksFileText.getText();
    String ranksName = getRanksName();
    EMDataSet dataset = getDataSet();
    RanksFileReaderTask task = new RanksFileReaderTask(rankFileName, dataset, ranksName, true);
    dialogTaskManager.execute(new TaskIterator(task), new TaskObserver() {

        @Override
        public void taskFinished(ObservableTask task) {
        }

        @Override
        public void allFinished(FinishStatus finishStatus) {
            resultRanksName = ranksName;
            dispose();
        }
    });
}

Example 19 with TaskIterator

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

the class PostAnalysisPanelMediator method addGeneSets.

private void addGeneSets(CyNetworkView netView, PostAnalysisParameters params) {
    CreateDiseaseSignatureTaskFactory taskFactory = signatureTaskFactoryFactory.create(netView, params);
    TaskIterator tasks = taskFactory.createTaskIterator();
    String errors = taskFactory.getErrors();
    if (errors.isEmpty()) {
        taskManager.execute(tasks, new DialogObserver());
    } else {
        JOptionPane.showMessageDialog(swingApplication.getJFrame(), errors, "Invalid Input", JOptionPane.WARNING_MESSAGE);
    }
}

Example 20 with TaskIterator

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

the class ClusterRankingOption method computeRanking.

@Override
public CompletableFuture<Optional<Map<Integer, RankValue>>> computeRanking(Collection<Integer> genes) {
    if (genes.size() < 2) {
        // The HierarchicalClusterTask requires at least 2 genes
        return CompletableFuture.completedFuture(Optional.of(Collections.emptyMap()));
    }
    HierarchicalClusterTask task = new HierarchicalClusterTask(map, genes, distance.getMetric());
    CompletableFuture<Optional<Map<Integer, RankValue>>> future = new CompletableFuture<>();
    taskManager.execute(new TaskIterator(task), new TaskObserver() {

        @Override
        public void taskFinished(ObservableTask task) {
            if (task instanceof HierarchicalClusterTask) {
                HierarchicalClusterTask clusterTask = (HierarchicalClusterTask) task;
                Optional<Map<Integer, RankValue>> ranking = clusterTask.getActualResults();
                future.complete(ranking);
            }
        }

        @Override
        public void allFinished(FinishStatus finishStatus) {
            // Don't see why this would ever happen
            if (!future.isDone()) {
                future.completeExceptionally(new RuntimeException("Failed"));
            }
        }
    });
    return future;
}