Java TaskMonitor类代码示例

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
	
	SmoothingService smoothingService = registrar.getService(SmoothingService.class);
	TimeSeries smoothedSeries = smoothingService.smooth(sourceTimeSeries, estimateX, provider, parameter, outputParameters.resultName, rowGrouping);
	
	registrar.getService(DataSeriesManager.class).registerDataSeries(smoothedSeries);
	
	if(outputParameters.mapResult)
	{
		MappingManipulationService manipulationService = registrar.getService(MappingManipulationService.class);					
		
		if(outputParameters.replaceMapping)
		{
			manipulationService.replaceMapping(sourceTimeSeries, smoothedSeries, rowGrouping); 
		}
		else
		{
			manipulationService.copyMapping(sourceTimeSeries, smoothedSeries, rowGrouping, outputParameters.mappingSuffix);
		}
	}
	
	registrar.unregisterAllServices(sourcePanel);
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
	SwingUtilities.invokeLater( () -> {
		final JFrame parent = registrar.getService(CySwingApplication.class).getJFrame();
		final JDialog frm = new JDialog(parent, "Manage data series mappings");
		frm.setLayout(new BorderLayout());
		frm.add(new MappingManagerPanel(registrar), BorderLayout.CENTER);
		JButton closeButton = new JButton("Close");
		closeButton.addActionListener(e -> frm.setVisible(false));
		frm.add(closeButton, BorderLayout.SOUTH);
		frm.pack();			
		frm.setModal(true);
		int x = (parent.getWidth() - frm.getWidth()) / 2;
		int y = (parent.getHeight() - frm.getHeight()) / 2;
		frm.setLocation(parent.getX() + x, parent.getY() + y);
		frm.setVisible(true);		
	});
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor tm) throws Exception {
	//DS is loaded during validation to let the user modify the options immediately after an import failure
	if(importedDS == null)
	{
		throw new DataSeriesException("Invalid import task state: series was not imported, although validation passed.");
	}
	dataSeriesManager.registerDataSeries(importedDS);
	if(mapAfterImport)
	{			
		MapColumnTask mapColumnTask = new MapColumnTask(registrar);
		mapColumnTask.dataSeries.setSelectedValue(importedDS);
		mapColumnTask.newColumnName = importedDS.getName();
		insertTasksAfterCurrentTask(mapColumnTask);
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor tm) throws Exception {
	tm.setTitle(TITLE);
	
	List<Cluster> clusters = new ArrayList<>(as.getClusters());
	clusters.sort(Comparator.comparing(Cluster::getNodeCount).thenComparing(Cluster::getLabel).reversed());
	
	try(BufferedWriter writer = new BufferedWriter(new FileWriter(file))) {
		writer.append("Cluster").append("\t").append("Nodes");
		writer.newLine();
		
		for(Cluster cluster : clusters) {
			writer.append(cluster.getLabel()).append("\t").append(String.valueOf(cluster.getNodeCount()));
			writer.newLine();
		}
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
	taskMonitor.setTitle(BuildProperties.APP_NAME);
	taskMonitor.setStatusMessage("Removing Clusters");
	
	ShapeAnnotation shape = annotationRenderer.removeShapeAnnoation(cluster);
	TextAnnotation text = annotationRenderer.removeTextAnnotation(cluster);
	
	// invokeAndWait forces the shape to update on the current thread
	if(shape != null) {
		if(SwingUtilities.isEventDispatchThread()) {
			shape.removeAnnotation();
		} else {
			SwingUtilities.invokeAndWait(shape::removeAnnotation);
		}
	}
	if(text != null) {
		if(SwingUtilities.isEventDispatchThread()) {
			text.removeAnnotation();
		} else {
			SwingUtilities.invokeAndWait(text::removeAnnotation);
		}
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) {
	taskMonitor.setTitle(BuildProperties.APP_NAME);
	taskMonitor.setStatusMessage("Removing Annotations");
	
	CyNetworkView networkView = networkViewSet.getNetworkView();
	List<Annotation> annotations = annotationManager.getAnnotations(networkView);
	if(annotations != null) { // seriously?
		for(Annotation annotation : annotations) {
			try {
				SwingUtilities.invokeAndWait(annotation::removeAnnotation);
			} catch (Exception e) {}
		}
	}
	
	for(Cluster cluster : networkViewSet.getAllClusters()) {
		annotationRenderer.removeShapeAnnoation(cluster);
		annotationRenderer.removeTextAnnotation(cluster);
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) {
	taskMonitor.setTitle(BuildProperties.APP_NAME);
	taskMonitor.setStatusMessage("Drawing Annotations");
	
	try {
		// So basically the task does nothing if the cluster is collapsed.
		// This just saves us from having to put an if-statement in the renderer.
		if(!cluster.isCollapsed()) {
			drawShape();
			drawLabel();
		}
	} catch(Exception e) {
		e.printStackTrace();
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
/**
 * This is fast because no events are fired while the summary network is being built. 
 * The summary network and view are registered at the end.
 */
@Override
public void run(TaskMonitor taskMonitor) {
	taskMonitor.setTitle(BuildProperties.APP_NAME);
	taskMonitor.setStatusMessage(SummaryNetworkAction.TITLE);
	
	
	CyNetwork originNetwork = annotationSet.getParent().getNetwork();
	List<SummaryCluster> summaryClusters = getSummaryClusters();
	
	// create summary network
	SummaryNetwork summaryNetwork = createSummaryNetwork(originNetwork, summaryClusters);
	
	// create summary network view
	CyNetworkView summaryNetworkView = createNetworkView(summaryNetwork);
	
	// apply visual style
	applyVisualStyle(annotationSet.getParent().getNetworkView(), summaryNetworkView, summaryNetwork);
	
	// register
	networkManager.addNetwork(summaryNetwork.network);
	networkViewManager.addNetworkView(summaryNetworkView);
	summaryNetworkView.fitContent();
	
	resultNetwork = summaryNetwork.network;
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
private void createSifNodeAttr(Model model, CyNetwork cyNetwork,
							   TaskMonitor taskMonitor) throws IOException
{
	taskMonitor.setStatusMessage("Updating SIF network node attributes from the BioPAX model...");

	// Set the Quick Find Default Index
	AttributeUtil.set(cyNetwork, cyNetwork, "quickfind.default_index", CyNetwork.NAME, String.class);
	if (cancelled) return;

	// Set node attributes from the Biopax Model
	for (CyNode node : cyNetwork.getNodeList()) {
		String uri = cyNetwork.getRow(node).get(CyNetwork.NAME, String.class);
		BioPAXElement e = model.getByID(uri);
		if(e instanceof EntityReference || e instanceof Entity) 
		{
			BioPaxMapper.createAttributesFromProperties(e, model, node, cyNetwork);
		} else if (e != null) {
			log.warn("SIF network has an unexpected node: " + uri + " of type " + e.getModelInterface());
			BioPaxMapper.createAttributesFromProperties(e, model, node, cyNetwork);
		} else { //should never happen anymore...
			log.error("(BUG) the biopax model does not have an object with URI=" + uri);
		}
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
    public void run(TaskMonitor tm) throws Exception {
        tm.setTitle("Adjacency Matrix import");
        tm.setStatusMessage("Adjacency Matrix import");
        
        CyNetwork n = readAdjFormat(inputStream, tm);
        this.networks = new CyNetwork[]{n};
        networkMgr.addNetwork(n);
//        GraphsWithValidation gv = checkSchema(inputStream, graphReader);
//        Graph[] graphs = gv.getGraphs();
//        tm.setProgress(0.50);
//
//        tm.setStatusMessage(format("Creating %d networks from \"%s\".", graphs.length, inputName));
//        this.networks = mapNetworks(graphs);
//        for (CyNetwork n : this.networks)
//            networkMgr.addNetwork(n);
//
//        // set up evidence table if we have cytoscape networks
//        if (this.networks.length > 0) {
//            CyTable table = getOrCreateEvidenceTable();
//            mapGraphsToEvidenceTable(graphs, table);
//            tableMgr.addTable(table);
//        }
//        m.setProgress(1.0);
    }
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    for (VisualStyle style : visualMappingManager.getAllVisualStyles()) {
        if (style.getTitle().equals(GFDNET_VIZMAP_FILE)) {
            return;
        }
    }
    URL url = this.getClass().getClassLoader().getResource(GFDNET_VIZMAP_FILE);
    VizmapReader reader = vizmapReaderManager.getReader(url.toURI(), url.getPath());

    if (reader == null) {
        throw new NullPointerException("Failed to find Default Vizmap loader.");
    }

    insertTasksAfterCurrentTask(reader, new AddVisualStylesTask(reader));
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
/**
 * {@inheritDoc}
 */
@Override
public void run(TaskMonitor m) throws Exception {
    m.setTitle("Import BEL JSON Graph");

    m.setStatusMessage(format("Read and validate \"%s\" against the BEL JSON Graph schema.", inputName));
    GraphsWithValidation gv = checkSchema(inputStream, graphReader);
    Graph[] graphs = gv.getGraphs();
    m.setProgress(0.50);

    m.setStatusMessage(format("Creating %d networks from \"%s\".", graphs.length, inputName));
    this.networks = mapNetworks(graphs);
    for (CyNetwork n : this.networks)
        networkMgr.addNetwork(n);

    // set up evidence table if we have cytoscape networks
    if (this.networks.length > 0) {
        CyTable table = getOrCreateEvidenceTable();
        mapGraphsToEvidenceTable(graphs, table);
        tableMgr.addTable(table);
    }
    m.setProgress(1.0);
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
public List<Cluster> execute(InputTask input, TaskMonitor progress) throws Exception {
	List<Cluster> results = new ArrayList<Cluster>();
	int cores = Runtime.getRuntime().availableProcessors() * 2;
	List<List<Cluster>> jobs = ClusterUtil.divideWork(candidates, cores);
	executor = Executors.newFixedThreadPool(cores);
	Phaser phaser = new Phaser();

	for (List<Cluster> job: jobs) {
		Runnable searchThread = new SeedSearch(model, job, phaser, input, candidates);
		phaser.register();
		executor.execute(searchThread);
	}
	executor.shutdown();
       while (!executor.isTerminated()) {}
	
	//Filter out clusters that are too small or too low-scoring and copy good ones to results
	for (Cluster complex: candidates) {
		if ((complex.getNodes().size() >= input.minSize) && (ClusterScore.score(complex, model) >= input.minScoreThreshold))
			results.add(complex);
		else
			complex.destroy();
	}
	
	return results;
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor arg0) throws Exception {
	// TODO Auto-generated method stub
	synchronized (this) {
		MyControlPanel mainPanel = null;
		
		// First we must make sure that the app is not already open
		if (!isOpen()) {
			mainPanel = new MyControlPanel(swingApplication, registrar, appManager);

			registrar.registerService(mainPanel, CytoPanelComponent.class, new Properties());
		} else {
			mainPanel = getMainPanel();
		}

		if (mainPanel != null) {
			CytoPanel cytoPanel = swingApplication.getCytoPanel(CytoPanelName.WEST);;
			int index = cytoPanel.indexOfComponent(mainPanel);
			cytoPanel.setSelectedIndex(index);
		}
	}
	
}
 

import org.cytoscape.work.TaskMonitor; //导入依赖的package包/类
@Override
public void run(TaskMonitor monitor) throws Exception {
	monitor.setStatusMessage("Executing ForceAtlas2 layout"); 

	List<ExtensionCall> calls = exec.buildExtensionCalls();

	double progress = 0.0;
	for(ExtensionCall call : calls){
		Object callRetValue = plugin.getInteractor().executeExtensionCall(call,false);
		exec.processCallResponse(call,callRetValue);
		++progress;
		monitor.setProgress(progress / ((double)calls.size()));
		
	}
	
}