Java TaskMonitor.setProgress方法代码示例

import org.cytoscape.work.TaskMonitor; //导入方法依赖的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; //导入方法依赖的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()));
		
	}
	
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
	if (taskMonitor != null) {
		taskMonitor.setTitle("Writing to D3-Style JSON");
		taskMonitor.setStatusMessage("Writing network in D3.js format...");
		taskMonitor.setProgress(-1.0);
	}

	network2jsonMapper.writeValue(new OutputStreamWriter(outputStream, EncodingUtil.getEncoder()), network);
	outputStream.close();

	if (taskMonitor != null) {
		taskMonitor.setStatusMessage("Success.");
		taskMonitor.setProgress(1.0);
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
/**
 * Calculate theta corresponding to theta
 * @param d1
 * @param d2
 * @param l1
 * @param l2
 * @param varList
 * @param M
 * @param delta
 * @param monitor 
 * @param secondStep 
 * @param firstStep 
 * @return
 * @throws InterruptedException
 */
public static double findTheta(double[][] d1, double[][] d2,
		double l1, double l2, String[] varList, int M,
		double delta, TaskMonitor monitor, double firstStep, double secondStep) throws InterruptedException {
	   	
	double portion = 0.2;
	double remaining = secondStep;
	
	standardizeData(d1);
   	standardizeData(d2);
   	
   	KddnSettings dataSetting = new KddnSettings(l1, l2, 0.05, d1, d2, varList, 0.05);
   	KddnResults dataResult = solveDDN(dataSetting);

   	double high = 0.5;
   	double low = 0.02;
   	double mid = (high-low) / 2 + low;

   	double deviation = thetaError(d1, d2, l1, l2, varList, M, mid, dataResult);
   	
   	while(high - low > 0.01) {
   		if(deviation > delta) {
   			high = mid;
   			mid = (high-low) / 2 + low;
   			deviation = thetaError(d1, d2, l1, l2, varList, M, mid, dataResult);
   		} else {
   			low = mid;
   			mid = (high-low) / 2 + low;
   			deviation = thetaError(d1, d2, l1, l2, varList, M, mid, dataResult);
   		}
   		
   		double progress = remaining * portion;
   		remaining -= progress;
   		portion += 0.05;
   		
   		monitor.setProgress(firstStep + secondStep - remaining);
   	}
   	
	return mid;
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
	if (taskMonitor != null) {
		taskMonitor.setTitle("Writing Network View to D3-Style JSON");
		taskMonitor.setStatusMessage("Writing D3 style JSON...");
		taskMonitor.setProgress(-1.0);
	}
	networkView2jsonMapper.writeValue(new OutputStreamWriter(outputStream, EncodingUtil.getEncoder()), view);
	outputStream.close();

	if (taskMonitor != null) {
		taskMonitor.setStatusMessage("Success.");
		taskMonitor.setProgress(1.0);
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
	if (network == null) return;
	
	taskMonitor.setStatusMessage("Removing groups.");
	int i = 0;
	Set<CyGroup> groupSet = groupManager.getGroupSet(network);
	for (CyGroup group : groupSet) {
		groupManager.destroyGroup(group);
		
		i++;
		taskMonitor.setProgress((double) i / (double) groupSet.size());
	}
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
@Override
public void run(TaskMonitor tm) {
	if (parentNetwork == null) {
		tm.showMessage(TaskMonitor.Level.ERROR, "Source network must be specified.");
		return;
	}
	
	tm.setProgress(0.2);

	// create subnetwork and add selected nodes and appropriate edges
	final CySubNetwork newNet = rootNetMgr.getRootNetwork(parentNetwork).addSubNetwork();
	
	//We need to cpy the columns to local tables, since copying them to default table will duplicate the virtual columns.
	addColumns(parentNetwork.getTable(CyNode.class, CyNetwork.LOCAL_ATTRS), newNet.getTable(CyNode.class, CyNetwork.LOCAL_ATTRS));
	addColumns(parentNetwork.getTable(CyEdge.class, CyNetwork.LOCAL_ATTRS), newNet.getTable(CyEdge.class, CyNetwork.LOCAL_ATTRS) );
	addColumns(parentNetwork.getTable(CyNetwork.class, CyNetwork.LOCAL_ATTRS), newNet.getTable(CyNetwork.class, CyNetwork.LOCAL_ATTRS));

	tm.setProgress(0.3);
	
	for(CyNode node : nodes) {
		newNet.addNode(node);
		cloneRow(parentNetwork.getRow(node), newNet.getRow(node));
		//Set rows and edges to not selected state to avoid conflicts with table browser
		newNet.getRow(node).set(CyNetwork.SELECTED, false);
	}

	tm.setProgress(0.4);
	
	for (final CyEdge edge : getEdges(parentNetwork, nodes)) {
		newNet.addEdge(edge);
		cloneRow(parentNetwork.getRow(edge), newNet.getRow(edge));
		//Set rows and edges to not selected state to avoid conflicts with table browser
		newNet.getRow(edge).set(CyNetwork.SELECTED, false);
	}
	
	tm.setProgress(0.5);
	
	newNet.getRow(newNet).set(CyNetwork.NAME, getNetworkName());

	resultNetwork = newNet;
	tm.setProgress(1.0);
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
@Override
public void run(final TaskMonitor taskMonitor) throws Exception{
	CyNetwork outputNet = null, trainedNet = null, modelNetwork = null;
	taskMonitor.setTitle("SCODE Progress");
	try {
		
		if (userInput.trainNewModel){
			// Train a template
			if (userInput.customModel) {
				// Load custom template
				modelNetwork = getNetwork(userInput.bayesModel.getSelectedValue());
			} else {
				// Load built-in template
				modelNetwork = ClusterUtil.getDefaultModel(userInput.weightName.getSelectedValue(), SavePolicy.DO_NOT_SAVE);
			}
			// Create empty network for saving state of model
			outputNet = CyActivator.networkFactory.createNetwork();
			outputNet.getRow(outputNet).set(CyNetwork.NAME, CyActivator.networkNaming.getSuggestedNetworkTitle("Supervised Complex Model"));
			
			// Set task monitor progress
			taskMonitor.setProgress(0.1);
			taskMonitor.setStatusMessage("Training...");
			clusterModel = new SupervisedModel(rootNetwork, modelNetwork,outputNet, userInput);
			CyActivator.networkManager.addNetwork(outputNet); 
			taskMonitor.setStatusMessage("Training is done.");
			taskMonitor.setProgress(1.0);
		}
		else {
			// Use an existing model
			taskMonitor.setProgress(0.1);
			taskMonitor.setStatusMessage("Loading model...");
			trainedNet = getNetwork(userInput.existingModel.getSelectedValue());
			clusterModel = new SupervisedModel(rootNetwork, trainedNet, userInput);
			
			taskMonitor.setStatusMessage("Model loaded.");
			taskMonitor.setProgress(1.0);
		}
	
	} catch ( Exception e){
		e.printStackTrace();
		throw new Exception("Training didn't work out so well..." + e.getMessage());
	}
   
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
/**
 * calculate DDN and p-value
 * @param network
 * @param paras
 * @param numPermutation 
 * @param monitor 
 * @param firstStep 
 * @param secondStep 
 * @return
 * @throws InterruptedException 
 */
public static KddnResults calculatePvalue(KddnResults network, 
		final KddnSettings paras, 
		int numPermutation, TaskMonitor monitor, 
		double firstStep, double secondStep) throws InterruptedException {

	// copy settings
	double pValueCutoff = paras.pValueCutoff;
    String[] varList = paras.varList;
    double[][] data1 = paras.data1;
    double[][] data2 = paras.data2;
    double lambda1 = paras.lambda1;
    double lambda2 = paras.lambda2;
    double alpha = paras.alpha;
    int p = paras.p;
    int N1 = paras.N1;
    int N2 = paras.N2;
    double theta = paras.theta;
    int[][] W = paras.W;
    double delta = paras.delta;
    
    int[][] difNet = network.getDifferentialNetwork();
    int[][] permNet = new int[p][p];
    int numDif = 0;
    for(int i=0; i<p; i++)
    	for(int j=0; j<p; j++) {
    		permNet[i][j] = 0;
    		if(difNet[i][j] != 0)
    			numDif++;
    	}
            
    double thirdStep = 1 - firstStep - secondStep;
    double progress = firstStep + secondStep;
    
    for(int i=0; i<numPermutation; i++) {
    	int[] permId = permutation(N1+N2);
    	double[][] pd1 = permute(data1, data2, permId, 0, N1-1);
    	double[][] pd2 = permute(data1, data2, permId, N1, N1+N2-1);
    	
    	standardizeData(pd1);
    	standardizeData(pd2);
    	
    	KddnSettings aRun = new KddnSettings(lambda1, lambda2, pValueCutoff, theta, W, pd1, pd2, varList, alpha, delta);
    	KddnResults aResult = solveDDN(aRun);
    	permNet = addMatrix(permNet, aResult.getDifferentialBeta());

    	progress = firstStep + secondStep + thirdStep * (i+1) / numPermutation;
		monitor.setProgress(progress);
    }
    
    double[][] pValue = new double[numDif][4];
    int rowId = 0;
    for(int i=0; i<p-1; i++)
    	for(int j=i+1; j<p; j++) {
    		if(difNet[i][j] != 0) {
    			pValue[rowId][0] = i;
    			pValue[rowId][1] = j;
    			double p1 = (double) permNet[i][j] / numPermutation;
    			double p2 = (double) permNet[j][i] / numPermutation;
    			pValue[rowId][2] = Math.min(p1, p2);
    			if(difNet[i][j] == 1)
    				pValue[rowId][3] = 1;
    			else
    				pValue[rowId][3] = 2;
    			
    			rowId++;
    		}
    	}
    
	return new KddnResults(paras.varList, network.adjacentMatrix, network.beta, pValue);
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
@Override
public void run(final TaskMonitor taskMonitor)
{
    taskMonitor.setTitle("Retrieving features...");
    taskMonitor.setProgress(0.0d);

    // if merge strategy is retain, skip to end
    // foreach node in model
    //   retrieve existing features from node --> feature mapping
    //   foreach ensembl gene id per node
    //     retrieve feature for ensembl gene id
    //       if merge strategy is replace, remove existing node --> feature mappings and features from features and add new ones
    //       else if merge strategy is merge, remove existing node --> feature mappings and features from features, perform the merge and re-add merged ones
    //       (note that removing feature mappings should also remove downstream variations and consequences, and should update counts in node table)
    if (!mergeStrategy.isRetain())
    {
        final Lock nodesReadLock = model.nodes().getReadWriteLock().readLock();
        final Lock featuresWriteLock = model.features().getReadWriteLock().writeLock();
        nodesReadLock.lock();
        featuresWriteLock.lock();
        try
        {
            for (int i = 0, size = model.nodes().size(); i < size; i++)
            {
                CyNode node = model.nodes().get(i);
                for (String ensemblGeneId : ensemblGeneIds(node, model.getNetwork(), model.getEnsemblGeneIdColumn()))
                {
                    if (StringUtils.isNotBlank(ensemblGeneId))
                    {
                        taskMonitor.setStatusMessage("Retrieving genome feature for Ensembl Gene " + ensemblGeneId + "...");
                        /*
                          
                          todo:  retrofit.RetrofitError with current version of ensembl-rest-client (1.2)
                          
                          retrofit.RetrofitError
                          at retrofit.RetrofitError.httpError(RetrofitError.java:37)
                          at retrofit.RestAdapter$RestHandler.invokeRequest(RestAdapter.java:343)
                          at retrofit.RestAdapter$RestHandler.invoke(RestAdapter.java:222)
                          at com.sun.proxy.$Proxy38.lookup(Unknown Source)
                          at org.dishevelled.variation.ensembl.EnsemblRestClientFeatureService.feature(EnsemblRestClientFeatureService.java:69)
                          at org.dishevelled.variation.cytoscape3.internal.RetrieveFeaturesTask.run(RetrieveFeaturesTask.java:94)
                          at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
                          at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)
                          at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
                          at java.util.concurrent.FutureTask.run(FutureTask.java:262)
                          at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
                          at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
                          at java.lang.Thread.run(Thread.java:745)

                          Ensembl search says:
                          Ensembl gene ENSG00000157763 is no longer in the database but it has been mapped to 1 deprecated identifier. Not a Primary Assembly Gene.

                          Fixed with new Ensembl gene identifiers for HLA-A, HLA-B, HLA-C, HLA-DQB1.
                          Need to handle this error appropriately; should probably use custom error handler in ensembl-rest-client APIs

                          MOVE THIS TO VARIATION LIBRARY INSIDE feature CALL

                        */
                        Feature feature = model.getFeatureService().feature(model.getSpecies(), model.getReference(), ensemblGeneId);
                        taskMonitor.setStatusMessage(resultStatusMessage(feature == null ? 0 : 1, "genome feature", "Ensembl Gene", ensemblGeneId));
                        if (feature != null)
                        {
                            model.add(node, feature);
                        }
                    }
                }
                taskMonitor.setProgress(i / (double) size);
            }
        }
        finally
        {
            nodesReadLock.unlock();
            featuresWriteLock.unlock();
        }
    }
    taskMonitor.setProgress(1.0d);
}
 

import org.cytoscape.work.TaskMonitor; //导入方法依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
	taskMonitor.setTitle("PathwayCommons: Expanding Selected Nodes to a New Network");
	if(cancelled) return;
	
	final String column = columnSelection.getSelectedValue();
	final String graphType = querySelection.getSelectedValue();
	taskMonitor.setStatusMessage("Getting the specified attribute values (IDs) from selected nodes");
	//collect the specified column values from the selected nodes
	Set<String> values = new HashSet<String>();
	for(CyNode node : network.getNodeList()) {
		if (!network.getRow(node).get(CyNetwork.SELECTED, Boolean.class))
			continue;			
		String val = network.getRow(node).get(column, String.class);
		if(val != null && !val.isEmpty())
			values.add(val);
	}
	
	if(values.isEmpty()) {
		taskMonitor.setStatusMessage("No values (IDs) " +
				"found in the attribute column of currently selected nodes.");
		cancel();
		return;
	}
	
	taskMonitor.setProgress(0.1);
	
	//execute, create a new network and view (if any data will be returned from the server)
	taskMonitor.setStatusMessage("Executing " + graphType + " query (in Pathway Commons)");		
	final CPathGraphQuery graphQ = App.client.createGraphQuery()
   			.kind(("NEIGHBORHOOD".equals(graphType)) ? GraphType.NEIGHBORHOOD : GraphType.PATHSBETWEEN)
   			.sources(values)
   			.datasourceFilter(App.options.selectedDatasources())
			.direction(("NEIGHBORHOOD".equals(graphType)) ? Direction.UNDIRECTED : null)
   			//.limit(1) TODO set limit via tunables (default is 1)
   			.organismFilter(App.options.selectedOrganisms());
   	App.cyServices.taskManager.execute(new TaskIterator(
   			new NetworkAndViewTask(graphQ, null)
       		));	
	
   	taskMonitor.setStatusMessage("Done");   	
	taskMonitor.setProgress(1.0);
}