@Override
protected void complete(TaskMonitor tm) throws Exception {
tm.setProgress(0.4);
tm.setTitle("Set network tables");
tm.setStatusMessage("Setting network tables...");
mergeNetworkTables();
tm.setProgress(0.5);
tm.setTitle("Restore virtual columns");
tm.setStatusMessage("Restoring virtual columns...");
restoreVirtualColumns();
tm.setProgress(0.6);
tm.setTitle("Extract network views");
tm.setStatusMessage("Extracting network views...");
// Read the session file again, this time to extract the network views
networksExtracted = true;
readSessionFile(tm);
tm.setProgress(0.8);
tm.setTitle("Update SUID columns");
tm.setStatusMessage("Updating SUID columns...");
updateSUIDColumns();
super.complete(tm);
}
@Override
public void run(TaskMonitor taskMonitor) {
taskMonitor.setProgress(0.0);
taskMonitor.setTitle("PRWP with Priors ranking of clusters");
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Fetching clusters...");
taskMonitor.setProgress(0.1);
List<NodeCluster> clusters = ClusterUtils.fetchClusters(network);
taskMonitor.setProgress(0.5);
initVariables();
clusters.forEach(NodeCluster::initNodeScores);
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Setting node scores in clusters");
addNodes();
taskMonitor.setProgress(0.6);
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Setting edge scores in clusters");
addEdges();
taskMonitor.setProgress(0.7);
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Calculating PageRank scores");
PageRank<PRNode, PREdge> pageRank = performPageRank();
taskMonitor.setProgress(0.8);
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Inserting scores into clusters");
insertScores(clusters, pageRank);
taskMonitor.setProgress(0.9);
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Insert cluster information in tables");
ClusterUtils.insertResultsInColumns(network, clusters, SHORTNAME);
taskMonitor.setProgress(1.0);
taskMonitor.showMessage(TaskMonitor.Level.INFO, "Done...");
}
@Override
public void run(TaskMonitor monitor) throws Exception {
// TODO Auto-generated method stub
monitor.setTitle("Building the User Interface");
DynNetworkView<T> view = dynNetViewManager.getDynNetworkView(cyNetworkView);
DynNetwork<T> dynamicnetwork = view.getNetwork();
GraphMetricsPanel<T, C> graphMetricsPanel =
new GraphMetricsPanel<T, C>(this.cyActivator, dynamicnetwork);
this.cyActivator
.getCyServiceRegistrar()
.registerService(graphMetricsPanel, CytoPanelComponent.class, new Properties());
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Loading Gene Association File");
taskMonitor.setStatusMessage("Importing annotation file. Please wait...");
taskMonitor.setProgress(-1.0);
this.ontologyDAG = OntologyDAGManager.getOntologyDAG(ontologyDagName);
if (ontologyDAG == null) logger.warn("Could not find associated Ontology DAG.");
else {
termIDList =
ontologyDAG.getDefaultNodeTable().getColumn(CyNetwork.NAME).getValues(String.class);
}
BufferedReader bufRd =
new BufferedReader(new InputStreamReader(is, Charset.forName("UTF-8").newDecoder()));
String line = null;
String[] parts;
while ((line = bufRd.readLine()) != null) {
// Validate.
if (line.contains(COMPATIBLE_VERSION)) break;
}
// Create result table
table =
serviceRegistrar
.getService(CyTableFactory.class)
.createTable(tableName, CyNetwork.NAME, String.class, true, true);
createColumns();
while ((line = bufRd.readLine()) != null) {
if (line.startsWith("!")) continue;
parts = line.split(GA_DELIMITER);
// GA is a fixed format file. Read only valid lines.
if (parts.length >= EXPECTED_COL_COUNT) {
parseGA(parts);
}
}
bufRd.close();
is.close();
is = null;
tables = new CyTable[1];
tables[0] = table;
serviceRegistrar.getService(CyTableManager.class).addTable(table);
}
@Override
public void run(TaskMonitor tm) throws Exception {
tm.setTitle("Loading network from table");
tm.setProgress(0.0);
tm.setStatusMessage("Loading network...");
Workbook workbook = null;
// Load Spreadsheet data for preview.
if (fileType != null
&& (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
|| fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension()))
&& workbook == null) {
try {
workbook = WorkbookFactory.create(is);
} catch (InvalidFormatException e) {
throw new IllegalArgumentException(
"Could not read Excel file. Maybe the file is broken?", e);
} finally {
if (is != null) is.close();
}
}
try {
if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
|| this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
String networkName = ntmp.getName();
if (networkName == null) networkName = workbook.getSheetName(0);
final Sheet sheet = workbook.getSheet(networkName);
reader =
new ExcelNetworkSheetReader(
networkName, sheet, ntmp, nMap, rootNetwork, serviceRegistrar);
} else {
reader = new NetworkTableReader(inputName, is, ntmp, nMap, rootNetwork, serviceRegistrar);
}
} catch (Exception ioe) {
tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
return;
}
loadNetwork(tm);
tm.setProgress(1.0);
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Updating Organism Interactome Data Files");
taskMonitor.setProgress(-1);
taskMonitor.setStatusMessage("Downloading data from BioGRID...");
BiogridDataLoader task = new BiogridDataLoader(props, dataSource, settingFileLocation);
task.extract(true);
final String version = task.getVersion();
taskMonitor.setProgress(1.0d);
taskMonitor.setStatusMessage(
"Organism network data files has been updated to BioGRID version "
+ version
+ ". Please restart Cytoscape to use new data.");
}
/** Executes Task. */
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Loading Network");
taskMonitor.setProgress(0);
taskMonitor.setStatusMessage("Reading in Network Data...");
try {
CyNetworkReaderManager readerManager = factory.getCyNetworkViewReaderManager();
CyNetworkReader reader = readerManager.getReader(url.toURI(), url.getFile());
if (reader == null) {
JOptionPane.showMessageDialog(
factory.getCySwingApplication().getJFrame(),
"Unable to connect to URL " + url,
"URL Connect Error",
JOptionPane.ERROR_MESSAGE);
return;
}
taskMonitor.setStatusMessage("Creating Cytoscape Network...");
reader.run(taskMonitor);
CyNetwork[] networks = reader.getNetworks();
CyNetwork cyNetwork = networks[0];
// TODO: Does CPath2 listen for this?
// Object[] ret_val = new Object[2];
// ret_val[0] = cyNetwork;
// ret_val[1] = url.toString();
//
// Cytoscape.firePropertyChange(Cytoscape.NETWORK_LOADED, null, ret_val);
if (cyNetwork != null) {
informUserOfGraphStats(cyNetwork, taskMonitor);
} else {
StringBuffer sb = new StringBuffer();
sb.append("Could not read network from: ");
sb.append(url);
sb.append("\nThis file may not be a valid file format.");
throw new IOException(sb.toString());
}
taskMonitor.setProgress(1.0);
} catch (Exception e) {
throw new Exception("Unable to load network.", e);
}
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
parentTaskMonitor = taskMonitor;
long start = System.currentTimeMillis();
taskMonitor.setProgress(0.01d);
taskMonitor.setTitle("Loading PSI-MI 2.5.x XML File ");
taskMonitor.setStatusMessage("Loading data file in PSI-MI 2.5 XML format.");
// support to add network into existing collection
this.initNodeMap();
PsimiXmlReader reader = new PsimiXmlReader();
EntrySet result = reader.read(inputStream);
taskMonitor.setProgress(0.4d);
taskMonitor.setStatusMessage("Data Loaded. Mapping Data to Network...");
if (cancelFlag) {
inputStream.close();
reader = null;
result = null;
return;
}
// network = cyNetworkFactory.createNetwork();
String networkCollectionName = this.rootNetworkList.getSelectedValue().toString();
if (networkCollectionName.equalsIgnoreCase(CRERATE_NEW_COLLECTION_STRING)) {
// This is a new network collection, create a root network and a subnetwork, which is a base
// subnetwork
network = cyNetworkFactory.createNetwork();
} else {
// Add a new subNetwork to the given collection
network = this.name2RootMap.get(networkCollectionName).addSubNetwork();
}
mapper = new PSIMI25EntryMapper(network, result);
mapper.map();
taskMonitor.setProgress(1.0d);
logger.info(
"PSI-MI XML Data Import finihsed in " + (System.currentTimeMillis() - start) + " msec.");
}
@Override
public void run(final TaskMonitor taskMonitor) {
taskMonitor.setTitle("Adding variations...");
taskMonitor.setProgress(0.0d);
if (!mergeStrategy.isRetain()) {
final Lock nodesReadLock = model.nodes().getReadWriteLock().readLock();
final Lock featuresReadLock = model.features().getReadWriteLock().readLock();
final Lock variationsWriteLock = model.variations().getReadWriteLock().writeLock();
nodesReadLock.lock();
featuresReadLock.lock();
variationsWriteLock.lock();
try {
for (int i = 0, size = model.features().size(); i < size; i++) {
Feature feature = model.features().get(i);
taskMonitor.setStatusMessage(
"Retrieving variations associated with feature " + feature + "...");
final List<Variation> variations = model.getVariationService().variations(feature);
taskMonitor.setStatusMessage(
resultStatusMessage(variations.size(), "variation", "feature", feature));
// todo: merge strategy
for (Variation variation : variations) {
if (!model.variations().contains(variation)) {
model.variations().add(variation);
}
}
// todo: count doesn't consider existing variations
for (CyNode node : model.nodesFor(feature)) {
addCount(node, model.getNetwork(), "variation_count", variations.size());
}
taskMonitor.setProgress(i / (double) size);
}
} finally {
nodesReadLock.unlock();
featuresReadLock.unlock();
variationsWriteLock.unlock();
}
}
taskMonitor.setProgress(1.0d);
}
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Exiting Chimera");
structureManager.exitChimera();
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
desktopApp.getJFrame().getGlassPane().setVisible(true);
taskMonitor.setTitle("Gene Set / Mutation Analysis");
taskMonitor.setStatusMessage("Loading file...");
taskMonitor.setProgress(.25d);
try {
Map<String, Integer> geneToSampleNumber = null;
Map<String, String> geneToSampleString = null;
Map<String, Set<String>> sampleToGenes = null;
Set<String> selectedGenes = null;
if (format.equals("MAF")) {
sampleToGenes =
new MATFileLoader().loadSampleToGenes(file.getAbsolutePath(), chooseHomoGenes);
selectedGenes =
CancerAnalysisUtilitites.selectGenesInSamples(sampleCutoffValue, sampleToGenes);
} else if (format.equals("GeneSample")) {
geneToSampleNumber = new HashMap<String, Integer>();
geneToSampleString = new HashMap<String, String>();
loadGeneSampleFile(file, geneToSampleNumber, geneToSampleString);
selectedGenes = selectGenesBasedOnSampleCutoff(geneToSampleNumber, sampleCutoffValue);
} else if (format.equals("GeneSet")) {
selectedGenes = loadGeneSetFile(file);
}
// Check if it is possible to construct the network
// given the sample size.
if (useLinkers) {
taskMonitor.setStatusMessage("Checking FI Network size...");
FINetworkService fiService = PlugInScopeObjectManager.getManager().getNetworkService();
Integer cutoff = fiService.getNetworkBuildSizeCutoff();
if (cutoff != null && selectedGenes.size() >= cutoff) {
JOptionPane.showMessageDialog(
desktopApp.getJFrame(),
"The size of the gene set is too big. Linker genes should not be used!\n"
+ "Please try again without using linker genes.",
"Error in Building Network",
JOptionPane.ERROR_MESSAGE);
desktopApp.getJFrame().getGlassPane().setVisible(false);
return;
}
}
CytoPanel controlPane = desktopApp.getCytoPanel(CytoPanelName.WEST);
int selectedIndex = controlPane.getSelectedIndex();
taskMonitor.setStatusMessage("Constructing FI Network...");
taskMonitor.setProgress(.50d);
CyNetwork network = constructFINetwork(selectedGenes, file.getName());
network.getDefaultNetworkTable().getRow(network.getSUID()).set("name", file.getName());
if (network == null) {
JOptionPane.showMessageDialog(
desktopApp.getJFrame(),
"Cannot find any functional interaction among provided genes.\n"
+ "No network can be constructed.\n"
+ "Note: only human gene names are supported.",
"Empty Network",
JOptionPane.INFORMATION_MESSAGE);
desktopApp.getJFrame().getGlassPane().setVisible(false);
return;
}
netManager.addNetwork(network);
// Fix for missing default value persistence in CyTables
// Should be remedied in the 3.1 api
CyTable nodeTable = network.getDefaultNodeTable();
for (Object name : network.getNodeList()) {
CyNode node = (CyNode) name;
Long nodeSUID = node.getSUID();
nodeTable.getRow(nodeSUID).set("isLinker", false);
}
controlPane.setSelectedIndex(selectedIndex);
if (sampleToGenes != null) {
geneToSampleNumber = new HashMap<String, Integer>();
geneToSampleString = new HashMap<String, String>();
Map<String, Set<String>> geneToSamples =
InteractionUtilities.switchKeyValues(sampleToGenes);
geneToSamples.keySet().retainAll(selectedGenes);
for (String gene : geneToSamples.keySet()) {
Set<String> samples = geneToSamples.get(gene);
geneToSampleNumber.put(gene, samples.size());
geneToSampleString.put(gene, InteractionUtilities.joinStringElements(";", samples));
}
}
taskMonitor.setStatusMessage("Formatting network attributes...");
taskMonitor.setProgress(.65d);
CyTableManager tableManager = new CyTableManager();
CyNetworkView view = viewFactory.createNetworkView(network);
tableManager.storeFINetworkVersion(view);
tableManager.storeDataSetType(network, CyTableFormatter.getSampleMutationData());
viewManager.addNetworkView(view);
if (geneToSampleNumber != null && !geneToSampleNumber.isEmpty()) {
tableManager.loadNodeAttributesByName(view, "sampleNumber", geneToSampleNumber);
}
if (geneToSampleString != null && !geneToSampleString.isEmpty()) {
tableManager.loadNodeAttributesByName(view, "samples", geneToSampleString);
}
// Check if linker genes are to be used.
if (useLinkers) {
taskMonitor.setStatusMessage("Fetching linker genes...");
Map<String, Boolean> geneToIsLinker = new HashMap<String, Boolean>();
for (Object name : network.getNodeList()) {
CyNode node = (CyNode) name;
Long suid = node.getSUID();
String nodeName = network.getDefaultNodeTable().getRow(suid).get("name", String.class);
geneToIsLinker.put(nodeName, !selectedGenes.contains(nodeName));
}
tableManager.loadNodeAttributesByName(view, "isLinker", geneToIsLinker);
}
if (fetchFIAnnotations) {
taskMonitor.setStatusMessage("Fetching FI annotations...");
new FIAnnotationHelper().annotateFIs(view, new RESTFulFIService(), tableManager);
}
if (view.getModel().getEdgeCount() != 0) {
for (CyEdge edge : view.getModel().getEdgeList()) {
tableManager.storeEdgeName(edge, view);
}
}
BundleContext context = PlugInScopeObjectManager.getManager().getBundleContext();
ServiceReference visHelperRef = context.getServiceReference(FIVisualStyle.class.getName());
if (visHelperRef != null) {
FIVisualStyleImpl styleHelper = (FIVisualStyleImpl) context.getService(visHelperRef);
styleHelper.setVisualStyle(view);
styleHelper.setLayout();
}
// BundleContext context =
// PlugInScopeObjectManager.getManager().getBundleContext();
// ServiceReference styleHelperRef =
// context.getServiceReference(FIVisualStyleImpl.class.getName());
// FIVisualStyleImpl styleHelper = (FIVisualStyleImpl)
// context.getService(styleHelperRef);
taskMonitor.setProgress(1.0d);
} catch (Exception e) {
JOptionPane.showMessageDialog(
desktopApp.getJFrame(),
"Error in Loading File: " + e.getMessage(),
"Error in Loading",
JOptionPane.ERROR_MESSAGE);
desktopApp.getJFrame().getGlassPane().setVisible(false);
}
desktopApp.getJFrame().getGlassPane().setVisible(false);
}
@SuppressWarnings("unchecked")
@Override
protected void doLayout(TaskMonitor taskMonitor) {
if (!context.m_cancel && networkView != null && dynView != null) {
taskMonitor.setTitle("Compute Dynamic Kamada Kawai Force Layout");
taskMonitor.setStatusMessage("Running energy minimization...");
taskMonitor.setProgress(0);
// int size = (int) (4*50*Math.sqrt(nodesToLayOut.size()));
int size =
(int)
(dynView.getCurrentVisualStyle().getDefaultValue(BasicVisualLexicon.NODE_SIZE)
* Math.sqrt(nodesToLayOut.size()));
// int size =(int)
// dynView.getCurrentVisualStyle().getDefaultValue(BasicVisualLexicon.NETWORK_HEIGHT).floatValue();
snap = new DynNetworkSnapshotImpl<T>(dynView, context.m_attribute_name);
kklayout = new KKLayout<T>(snap, new Dimension(4 * size, 4 * size));
List<Double> events = context.m_event_list;
// Full KK evaluation to initialize the network at time t=0
kklayout.setAdjustForGravity(true);
kklayout.setExchangeVertices(context.m_exchange_nodes);
kklayout.setAutoscaling(context.m_autoscale);
kklayout.setMaxIterations(1000);
// Compute incremental KK. The number of iterations is proportional to the time to the next
// event.
double t0, t1;
for (int t = 0; t < events.size() - 1; t++) {
t0 = events.get(Math.max(0, t - context.m_past_events));
t1 = events.get(Math.min(events.size() - 1, t + 1 + context.m_future_events));
snap.setInterval((DynInterval<T>) new DynIntervalDouble(t0, t1), t, 1000, 1000);
if (!context.m_attribute_name.equals("none"))
kklayout.setDistance(new DijkstraShortestPath<T>(snap, snap.getWeightMap(), 100));
else kklayout.setDistance(new UnweightedShortestPath<T>(snap));
kklayout.initialize();
kklayout.run();
updateGraph((DynInterval<T>) new DynIntervalDouble(events.get(t), events.get(t + 1)));
kklayout.setMaxIterations(
(int) (context.m_iteration_rate * (events.get(t + 1) - events.get(t))));
if (t % 10 == 0) taskMonitor.setProgress(((double) t) / (double) events.size());
taskMonitor.setStatusMessage("Running energy minimization... " + t + "/" + events.size());
}
// Finalize layout
layout.finalize();
taskMonitor.setProgress(1);
// Set the current network view
initializePositions(size);
layout.initNodePositions(timeInterval);
view.fitContent();
view.updateView();
}
}
public void run(TaskMonitor monitor) {
monitor.setTitle("Performing MCL cluster");
this.monitor = monitor;
if (network == null) network = clusterManager.getNetwork();
context.setNetwork(network);
NodeCluster.init();
DistanceMatrix matrix = context.edgeAttributeHandler.getMatrix();
if (matrix == null) {
monitor.showMessage(
TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
return;
}
// Update our tunable results
clusterAttributeName = context.getClusterAttribute();
createGroups = context.advancedAttributes.createGroups;
if (canceled) return;
// Cluster the nodes
runMCL =
new RunMCL(
matrix,
context.inflation_parameter,
context.iterations,
context.clusteringThresh,
context.maxResidual,
context.maxThreads,
monitor);
runMCL.setDebug(debug);
if (canceled) return;
monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
// results = runMCL.run(monitor);
List<NodeCluster> clusters = runMCL.run(network, monitor);
if (clusters == null) return; // Canceled?
monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
// Remove any leftover groups from previous runs
removeGroups(network, GROUP_ATTRIBUTE);
monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
params = new ArrayList<String>();
context.edgeAttributeHandler.setParams(params);
List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
results = new AbstractClusterResults(network, nodeClusters);
monitor.showMessage(TaskMonitor.Level.INFO, "MCL results:\n" + results);
if (context.vizProperties.showUI) {
monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
insertTasksAfterCurrentTask(
new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges));
}
}
