@Override
public void run(TaskMonitor taskMonitor) throws Exception {
JAXBContext jaxbContext =
JAXBContext.newInstance(CYTABLES_PACKAGE, getClass().getClassLoader());
taskMonitor.setProgress(0.33);
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
taskMonitor.setProgress(0.67);
cyTables = (CyTables) unmarshaller.unmarshal(inputStream);
taskMonitor.setProgress(1);
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
if (network == null) network = appMgr.getCurrentNetwork();
views = new ArrayList<CyNetworkView>(viewMgr.getNetworkViews(network));
taskMonitor.showMessage(
TaskMonitor.Level.INFO, "Views for network " + DataUtils.getNetworkTitle(network));
for (CyNetworkView view : views) {
taskMonitor.showMessage(TaskMonitor.Level.INFO, " " + view);
return;
}
}
@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()));
}
}
@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);
}
private void loadNetwork(TaskMonitor tm) throws IOException {
final CyNetwork network = this.rootNetwork.addSubNetwork();
tm.setProgress(0.10);
this.reader.setNetwork(network);
if (this.cancelled) return;
this.reader.read();
tm.setProgress(0.80);
if (this.cancelled) return;
networks = new CyNetwork[] {network};
tm.setProgress(1.0);
}
/**
* Inform User of Network Stats.
*
* @param taskMonitor
*/
private void informUserOfGraphStats(CyNetwork newNetwork, TaskMonitor taskMonitor) {
NumberFormat formatter = new DecimalFormat("#,###,###");
StringBuffer sb = new StringBuffer();
// Give the user some confirmation
sb.append("Successfully loaded network from: ");
sb.append(url);
sb.append("\n\nNetwork contains " + formatter.format(newNetwork.getNodeCount()));
sb.append(" nodes and " + formatter.format(newNetwork.getEdgeCount()));
sb.append(" edges.\n\n");
// TODO: Port this
// if (newNetwork.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties()
//
// .getProperty("viewThreshold"))) {
// sb.append("Network is under "
// + CytoscapeInit.getProperties().getProperty("viewThreshold")
// + " nodes. A view will be automatically created.");
// } else {
// sb.append("Network is over "
// + CytoscapeInit.getProperties().getProperty("viewThreshold")
// + " nodes. A view has not been created."
// + " If you wish to view this network, use "
// + "\"Create View\" from the \"Edit\" menu.");
// }
taskMonitor.setStatusMessage(sb.toString());
}
@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 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 CyNetworkView buildCyNetworkView(final CyNetwork network) {
final CyNetworkView view = networkViewFactory.createNetworkView(network);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
TaskIterator itr =
layout.createTaskIterator(
view, layout.getDefaultLayoutContext(), CyLayoutAlgorithm.ALL_NODE_VIEWS, "");
Task nextTask = itr.next();
try {
nextTask.run(parentTaskMonitor);
} catch (Exception e) {
throw new RuntimeException("Could not finish layout", e);
}
parentTaskMonitor.setProgress(1.0d);
return view;
}
@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);
}
@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
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);
}
/**
* Calculates the node distances.
*
* @return the <code>int[][]</code> array of calculated distances or null if the task was canceled
* or there was an error
*/
public int[][] calculate() {
int currentProgress = 0;
this.maxValue = distances.length;
CyNode[] nodes = new CyNode[nodesList.size()];
// TODO: REMOVE
// System.err.println( "Calculating all node distances.. for: "
// +nodesList.size()+" and "+nodes.length );
// We don't have to make new Integers all the time, so we store the index
// Objects in this array for reuse.
Integer[] integers = new Integer[nodes.length];
// Fill the nodes array with the nodes in their proper index locations.
// int index;
CyNode from_node;
for (int i = 0; i < nodes.length; i++) {
from_node = (CyNode) nodesList.get(i);
if (from_node == null) {
continue;
}
int index = ((Integer) nodeIndexToMatrixIndexMap.get(from_node.getSUID())).intValue();
// index = ((Integer) nodeIndexToMatrixIndexMap.get(new
// Integer(from_node.getRootGraphIndex()))).intValue();
if ((index < 0) || (index >= nodes.length)) {
System.err.println(
"WARNING: GraphNode \""
+ from_node
+ "\" has an index value that is out of range: "
+ index
+ ". Graph indices should be maintained such "
+ "that no index is unused.");
return null;
}
if (nodes[index] != null) {
System.err.println(
"WARNING: GraphNode \""
+ from_node
+ "\" has an index value ( "
+ index
+ " ) that is the same as "
+ "that of another GraphNode ( \""
+ nodes[index]
+ "\" ). Graph indices should be maintained such "
+ "that indices are unique.");
return null;
}
nodes[index] = from_node;
Integer in = new Integer(index);
integers[index] = in;
}
LinkedList queue = new LinkedList();
boolean[] completed_nodes = new boolean[nodes.length];
Iterator neighbors;
CyNode to_node;
CyNode neighbor;
int neighbor_index;
int to_node_distance;
int neighbor_distance;
for (int from_node_index = 0; from_node_index < nodes.length; from_node_index++) {
if (this.interrupted) {
// The task was canceled
this.distances = null;
return this.distances;
}
from_node = nodes[from_node_index];
if (from_node == null) {
// Make the distances in this row all Integer.MAX_VALUE.
if (distances[from_node_index] == null) {
distances[from_node_index] = new int[nodes.length];
}
Arrays.fill(distances[from_node_index], Integer.MAX_VALUE);
continue;
}
// TODO: REMOVE
// System.err.print( "Calculating node distances from graph node " +
// from_node );
// System.err.flush();
// Make the distances row and initialize it.
if (distances[from_node_index] == null) {
distances[from_node_index] = new int[nodes.length];
}
Arrays.fill(distances[from_node_index], Integer.MAX_VALUE);
distances[from_node_index][from_node_index] = 0;
// Reset the completed nodes array.
Arrays.fill(completed_nodes, false);
// Add the start node to the queue.
queue.add(integers[from_node_index]);
while (!(queue.isEmpty())) {
if (this.interrupted) {
// The task was canceled
this.distances = null;
return this.distances;
}
int index = ((Integer) queue.removeFirst()).intValue();
if (completed_nodes[index]) {
continue;
}
completed_nodes[index] = true;
to_node = nodes[index];
to_node_distance = distances[from_node_index][index];
if (index < from_node_index) {
// Oh boy. We've already got every distance from/to this node.
int distance_through_to_node;
for (int i = 0; i < nodes.length; i++) {
if (distances[index][i] == Integer.MAX_VALUE) {
continue;
}
distance_through_to_node = to_node_distance + distances[index][i];
if (distance_through_to_node <= distances[from_node_index][i]) {
// Any immediate neighbor of a node that's already been
// calculated for that does not already have a shorter path
// calculated from from_node never will, and is thus complete.
if (distances[index][i] == 1) {
completed_nodes[i] = true;
}
distances[from_node_index][i] = distance_through_to_node;
}
} // End for every node, update the distance using the distance from
// to_node.
// So now we don't need to put any neighbors on the queue or
// anything, since they've already been taken care of by the previous
// calculation.
continue;
} // End if to_node has already had all of its distances calculated.
neighbors = getNeighbors(to_node).iterator();
// neighbors = perspective.neighborsList(to_node).iterator();
while (neighbors.hasNext()) {
if (this.interrupted) {
this.distances = null;
return this.distances;
}
neighbor = (CyNode) neighbors.next();
neighbor_index = ((Integer) nodeIndexToMatrixIndexMap.get(neighbor.getSUID())).intValue();
// neighbor_index = ((Integer) nodeIndexToMatrixIndexMap.get(new
// Integer(neighbor.getRootGraphIndex()))).intValue();
// If this neighbor was not in the incoming List, we cannot include
// it in any paths.
if (nodes[neighbor_index] == null) {
distances[from_node_index][neighbor_index] = Integer.MAX_VALUE;
continue;
}
if (completed_nodes[neighbor_index]) {
// We've already done everything we can here.
continue;
}
neighbor_distance = distances[from_node_index][neighbor_index];
if ((to_node_distance != Integer.MAX_VALUE)
&& (neighbor_distance > (to_node_distance + 1))) {
distances[from_node_index][neighbor_index] = (to_node_distance + 1);
queue.addLast(integers[neighbor_index]);
}
// TODO: REMOVE
// System.out.print( "." );
// System.out.flush();
} // For each of the next nodes' neighbors
// TODO: REMOVE
// System.out.print( "|" );
// System.out.flush();
} // For each to_node, in order of their (present) distances
// TODO: REMOVE
/*
System.err.println( "done." );
*/
// Calculate Percentage. This must be a value between 0..100.
int percentComplete = (int) (((double) currentProgress / maxValue) * 100);
// Estimate Time Remaining
long timeRemaining = maxValue - currentProgress;
// Update the Task Monitor.
// This automatically updates the UI Component w/ progress bar.
if (taskMonitor != null) {
taskMonitor.setProgress(percentComplete);
taskMonitor.setStatusMessage(
"Calculating Node Distances: " + currentProgress + "of " + maxValue);
// taskMonitor.setEstimatedTimeRemaining(timeRemaining);
}
currentProgress++;
} // For each from_node
// TODO: REMOVE
// System.err.println( "..Done calculating all node distances." );
return distances;
} // calculate
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));
}
}
@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 taskMonitor) throws Exception {
CaseList caseList = (CaseList) caseSetComboBox.getSelectedItem();
Object[] profiles = profileList.getSelectedValues();
String geneSymbolField = (String) geneSymbolComboBox.getSelectedItem();
// update the configuration to store this field
MondrianApp app = MondrianApp.getInstance();
CyNetwork currentNetwork = app.getAppManager().getCurrentNetwork();
// call the next two lines in the right order!
app.getMondrianConfiguration()
.setNetworkGeneSymbolAttr(currentNetwork.getSUID(), geneSymbolField);
Map<String, Long> geneSymbolMap =
app.getMondrianConfiguration().getGeneNodeMap(currentNetwork.getSUID());
List<String> genes = new ArrayList<String>(geneSymbolMap.keySet());
// Extract data from web service
int p = 1;
List<GeneticProfile> profileList = new ArrayList<GeneticProfile>();
List<MondrianCyTable> importedTables = new ArrayList<MondrianCyTable>();
CyNetwork network = app.getAppManager().getCurrentNetwork();
CancerStudy study = (CancerStudy) cancerStudyComboBox.getSelectedItem();
for (Object obj : profiles) {
GeneticProfile profile = (GeneticProfile) obj;
profileList.add(profile);
taskMonitor.setStatusMessage("Loading genetic profile: " + profile.getName());
taskMonitor.setProgress(p++ / (double) profiles.length);
CyTable table =
MondrianApp.getInstance()
.getTableFactory()
.createTable(profile.getName(), CyIdentifiable.SUID, Long.class, true, true);
DataTypeMatrix matrix = portalClient.getProfileData(caseList, profile, genes);
List<String> dataColNames = matrix.getDataColNames();
for (String colName : dataColNames) {
if (profile.getType() == GENETIC_PROFILE_TYPE.MUTATION_EXTENDED) {
table.createColumn(colName, String.class, false);
} else {
table.createColumn(colName, Double.class, false);
}
}
// Add rows
for (String rowName : matrix.getRowNames()) {
long suid = geneSymbolMap.get(rowName);
CyRow row = table.getRow(suid);
// row.set("selected", currentNetwork.getDefaultNodeTable().getRow(suid).get("selected",
// Boolean.class));
// row.set(geneSymbolField, rowName);
int i = 0;
for (String colName : dataColNames) {
row.set(colName, matrix.getDataRow(rowName).get(i++));
}
}
log.debug(
"Loading genetic profile: "
+ profile.getName()
+ "; Insert Table: "
+ matrix.getNumRows()
+ ", "
+ matrix.getDataColNames().size());
MondrianCyTable mondrianCyTable = new MondrianCyTable(study, profile, caseList, table);
importedTables.add(mondrianCyTable);
//
}
app.getMondrianConfiguration().registerMondrianTables(network, importedTables);
// app.getMondrianConfiguration().cbioDataImport(currentNetwork.getSUID(), profileList,
// caseList);
}
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);
}
private void readInput(TaskMonitor tm) throws IOException {
this.parentTaskMonitor = tm;
tm.setProgress(0.0);
String line;
final BufferedReader br =
new BufferedReader(
new InputStreamReader(inputStream, Charset.forName("UTF-8").newDecoder()), 128 * 1024);
String networkCollectionName = this.rootNetworkList.getSelectedValue().toString();
CySubNetwork subNetwork;
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
CyNetwork rootNetwork = cyNetworkFactory.createNetwork();
subNetwork = this.cyRootNetworkManager.getRootNetwork(rootNetwork).addSubNetwork();
} else {
// Add a new subNetwork to the given collection
subNetwork = this.name2RootMap.get(networkCollectionName).addSubNetwork();
}
// Build a Map based on the key attribute for the entire collection,
// For SIF network, the 'shared name' attribute is the primary key
this.initNodeMap(subNetwork.getRootNetwork(), "shared " + CyNetwork.NAME);
tm.setProgress(0.1);
// Generate bundled event to avoid too many events problem.
final String firstLine = br.readLine();
if (firstLine.contains(TAB)) delimiter = TAB;
createEdge(new Interaction(firstLine.trim(), delimiter), subNetwork);
tm.setProgress(0.15);
tm.setStatusMessage("Processing the interactions...");
int numInteractionsRead = 0;
while ((line = br.readLine()) != null) {
if (cancelled) {
// Cancel called. Clean up the garbage.
nMap.clear();
nMap = null;
subNetwork = null;
br.close();
return;
}
if (line.trim().length() <= 0) continue;
try {
final Interaction itr = new Interaction(line, delimiter);
createEdge(itr, subNetwork);
} catch (Exception e) {
// Simply ignore invalid lines.
continue;
}
if ((++numInteractionsRead % 1000) == 0)
tm.setStatusMessage("Processed " + numInteractionsRead + " interactions so far.");
}
br.close();
tm.setStatusMessage("Processed " + numInteractionsRead + " interactions in total.");
nMap.clear();
nMap = null;
this.cyNetworks = new CyNetwork[] {subNetwork};
tm.setProgress(1.0);
logger.debug("SIF file loaded: ID = " + subNetwork.getSUID());
}
@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();
}
}