private void display() {
CyServiceRegistrarImpl register = new CyServiceRegistrarImpl(bc);
CyNetworkViewManager viewManager = register.getService(CyNetworkViewManager.class);
CyNetworkViewFactory viewFactory = register.getService(CyNetworkViewFactory.class);
CyNetworkView networkView = viewFactory.createNetworkView(network);
viewManager.addNetworkView(networkView);
VisualMappingFunctionFactory passthroughFactory =
register.getService(VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");
VisualMappingFunctionFactory continuousFactory =
register.getService(VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
VisualMappingManager vmManager = register.getService(VisualMappingManager.class);
VisualStyleFactory vsFactory = register.getService(VisualStyleFactory.class);
VisualStyle vs =
vsFactory.createVisualStyle(
network.getDefaultNetworkTable().getRow(network.getSUID()).get("name", String.class));
PassthroughMapping pMapping =
(PassthroughMapping)
passthroughFactory.createVisualMappingFunction(
"name", String.class, BasicVisualLexicon.NODE_LABEL);
vs.addVisualMappingFunction(pMapping);
vs.apply(networkView);
ContinuousMapping mapping =
(ContinuousMapping)
continuousFactory.createVisualMappingFunction(
"score", Double.class, BasicVisualLexicon.NODE_FILL_COLOR);
Double val1 = getMinimum(network.getDefaultNodeTable().getColumn("score"));
BoundaryRangeValues<Paint> brv1 =
new BoundaryRangeValues<Paint>(Color.GREEN, Color.GREEN, Color.GREEN);
Double val3 = getMaximum(network.getDefaultNodeTable().getColumn("score"));
BoundaryRangeValues<Paint> brv3 =
new BoundaryRangeValues<Paint>(Color.RED, Color.RED, Color.RED);
Double val2 = (val1 + val3 + val1 + val1) / 4;
BoundaryRangeValues<Paint> brv2 =
new BoundaryRangeValues<Paint>(Color.YELLOW, Color.YELLOW, Color.YELLOW);
mapping.addPoint(val1, brv1);
mapping.addPoint(val2, brv2);
mapping.addPoint(val3, brv3);
vs.addVisualMappingFunction(mapping);
vs.apply(networkView);
vmManager.addVisualStyle(vs);
vmManager.setVisualStyle(vs, networkView);
networkView.updateView();
}
protected final Set<CyNetwork> getNetworksByQuery(final String query, final String column) {
final Set<CyNetwork> networks = networkManager.getNetworkSet();
final Set<CyNetwork> matchedNetworks = new HashSet<>();
for (final CyNetwork network : networks) {
// First, check shared table
CyTable table = network.getDefaultNetworkTable();
if (table.getColumn(column) == null) {
table = network.getTable(CyNetwork.class, CyNetwork.LOCAL_ATTRS);
}
// If column does not exists in the default table, check local one:
if (table.getColumn(column) == null) {
// Still not found? Give up and continue.
// TODO: should we check hidden tables, too?
continue;
}
final Object rawQuery = MapperUtil.getRawValue(query, table.getColumn(column).getType());
final Collection<CyRow> rows = table.getMatchingRows(column, rawQuery);
if (rows.isEmpty() == false) {
matchedNetworks.add(network);
}
}
return matchedNetworks;
}
@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);
}
