protected CyNode getNodeByName(CyNetwork net, String name) {
for (CyNode n : net.getNodeList()) {
if (name.equals(net.getRow(n).get(NAME, String.class))) return n;
}
return null;
}
/** Will fail if it doesn't find the specified interaction. */
protected void findInteraction(
CyNetwork net, String source, String target, String interaction, int count) {
for (CyNode n : net.getNodeList()) {
String sname = net.getRow(n).get(CyNetwork.NAME, String.class);
assertNotNull("Source name is NULL", sname);
if (source.equals(sname)) {
List<CyNode> neigh = net.getNeighborList(n, CyEdge.Type.ANY);
assertEquals("wrong number of neighbors", count, neigh.size());
for (CyNode nn : neigh) {
String tname = net.getRow(nn).get(CyNetwork.NAME, String.class);
assertNotNull("Target name is NULL", tname);
if (tname.equals(target)) {
List<CyEdge> con = net.getConnectingEdgeList(n, nn, CyEdge.Type.ANY);
assertTrue("Connecting edge list is empty", con.size() > 0);
for (CyEdge e : con) {
String inter = net.getRow(e).get(CyEdge.INTERACTION, String.class);
assertNotNull("Edge interaction is NULL", inter);
if (inter.equals(interaction)) {
return;
}
}
}
}
}
}
fail("couldn't find interaction: " + source + " " + interaction + " " + target);
}
public boolean isReady(CyNetwork network) {
if (scope == Scope.ALLNODES && settings.hasNodeCompounds(network.getNodeList())) return true;
if (scope == Scope.SELECTEDNODES) return selectedNodesReady(network);
return false;
}
/** all lines have the degenerate form "node1" that is, with no interaction type and no target */
@Test
public void testReadFileWithNoInteractions() throws Exception {
List<CyNetworkView> views = getViews("degenerate.sif");
CyNetwork net = checkSingleNetwork(views, 9, 0);
for (CyNode n : net.getNodeList())
assertTrue(net.getRow(n).get("name", String.class).startsWith("Y"));
}
private void initVariables() {
edgeAttributes = context.getSelectedEdgeAttributes();
graph = new DirectedSparseMultigraph<>();
idToNode = new HashMap<>();
nodeList = network.getNodeList();
edgeList = network.getEdgeList();
nodeTable = network.getDefaultNodeTable();
edgeTable = network.getDefaultEdgeTable();
}
public TaskIterator createTaskIterator(CyNetwork network) {
if (scope == Scope.ALLNODES)
return new TaskIterator(
new SMARTSSearchTask(network, network.getNodeList(), scope, showResult, settings));
else {
List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
return new TaskIterator(
new SMARTSSearchTask(network, selectedNodes, scope, showResult, settings));
}
}
/**
* Save node attributes computed by NetworkAnalyzer for this network into a tab-delimited file
* with extension "nattributes" (1st column corresponds to the node ids, each subsequent column
* contains the values of a node attribute).
*
* @param aNetwork Target network.
* @param aDir Flag indicating if the network interpretation is directed.
* @param aOutputDir Output directory for writing files as chosen by the user.
* @param aExtendedName Name of the analyzed network including the current interpretation.
* @return <code>true</code> if any node attributes where present and have been saved, and <code>
* false</code> otherwise.
*/
private boolean saveNodeAttributes(
CyNetwork aNetwork, boolean aDir, File aOutputDir, String aExtendedName) {
// get node attributes computed in the last analysis run
Set<String> netAnayzerAttr = new HashSet<String>();
if (aDir) {
netAnayzerAttr = Messages.getDirNodeAttributes();
} else {
netAnayzerAttr = Messages.getUndirNodeAttributes();
}
if (netAnayzerAttr.size() == 0) {
return false;
}
// save chosen node attributes in a file, 1st column corresponds to the node ids, each
// subsequent column
// contains the values of a node attribute
try {
final FileWriter writer = new FileWriter(new File(outputDir, aExtendedName + ".nattributes"));
writer.write("Node ID");
for (final String attr : netAnayzerAttr) {
writer.write("\t" + attr);
}
writer.write("\n");
for (CyNode n : aNetwork.getNodeList()) {
final String id = aNetwork.getRow(n).get("name", String.class);
writer.write(id);
for (final String attr : netAnayzerAttr) {
final Object attrValue = aNetwork.getRow(n).getRaw(attr);
if (attrValue != null) {
writer.write("\t" + attrValue.toString());
}
}
writer.write("\n");
}
writer.close();
} catch (IOException ex) {
// attributes file could not be written
return false;
}
return true;
}
public BellmanFordStatsImpl findPath(
CyNetwork network, CyNode source, boolean directed, WeightFunction function) {
Map<CyNode, MetaNode> nodeToMetaNodeMap = new IdentityHashMap<CyNode, MetaNode>();
boolean negativeCycle = true;
for (CyNode node : network.getNodeList()) {
MetaNode metaNode = new MetaNode(node, Double.POSITIVE_INFINITY, null);
nodeToMetaNodeMap.put(node, metaNode);
}
nodeToMetaNodeMap.get(source).setDistance(0.0);
for (int i = 0; i < network.getNodeCount() - 1; i++) {
for (CyEdge edge : network.getEdgeList()) {
MetaNode sourceMetaNode = nodeToMetaNodeMap.get(edge.getSource());
MetaNode targetMetaNode = nodeToMetaNodeMap.get(edge.getTarget());
if (targetMetaNode.getDistance()
> sourceMetaNode.getDistance() + function.getWeight(edge)) {
targetMetaNode.setDistance(sourceMetaNode.getDistance() + function.getWeight(edge));
targetMetaNode.setPredecessor(sourceMetaNode.getNode());
}
}
}
for (CyEdge edge : network.getEdgeList()) {
MetaNode sourceMetaNode = nodeToMetaNodeMap.get(edge.getSource());
MetaNode targetMetaNode = nodeToMetaNodeMap.get(edge.getTarget());
if (targetMetaNode.getDistance() > sourceMetaNode.getDistance() + function.getWeight(edge))
negativeCycle = false;
}
return new BellmanFordStatsImpl(source, nodeToMetaNodeMap, negativeCycle);
}
@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);
}
@Override
public void serialize(CyNetworkView networkView, JsonGenerator jgen, SerializerProvider provider)
throws IOException, JsonProcessingException {
jgen.useDefaultPrettyPrinter();
jgen.writeStartObject();
jgen.writeStringField(
CytoscapeJsNetworkModule.FORMAT_VERSION_TAG, CytoscapeJsNetworkModule.FORMAT_VERSION);
jgen.writeStringField(CytoscapeJsNetworkModule.GENERATED_BY_TAG, "cytoscape-" + version);
jgen.writeStringField(
CytoscapeJsNetworkModule.TARGET_CYJS_VERSION_TAG,
CytoscapeJsNetworkModule.CYTOSCAPEJS_VERSION);
final CyNetwork network = networkView.getModel();
// Serialize network data table
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeObject(network.getRow(network));
jgen.writeEndObject();
jgen.writeObjectFieldStart(ELEMENTS.getTag());
// Write array
final List<CyNode> nodes = network.getNodeList();
final List<CyEdge> edges = network.getEdgeList();
jgen.writeArrayFieldStart(NODES.getTag());
for (final CyNode node : nodes) {
jgen.writeStartObject();
// Data field
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeStringField(ID.getTag(), node.getSUID().toString());
// Write CyRow in "data" field
jgen.writeObject(network.getRow(node));
jgen.writeEndObject();
// Position and other visual props
jgen.writeObject(networkView.getNodeView(node));
// Special case for cytoscape.js format:
// - Selected
jgen.writeBooleanField(
CyNetwork.SELECTED, network.getRow(node).get(CyNetwork.SELECTED, Boolean.class));
jgen.writeEndObject();
}
jgen.writeEndArray();
jgen.writeArrayFieldStart(EDGES.getTag());
for (final CyEdge edge : edges) {
jgen.writeStartObject();
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeStringField(ID.getTag(), edge.getSUID().toString());
jgen.writeStringField(SOURCE.getTag(), edge.getSource().getSUID().toString());
jgen.writeStringField(TARGET.getTag(), edge.getTarget().getSUID().toString());
// Write CyRow in "data" field
jgen.writeObject(network.getRow(edge));
jgen.writeEndObject();
// Special case for cytoscape.js format:
// - Selected
jgen.writeBooleanField(
CyNetwork.SELECTED, network.getRow(edge).get(CyNetwork.SELECTED, Boolean.class));
jgen.writeEndObject();
}
jgen.writeEndArray();
jgen.writeEndObject();
}
void cyLoad(CyNetwork gp) {
net = gp;
nodes = new ArrayList<CyNode>(net.getNodeList());
edges = new ArrayList<CyEdge>(net.getEdgeList());
}
