private void checkView(final CyNetworkView view) {
assertEquals(Color.BLACK, view.getVisualProperty(NETWORK_BACKGROUND_PAINT));
assertEquals(new Double(639.0d), view.getVisualProperty(NETWORK_WIDTH));
assertEquals(new Double(624.0d), view.getVisualProperty(NETWORK_HEIGHT));
assertEquals(
new Double(3091.2991395970175d), view.getVisualProperty(NETWORK_CENTER_X_LOCATION));
assertEquals(new Double(3610.396738076269d), view.getVisualProperty(NETWORK_CENTER_Y_LOCATION));
assertEquals(new Double(0.05044042295795177d), view.getVisualProperty(NETWORK_SCALE_FACTOR));
// All nodes have the same size, border and shape
final View<CyNode> nv = view.getNodeView(view.getModel().getNodeList().iterator().next());
assertEquals(80, nv.getVisualProperty(NODE_WIDTH).intValue());
assertEquals(30, nv.getVisualProperty(NODE_HEIGHT).intValue());
assertEquals(NodeShapeVisualProperty.ROUND_RECTANGLE, nv.getVisualProperty(NODE_SHAPE));
assertEquals(180, nv.getVisualProperty(NODE_TRANSPARENCY).intValue());
assertEquals(2, nv.getVisualProperty(NODE_BORDER_WIDTH).intValue());
assertEquals(LineTypeVisualProperty.SOLID, nv.getVisualProperty(NODE_BORDER_LINE_TYPE));
assertEquals(new Color(153, 153, 255), nv.getVisualProperty(NODE_BORDER_PAINT));
assertEquals(255, nv.getVisualProperty(NODE_BORDER_TRANSPARENCY).intValue());
assertEquals(new Color(255, 255, 255), nv.getVisualProperty(NODE_LABEL_COLOR));
assertEquals(255, nv.getVisualProperty(NODE_LABEL_TRANSPARENCY).intValue());
// All edges have the same width and other properties
final View<CyEdge> ev = view.getEdgeView(view.getModel().getEdgeList().iterator().next());
assertEquals(new Double(1.0), ev.getVisualProperty(EDGE_WIDTH));
assertEquals(255, ev.getVisualProperty(EDGE_TRANSPARENCY).intValue());
assertEquals(ArrowShapeVisualProperty.NONE, ev.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
assertEquals(ArrowShapeVisualProperty.NONE, ev.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
}
@GET
@Path("/{viewId}/{objectType}/{objectId}/{visualProperty}")
@Produces(MediaType.APPLICATION_JSON)
public String getSingleVisualPropertyValue(
@PathParam("networkId") Long networkId,
@PathParam("viewId") Long viewId,
@PathParam("objectType") String objectType,
@PathParam("objectId") Long objectId,
@PathParam("visualProperty") String visualProperty) {
final CyNetworkView networkView = getView(networkId, viewId);
Collection<VisualProperty<?>> vps = null;
View<? extends CyIdentifiable> view = null;
if (nodeLexicon == null) {
initLexicon();
}
if (objectType.equals("nodes")) {
view = networkView.getNodeView(networkView.getModel().getNode(objectId));
vps = nodeLexicon;
} else if (objectType.equals("edges")) {
view = networkView.getNodeView(networkView.getModel().getNode(objectId));
vps = edgeLexicon;
}
if (view == null) {
throw getError(
"Could not find view.", new IllegalArgumentException(), Response.Status.NOT_FOUND);
}
return getSingleVp(visualProperty, view, vps);
}
public TaskIterator createTaskIterator(View<CyNode> nView, CyNetworkView netView) {
List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(netView.getModel(), CyNetwork.SELECTED, true);
if (selectedNodes == null || selectedNodes.size() == 0)
selectedNodes = Collections.singletonList(nView.getModel());
return new TaskIterator(
new SMARTSSearchTask(netView.getModel(), selectedNodes, scope, showResult, settings));
}
/**
* By passing list of key-value pair for each Visual Property, update node view.
*
* <p>The body should have the following JSON:
*
* <pre>
* [
* {
* "SUID": SUID of node,
* "view": [
* {
* "visualProperty": "Visual Property Name, like NODE_FILL_COLOR",
* "value": "Serialized form of value, like 'red.'"
* },
* ...
* {}
* ]
* },
* ...
* {}
* ]
* </pre>
*
* Note that this API directly set the value to the view objects, and once Visual Style applied,
* those values are overridden by the Visual Style.
*
* @summary Update node/edge view objects at once
* @param networkId Network SUID
* @param viewId Network view SUID
* @param objectType Type of objects ("nodes" or "edges")
*/
@PUT
@Path("/{viewId}/{objectType}")
@Consumes(MediaType.APPLICATION_JSON)
public Response updateViews(
@PathParam("networkId") Long networkId,
@PathParam("viewId") Long viewId,
@PathParam("objectType") String objectType,
final InputStream is) {
final CyNetworkView networkView = getView(networkId, viewId);
final ObjectMapper objMapper = new ObjectMapper();
try {
// This should be an JSON array.
final JsonNode rootNode = objMapper.readValue(is, JsonNode.class);
for (JsonNode entry : rootNode) {
final Long objectId = entry.get(CyIdentifiable.SUID).asLong();
final JsonNode viewNode = entry.get("view");
if (objectId == null || viewNode == null) {
continue;
}
View<? extends CyIdentifiable> view = null;
if (objectType.equals("nodes")) {
view = networkView.getNodeView(networkView.getModel().getNode(objectId));
} else if (objectType.equals("edges")) {
view = networkView.getEdgeView(networkView.getModel().getEdge(objectId));
} else if (objectType.equals("network")) {
view = networkView;
} else {
throw getError(
"Method not supported.",
new IllegalStateException(),
Response.Status.INTERNAL_SERVER_ERROR);
}
if (view == null) {
throw getError(
"Could not find view.", new IllegalArgumentException(), Response.Status.NOT_FOUND);
}
styleMapper.updateView(view, viewNode, getLexicon());
}
// Repaint
networkView.updateView();
} catch (Exception e) {
throw getError(
"Could not parse the input JSON for updating view because: " + e.getMessage(),
e,
Response.Status.INTERNAL_SERVER_ERROR);
}
return Response.ok().build();
}
void setNetworkView(final CyNetworkView view) {
getApplyBtn().setEnabled(view != null);
if (layoutAttrPnl == null) return;
layoutAttrPnl.removeAll();
layoutAttrTunable = new LayoutAttributeTunable();
if (view != null) {
List<String> attributeList =
getAttributeList(
view.getModel(),
currentLayout.getSupportedNodeAttributeTypes(),
currentLayout.getSupportedEdgeAttributeTypes());
if (attributeList.size() > 0) {
layoutAttrTunable.layoutAttribute = new ListSingleSelection<String>(attributeList);
layoutAttrTunable.layoutAttribute.setSelectedValue(attributeList.get(0));
final PanelTaskManager taskMgr = serviceRegistrar.getService(PanelTaskManager.class);
JPanel panel = taskMgr.getConfiguration(null, layoutAttrTunable);
setPanelsTransparent(panel);
layoutAttrPnl.add(panel);
panel.invalidate();
}
}
}
private boolean hasSelectedNodes(final CyNetworkView view) {
if (view == null) return false;
final CyNetwork network = view.getModel();
final CyTable table = network.getDefaultNodeTable();
return table.countMatchingRows(CyNetwork.SELECTED, Boolean.TRUE) > 0;
}
/** 'typical' means that all lines have the form "node1 pd node2 [node3 node4 ...] */
@Test
public void testReadFromTypicalFile() throws Exception {
List<CyNetworkView> views = getViews("sample.sif");
for (CyNetworkView view : views) {
for (CyNode n : view.getModel().getNodeList()) {
System.out.println(
"sample.sif: NODE " + view.getModel().getRow(n).get("name", String.class));
}
for (CyEdge e : view.getModel().getEdgeList()) {
System.out.println(
"sample.sif: EDGE " + view.getModel().getRow(e).get("name", String.class));
}
}
CyNetwork net = checkSingleNetwork(views, 31, 27);
findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
}
@Override
public boolean isReady(CyNetworkView networkView) {
if (!super.isReady(networkView)) return false;
// Make sure we've got something selected
List<CyNode> selNodes =
CyTableUtil.getNodesInState(networkView.getModel(), CyNetwork.SELECTED, true);
if (selNodes != null && selNodes.size() > 0) return true;
return false;
}
private Set<View<CyNode>> getLayoutNodes(CyLayoutAlgorithm layout, CyNetworkView networkView) {
if (layout.getSupportsSelectedOnly() && selectedTunable.selectedNodesOnly) {
Set<View<CyNode>> nodeViews = new HashSet<View<CyNode>>();
CyNetwork network = networkView.getModel();
for (View<CyNode> view : networkView.getNodeViews()) {
if (network.getRow(view.getModel()).get(CyNetwork.SELECTED, Boolean.class)
&& view.getVisualProperty(BasicVisualLexicon.NODE_VISIBLE)) {
nodeViews.add(view);
}
}
return nodeViews;
}
return CyLayoutAlgorithm.ALL_NODE_VIEWS;
}
/**
* @summary Get view object for the specified type (node or edge)
* @param networkId Network SUID
* @param viewId Network view SUID
* @param objectType nodes or edges
* @param objectId Object's SUID
*/
@GET
@Path("/{viewId}/{objectType}/{objectId}")
@Produces(MediaType.APPLICATION_JSON)
public String getView(
@PathParam("networkId") Long networkId,
@PathParam("viewId") Long viewId,
@PathParam("objectType") String objectType,
@PathParam("objectId") Long objectId) {
final CyNetworkView networkView = getView(networkId, viewId);
View<? extends CyIdentifiable> view = null;
Collection<VisualProperty<?>> lexicon = null;
if (nodeLexicon == null) {
initLexicon();
}
if (objectType.equals("nodes")) {
view = networkView.getNodeView(networkView.getModel().getNode(objectId));
lexicon = nodeLexicon;
} else if (objectType.equals("edges")) {
view = networkView.getNodeView(networkView.getModel().getNode(objectId));
lexicon = edgeLexicon;
}
if (view == null) {
throw getError(
"Could not find view.", new IllegalArgumentException(), Response.Status.NOT_FOUND);
}
try {
return styleSerializer.serializeView(view, lexicon);
} catch (IOException e) {
throw getError(
"Could not serialize the view object.", e, Response.Status.INTERNAL_SERVER_ERROR);
}
}
/**
* Sets the given AnnotationSet as the "selected" one. If null is passed then all AnnotationSets
* will be unselected.
*
* <p>Note: Currently switching selection is not supported when the currently selected
* AnnotationSet has collapsed clusters. It is the responsibility of the UI to expand all the
* clusters before switching the AnnotationSet.
*
* <p>MKTODO: It would be better for the model to handle expanding the clusters, but for now we
* will force the UI to do it.
*
* @throws IllegalStateException If the currently active AnnotationSet has collapsed clusters.
*/
public void select(AnnotationSet annotationSet) {
if (annotationSet == null || annotationSets.contains(annotationSet)) {
if (Optional.ofNullable(annotationSet).equals(activeSet)) {
return;
}
if (activeSet.map(AnnotationSet::hasCollapsedCluster).orElse(false)) {
throw new IllegalStateException("Current AnnotationSet has collapsed clusters");
}
CyNetwork network = networkView.getModel();
activeSet = Optional.ofNullable(annotationSet);
// ModelManager.handle(AboutToRemoveNodesEvent) only removes nodes from the active annotation
// set.
// When switching to a new annotation set we need to "fix" the clusters to remove any nodes
// that
// were deleted previously.
// MKTODO: probably need to test for deleted nodes when serializing the model
if (annotationSet != null) {
Set<Cluster> clusters = annotationSet.getClusters();
for (Cluster cluster :
new HashSet<>(
clusters)) { // avoid ConcurrentModificationException because removeNodes() can call
// delete()
Set<CyNode> nodesToRemove =
cluster
.getNodes()
.stream()
.filter(node -> !network.containsNode(node))
.collect(Collectors.toSet());
// Fires ClusterChangedEvent, UI listeners should test if the cluster is part of the
// active annotation set.
if (!nodesToRemove.isEmpty()) {
cluster.removeNodes(nodesToRemove);
}
}
}
parent.postEvent(new ModelEvents.AnnotationSetSelected(this, activeSet));
}
}
public CyNetwork getNetwork() {
return networkView.getModel();
}
@Override
public List<BarLayer> getLayers(
CyNetworkView networkView, View<? extends CyIdentifiable> nodeView) {
CyNetwork network = networkView.getModel();
if (!(nodeView.getModel() instanceof CyNode)) return null;
layers = new ArrayList<>();
CyNode node = (CyNode) nodeView.getModel();
// Create all of our pie slices. Each slice becomes a layer
if (attributes != null && attributes.size() > 0) {
// System.out.println("Getting data from attributes for node "+node);
values = getDataFromAttributes(network, node, attributes, labels);
// System.out.println("Data from attributes returns "+values.size()+" values");
colorList = convertInputToColor(colorString, values);
}
// Protect against missing values in the input stream
// if (values == null || colorList == null) return layers;
if (labels != null
&& labels.size() > 0
&& (labels.size() != values.size() || labels.size() != colorList.size())) {
logger.error(
"barchart: number of labels ("
+ labels.size()
+ "), values ("
+ values.size()
+ "), and colors ("
+ colorList.size()
+ ") don't match");
return null;
}
List<BarLayer> labelList = new ArrayList<BarLayer>();
double minValue = 0.000001;
double maxValue = -minValue;
for (Double val : values) {
if (val == null) continue;
minValue = Math.min(minValue, val);
maxValue = Math.max(maxValue, val);
}
double labelMin = minValue;
if (normalized) {
minValue = rangeMin;
maxValue = rangeMax;
}
int nBars = values.size();
Font font = getFont();
for (int bar = 0; bar < nBars; bar++) {
String label = null;
if (labels != null && labels.size() > 0) label = labels.get(bar);
if (values.get(bar) == null || values.get(bar) == 0.0) continue;
// System.out.println("Creating bar #"+bar);
// Create the slice
BarLayer bl =
new BarLayer(
bar,
nBars,
separation,
values.get(bar),
minValue,
maxValue,
normalized,
ybase,
colorList.get(bar),
showAxes,
borderWidth,
scale);
if (bl == null) continue;
layers.add(bl);
// System.out.println("BarLayer: "+bar+" bounds: "+bl.getShape().getBounds2D());
if (label != null) {
// System.out.println("Creating label for bar #"+bar);
// Now, create the label
BarLayer labelLayer =
new BarLayer(
bar,
nBars,
separation,
minValue,
maxValue,
normalized,
labelMin,
ybase,
label,
font,
labelColor,
showAxes,
scale);
if (labelLayer != null) labelList.add(labelLayer);
}
}
// System.out.println("Created "+layers.size()+" bar layers");
// Now add all of our labels so they will be on top of our slices
if (labelList != null && labelList.size() > 0) layers.addAll(labelList);
// System.out.println("Created "+layers.size()+" total layers");
shapeLayers = layers;
return layers;
}
@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();
}
public boolean isReady(View<CyNode> nView, CyNetworkView netView) {
if (nView != null && settings.hasNodeCompounds(Collections.singletonList(nView.getModel())))
return true;
return selectedNodesReady(netView.getModel());
}
