/**
* By passing a list of key-value pairs for each Visual Property, update network view.
*
* <p>The body should have the following JSON:
*
* <pre>
* [
* {
* "visualProperty": "Visual Property Name, like NETWORK_BACKGROUND_PAINT",
* "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 single network view value, such as background color or zoom level.
* @param networkId Network SUID
* @param viewId Network view SUID
*/
@PUT
@Path("/{viewId}/network")
@Consumes(MediaType.APPLICATION_JSON)
public Response updateNetworkView(
@PathParam("networkId") Long networkId,
@PathParam("viewId") Long viewId,
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);
styleMapper.updateView(networkView, rootNode, getLexicon());
} catch (Exception e) {
throw getError(
"Could not parse the input JSON for updating view because: " + e.getMessage(),
e,
Response.Status.INTERNAL_SERVER_ERROR);
}
// Repaint
networkView.updateView();
return Response.ok().build();
}
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();
}
/**
* 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();
}
public void redo() {
;
final CyNetworkView view = viewFactory.createNetworkView(network);
networkViewManager.addNetworkView(view);
for (final View<CyNode> nodeView : view.getNodeViews())
nodesAndLocations.get(nodeView.getModel()).restoreLocations(nodeView);
view.setVisualProperty(NETWORK_CENTER_X_LOCATION, networkCenterX);
view.setVisualProperty(NETWORK_CENTER_Y_LOCATION, networkCenterY);
view.setVisualProperty(NETWORK_CENTER_Z_LOCATION, networkCenterZ);
view.setVisualProperty(NETWORK_SCALE_FACTOR, networkScaleFactor);
eventHelper.flushPayloadEvents();
view.updateView();
}
private final void clearAll(
final CyNetworkView netView, final View<? extends CyIdentifiable> nodeView) {
boolean needToUpdateView = false;
final VisualStyle style = vmm.getCurrentVisualStyle();
for (VisualProperty<?> vp : vpSet) {
final boolean lock = nodeView.isDirectlyLocked(vp);
if (lock) {
nodeView.clearValueLock(vp);
needToUpdateView = true;
}
}
if (needToUpdateView) {
style.apply(netView);
netView.updateView();
}
}
/**
* Apply bypass
*
* @param netView
* @param graphObjectView
* @param vp
*/
private final void applBypassValue(
final CyNetworkView netView,
final View<? extends CyIdentifiable> graphObjectView,
VisualProperty<?> vp) {
final ValueEditor<Object> editor =
(ValueEditor<Object>) editorManager.getValueEditor(vp.getRange().getType());
final Object bypassValue = editor.showEditor(null, graphObjectView.getVisualProperty(vp));
// Set lock for the vp
graphObjectView.setLockedValue(vp, bypassValue);
// Apply the new value only for the given view
// TODO don't do this, because it overwrites some bypassed values with default ones!!! Calling
// setLockedValue should be enough
// final CyRow row = netView.getModel().getRow(graphObjectView.getModel());
// vmm.getCurrentVisualStyle().apply(row, graphObjectView);
// Redraw the view
netView.updateView();
}
@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();
}
}