/** * Update view of each network * * @param network */ private final void updateViews(final CyNetwork network) { final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(network); for (final CyNetworkView view : views) { view.updateView(); } }
@Override public void handleEvent(SetCurrentNetworkEvent e) { final CyNetwork net = e.getNetwork(); CyNetworkView view = null; if (net != null) { final Collection<CyNetworkView> views = netViewMgr.getNetworkViews(net); if (!views.isEmpty()) view = views.iterator().next(); } // Do not use invokeLater() here. It cause all kinds of threading problem. setFocus(view); }
protected final Collection<CyNetworkView> getCyNetworkViews(final Long id) { final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(getCyNetwork(id)); if (views.isEmpty()) { throw new NotFoundException("No view is available for network with SUID: " + id); } return views; }
private boolean isNetworkViewRegistered() { final CyNetworkViewManager netViewMgr = servicesUtil.get(CyNetworkViewManager.class); return netViewMgr.getNetworkViews(netView.getModel()).contains(netView); }
private boolean isNetworkViewRegistered() { final CyNetworkViewManager netViewMgr = servicesUtil.get(CyNetworkViewManager.class); return netViewMgr.getNetworkViews(netView.getModel()).contains(netView); }
/** * Cytoscape can have multiple views per network model. This feature is not * exposed to end-users, but you can access it from this API. * * @summary Get number of views for the given network model * * @param networkId * Network SUID * * @return Number of views for the network model * */ @GET @Path("/count") @Produces(MediaType.APPLICATION_JSON) public String getNetworkViewCount(@PathParam("networkId") Long networkId) { return getNumberObjectString(JsonTags.COUNT, networkViewManager.getNetworkViews(getCyNetwork(networkId)).size()); }
/** * If view(s) exists for the current network, update them. */ private void updateView() { final Collection<CyNetworkView> views = viewManager.getNetworkViews(network); CyNetworkView targetView = null; if(views.size() != 0) targetView = views.iterator().next(); if(targetView != null) targetView.updateView(); final CyNetworkView view = appManager.getCurrentNetworkView(); if(view != null ) view.updateView(); }
/** * * In general, a network has one view. But if there are multiple views, this * deletes all of them. * * @summary Delete all network views * * @param networkId * Network SUID * */ @DELETE @Path("/") @Produces(MediaType.APPLICATION_JSON) public Response deleteAllNetworkViews(@PathParam("networkId") Long networkId) { try { final Collection<CyNetworkView> views = this.networkViewManager.getNetworkViews(getCyNetwork(networkId)); final Set<CyNetworkView> toBeDestroyed = new HashSet<CyNetworkView>(views); for (final CyNetworkView view : toBeDestroyed) { networkViewManager.destroyNetworkView(view); } return Response.ok().build(); } catch (Exception e) { throw getError("Could not delete network views for network with SUID: " + networkId, e, Response.Status.INTERNAL_SERVER_ERROR); } }
final Collection<CyNetworkView> views = factory.getCyNetworkViewManager().getNetworkViews(cyNetwork); CyNetworkView view = null; if(views.size() != 0)
private final void apply() { final Collection<CyNetworkView> views = viewManager.getNetworkViews(network); if(views.isEmpty()) return;
@Override public void run(final TaskMonitor taskMonitor) { if (network == null) network = appMgr.getCurrentNetwork(); Collection<CyNetworkView> views = viewMgr.getNetworkViews(network); nodes = nodeList.getValue(); for (CyNetworkView view: views) { Set<View<CyNode>> nodeViews = new HashSet<View<CyNode>>(); if (nodes == null || nodes.size() == 0) { nodeViews = CyLayoutAlgorithm.ALL_NODE_VIEWS; } else { for (CyNode node: nodes) nodeViews.add(view.getNodeView(node)); } insertTasksAfterCurrentTask(algorithm.createTaskIterator(view, layoutContext, nodeViews,"")); } }
.getNetworkViews(network); if (views.isEmpty()) { throw new NotFoundException(
.getNetworkViews(network); if (views.isEmpty()) { throw new NotFoundException(
.getNetworkViews(network); if (views.isEmpty()) { throw new NotFoundException(
/** * Method for any post processing of recently loaded network. * * @param cyNetwork CyNetwork * @param doLayout boolean */ private void postProcess(final CyNetwork cyNetwork, boolean doLayout) { // ref to view used below final Collection<CyNetworkView> views = factory.getCyNetworkViewManager().getNetworkViews(cyNetwork); CyNetworkView view = null; if(views.size() != 0) view = views.iterator().next(); // setup web services url to pc attribute - used by nodeContextMenuListener if (webServicesURL != null) { AttributeUtil.set(cyNetwork, cyNetwork, "biopax.web_services_url", webServicesURL, String.class); } // setup data sources attribute - used by nodeContextMenuListener - remains encoded if (dataSources != null) { AttributeUtil.set(cyNetwork, cyNetwork, "biopax.data_sources", dataSources, String.class); } // setup the context menu //view.addNodeContextMenuListener(nodeContextMenuListener); // set focus current factory.getCyApplicationManager().setCurrentNetworkView(view); }
final Collection<CyNetworkView> views = netViewMgr.getNetworkViews(n); final Collection<CyNetworkView> cnViews = cn != null ? netViewMgr.getNetworkViews(cn) : null; cv = (cnViews == null || cnViews.isEmpty()) ? null : cnViews.iterator().next();
final Collection<CyNetworkView> views = factory.getCyNetworkViewManager().getNetworkViews(cyNetwork); CyNetworkView view = null; if(views.size() != 0)
@Override public void run(TaskMonitor tm) throws Exception { final CyNode node = nodeView.getModel(); final CyNetwork netPointer = node.getNetworkPointer(); if (netPointer != null && netMgr.networkExists(netPointer.getSUID())) { CyNetworkView pointerView = null; Collection<CyNetworkView> views = netViewMgr.getNetworkViews(netPointer); for (CyNetworkView nv : views) { // Get the first view pointerView = nv; break; } if (pointerView == null) { // Create a network view final Set<CyNetwork> networks = new HashSet<CyNetwork>(); networks.add(netPointer); TaskIterator iter = createViewFactory.createTaskIterator(networks); this.insertTasksAfterCurrentTask(iter); } else { // Just set the existing one as current appMgr.setCurrentNetworkView(pointerView); } } } }
@Override public CyNetworkView buildCyNetworkView(final CyNetwork network) { CyNetworkView view; //visual style depends on the tunable // VisualStyle style = null; ReaderMode currentMode = ReaderMode.valueOf(readerMode.getSelectedValue()); switch (currentMode) { case DEFAULT: // style = visualStyleUtil.getBioPaxVisualStyle(); view = cyServices.networkViewFactory.createNetworkView(network); break; case SIF: // style = visualStyleUtil.getBinarySifVisualStyle(); view = anotherReader.buildCyNetworkView(network); break; case SBGN: default: view = anotherReader.buildCyNetworkView(network); //TODO: a layout for SBGN views (if not already done)? break; } if(!cyServices.networkViewManager.getNetworkViews(network).contains(view)) cyServices.networkViewManager.addNetworkView(view); return view; }
cPathFactory.getCyNetworkViewManager().getNetworkViews(mergedNetwork); if(!networkViews.isEmpty()) { cPathFactory.getCyApplicationManager().setCurrentNetwork(mergedNetwork);