/** * DOCUMENT ME! * * @return DOCUMENT ME! */ public CyNetwork getNetwork() { return networkView.getNetwork(); }
/** * Create String set of node/edge ID. * * @param isNode * @return set of ID */ private static Set<Object> loadID(final boolean isNode) { final Set<Object> ids = new TreeSet<Object>(); final List<GraphObject> obj; if (isNode) obj = Cytoscape.getCurrentNetworkView().getNetwork().nodesList(); else obj = Cytoscape.getCurrentNetworkView().getNetwork().edgesList(); for (GraphObject o : obj) ids.add(o.getIdentifier()); return ids; }
public List<JMenuItem> getNodeContextMenuItems(NodeView nodeView) { CyNetworkView networkView = (CyNetworkView) nodeView.getGraphView(); CyNetwork cyNetwork = networkView.getNetwork(); CyAttributes networkAttributes = Cytoscape.getNetworkAttributes(); Boolean b = networkAttributes.getBooleanAttribute(cyNetwork.getIdentifier(), BinarySifVisualStyleUtil.BINARY_NETWORK); if (b != null) { List<JMenuItem> menuList = new ArrayList<JMenuItem>(); JMenuItem menuItem = new JMenuItem ("Get Neighbors"); menuItem.addActionListener(new ExpandNode(nodeView)); menuList.add(menuItem); return menuList; } return null; }
/** * Property change listener - to get network/network view destroy events. * * @param event PropertyChangeEvent */ public void propertyChange(PropertyChangeEvent event) { final QuickFind quickFind = QuickFindFactory.getGlobalQuickFindInstance(); if (event.getPropertyName() != null) { if (event.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_CREATED)) { final CyNetwork cyNetwork = Cytoscape.getCurrentNetwork(); // Run Indexer in separate background daemon thread. Thread thread = new Thread() { public void run() { quickFind.addNetwork(cyNetwork, new TaskMonitorBase()); } }; thread.start(); } else if (event.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_DESTROYED)) { CyNetworkView networkView = (CyNetworkView) event.getNewValue(); CyNetwork cyNetwork = networkView.getNetwork(); quickFind.removeNetwork(cyNetwork); swapCurrentNetwork(quickFind); } else if (event.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_FOCUS)) { swapCurrentNetwork(quickFind); } } }
updateNodeViews(view.getNetwork(), view); final List<String> parents = Cytoscape.getNetworkAttributes().getListAttribute(view.getNetwork().getIdentifier(), CyNode.PARENT_NODES_ATTR); if (parents == null || parents.isEmpty()) {
protected void initialize() { networkView = Cytoscape.getCurrentNetworkView(); cyNetwork = networkView.getNetwork(); nodeAttributes = Cytoscape.getNodeAttributes(); edgeAttributes = Cytoscape.getEdgeAttributes();
int modificationCount) { CyNetwork cyNetwork = networkView.getNetwork(); NodeView nodeView = networkView.getNodeView(node); DNodeView dingNodeView = (DNodeView) nodeView;
CyNetwork cyNet = myView.getNetwork(); List<EdgeView> edgeViews = myView.getSelectedEdges(); List<NodeView> nodeViews = myView.getSelectedNodes();
String webServicesURL = networkAttributes.getStringAttribute(view.getNetwork().getIdentifier(), "biopax.web_services_url"); if (webServicesURL.startsWith("http://")) { String dataSources = networkAttributes.getStringAttribute(view.getNetwork().getIdentifier(), "biopax.data_sources");
final double yOff = minY - border; final FixedGraph fixedGraph = (FixedGraph) (graphView.getNetwork());
CyNetwork cyNetwork = networkView.getNetwork(); CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
if (networkViewMap.containsKey(view.getNetwork().getIdentifier())) return; internalFrameComponentMap.put(view.getNetwork().getIdentifier(), internalFrameComp); } else { logger.info("NetworkViewManager.createContainer() - DGraphView not found!"); iframe.setResizable(true); networkViewMap.put(view.getNetwork().getIdentifier(), iframe); componentMap.put(iframe, view.getNetwork().getIdentifier()); view.getNetwork().getIdentifier());
/** * DOCUMENT ME! * * @param edgeView * DOCUMENT ME! * @param network_view * DOCUMENT ME! */ public void vizmapEdge(EdgeView edgeView, CyNetworkView network_view) { CyEdge edge = (CyEdge) edgeView.getEdge(); List<VisualPropertyType> bypassedVPs = getBypassedVPs("EDGE", Cytoscape .getEdgeAttributes()); EdgeAppearanceCalculator edgeAppearanceCalculator = activeVS .getEdgeAppearanceCalculator(); edgeAppearanceCalculator.calculateEdgeAppearance(myEdgeApp, edge, network_view.getNetwork(), bypassedVPs); myEdgeApp.applyAppearance(edgeView, activeVS.getDependency()); }
/** * DOCUMENT ME! * * @param nodeView * DOCUMENT ME! * @param network_view * DOCUMENT ME! */ public void vizmapNode(NodeView nodeView, CyNetworkView network_view) { CyNode node = (CyNode) nodeView.getNode(); List<VisualPropertyType> bypassedVPs = getBypassedVPs("NODE", Cytoscape .getNodeAttributes()); NodeAppearanceCalculator nodeAppearanceCalculator = activeVS .getNodeAppearanceCalculator(); nodeAppearanceCalculator.calculateNodeAppearance(myNodeApp, node, network_view.getNetwork(), bypassedVPs); myNodeApp.applyAppearance(nodeView, activeVS.getDependency()); }
Cytoscape.getDesktop().getNetworkViewManager() .firePropertyChange(CytoscapeDesktop.NETWORK_VIEW_FOCUSED, null, Cytoscape.getCurrentNetworkView().getNetwork() .getIdentifier());
String text; for (Object node : net.getNetwork().nodesList()) { text = net.getNodeView((Node) node).getLabel().getText(); strLen = text.length(); String text; for (Object node : net.getNetwork().nodesList()) { text = net.getNodeView((Node) node).getLabel().getText(); strLen = text.length();
return; this.network = networkView.getNetwork();