1 //First, get a handler to the cytoPanel west, which is the control panel
   2 CytoPanelImp ctrlPanel = (CytoPanelImp) Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
   3 
   4 //Create a JPanel object (a class extends JPanel, say, MyPanel)
   5 MyPanel myPanel = new MyPanel();
   6 
   7 //Add it to the control panel.
   8 ctrlPanel.add("myPanel", myPanel);
   9 

   1 ImageIcon icon = new ImageIcon(getClass().getResource("/tiger.jpg"));
   2 MyPluginToolBarAction toolbarAction = new MyPluginToolBarAction(icon, this);
   3 

   1 Cytoscape.getDesktop().getCyMenus().addCytoscapeAction((CytoscapeAction) toolbarAction);
   2 

   1 //create a network without a view CyNetwork
   2 yNetwork = Cytoscape.createNetwork("network1", false);
   3 
   4 CyNode node0 = Cytoscape.getCyNode("rain", true);
   5 CyNode node1 = Cytoscape.getCyNode("rainbow", true);
   6 CyNode node2 = Cytoscape.getCyNode("rabbit", true);
   7 CyNode node3 = Cytoscape.getCyNode("yellow", true);
   8 
   9 cyNetwork.addNode(node0);
  10 cyNetwork.addNode(node1);
  11 cyNetwork.addNode(node2);
  12 cyNetwork.addNode(node3);
  13 
  14 CyEdge edge0 = Cytoscape.getCyEdge(node0, node1, Semantics.INTERACTION, "pp", true);
  15 CyEdge edge1 = Cytoscape.getCyEdge(node0, node2, Semantics.INTERACTION, "pp", true);
  16 CyEdge edge2 = Cytoscape.getCyEdge(node0, node3, Semantics.INTERACTION, "pp", true);
  17 
  18 cyNetwork.addEdge(edge0);
  19 cyNetwork.addEdge(edge1);
  20 cyNetwork.addEdge(edge2);
  21 

   1 cyNetwork.removeNode(node1.getRootGraphIndex(), true);
   2 

   1 Cytoscape.destroyNetwork(cyNetwork);
   2 

   1 // Create a view for the network CyNetworkView
   2 cyView = Cytoscape.createNetworkView(cyNetwork, "MyNetwork");
   3 

   1 // hide a node
   2 cyNetwork.hideNode(node1.getRootGraphIndex());
   3 

   1 Cytoscape.destroyNetworkView(cyView);
   2 

   1 CyNetwork current_network = Cytoscape.getCurrentNetwork();
   2 Set selectedNodes = current_network.getSelectedNodes();
   3 
   4 Iterator<Node> it = selectedNodes.iterator();
   5 while (it.hasNext()) {
   6         Node aNode = (Node) it.next();
   7         System.out.println(aNode.getIdentifier());
   8 }
   9 

   1 // Handle PropertyChangeEvent
   2 public void propertyChange(PropertyChangeEvent e) {
   3 if (e.getPropertyName().equalsIgnoreCase(Cytoscape.ATTRIBUTES_CHANGED))
   4 {
   5         System.out.println("Received an event -- Cytoscape.ATTRIBUTES_CHANGED!");
   6 }
   7 if (e.getPropertyName().equalsIgnoreCase(CytoscapeDesktop.NETWORK_VIEW_FOCUSED))
   8 {
   9                                 System.out.println("Received an event -- CytoscapeDesktop.NETWORK_VIEW_FOCUSED!");
  10 }
  11 
  12 
  13 }
  14 

   1 //Let user choose a color
   2 Color bkColor = JColorChooser.showDialog(Cytoscape.getDesktop(), "Please choose a background color", Color.white);
   3 
   4 // Change the background color for current view
   5 DingNetworkView  theView = (DingNetworkView) Cytoscape.getCurrentNetworkView();
   6 DingCanvas backgroundCanvas = theView.getCanvas(DGraphView.Canvas.BACKGROUND_CANVAS);
   7 backgroundCanvas.setBackground(bkColor);
   8 
   9 // Refresh the view
  10 Cytoscape.getCurrentNetworkView().updateView();
  11 

   1 // Get reference to the view
   2 final CyNetworkView networkView = Cytoscape.getCurrentNetworkView();
   3 
   4 networkView.setZoom(scaleFactor);
   5 networkView.updateView();
   6 

   1 String attributeName = "testAttribute";
   2 String AttributeValue = "testValue";
   3 CyAttributes cyNodeAttrs = Cytoscape.getNodeAttributes();
   4 cyNodeAttrs.setAttribute(node.getIdentifier(), attributeName, AttributeValue);
   5 

   1 // inform others via property change event.
   2 Cytoscape.firePropertyChange(Cytoscape.ATTRIBUTES_CHANGED, null, null);
   3 

   1 CyAttributes cyNodeAttrs = Cytoscape.getNodeAttributes();
   2 cyNodeAttrs.deleteAttribute(attributeName);
   3 

   1 WebServiceClient<EUtilsServiceSoap> client =
   2         WebServiceClientManager.getClient("tutorial13");
   3 
   4 if (client == null) {
   5 System.out.println("Web service client tutorial13 is not found!");
   6         return;
   7 }
   8 

   1 // eInfo utility returns a list of available databases
   2 EUtilsServiceSoap utils = (EUtilsServiceSoap) client.getClientStub();
   3 
   4 // call NCBI EInfo utility, "Available databases from NCBI";
   5 EInfoResult res = utils.run_eInfo(new EInfoRequest());
   6 

   1 WebServiceClientManager.registerClient(My_NCBIClient.getClient());
   2 

   1 VisualMappingManager vmm = Cytoscape.getVisualMappingManager();
   2 Set<String> names = vmm.getCalculatorCatalog().getVisualStyleNames();
   3 

   1       public static final String vsName = "Example Visual Style";
   2         VisualStyle createVisualStyle(CyNetwork network) {
   3 
   4                 NodeAppearanceCalculator nodeAppCalc = new NodeAppearanceCalculator();
   5                 EdgeAppearanceCalculator edgeAppCalc = new EdgeAppearanceCalculator();
   6                 GlobalAppearanceCalculator globalAppCalc = new GlobalAppearanceCalculator();
   7 
   8 
   9                 // Passthrough Mapping - set node label
  10                 //PassThroughMapping pm = new PassThroughMapping(new String(), "attr2");
  11                 PassThroughMapping pm = new PassThroughMapping(new String(), "attr2asdf");
  12                 Calculator nlc = new BasicCalculator("Example Node Label Calculator",
  13                                                      pm, VisualPropertyType.NODE_LABEL);
  14                 nodeAppCalc.setCalculator(nlc);
  15 
  16 
  17                 // Discrete Mapping - set node shapes
  18                 DiscreteMapping disMapping = new DiscreteMapping(NodeShape.RECT,
  19                                                                  ObjectMapping.NODE_MAPPING);
  20                 disMapping.setControllingAttributeName("attr1", network, false);
  21                 disMapping.putMapValue(new Integer(1), NodeShape.DIAMOND);
  22                 disMapping.putMapValue(new Integer(2), NodeShape.ELLIPSE);
  23                 disMapping.putMapValue(new Integer(3), NodeShape.TRIANGLE);
  24 
  25                 Calculator shapeCalculator = new BasicCalculator("Example Node Shape Calculator",
  26                                                                   disMapping,
  27                                                                                                                   VisualPropertyType.NODE_SHAPE);
  28                 nodeAppCalc.setCalculator(shapeCalculator);
  29 
  30 
  31                 // Continuous Mapping - set node color
  32                 ContinuousMapping continuousMapping = new ContinuousMapping(Color.WHITE,
  33                                                             ObjectMapping.NODE_MAPPING);
  34                 continuousMapping.setControllingAttributeName("attr3", network, false);
  35 
  36         Interpolator numToColor = new LinearNumberToColorInterpolator();
  37         continuousMapping.setInterpolator(numToColor);
  38 
  39                 Color underColor = Color.GRAY;
  40                 Color minColor = Color.RED;
  41                 Color midColor = Color.WHITE;
  42                 Color maxColor = Color.GREEN;
  43                 Color overColor = Color.BLUE;
  44 
  45                 // Create boundary conditions                  less than,   equals,  greater than
  46                 BoundaryRangeValues bv0 = new BoundaryRangeValues(underColor, minColor, minColor);
  47                 BoundaryRangeValues bv1 = new BoundaryRangeValues(midColor, midColor, midColor);
  48                 BoundaryRangeValues bv2 = new BoundaryRangeValues(maxColor, maxColor, overColor);
  49 
  50         // Set the attribute point values associated with the boundary values
  51                 continuousMapping.addPoint(0.0, bv0);
  52                 continuousMapping.addPoint(1.0, bv1);
  53                 continuousMapping.addPoint(2.0, bv2);
  54 
  55                 Calculator nodeColorCalculator = new BasicCalculator("Example Node Color Calc",
  56                                                                 continuousMapping,
  57                                                                                                          VisualPropertyType.NODE_FILL_COLOR);
  58                 nodeAppCalc.setCalculator(nodeColorCalculator);
  59 
  60 
  61                 // Discrete Mapping - Set edge target arrow shape
  62                 DiscreteMapping arrowMapping = new DiscreteMapping(ArrowShape.NONE,
  63                                                                    ObjectMapping.EDGE_MAPPING);
  64                 arrowMapping.setControllingAttributeName("interaction", network, false);
  65                 arrowMapping.putMapValue("pp", ArrowShape.ARROW);
  66                 arrowMapping.putMapValue("pd", ArrowShape.CIRCLE);
  67 
  68                 Calculator edgeArrowCalculator = new BasicCalculator("Example Edge Arrow Shape Calculator",
  69                                               arrowMapping, VisualPropertyType.EDGE_TGTARROW_SHAPE);
  70                 edgeAppCalc.setCalculator(edgeArrowCalculator);
  71 
  72 
  73                 // Create the visual style
  74                 VisualStyle visualStyle = new VisualStyle(vsName, nodeAppCalc, edgeAppCalc, globalAppCalc);
  75 
  76                 return visualStyle;
  77         }
  78 

   1                 // get the network and view
   2                 CyNetwork network = Cytoscape.getCurrentNetwork();
   3                 CyNetworkView networkView = Cytoscape.getCurrentNetworkView();
   4 
   5                 // get the VisualMappingManager and CalculatorCatalog
   6                 VisualMappingManager manager = Cytoscape.getVisualMappingManager();
   7                 CalculatorCatalog catalog = manager.getCalculatorCatalog();
   8 
   9                 // check to see if a visual style with this name already exists
  10                 VisualStyle vs = catalog.getVisualStyle(vsName);
  11                 if (vs == null) {
  12                         // if not, create it and add it to the catalog
  13                         vs = createVisualStyle(network);
  14                         catalog.addVisualStyle(vs);
  15                 }
  16 
  17                 networkView.setVisualStyle(vs.getName()); // not strictly necessary
  18 
  19                 // actually apply the visual style
  20                 manager.setVisualStyle(vs);
  21                 networkView.redrawGraph(true,true);
  22 

   1 // Create a node color calculator for "Degree" attribute
   2 Calculator nodeColorCalculator = createCalculator(); // see below
   3 
   4 // Set the calculator to the visualStyle
   5 vs.getNodeAppearanceCalculator().setCalculator(nodeColorCalculator);
   6 

   1 VisualPropertyType type = VisualPropertyType.NODE_FILL_COLOR;
   2 final Object defaultObj = type.getDefault(Cytoscape.getVisualMappingManager().getVisualStyle());
   3 
   4 ContinuousMapping cm = new ContinuousMapping(defaultObj, ObjectMapping.NODE_MAPPING);
   5 // Set controlling Attribute
   6 cm.setControllingAttributeName("Degree", Cytoscape.getCurrentNetwork(), false);
   7 
   8 Interpolator numToColor = new LinearNumberToColorInterpolator();
   9 cm.setInterpolator(numToColor);
  10 
  11 Color underColor = Color.GRAY;
  12 Color minColor = Color.RED;
  13 Color midColor = Color.WHITE;
  14 Color maxColor = Color.GREEN;
  15 Color overColor = Color.BLUE;
  16 
  17 BoundaryRangeValues bv0 = new BoundaryRangeValues(underColor, minColor, minColor);
  18 BoundaryRangeValues bv1 = new BoundaryRangeValues(midColor, midColor, midColor);
  19 BoundaryRangeValues bv2 = new BoundaryRangeValues(maxColor, maxColor, overColor);
  20 
  21 // Set the attribute point values associated with the boundary values
  22 // The points p1, p2, p3 are the values between (min~max) of the degree
  23 cm.addPoint(p1, bv0); cm.addPoint(p2, bv1); cm.addPoint(p3, bv2);
  24 
  25 // Create a calculator
  26 BasicCalculator myCalculator = new BasicCalculator("My degree calcualtor", cm, VisualPropertyType.NODE_FILL_COLOR);
  27 

   1 Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED, null, file.getAbsolutePath());
   2 

   1 CyLayouts.addLayout(new MyLayout(), "My Layouts");
   2 

   1 layoutProperties.add(new Tunable("groupcount", "Number of random groups ",
   2 Tunable.INTEGER, new Integer(2)));
   3 

   1 MyGroupViewer myView = new MyGroupViewer();
   2 // Register with CyGroup
   3 CyGroupManager.registerGroupViewer(myView);
   4 

   1 class MyNodeContextMenuListener implements NodeContextMenuListener {
   2         public void addNodeContextMenuItems(NodeView nodeView, JPopupMenu menu)
   3         {
   4                 JMenuItem myMenuItem = new JMenuItem("MyNodeMenuItem");
   5 
   6                 myMenuItem.addActionListener(new MyNodeAction(nodeView));
   7                 if (menu == null) {
   8                         menu = new JPopupMenu();
   9                 }
  10                 menu.add(myMenuItem);
  11         }
  12 }
  13 

   1 MyNodeContextMenuListener l = new MyNodeContextMenuListener();
   2 Cytoscape.getCurrentNetworkView().addNodeContextMenuListener(l);
   3 

   1 import browser.AttributeBrowserPlugin;
   2 …
   3 
   4 JMenuItem menuItem = new JMenuItem("MyMenuItem_browser");
   5 menuItem.addActionListener(actionListener);
   6 AttributeBrowserPlugin.addMenuItem(browser.DataObjectType.NODES, menuItem);
   7 

   1 /**
   2 * Save global state to "tutorial21.props"
   3 */
   4 public void onCytoscapeExit() {}
   5 
   6 // restore state
   7 public void restoreInitState() {
   8         File global_prop_file = CytoscapeInit.getConfigFile("tutorial21.props");
   9 }
  10 

   1 public void saveSessionStateFiles(List<File> pFileList) {}
   2 public void restoreSessionState(List<File> pStateFileList) {}
   3 

   1 package cytoscape.tutorial23;
   2 
   3 
   4 import cytoscape.data.eqn_attribs.AttribParser;
   5 import cytoscape.data.eqn_attribs.Parser;
   6 import cytoscape.plugin.CytoscapePlugin;
   7 
   8 
   9 public class Tutorial23 extends CytoscapePlugin {
  10         public Tutorial23() {
  11                 final AttribParser theParser = Parser.getParser();
  12                 theParser.registerFunction(new IXor());
  13         }
  14 }
  15 

   1         /**                                                                                                                                                                                                                                                  
   2          *  Used to parse the function string.  This name is treated in a case-insensitive manner!                                                                                                                                                           
   3          *  @returns the name by which you must call the function when used in an attribute equation.                                                                                                                                                        
   4          */
   5         public String getName() { return "IXOR"; }
   6 
   7         /**                                                                                                                                                                                                                                                  
   8          *  Used to provide help for users.                                                                                                                                                                                                                  
   9          *  @returns a description of what this function does                                                                                                                                                                                                
  10          */
  11         public String getFunctionSummary() { return "Returns an integer value that is the exclusive-or of 2 other integer values."; }
  12 
  13         /**                                                                                                                                                                                                                                                  
  14          *  Used to provide help for users.                                                                                                                                                                                                                  
  15          *  @returns a description of how to use this function                                                                                                                                                                                               
  16          */
  17         public String getUsageDescription() { return "Call this with \"IXOR(integer1,integer2)\""; }
  18 

   1 public Class getReturnType() { return Long.class; }
   2 

   1         public Class validateArgTypes(final Class[] argTypes) {
   2                 if (argTypes.length != 2 || (argTypes[0] != Long.class && argTypes[0] != Double.class)
   3                     || (argTypes[1] != Long.class && argTypes[1] != Double.class))
   4                         return null;
   5 
   6                 return Long.class;
   7         }
   8