addAction(new NewSessionAction()); addAction(new NewWindowSelectedNodesOnlyAction()); addAction(new NewWindowSelectedNodesEdgesAction()); addAction(new CloneGraphInNewWindowAction()); addAction(new NewNetworkAction()); addAction(new OpenSessionAction(),1); addAction(new SaveSessionAction("Save"),2); addAction(new SaveSessionAsAction("Save as..."),3); addAction(new ImportGraphFileAction(this)); addAction(new WebServiceNetworkImportAction()); addAction(new ImportNodeAttributesAction()); addAction(new ImportEdgeAttributesAction()); addAction(new ImportExpressionMatrixAction()); addAction(new ImportVizmapAction()); addAction(new ExportAsXGMMLAction()); addAction(new ExportAsGMLAction()); addAction(new ExportAsInteractionsAction()); addAction(new ExportNetworksAsNNFAction()); addAction(new ExportNodeAttributesAction()); addAction(new ExportEdgeAttributesAction()); addAction(new ExportVizmapAction()); addAction(new ExportAsGraphicsAction("PDF"));
/** * Constructor. * This method is called by the main Cytoscape Application upon startup. */ public BiopaxPlugin() { ImportHandler importHandler = new ImportHandler(); importHandler.addFilter(new BioPaxFilter()); // Optionally set up HTTP Proxy Properties cytoProps = CytoscapeInit.getProperties(); String proxyHost = (String) cytoProps.get(PROXY_HOST_PROPERTY); String proxyPort = (String) cytoProps.get(PROXY_PORT_PROPERTY); if ((proxyHost != null) && (proxyPort != null)) { System.getProperties().put("proxySet", "true"); System.getProperties().put("proxyHost", proxyHost); System.getProperties().put("proxyPort", proxyPort); } // add export to BioPAX menu CyMenus cyMenus = Cytoscape.getDesktop().getCyMenus(); cyMenus.addAction(new ExportAsBioPAXAction()); // to start listening to network events, like a load of a network from a session, // we create an instance of a BioPaxContainerClass this contains the network listener BioPaxContainer.getInstance(); }
/** * PSI-MI Plugin */ public PsiMiPlugIn() { // Register PsiMiFilter ImportHandler importHandler = new ImportHandler(); importHandler.addFilter(new PsiMiFilter()); Cytoscape.getDesktop().getCyMenus().addAction(new ExportNetworkAsPsiMiOne()); Cytoscape.getDesktop().getCyMenus().addAction(new ExportNetworkAsPsiMiTwoFive()); } }
/** * Creates a new ManualLayoutPlugin object. */ public ManualLayoutPlugin() { // create the panels RotatePanel rotatePanel = new RotatePanel(); ScalePanel scalePanel = new ScalePanel(); ControlPanel controlPanel = new ControlPanel(); // add them to the cytopanel Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH_WEST) .add("Align and Distribute", controlPanel); Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH_WEST).add("Rotate", rotatePanel); Cytoscape.getDesktop().getCytoPanel(SwingConstants.SOUTH_WEST).add("Scale", scalePanel); // create the actions Cytoscape.getDesktop().getCyMenus().addAction( new ControlPanelAction(), 0); Cytoscape.getDesktop().getCyMenus().addAction( new RotatePanelAction(), 1); Cytoscape.getDesktop().getCyMenus().addAction( new ScalePanelAction(), 2); } }