/* File: CytoscapeDesktop.java Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org) This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder is on an "as is" basis, and the Institute for Systems Biology and the Whitehead Institute have no obligations to provide maintenance, support, updates, enhancements or modifications. In no event shall the Institute for Systems Biology and the Whitehead Institute be liable to any party for direct, indirect, special, incidental or consequential damages, including lost profits, arising out of the use of this software and its documentation, even if the Institute for Systems Biology and the Whitehead Institute have been advised of the possibility of such damage. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. */ package cytoscape.view; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.Toolkit; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.util.List; import java.util.Properties; import javax.help.CSH; import javax.swing.ImageIcon; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSplitPane; import javax.swing.JTabbedPane; import javax.swing.SwingConstants; import javax.swing.WindowConstants; import javax.swing.border.EmptyBorder; import javax.swing.event.SwingPropertyChangeSupport; import cytoscape.CyNetwork; import cytoscape.Cytoscape; import cytoscape.CytoscapeInit; import cytoscape.CytoscapeVersion; import cytoscape.data.webservice.ui.WebServiceContextMenuListener; import cytoscape.util.undo.CyUndo; import cytoscape.view.cytopanels.BiModalJSplitPane; import cytoscape.view.cytopanels.CytoPanel; import cytoscape.view.cytopanels.CytoPanelImp; import cytoscape.view.cytopanels.CytoPanelState; import cytoscape.visual.VisualMappingManager; import cytoscape.visual.VisualStyle; import cytoscape.visual.ui.HideEdgeListener; import cytoscape.visual.ui.HideNodeListener; import cytoscape.visual.ui.NestedNetworkListener; import cytoscape.visual.ui.VizMapBypassNetworkListener; import cytoscape.visual.ui.VizMapperMainPanel; /** * The CytoscapeDesktop is the central Window for working with Cytoscape */ public class CytoscapeDesktop extends JFrame implements PropertyChangeListener { private static final long serialVersionUID = 2986320083629749014L; protected long lastPluginRegistryUpdate; protected int returnVal; // Default sizes of components private static final Dimension DEF_DESKTOP_SIZE = new Dimension(1000, 720); private static final int DEF_CONTROL_PANEL_WIDTH = 400; private static final int DEF_DATAPANEL_HEIGHT = 300; private static final int DEVIDER_SIZE = 4; /** * */ public static final String NETWORK_VIEWS_SELECTED = "NETWORK_VIEWS_SELECTED"; /** * */ public static final String NETWORK_VIEW_FOCUSED = "NETWORK_VIEW_FOCUSED"; /** * */ public static final String NETWORK_VIEW_FOCUS = "NETWORK_VIEW_FOCUS"; /** * */ public static final String NETWORK_VIEW_CREATED = "NETWORK_VIEW_CREATED"; /** * */ public static final String NETWORK_VIEW_DESTROYED = "NETWORK_VIEW_DESTROYED"; // state variables /** * */ public static final String VISUAL_STYLE = "VISUAL_STYLE"; /** * */ public static final String VIZMAP_ENABLED = "VIZMAP_ENABLED"; private static final String SMALL_ICON = "images/c16.png"; protected VisualStyle defaultVisualStyle; /** * The network panel that sends out events when a network is selected from * the Tree that it contains. */ protected NetworkPanel networkPanel; /** * The CyMenus object provides access to the all of the menus and toolbars * that will be needed. */ protected CyMenus cyMenus; /** * The NetworkViewManager can support three types of interfaces. * Tabbed/InternalFrame/ExternalFrame */ protected NetworkViewManager networkViewManager; /** * provides support for property change events */ protected final SwingPropertyChangeSupport pcs = new SwingPropertyChangeSupport(this); /** * The GraphViewController for all NetworkViews that we know about */ protected GraphViewController graphViewController; /** * Provides Operations for Mapping Data Attributes of CyNetworks to * CyNetworkViews */ protected VisualMappingManager vmm; /** * New VizMapper UI */ protected VizMapperMainPanel vizmapperUI; /** * Current network and view. */ protected String currentNetworkID; protected String currentNetworkViewID; // CytoPanels protected CytoPanelImp cytoPanelWest; protected CytoPanelImp cytoPanelEast; protected CytoPanelImp cytoPanelSouth; protected CytoPanelImp cytoPanelSouthWest; // Status Bar protected JLabel statusBar; protected final JPanel main_panel; // This is used to keep track of the visual style combo box. // This is the index of the box in the toolbar. We use this so that we can // add and remove the stylebox from the same place. protected int styleBoxIndex = -1; // Overview Window; private BirdsEyeViewHandler bevh; // These values will be calculated based on start-up window size. private int defaultControlPanelWidth; private int defaultDataPanelHeight; // Desktop and Result Panel private BiModalJSplitPane topRightPane; // Desktop and Data Panel private BiModalJSplitPane rightPane; // Network Panel and Desktop private BiModalJSplitPane masterPane; /** * Creates a new CytoscapeDesktop object. */ public CytoscapeDesktop() { super("Cytoscape Desktop (New Session)"); setIconImage(Toolkit.getDefaultToolkit().getImage(Cytoscape.class.getResource(SMALL_ICON))); main_panel = new JPanel(); main_panel.setLayout(new BorderLayout()); // ------------------------------// // Set up the Panels, Menus, and Event Firing networkViewManager = new NetworkViewManager(this); getBirdsEyeViewHandler(); getSwingPropertyChangeSupport().addPropertyChangeListener(bevh); Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(bevh); networkPanel = new NetworkPanel(this); networkPanel.setNavigator(bevh.getBirdsEyeView()); cyMenus = new CyMenus(); // Listener Setup // ---------------------------------------- // |----------| // | CyMenus | // |----------| // | // | // |-----| |---------| |------| |-------| // | N P |------| Desktop |----| NVM |--| Views | // |-----| |---------| |------| |-------| // | // | // |-----------| // | Cytoscape | // |-----------| // The CytoscapeDesktop listens to NETWORK_VIEW_CREATED events, // and passes them on, The NetworkPanel listens for them // The Desktop also keeps Cytoscape up2date, but NOT via events Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(this); // The Networkviewmanager listens to the CytoscapeDesktop to know when // to // put new NetworkViews in the userspace and to get passed focus events // from // the NetworkPanel. The CytoscapeDesktop also listens to the NVM this.getSwingPropertyChangeSupport().addPropertyChangeListener(networkViewManager); networkViewManager.getSwingPropertyChangeSupport().addPropertyChangeListener(this); // The NetworkPanel listens to the CytoscapeDesktop for // NETWORK_CREATED_EVENTS a // as well as for passing focused events from the Networkviewmanager. // The // CytoscapeDesktop also listens to the NetworkPanel this.getSwingPropertyChangeSupport().addPropertyChangeListener(networkPanel); networkPanel.getSwingPropertyChangeSupport().addPropertyChangeListener(this); // add a listener for node bypass Cytoscape.getSwingPropertyChangeSupport() .addPropertyChangeListener(new VizMapBypassNetworkListener()); // add a listener for nestedNetwork Cytoscape.getSwingPropertyChangeSupport() .addPropertyChangeListener(new NestedNetworkListener()); // Web Service Client context menu. Cytoscape.getSwingPropertyChangeSupport() .addPropertyChangeListener(new WebServiceContextMenuListener()); Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(new HideNodeListener()); Cytoscape.getSwingPropertyChangeSupport().addPropertyChangeListener(new HideEdgeListener()); // initialize Menus cyMenus.initializeMenus(); // create the CytoscapeDesktop masterPane = setupCytoPanels(networkPanel, networkViewManager); // note - proper networkViewManager has been properly selected in // setupCytoPanels() main_panel.add(masterPane, BorderLayout.CENTER); main_panel.add(cyMenus.getToolBar(), BorderLayout.NORTH); // Remove status bar. initStatusBar(main_panel); setJMenuBar(cyMenus.getMenuBar()); // Set up the VizMapper //setupVizMapper(); getVizMapperUI(); // don't automatically close window. Let Cytoscape.exit(returnVal) // handle this, // based upon user confirmation. setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent we) { Cytoscape.exit(returnVal); } }); setContentPane(main_panel); setSize(DEF_DESKTOP_SIZE); pack(); // Calculate panel sizes based on current window size. calculateProperPanelSize(); // Set the width of Cytopanel West masterPane.setDividerLocation(defaultControlPanelWidth); rightPane.setDividerLocation(getSize().height - defaultDataPanelHeight); masterPane.setDividerSize(DEVIDER_SIZE); // Set desktop location setDesktopLocation(); // show the Desktop setVisible(true); toFront(); // sets the top level identifier for java help CSH.setHelpIDString(this,"Cytoscape User Manual"); } private void calculateProperPanelSize() { final Dimension windowSize = this.getSize(); this.defaultControlPanelWidth = (int)(windowSize.width * 0.4); if (defaultControlPanelWidth>DEF_CONTROL_PANEL_WIDTH) defaultControlPanelWidth = DEF_CONTROL_PANEL_WIDTH; this.defaultDataPanelHeight = (int)(windowSize.getHeight() * 0.3); if(defaultDataPanelHeight > DEF_DATAPANEL_HEIGHT) defaultControlPanelWidth = DEF_DATAPANEL_HEIGHT; } private void setDesktopLocation(){ //restore desktop to previous location try { Properties props = new Properties(); File desktop_prop_file = new File(CytoscapeInit.getConfigVersionDirectory(), "desktop.props"); props.load(new FileInputStream(desktop_prop_file)); this.setLocation(new Integer(props.get("x").toString()).intValue(), new Integer(props.get("y").toString()).intValue()); this.setSize(new Integer(props.get("w").toString()).intValue(), new Integer(props.get("h").toString()).intValue()); } catch (Exception e){ setLocationRelativeTo(null); } } private void initStatusBar(JPanel panel) { statusBar = new JLabel(); statusBar.setFont(new Font("SansSerif", Font.PLAIN, 10)); statusBar.setBorder(new EmptyBorder(0, 7, 0, 7)); statusBar.setForeground(new Color(40, 40, 40)); panel.add(statusBar, BorderLayout.SOUTH); setStatusBarMsg("Welcome to Cytoscape " + CytoscapeVersion.version + " Right-click + drag to ZOOM Middle-click + drag to PAN"); } /** * Sets the Status Bar Message. * * @param msg * Status Bar Message. */ public void setStatusBarMsg(String msg) { statusBar.setText(msg); } /** * Clears the Status Bar Message. */ public void clearStatusBar() { // By using mutiple white spaces, layout for the statusBar is preserved. statusBar.setText(" "); } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public NetworkPanel getNetworkPanel() { return networkPanel; } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public CyMenus getCyMenus() { return cyMenus; } /** * DOCUMENT ME! * * @param newNetwork DOCUMENT ME! */ public void setNewNetwork(CyNetwork newNetwork) { } /** * Returns new vizmapper GUI. * * @return DOCUMENT ME! */ public VizMapperMainPanel getVizMapperUI() { if (vizmapperUI == null) { this.vmm = Cytoscape.getVisualMappingManager(); vizmapperUI = VizMapperMainPanel.getVizMapperUI(); getCytoPanel(SwingConstants.WEST).add("VizMapper\u2122", vizmapperUI); this.getSwingPropertyChangeSupport().addPropertyChangeListener(vizmapperUI); } return vizmapperUI; } /** * @param style the NEW VisualStyle * @return the OLD VisualStyle * * @deprecated use VisualMappingManager.setVisualStyle(VisualStyle style) instead. */ @Deprecated public VisualStyle setVisualStyle(VisualStyle style) { vmm.setVisualStyle(style); return null; } protected void updateFocus(String network_id) { final VisualStyle old_style = vmm.getVisualStyle(); final CyNetworkView old_view = Cytoscape.getCurrentNetworkView(); if (old_view != null) { old_view.putClientData(VISUAL_STYLE, old_style); old_view.putClientData(VIZMAP_ENABLED, new Boolean(old_view.getVisualMapperEnabled())); } // set the current Network/View Cytoscape.setCurrentNetwork(network_id); if (Cytoscape.setCurrentNetworkView(network_id)) { // deal with the new Network final CyNetworkView new_view = Cytoscape.getCurrentNetworkView(); // VisualStyle new_style = (VisualStyle) new_view.getClientData(VISUAL_STYLE); VisualStyle new_style = new_view.getVisualStyle(); Boolean vizmap_enabled = ((Boolean) new_view.getClientData(VIZMAP_ENABLED)); if (new_style == null) new_style = vmm.getCalculatorCatalog().getVisualStyle("default"); if (vizmap_enabled == null) vizmap_enabled = true; vmm.setNetworkView(new_view); if (new_style.getName().equals(old_style.getName()) == false) { vmm.setVisualStyle(new_style); // Redraw Graph only when current network view's style is not equal to the selected style. final CyNetworkView curView = Cytoscape.getCurrentNetworkView(); final VisualStyle curViewStyle = curView.getVisualStyle(); if (curView != Cytoscape.getNullNetworkView() && curViewStyle != null) { if (new_style.getName().equals(curViewStyle.getName()) == false) Cytoscape.getCurrentNetworkView().redrawGraph(false, true); } } } } /** * TODO: We should remove one of this event! * * @param network_id DOCUMENT ME! */ public void setFocus(String network_id) { pcs.firePropertyChange(new PropertyChangeEvent(this, NETWORK_VIEW_FOCUSED, null, network_id)); pcs.firePropertyChange(new PropertyChangeEvent(this, NETWORK_VIEW_FOCUS, null, network_id)); } /** * TO keep things clearer there is one GraphView Controller per * CytoscapeDesktop */ public GraphViewController getGraphViewController() { if (graphViewController == null) graphViewController = new GraphViewController(); return graphViewController; } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public SwingPropertyChangeSupport getSwingPropertyChangeSupport() { return pcs; } /** * DOCUMENT ME! * * @param e DOCUMENT ME! */ public void propertyChange(PropertyChangeEvent e) { if (NETWORK_VIEW_CREATED.equals(e.getPropertyName())) { // add the new view to the GraphViewController getGraphViewController().addGraphView((CyNetworkView) e.getNewValue()); // pass on the event pcs.firePropertyChange(e); } else if (NETWORK_VIEW_FOCUSED.equals(e.getPropertyName())) { // get focus event from NetworkViewManager updateFocus(e.getNewValue().toString()); pcs.firePropertyChange(e); } else if (NETWORK_VIEW_FOCUS.equals(e.getPropertyName())) { // get Focus from NetworkPanel updateFocus(e.getNewValue().toString()); pcs.firePropertyChange(e); } else if (NETWORK_VIEWS_SELECTED.equals(e.getPropertyName())) { Cytoscape.setSelectedNetworkViews( (List)(e.getNewValue()) ); Cytoscape.setSelectedNetworks( (List)(e.getNewValue()) ); pcs.firePropertyChange(e); } else if (Cytoscape.NETWORK_CREATED.equals(e.getPropertyName())) { // fire the event so that the NetworkPanel can catch it pcs.firePropertyChange(e); } else if (Cytoscape.NETWORK_DESTROYED.equals(e.getPropertyName())) { // fire the event so that the NetworkPanel can catch it pcs.firePropertyChange(e); // Check new session or not if ((Cytoscape.getNetworkSet().size() == 0) && (Cytoscape.getSessionstate() != Cytoscape.SESSION_OPENED)) { String message = "Do you want to create a new session?.\n(All attributes will be lost!)"; int result = JOptionPane.showConfirmDialog(this, message, "Create New Session?", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, null); if (result == JOptionPane.YES_OPTION) Cytoscape.createNewSession(); } } else if (NETWORK_VIEW_DESTROYED.equals(e.getPropertyName())) { // remove the view from the GraphViewController getGraphViewController().removeGraphView((CyNetworkView) e.getNewValue()); // pass on the event pcs.firePropertyChange(e); } else if (e.getPropertyName().equalsIgnoreCase(Cytoscape.CYTOSCAPE_EXIT)){ // save Desktop location into property file "desktop.prop" File desktop_prop_file = new File(CytoscapeInit.getConfigVersionDirectory(), "desktop.props"); Properties props = new Properties(); props.setProperty("x", new Integer(this.getX()).toString()); props.setProperty("y", new Integer(this.getY()).toString()); props.setProperty("w", new Integer(this.getWidth()).toString()); props.setProperty("h", new Integer(this.getHeight()).toString()); try { props.store(new FileOutputStream(desktop_prop_file), "Remember desktop frame location"); } catch (IOException ioe){ } try { Cytoscape.getRecentlyOpenedSessionTracker().writeOut(); } catch (final IOException ioe) { System.err.println("failed to save recent session URLs!"); } } } // ---------------------------------------------------------------------------// // Cytopanels - Public and Protected methods /** * Gets a cytoPanel given a Compass direction. * * @param compassDirection * Compass Direction (SwingConstants.{SOUTH,EAST,WEST}). * @return CytoPanel The CytoPanel that lives in the region specified by * compass direction. */ public CytoPanel getCytoPanel(int compassDirection) { // return appropriate cytoPanel based on compass direction switch (compassDirection) { case SwingConstants.SOUTH: return (CytoPanel) cytoPanelSouth; case SwingConstants.EAST: return (CytoPanel) cytoPanelEast; case SwingConstants.WEST: return (CytoPanel) cytoPanelWest; case SwingConstants.SOUTH_WEST: return (CytoPanel) cytoPanelSouthWest; } // Houston we have a problem! throw new IllegalArgumentException("Illegal Argument: " + compassDirection + ". Must be one of: SwingConstants.{SOUTH,EAST,WEST,SOUTH_WEST}."); } /** * Create the CytoPanels UI. * * @param networkPanel * to load on left side of right bimodal. * @param networkViewManager * to load on left side (CytoPanel West). * @return BiModalJSplitPane Object. */ private BiModalJSplitPane setupCytoPanels(NetworkPanel networkPanel, NetworkViewManager networkViewManager) { // bimodals that our Cytopanels Live within topRightPane = createTopRightPane(networkViewManager); rightPane = createRightPane(topRightPane); masterPane = createMasterPane(networkPanel, rightPane); createBottomLeft(); return masterPane; } protected void createBottomLeft() { cytoPanelSouthWest = new CytoPanelImp(SwingConstants.SOUTH_WEST, JTabbedPane.TOP, CytoPanelState.HIDE); final BiModalJSplitPane split = new BiModalJSplitPane(this, JSplitPane.VERTICAL_SPLIT, BiModalJSplitPane.MODE_HIDE_SPLIT, new JPanel(), cytoPanelSouthWest); split.setResizeWeight(0); cytoPanelSouthWest.setCytoPanelContainer(split); cytoPanelSouthWest.setMinimumSize(new Dimension(180, 330)); cytoPanelSouthWest.setMaximumSize(new Dimension(180, 330)); cytoPanelSouthWest.setPreferredSize(new Dimension(180, 330)); split.setDividerSize(DEVIDER_SIZE); new ToolCytoPanelListener( split, (CytoPanelImp)cytoPanelWest, cytoPanelSouthWest ); } /** * Creates the TopRight Pane. * * @param networkViewManager * to load on left side of top right bimodal. * @return BiModalJSplitPane Object. */ protected BiModalJSplitPane createTopRightPane(NetworkViewManager networkViewManager) { // create cytopanel with tabs along the top cytoPanelEast = new CytoPanelImp(SwingConstants.EAST, JTabbedPane.TOP, CytoPanelState.HIDE); // create the split pane - we show this on startup final BiModalJSplitPane splitPane = new BiModalJSplitPane(this, JSplitPane.HORIZONTAL_SPLIT, BiModalJSplitPane.MODE_HIDE_SPLIT, networkViewManager.getDesktopPane(), cytoPanelEast); // set the cytopanelcontainer cytoPanelEast.setCytoPanelContainer(splitPane); // set the resize weight - left component gets extra space splitPane.setResizeWeight(1.0); // outta here return splitPane; } /** * Creates the Right Panel. * * @param topRightPane * TopRightPane Object. * @return BiModalJSplitPane Object */ protected BiModalJSplitPane createRightPane(BiModalJSplitPane topRightPane) { // create cytopanel with tabs along the bottom cytoPanelSouth = new CytoPanelImp(SwingConstants.SOUTH, JTabbedPane.BOTTOM, CytoPanelState.HIDE); // create the split pane - hidden by default final BiModalJSplitPane splitPane = new BiModalJSplitPane(this, JSplitPane.VERTICAL_SPLIT, BiModalJSplitPane.MODE_HIDE_SPLIT, topRightPane, cytoPanelSouth); // set the cytopanel container cytoPanelSouth.setCytoPanelContainer(splitPane); splitPane.setDividerSize(DEVIDER_SIZE); // set resize weight - top component gets all the extra space. splitPane.setResizeWeight(1.0); // outta here return splitPane; } /** * Creates the Master Split Pane. * * @param networkPanel * to load on left side of CytoPanel (cytoPanelWest). * @param rightPane * BiModalJSplitPane Object. * @return BiModalJSplitPane Object. */ protected BiModalJSplitPane createMasterPane(NetworkPanel networkPanel, BiModalJSplitPane rightPane) { // create cytopanel with tabs along the top cytoPanelWest = new CytoPanelImp(SwingConstants.WEST, JTabbedPane.TOP, CytoPanelState.DOCK); // add the network panel to our tab String tab1Name = new String("Network"); cytoPanelWest.add(tab1Name, new ImageIcon(Cytoscape.class.getResource("images/class_hi.gif")), networkPanel, "Cytoscape Network List"); // create the split pane - hidden by default final BiModalJSplitPane splitPane = new BiModalJSplitPane(this, JSplitPane.HORIZONTAL_SPLIT, BiModalJSplitPane.MODE_SHOW_SPLIT, cytoPanelWest, rightPane); splitPane.setDividerSize(DEVIDER_SIZE); // set the cytopanel container cytoPanelWest.setCytoPanelContainer(splitPane); // outta here return splitPane; } // End Cytopanels - Public and Protected methods // ---------------------------------------------------------------------------// /** * Gets the NetworkView Manager. * * @return NetworkViewManager Object. */ public NetworkViewManager getNetworkViewManager() { return this.networkViewManager; } /** * DOCUMENT ME! * * @return DOCUMENT ME! */ public BirdsEyeViewHandler getBirdsEyeViewHandler() { if (bevh == null) bevh = new BirdsEyeViewHandler(networkViewManager.getDesktopPane()); return bevh; } /** * DOCUMENT ME! * * @param vt DOCUMENT ME! * * @return DOCUMENT ME! * @deprecated View types are no longer support so stop using this. Will be removed August 2008. */ public static int parseViewType(String vt) { return 1; // What was internal } }