void createFileMenu() { List<JComponent> menuItems = new ArrayList<JComponent>(); MenuAction menuAction = null; // We disable certain load items when there is no genome. boolean genomeLoaded = GenomeManager.getInstance().getCurrentGenome() != null; menuItems.add(new JSeparator()); // Load menu items menuAction = new LoadFilesMenuAction("Load from File...", KeyEvent.VK_L, igv); menuAction.setToolTipText(UIConstants.LOAD_TRACKS_TOOLTIP); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); menuAction = new LoadFromURLMenuAction(LoadFromURLMenuAction.LOAD_FROM_URL, KeyEvent.VK_U, igv); menuAction.setToolTipText(UIConstants.LOAD_TRACKS_TOOLTIP); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); menuAction = new LoadFromServerAction("Load from Server...", KeyEvent.VK_S, igv); menuAction.setToolTipText(UIConstants.LOAD_SERVER_DATA_TOOLTIP); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); menuAction = new LoadFromURLMenuAction(LoadFromURLMenuAction.LOAD_FROM_DAS, KeyEvent.VK_D, igv); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); if (PreferenceManager.getInstance().getAsBoolean(PreferenceManager.DB_ENABLED)) { menuAction = new LoadFromDatabaseAction("Load from Database...", 0, igv); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); } String genomeId = IGV.getInstance().getGenomeManager().getGenomeId(); if (EncodeFileBrowser.genomeSupported(genomeId)) { menuAction = new BrowseEncodeAction("Load from ENCODE...", KeyEvent.VK_E, igv); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); } // Disable loading if no genome loaded. Something of an edge case if (!genomeLoaded) { for (JComponent menuItem : menuItems) { menuItem.setEnabled(false); } } menuItems.add(new JSeparator()); // Session menu items menuAction = new NewSessionMenuAction("New Session...", KeyEvent.VK_N, igv); menuAction.setToolTipText(UIConstants.NEW_SESSION_TOOLTIP); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); menuAction = new OpenSessionMenuAction("Open Session...", KeyEvent.VK_O, igv); menuAction.setToolTipText(UIConstants.RESTORE_SESSION_TOOLTIP); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); menuAction = new SaveSessionMenuAction("Save Session...", KeyEvent.VK_V, igv); menuAction.setToolTipText(UIConstants.SAVE_SESSION_TOOLTIP); JMenuItem saveSessionItem = MenuAndToolbarUtils.createMenuItem(menuAction); menuItems.add(saveSessionItem); saveSessionItem.setEnabled(genomeLoaded); menuItems.add(new JSeparator()); // ***** Snapshots // Snapshot Application menuAction = new MenuAction("Save Image ...", null, KeyEvent.VK_A) { @Override public void actionPerformed(ActionEvent e) { igv.saveImage(igv.getMainPanel()); } }; menuAction.setToolTipText(SAVE_IMAGE_TOOLTIP); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); // TODO -- change "Exit" to "Close" for BioClipse menuItems.add(new JSeparator()); // Exit menuAction = new MenuAction("Exit", null, KeyEvent.VK_X) { @Override public void actionPerformed(ActionEvent e) { doExitApplication(); } }; menuAction.setToolTipText(EXIT_TOOLTIP); menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction)); // Empty the recent sessions list before we start to do // anything with it igv.getRecentSessionList().clear(); // Retrieve the stored session paths String recentSessions = PreferenceManager.getInstance().getRecentSessions(); if (recentSessions != null) { String[] sessions = recentSessions.split(";"); for (String sessionPath : sessions) { if (!igv.getRecentSessionList().contains(sessionPath)) { igv.getRecentSessionList().add(sessionPath); } } } if (!IGV.getInstance().getRecentSessionList().isEmpty()) { menuItems.add(new JSeparator()); // Now add menu items for (final String session : IGV.getInstance().getRecentSessionList()) { OpenSessionMenuAction osMenuAction = new OpenSessionMenuAction(session, session, IGV.getInstance()); menuItems.add(MenuAndToolbarUtils.createMenuItem(osMenuAction)); } } MenuAction fileMenuAction = new MenuAction("File", null, KeyEvent.VK_F); if (fileMenu == null) { fileMenu = MenuAndToolbarUtils.createMenu(menuItems, fileMenuAction); } else { fileMenu.removeAll(); for (JComponent item : menuItems) { fileMenu.add(item); } } }