private JMenu createHelpMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
menuAction =
new MenuAction("User Guide ... ") {
@Override
public void actionPerformed(ActionEvent e) {
try {
BrowserLauncher.openURL(SERVER_BASE_URL + "igv/UserGuide");
} catch (IOException ex) {
log.error("Error opening browser", ex);
}
}
};
menuAction.setToolTipText(HELP_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
if (Desktop.isDesktopSupported()) {
final Desktop desktop = Desktop.getDesktop();
if (desktop.isSupported(Desktop.Action.MAIL)) {
menuAction =
new MenuAction("Help Forum...") {
@Override
public void actionPerformed(ActionEvent e) {
try {
URI uri = new URI("http://groups.google.com/forum/#!forum/igv-help");
Desktop.getDesktop().browse(uri);
} catch (Exception ex) {
log.error("Error opening igv-help uri", ex);
}
}
};
menuAction.setToolTipText("Email support");
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
}
}
menuAction =
new MenuAction("About IGV ") {
@Override
public void actionPerformed(ActionEvent e) {
(new AboutDialog(IGV.getMainFrame(), true)).setVisible(true);
}
};
menuAction.setToolTipText(ABOUT_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
MenuAction helpMenuAction = new MenuAction("Help");
return MenuAndToolbarUtils.createMenu(menuItems, helpMenuAction);
}
private JMenu createGenomeSpaceMenu() {
JMenu menu = new JMenu("GenomeSpace");
MenuAction menuAction = null;
menuAction = new LoadFromGSMenuAction("Load File from GenomeSpace...", KeyEvent.VK_U, igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.addSeparator();
menuAction =
new LoadGenomeFromGSMenuAction("Load Genome from GenomeSpace...", KeyEvent.VK_Z, igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.addSeparator();
menuAction = new GSSaveSessionMenuAction("Save Session to GenomeSpace...", igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new GSOpenSessionMenuAction("Load Session from GenomeSpace...", igv);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.add(new JSeparator());
menuAction =
new MenuAction("Logout") {
@Override
public void actionPerformed(ActionEvent e) {
GSUtils.logout();
if (MessageUtils.confirm(
"You must shutdown IGV to complete the GenomeSpace logout. Shutdown now?")) {
doExitApplication();
}
}
};
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.add(new JSeparator());
menuAction =
new MenuAction("Register... ") {
@Override
public void actionPerformed(ActionEvent e) {
try {
BrowserLauncher.openURL(GENOMESPACE_REG_PAGE);
} catch (IOException ex) {
log.error("Error opening browser", ex);
}
}
};
menuAction.setToolTipText(GENOMESPACE_REG_TOOLTIP);
menu.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menu.setVisible(
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.GENOME_SPACE_ENABLE));
return menu;
}
private JMenu createRegionsMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
menuAction = new NavigateRegionsMenuAction("Region Navigator ...", IGV.getInstance());
menuAction.setToolTipText(UIConstants.REGION_NAVIGATOR_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction =
new MenuAction("Gene Lists...", null, KeyEvent.VK_S) {
@Override
public void actionPerformed(ActionEvent e) {
(GeneListManagerUI.getInstance(IGV.getMainFrame())).setVisible(true);
}
};
menuAction.setToolTipText("Open gene list manager");
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
// Export Regions
menuAction =
new ExportRegionsMenuAction("Export Regions ...", KeyEvent.VK_E, IGV.getInstance());
menuAction.setToolTipText(UIConstants.EXPORT_REGION_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Import Regions
menuAction =
new ImportRegionsMenuAction("Import Regions ...", KeyEvent.VK_I, IGV.getInstance());
menuAction.setToolTipText(IMPORT_REGION_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Import Regions
// menuAction = new ClearRegionsMenuAction("Clear Regions ...", IGV.getInstance());
// menuAction.setToolTipText(IMPORT_REGION_TOOLTIP);
// menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
MenuAction dataMenuAction = new MenuAction("Regions", null, KeyEvent.VK_V);
viewMenu = MenuAndToolbarUtils.createMenu(menuItems, dataMenuAction);
return viewMenu;
}
private JMenu createTracksMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
// Sort Context
menuAction = new SortTracksMenuAction("Sort Tracks...", KeyEvent.VK_S, IGV.getInstance());
menuAction.setToolTipText(SORT_TRACKS_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new GroupTracksMenuAction("Group Tracks... ", KeyEvent.VK_G, IGV.getInstance());
menuAction.setToolTipText(UIConstants.GROUP_TRACKS_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Filter Tracks
filterTracksAction =
new FilterTracksMenuAction("Filter Tracks...", KeyEvent.VK_F, IGV.getInstance());
filterTracksAction.setToolTipText(UIConstants.FILTER_TRACKS_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(filterTracksAction));
menuItems.add(new JSeparator());
// Reset Tracks
menuAction =
new FitDataToWindowMenuAction("Fit Data to Window", KeyEvent.VK_W, IGV.getInstance());
menuAction.setToolTipText(UIConstants.FIT_DATA_TO_WINDOW_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Set track height
menuAction =
new SetTrackHeightMenuAction("Set Track Height...", KeyEvent.VK_H, IGV.getInstance());
menuAction.setToolTipText(UIConstants.SET_DEFAULT_TRACK_HEIGHT_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
MenuAction dataMenuAction = new MenuAction("Tracks", null, KeyEvent.VK_K);
// menuItems.add(exportData);
return MenuAndToolbarUtils.createMenu(menuItems, dataMenuAction);
}
private JMenu createViewMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
// Preferences
menuAction =
new MenuAction("Preferences...", null, KeyEvent.VK_P) {
@Override
public void actionPerformed(ActionEvent e) {
UIUtilities.invokeOnEventThread(
new Runnable() {
public void run() {
IGV.getInstance().doViewPreferences();
}
});
}
};
menuAction.setToolTipText(PREFERENCE_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction =
new MenuAction("Color Legends ...", null, KeyEvent.VK_H) {
@Override
public void actionPerformed(ActionEvent e) {
(new LegendDialog(IGV.getMainFrame())).setVisible(true);
}
};
menuAction.setToolTipText(SHOW_HEATMAP_LEGEND_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
menuAction =
new MenuAction("Show Name Panel", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
JCheckBoxMenuItem menuItem = (JCheckBoxMenuItem) e.getSource();
if (menuItem.isSelected()) {
IGV.getInstance().getMainPanel().expandNamePanel();
} else {
IGV.getInstance().getMainPanel().collapseNamePanel();
}
IGV.getInstance().doRefresh();
}
};
boolean isShowing = IGV.getInstance().getMainPanel().isExpanded();
JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem();
menuItem.setSelected(isShowing);
menuItem.setAction(menuAction);
menuItems.add(menuItem);
JMenuItem panelWidthmenuItem = new JMenuItem();
menuAction =
new MenuAction("Set Name Panel Width...", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
MainPanel mainPanel = IGV.getInstance().getMainPanel();
String currentValue = String.valueOf(mainPanel.getNamePanelWidth());
String newValue =
MessageUtils.showInputDialog("Enter track name panel width: ", currentValue);
if (newValue != null) {
try {
Integer w = Integer.parseInt(newValue);
if (w <= 0 || w == 1000) throw new NumberFormatException();
PreferenceManager.getInstance().put(PreferenceManager.NAME_PANEL_WIDTH, newValue);
mainPanel.setNamePanelWidth(w);
} catch (NumberFormatException ex) {
MessageUtils.showErrorMessage(
"Error: value must be a positive integer < 1000.", ex);
}
}
}
};
panelWidthmenuItem.setAction(menuAction);
menuItems.add(panelWidthmenuItem);
// Hide or Show the attribute panels
boolean isShow =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_ATTRIBUTE_VIEWS_KEY);
IGV.getInstance().doShowAttributeDisplay(isShow); // <= WEIRD doing IGV.getInstance() here!
menuAction =
new MenuAction("Show Attribute Display", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
JCheckBoxMenuItem menuItem = (JCheckBoxMenuItem) e.getSource();
PreferenceManager.getInstance().setShowAttributeView(menuItem.getState());
IGV.getInstance().getMainPanel().invalidate();
IGV.getInstance().doRefresh();
}
};
menuItem = MenuAndToolbarUtils.createMenuItem(menuAction, isShow);
menuItems.add(menuItem);
menuAction =
new MenuAction("Select Attributes to Show...", null, KeyEvent.VK_S) {
@Override
public void actionPerformed(ActionEvent e) {
IGV.getInstance().doSelectDisplayableAttribute();
}
};
menuAction.setToolTipText(SELECT_DISPLAYABLE_ATTRIBUTES_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction =
new MenuAction("Show Header Panel", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
JCheckBoxMenuItem menuItem = (JCheckBoxMenuItem) e.getSource();
if (menuItem.isSelected()) {
IGV.getInstance().getMainPanel().restoreHeader();
} else {
IGV.getInstance().getMainPanel().removeHeader();
}
IGV.getInstance().doRefresh();
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction, true));
menuItems.add(new JSeparator());
menuAction =
new MenuAction("Reorder Panels...", null, KeyEvent.VK_S) {
@Override
public void actionPerformed(ActionEvent e) {
ReorderPanelsDialog dlg = new ReorderPanelsDialog(IGV.getMainFrame());
dlg.setVisible(true);
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
menuItems.add(new HistoryMenu("Go to"));
// Add to IGVPanel menu
MenuAction dataMenuAction = new MenuAction("View", null, KeyEvent.VK_V);
viewMenu = MenuAndToolbarUtils.createMenu(menuItems, dataMenuAction);
return viewMenu;
}
private JMenu createGenomesMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
// Load genome
menuAction =
new MenuAction("Load Genome from File...", null, KeyEvent.VK_I) {
@Override
public void actionPerformed(ActionEvent event) {
try {
org.broad.igv.ui.util.ProgressMonitor monitor =
new org.broad.igv.ui.util.ProgressMonitor();
igv.doLoadGenome(monitor);
} catch (Exception e) {
MessageUtils.showErrorMessage(e.getMessage(), e);
}
}
};
menuAction.setToolTipText("Load a FASTA or .genome file...");
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Load genome from URL
menuAction = new LoadFromURLMenuAction(LoadFromURLMenuAction.LOAD_GENOME_FROM_URL, 0, igv);
menuAction.setToolTipText("Load a FASTA or .genome file...");
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Add genome to combo box from server
menuAction =
new MenuAction("Load Genome From Server...", null) {
@Override
public void actionPerformed(ActionEvent event) {
IGV.getInstance().loadGenomeFromServerAction();
}
};
menuAction.setToolTipText(LOAD_GENOME_SERVER_TOOLTIP);
loadFromServerMenuItem = MenuAndToolbarUtils.createMenuItem(menuAction);
menuItems.add(loadFromServerMenuItem);
menuItems.add(new JSeparator());
menuAction =
new MenuAction("Create .genome File...", null, KeyEvent.VK_D) {
@Override
public void actionPerformed(ActionEvent event) {
org.broad.igv.ui.util.ProgressMonitor monitor =
new org.broad.igv.ui.util.ProgressMonitor();
igv.doDefineGenome(monitor);
}
};
menuAction.setToolTipText(UIConstants.IMPORT_GENOME_TOOLTIP);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
// Add genome to combo box from server
menuAction =
new MenuAction("Manage Genome List...", null) {
@Override
public void actionPerformed(ActionEvent event) {
ManageGenomesDialog dialog2 = new ManageGenomesDialog(IGV.getMainFrame());
dialog2.setVisible(true);
boolean cancelled = dialog2.isCancelled();
List<GenomeListItem> removedValuesList = dialog2.getRemovedValuesList();
if (!cancelled) {
GenomeManager.getInstance().buildGenomeItemList();
igv.getContentPane().getCommandBar().refreshGenomeListComboBox();
if (removedValuesList != null && !removedValuesList.isEmpty()) {
try {
GenomeManager.getInstance().deleteDownloadedGenomes(removedValuesList);
} catch (IOException e) {
MessageUtils.showErrorMessage("Error deleting genome files", e);
}
GenomeManager.getInstance().updateImportedGenomePropertyFile();
notifyGenomesAddedRemoved(removedValuesList, false);
}
}
}
};
menuAction.setToolTipText("Add, remove, or reorder genomes which appear in the dropdown list");
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
MenuAction genomeMenuAction = new MenuAction("Genomes", null);
return MenuAndToolbarUtils.createMenu(menuItems, genomeMenuAction);
}
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);
}
}
}
