public final void doExitApplication() {
try {
IGV.getInstance().saveStateForExit();
Frame mainFrame = IGV.getMainFrame();
// Hide and close the application
mainFrame.setVisible(false);
mainFrame.dispose();
} finally {
System.exit(0);
}
}
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);
}
public void showAboutDialog() {
(new AboutDialog(IGV.getMainFrame(), true)).setVisible(true);
}
private JMenu createExtrasMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
final JCheckBoxMenuItem exomeModeItem = new JCheckBoxMenuItem("Exome mode");
exomeModeItem.setSelected(FrameManager.isExomeMode());
exomeModeItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent actionEvent) {
FrameManager.setExomeMode(exomeModeItem.isSelected(), true);
igv.resetFrames();
}
});
menuItems.add(exomeModeItem);
menuItems.add(new JSeparator());
// Preferences reset
menuAction = new ResetPreferencesAction("Reset Preferences", IGV.getInstance());
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
menuAction =
new MenuAction("Variant list ... *EXPERIMENTAL*") {
@Override
public void actionPerformed(ActionEvent e) {
VariantListManager.openNavigator(IGV.getMainFrame());
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuItems.add(new JSeparator());
// Set frame dimensions
menuAction =
new MenuAction("Set window dimensions", null, KeyEvent.VK_C) {
@Override
public void actionPerformed(ActionEvent e) {
String value = JOptionPane.showInputDialog("Enter dimensions, e.g. 800x400");
if (value != null) {
String[] vals = value.split("x");
if (vals.length == 2) {
int w = Integer.parseInt(vals[0]);
int h = Integer.parseInt(vals[1]);
IGV.getMainFrame().setSize(w, h);
}
}
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// Save entire window
menuAction =
new MenuAction("Save Screenshot ...", null, KeyEvent.VK_A) {
@Override
public void actionPerformed(ActionEvent e) {
IGV.getInstance().saveImage(IGV.getInstance().getContentPane());
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction = new ExportTrackNamesMenuAction("Export track names...", IGV.getInstance());
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
menuAction =
new MenuAction("Scatter Plot ...") {
@Override
public void actionPerformed(ActionEvent e) {
final ReferenceFrame defaultFrame = FrameManager.getDefaultFrame();
String chr = defaultFrame.getChrName();
int start = (int) defaultFrame.getOrigin();
int end = (int) defaultFrame.getEnd();
int zoom = defaultFrame.getZoom();
ScatterPlotUtils.openPlot(chr, start, end, zoom);
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
MenuAction extrasMenuAction = new MenuAction("Extras");
JMenu menu = MenuAndToolbarUtils.createMenu(menuItems, extrasMenuAction);
//
JMenu lfMenu = new JMenu("L&F");
LookAndFeel lf = UIManager.getLookAndFeel();
for (UIManager.LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {
final String lfName = info.getName();
JMenuItem cb = new JMenuItem(lfName);
// cb.setSelected(info.getClassName().equals(lf.getClass().getName());
cb.addActionListener(
new AbstractAction() {
public void actionPerformed(ActionEvent actionEvent) {
for (UIManager.LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {
if (lfName.equals(info.getName())) {
try {
UIManager.setLookAndFeel(info.getClassName());
} catch (Exception e) {
e.printStackTrace();
}
break;
}
}
}
});
lfMenu.add(cb);
}
menu.add(lfMenu);
menu.setVisible(false);
return menu;
}
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;
}
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);
}
}
}
/**
* Generate the "tools" menu. This is imperative, it is written to field {@code toolsMenu}. Reason
* being, when we add (TODO remove) a new tool, we need to refresh just this menu
*/
void refreshToolsMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>(10);
// batch script
MenuAction menuAction = new RunScriptMenuAction("Run Batch Script...", KeyEvent.VK_X, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
// igvtools
// menuItems.add(new JSeparator());
menuAction =
new SortTracksMenuAction("Run igvtools...", KeyEvent.VK_T, igv) {
@Override
public void actionPerformed(ActionEvent e) {
IgvToolsGui.launch(false, igv.getGenomeManager().getGenomeId());
}
};
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
List<JComponent> otherToolMenus = igv.getOtherToolMenus();
if (otherToolMenus.size() > 0) {
for (JComponent entry : otherToolMenus) {
menuItems.add(entry);
}
}
// menuItems.add(new JSeparator());
// -------------------------------------//
// "Add tool" option, for loading cli_plugin from someplace else
JMenuItem addTool = new JMenuItem("Add Tool...");
addTool.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File pluginFi = FileDialogUtils.chooseFile("Select cli_plugin .xml spec");
if (pluginFi == null) return;
try {
PluginSpecReader.addCustomPlugin(pluginFi.getAbsolutePath());
refreshToolsMenu();
} catch (IOException e1) {
MessageUtils.showErrorMessage("Error loading custom cli_plugin", e1);
}
}
});
// menuItems.add(addTool);
// menuItems.add(new JSeparator());
// -------------------------------------//
for (final PluginSpecReader pluginSpecReader : PluginSpecReader.getPlugins()) {
for (final PluginSpecReader.Tool tool : pluginSpecReader.getTools()) {
final String toolName = tool.name;
boolean toolVisible = tool.visible;
JMenuItem toolMenu;
if (toolVisible) {
final String toolPath = pluginSpecReader.getToolPath(tool);
final String tool_url = tool.toolUrl;
boolean isValid = PluginSpecReader.isToolPathValid(toolPath);
ActionListener invalidActionListener =
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String msg = String.format("%s executable not found at %s", toolName, toolPath);
if (tool_url != null) {
msg += "<br/>See " + tool_url + " to install";
}
MessageUtils.showMessage(msg);
}
};
toolMenu = new JMenu(toolName);
// Kind of overlaps with the side-pull menu, doesn't look great
// toolMenu.setToolTipText(tool.getAttribute("description"));
for (final PluginSpecReader.Command command : tool.commandList) {
final String cmdName = command.name;
JMenuItem cmdItem = new JMenuItem(cmdName);
toolMenu.add(cmdItem);
if (isValid || toolPath == null) {
cmdItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
RunPlugin runPlugin = null;
try {
runPlugin =
new RunPlugin(IGV.getMainFrame(), pluginSpecReader, tool, command);
} catch (IllegalStateException e1) {
MessageUtils.showErrorMessage(e1.getMessage(), e1);
return;
}
runPlugin.setVisible(true);
}
});
cmdItem.setEnabled(true);
} else {
cmdItem.setEnabled(false);
}
}
// Hack so we can have a tool which is just general command line stuff
// Don't let the user change the path in that case
if (tool.defaultPath != null) {
JMenuItem setPathItem = new JMenuItem(String.format("Set path to %s...", toolName));
setPathItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
(new SetPluginPathDialog(IGV.getMainFrame(), pluginSpecReader, tool))
.setVisible(true);
refreshToolsMenu();
}
});
toolMenu.add(setPathItem);
}
menuItems.add(toolMenu);
}
}
}
// -------------------------------------//
// -----------SQL DB Tools--------------//
boolean showDBEditor = Globals.isDevelopment();
if (showDBEditor) {
JMenu sqlDBProfileEditor = new JMenu("SQL DB Profile Editor");
JMenuItem createNewProfile = new JMenuItem("Create New Profile");
createNewProfile.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File file =
FileDialogUtils.chooseFile(
"Save DB Profile", DirectoryManager.getUserDirectory(), FileDialogUtils.SAVE);
if (file != null) {
DBProfileEditor editor =
new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
editor.setVisible(true);
}
}
});
JMenuItem editExistingProfile = new JMenuItem("Edit Existing Profile");
editExistingProfile.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
File file = FileDialogUtils.chooseFile("Select .dbxml database profile");
if (file != null) {
if (!file.exists()) {}
DBProfileEditor editor =
new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
editor.setVisible(true);
}
}
});
sqlDBProfileEditor.add(createNewProfile);
sqlDBProfileEditor.add(editExistingProfile);
menuItems.add(sqlDBProfileEditor);
}
// -------------------------------------//
// DataTrack Math------------------------//
if (Globals.isDevelopment()) {
JMenuItem combineDataItem = new JMenuItem("Combine Data Tracks");
combineDataItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
CombinedDataSourceDialog dialog = new CombinedDataSourceDialog(IGV.getMainFrame());
dialog.setVisible(true);
}
});
menuItems.add(combineDataItem);
}
// -------------------------------------//
MenuAction toolsMenuAction = new MenuAction("Tools", null);
if (toolsMenu == null) {
toolsMenu = MenuAndToolbarUtils.createMenu(menuItems, toolsMenuAction);
toolsMenu.setName("Tools");
} else {
toolsMenu.removeAll();
for (JComponent item : menuItems) {
toolsMenu.add(item);
}
}
}