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 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;
}
public void enableExtrasMenu() {
extrasMenu.setVisible(true);
}