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;
}
/**
* 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);
}
}
}