void windowMenu_menuSelected(MenuEvent e) {
// <<TODO:MAINTAINABILITY>> This algorithm is not robust. It assumes
// the Window
// menu has exactly one "regular" menu item (newWindowMenuItem). [Jon
// Aquino]
if (windowMenu.getItemCount() > 0
&& windowMenu.getItem(0) != null
&& windowMenu
.getItem(0)
.getText()
.equals(AbstractPlugIn.createName(CloneWindowPlugIn.class))) {
JMenuItem newWindowMenuItem = windowMenu.getItem(0);
windowMenu.removeAll();
windowMenu.add(newWindowMenuItem);
windowMenu.addSeparator();
} else {
// ezLink doesn't have a Clone Window menu [Jon Aquino]
windowMenu.removeAll();
}
// final TaskComponent[] frames = (TaskComponent[]) desktopPane.getAllFrames();
final JInternalFrame[] frames = desktopPane.getAllFrames();
for (int i = 0; i < frames.length; i++) {
JMenuItem menuItem = new JMenuItem();
// Increase truncation threshold from 20 to 40, for eziLink [Jon
// Aquino]
menuItem.setText(GUIUtil.truncateString(frames[i].getTitle(), 40));
associate(menuItem, frames[i]);
windowMenu.add(menuItem);
}
if (windowMenu.getItemCount() == 0) {
// For ezLink [Jon Aquino]
windowMenu.add(new JMenuItem("(No Windows)"));
}
}
/**
* initialize the symbols menu
*
* @param m menu
*/
public void initSymbolsMenu(JMenu m) {
m.removeAll();
for (int i = 0; i < glyphs.size(); i++) {
final MetSymbol metSymbol = (MetSymbol) glyphs.get(i);
JMenuItem mi = GuiUtils.makeMenuItem(metSymbol.getLabel(), this, "showProperties", metSymbol);
mi.addMouseListener(
new MouseAdapter() {
public void mousePressed(MouseEvent e) {
highlightedMetSymbol = null;
StationModelCanvas.this.repaint();
}
public void mouseReleased(MouseEvent e) {
highlightedMetSymbol = null;
StationModelCanvas.this.repaint();
}
public void mouseEntered(MouseEvent e) {
highlightedMetSymbol = metSymbol;
StationModelCanvas.this.repaint();
}
public void mouseExited(MouseEvent e) {
highlightedMetSymbol = null;
StationModelCanvas.this.repaint();
}
});
m.add(mi);
}
}
private void resetMarks() {
interpToMark.removeAll();
shiftToMark.removeAll();
Iterator marks = mediator.getMarkerModel().getLabels().iterator();
boolean hasMark = false;
while (marks.hasNext()) {
String mark = (String) marks.next();
if (!ChronicleViewer.CURR_FRAME_LABEL.equals(mark)) {
JMenuItem mi = new JMenuItem(mark);
mi.addActionListener(itmAction);
interpToMark.add(mi);
mi = new JMenuItem(mark);
mi.addActionListener(stmAction);
shiftToMark.add(mi);
hasMark = true;
}
}
shiftToMark.setEnabled(hasMark);
interpToMark.setEnabled(hasMark);
}
/** Make the view menu */
private void makeStationModelMenu() {
stationModelMenu.removeAll();
List symbols = smm.getResources();
List items = new ArrayList();
ObjectListener listener =
new ObjectListener(null) {
public void actionPerformed(ActionEvent ae) {
if (!okToChange()) {
return;
}
setStationModel((StationModel) theObject, true);
}
};
GuiUtils.makeMenu(stationModelMenu, makeStationModelMenuItems(symbols, listener, smm));
}
public void refreshSerialPortList() {
String[] serialPortList = SerialPortList.getPortNames();
portMenu.removeAll();
portMenu.add(refreshItem);
JMenuItem menuItem;
for (String serialPort : serialPortList) {
menuItem = new JMenuItem(serialPort);
menuItem.addActionListener(e -> onSerialPortClicked(e.getActionCommand()));
portMenu.add(menuItem);
}
}
/** Make the file menu */
private void makeFileMenu() {
fileMenu.removeAll();
fileMenu.add(makeMenuItem("New", 'n', GuiUtils.CMD_NEW));
fileMenu.addSeparator();
fileMenu.add(makeMenuItem("Save", 's', GuiUtils.CMD_SAVE));
fileMenu.add(makeMenuItem("Save As...", GuiUtils.CMD_SAVEAS));
fileMenu.add(makeMenuItem("Rename...", GuiUtils.CMD_RENAME));
fileMenu.addSeparator();
JMenuItem removeMenuItem = makeMenuItem("Remove", GuiUtils.CMD_REMOVE);
removeMenuItem.setEnabled(smm.isUsers(stationModel));
fileMenu.add(removeMenuItem);
fileMenu.addSeparator();
fileMenu.add(makeMenuItem("Import...", GuiUtils.CMD_IMPORT));
fileMenu.add(makeMenuItem("Export...", GuiUtils.CMD_EXPORT));
fileMenu.addSeparator();
fileMenu.add(makeMenuItem("Close", GuiUtils.CMD_CLOSE));
}
/**
* Creates an {@link OtrContactMenu} for each {@link Contact} contained in the
* <tt>metaContact</tt>.
*
* @param metaContact The {@link MetaContact} this {@link OtrMetaContactMenu} refers to.
*/
private void createOtrContactMenus(MetaContact metaContact) {
JMenu menu = getMenu();
// Remove any existing OtrContactMenu items.
menu.removeAll();
// Create the new OtrContactMenu items.
if (metaContact != null) {
Iterator<Contact> contacts = metaContact.getContacts();
if (metaContact.getContactCount() == 1) {
new OtrContactMenu(contacts.next(), inMacOSXScreenMenuBar, menu, false);
} else
while (contacts.hasNext()) {
new OtrContactMenu(contacts.next(), inMacOSXScreenMenuBar, menu, true);
}
}
}
@Override
public void run() {
if (androidMode.getSDK() == null) return;
final Devices devices = Devices.getInstance();
java.util.List<Device> deviceList = devices.findMultiple(false);
Device selectedDevice = devices.getSelectedDevice();
if (deviceList.size() == 0) {
// if (deviceMenu.getItem(0).isEnabled()) {
if (0 < deviceMenu.getItemCount()) {
deviceMenu.removeAll();
JMenuItem noDevicesItem = new JMenuItem("No connected devices");
noDevicesItem.setEnabled(false);
deviceMenu.add(noDevicesItem);
}
devices.setSelectedDevice(null);
} else {
deviceMenu.removeAll();
if (selectedDevice == null) {
selectedDevice = deviceList.get(0);
devices.setSelectedDevice(selectedDevice);
} else {
// check if selected device is still connected
boolean found = false;
for (Device device : deviceList) {
if (device.equals(selectedDevice)) {
found = true;
break;
}
}
if (!found) {
selectedDevice = deviceList.get(0);
devices.setSelectedDevice(selectedDevice);
}
}
for (final Device device : deviceList) {
final JCheckBoxMenuItem deviceItem = new JCheckBoxMenuItem(device.getName());
deviceItem.setEnabled(true);
if (device.equals(selectedDevice)) deviceItem.setState(true);
// prevent checkboxmenuitem automatic state changing onclick
deviceItem.addChangeListener(
new ChangeListener() {
@Override
public void stateChanged(ChangeEvent e) {
if (device.equals(devices.getSelectedDevice())) deviceItem.setState(true);
else deviceItem.setState(false);
}
});
deviceItem.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
devices.setSelectedDevice(device);
for (int i = 0; i < deviceMenu.getItemCount(); i++) {
((JCheckBoxMenuItem) deviceMenu.getItem(i)).setState(false);
}
deviceItem.setState(true);
}
});
deviceMenu.add(deviceItem);
}
}
}
private void updateSdkMenu(final JMenu sdkMenu) {
try {
ArrayList<AndroidSDK.SDKTarget> targets = androidMode.getSDK().getAvailableSdkTargets();
if (targets.size() != 0) sdkMenu.removeAll();
AndroidSDK.SDKTarget lowestTargetAvailable = null;
JCheckBoxMenuItem lowestTargetMenuItem = null;
String savedTargetVersion = Preferences.get("android.sdk.version");
boolean savedTargetSet = false;
for (final AndroidSDK.SDKTarget target : targets) {
if (target.version < 11) {
// We do not support API level less than 11
continue;
}
final JCheckBoxMenuItem item =
new JCheckBoxMenuItem("API " + target.name + " (" + target.version + ")");
if (savedTargetSet == false
&& (lowestTargetAvailable == null || lowestTargetAvailable.version > target.version)) {
lowestTargetAvailable = target;
lowestTargetMenuItem = item;
}
if (Integer.toString(target.version).equals(savedTargetVersion)) {
AndroidBuild.setSdkTarget(target, sketch);
item.setState(true);
savedTargetSet = true;
}
item.addChangeListener(
new ChangeListener() {
@Override
public void stateChanged(ChangeEvent e) {
if (target.name.equals(AndroidBuild.sdkName)) item.setState(true);
else item.setState(false);
}
});
item.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
AndroidBuild.setSdkTarget(target, sketch);
for (int i = 0; i < sdkMenu.getItemCount(); i++) {
((JCheckBoxMenuItem) sdkMenu.getItem(i)).setState(false);
}
item.setState(true);
}
});
sdkMenu.add(item);
}
if (!savedTargetSet) {
AndroidBuild.setSdkTarget(lowestTargetAvailable, sketch);
lowestTargetMenuItem.setState(true);
}
} catch (IOException e) {
e.printStackTrace();
}
}
public void clear() {
items.clear();
jMenu.removeAll();
}
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);
}
}
}
/** Remove all types from the menu. Then cycle through all available types, and add them. */
private void populateTypeMenu() {
typeMenu.removeAll();
for (String key : BibtexEntryType.getAllTypes()) {
typeMenu.add(new ChangeTypeAction(BibtexEntryType.getType(key), panel));
}
}
