/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.ui;
import apple.dts.samplecode.osxadapter.OSXAdapter;
import org.apache.log4j.Logger;
import org.broad.igv.DirectoryManager;
import org.broad.igv.Globals;
import org.broad.igv.annotations.ForTesting;
import org.broad.igv.charts.ScatterPlotUtils;
import org.broad.igv.cli_plugin.PluginSpecReader;
import org.broad.igv.cli_plugin.ui.RunPlugin;
import org.broad.igv.cli_plugin.ui.SetPluginPathDialog;
import org.broad.igv.dev.db.DBProfileEditor;
import org.broad.igv.feature.genome.GenomeListItem;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.ga4gh.Ga4ghAPIHelper;
import org.broad.igv.ga4gh.OAuthUtils;
import org.broad.igv.gs.GSOpenSessionMenuAction;
import org.broad.igv.gs.GSSaveSessionMenuAction;
import org.broad.igv.gs.GSUtils;
import org.broad.igv.lists.GeneListManagerUI;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.tools.IgvToolsGui;
import org.broad.igv.tools.motiffinder.MotifFinderPlugin;
import org.broad.igv.track.CombinedDataSourceDialog;
import org.broad.igv.ui.action.*;
import org.broad.igv.event.GenomeChangeEvent;
import org.broad.igv.event.IGVEventBus;
import org.broad.igv.event.IGVEventObserver;
import org.broad.igv.ui.legend.LegendDialog;
import org.broad.igv.ui.panel.FrameManager;
import org.broad.igv.ui.panel.MainPanel;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.panel.ReorderPanelsDialog;
import org.broad.igv.ui.util.*;
import org.broad.igv.util.BrowserLauncher;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.LongRunningTask;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.blat.BlatClient;
import org.broad.igv.util.encode.EncodeFileBrowser;
import javax.swing.*;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
import javax.swing.plaf.basic.BasicBorders;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import static org.broad.igv.prefs.Constants.*;
import static org.broad.igv.ui.UIConstants.*;
/**
* Main menu bar at top of window. File / genomes / view / etc.
* Singleton
*
* @author jrobinso
* @date Apr 4, 2011
*/
public class IGVMenuBar extends JMenuBar implements IGVEventObserver {
private static Logger log = Logger.getLogger(IGVMenuBar.class);
public static final String GENOMESPACE_REG_TOOLTIP = "Register for GenomeSpace";
public static final String GENOMESPACE_REG_PAGE = "http://www.genomespace.org/register";
private JMenu extrasMenu;
private FilterTracksMenuAction filterTracksAction;
private JMenu viewMenu;
IGV igv;
private JMenu toolsMenu;
/**
* We store this as a field because we alter it if
* we can't access genome server list
*/
private JMenuItem loadFromServerMenuItem;
private static final String LOAD_GENOME_SERVER_TOOLTIP = "Select genomes available on the server to appear in menu.";
private static final String CANNOT_LOAD_GENOME_SERVER_TOOLTIP = "Could not reach genome server";
private static IGVMenuBar instance;
private JMenu googleMenu;
private JMenuItem encodeMenuItem;
public void notifyGenomeServerReachable(boolean reachable) {
if (loadFromServerMenuItem != null) {
UIUtilities.invokeOnEventThread(() -> {
loadFromServerMenuItem.setEnabled(reachable);
String tooltip = reachable ? LOAD_GENOME_SERVER_TOOLTIP : CANNOT_LOAD_GENOME_SERVER_TOOLTIP;
loadFromServerMenuItem.setToolTipText(tooltip);
});
}
}
public void showAboutDialog() {
(new AboutDialog(IGV.getMainFrame(), true)).setVisible(true);
}
static IGVMenuBar createInstance(IGV igv) {
if (instance != null) {
if (igv == instance.igv) {
return instance;
}
throw new IllegalStateException("Cannot create another IGVMenuBar, use getInstance");
}
UIUtilities.invokeAndWaitOnEventThread(() ->instance = new IGVMenuBar(igv));
return instance;
}
public static IGVMenuBar getInstance() {
return instance;
}
private IGVMenuBar(IGV igv) {
this.igv = igv;
setBorder(new BasicBorders.MenuBarBorder(Color.GRAY, Color.GRAY));
setBorderPainted(true);
for (AbstractButton menu : createMenus()) {
add(menu);
}
IGVEventBus.getInstance().subscribe(GenomeChangeEvent.class, this);
//This is for Macs, so showing the about dialog
//from the command bar does what we want.
if (Globals.IS_MAC) {
try {
OSXAdapter.setAboutHandler(this, getClass().getDeclaredMethod("showAboutDialog", (Class[]) null));
OSXAdapter.setQuitHandler(ShutdownThread.class, ShutdownThread.class.getDeclaredMethod("runS", (Class[]) null));
} catch (Exception e) {
log.error("Error setting apple-specific about and quit handlers", e);
}
}
}
private List<AbstractButton> createMenus() {
List<AbstractButton> menus = new ArrayList<AbstractButton>();
menus.add(createFileMenu());
menus.add(createGenomesMenu());
menus.add(createViewMenu());
menus.add(createTracksMenu());
menus.add(createRegionsMenu());
refreshToolsMenu();
menus.add(toolsMenu);
menus.add(createGenomeSpaceMenu());
extrasMenu = createExtrasMenu();
//extrasMenu.setVisible(false);
menus.add(extrasMenu);
googleMenu = createGoogleMenu();
googleMenu.setVisible(PreferencesManager.getPreferences().getAsBoolean(ENABLE_GOOGLE_MENU));
menus.add(googleMenu);
menus.add(createHelpMenu());
// Experimental -- remove for production release
return menus;
}
/**
* 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
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));
// Motif finder
menuItems.add(MotifFinderPlugin.getMenuItem());
// BLAT
menuItems.add(BlatClient.getMenuItem());
// Combine data tracks
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);
List<JComponent> otherToolMenus = igv.getOtherToolMenus();
menuItems.add(new JSeparator());
if (otherToolMenus.size() > 0) {
for (JComponent entry : otherToolMenus) {
menuItems.add(entry);
}
}
//-------------------------------------//
//"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 (Exception 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(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------------------------//
//-------------------------------------//
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);
}
}
}
public void enableExtrasMenu() {
extrasMenu.setVisible(true);
}
JMenu createFileMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = 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 (PreferencesManager.getPreferences().getAsBoolean(DB_ENABLED)) {
menuAction = new LoadFromDatabaseAction("Load from Database...", 0, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
}
encodeMenuItem = MenuAndToolbarUtils.createMenuItem(new BrowseEncodeAction("Load from ENCODE (2012)...", KeyEvent.VK_E, igv));
menuItems.add(encodeMenuItem);
String genomeId = IGV.getInstance().getGenomeManager().getGenomeId();
encodeMenuItem.setVisible (EncodeFileBrowser.genomeSupported(genomeId));
menuAction = new BrowseGa4ghAction("Load from Ga4gh...", KeyEvent.VK_G, igv);
menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
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);
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 = PreferencesManager.getPreferences().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);
JMenu fileMenu = MenuAndToolbarUtils.createMenu(menuItems, fileMenuAction);
return fileMenu;
}
private void notifyGenomesAddedRemoved(List<GenomeListItem> selectedValues, boolean added) {
if (selectedValues == null || selectedValues.size() == 0) return;
int size = selectedValues.size();
String msg = "";
if (size == 1) {
msg += selectedValues.get(0) + " genome";
} else {
msg += size + " genomes";
}
if (added) {
msg += " added to";
} else {
msg += " removed from";
}
msg += " list";
MessageUtils.setStatusBarMessage(msg);
}
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 {
File importDirectory = PreferencesManager.getPreferences().getLastGenomeImportDirectory();
if (importDirectory == null) {
PreferencesManager.getPreferences().setLastGenomeImportDirectory(DirectoryManager.getUserDirectory());
}
// Display the dialog
File file = FileDialogUtils.chooseFile("Load Genome", importDirectory, FileDialog.LOAD);
// If a file selection was made
if (file != null) {
GenomeManager.getInstance().loadGenome(file.getAbsolutePath(), null);
}
} 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().loadGenomeFromServer();
}
};
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) {
javax.swing.ProgressMonitor monitor = new javax.swing.ProgressMonitor(IGV.getInstance().getMainPanel(),
"Creating genome", null, 0, 100);
igv.defineGenome(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) {
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);
String defaultGenomeKey = PreferencesManager.getPreferences().get(DEFAULT_GENOME);
for (GenomeListItem item : removedValuesList) {
if (defaultGenomeKey.equals(item.getId())) {
PreferencesManager.getPreferences().remove(DEFAULT_GENOME);
break;
}
}
}
GenomeManager.getInstance().buildGenomeItemList();
igv.getContentPane().getCommandBar().refreshGenomeListComboBox();
}
}
};
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);
}
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();
PreferencesManager.getPreferences().put(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 = PreferencesManager.getPreferences().getAsBoolean(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();
PreferencesManager.getPreferences().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 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 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("Check for Updates...") {
@Override
public void actionPerformed(ActionEvent e) {
checkVersion();
}
};
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 void checkVersion() {
int readTimeout = Globals.READ_TIMEOUT;
int connectTimeout = Globals.CONNECT_TIMEOUT;
try {
Main.Version thisVersion = Main.Version.getVersion(Globals.VERSION);
if (thisVersion != null) {
Globals.CONNECT_TIMEOUT = 5000;
Globals.READ_TIMEOUT = 1000;
final String serverVersionString = HttpUtils.getInstance().getContentsAsString(new URL(Globals.getVersionURL())).trim();
// See if user has specified to skip this update
final String skipString = PreferencesManager.getPreferences().get(SKIP_VERSION);
HashSet<String> skipVersion = new HashSet<String>(Arrays.asList(skipString.split(",")));
if (skipVersion.contains(serverVersionString)) return;
Main.Version serverVersion = Main.Version.getVersion(serverVersionString.trim());
if (serverVersion == null) return;
if (thisVersion.lessThan(serverVersion)) {
log.info("A later version of IGV is available (" + serverVersionString + ")");
final VersionUpdateDialog dlg = new VersionUpdateDialog(serverVersionString);
dlg.setVisible(true);
if (dlg.isSkipVersion()) {
String newSkipString = skipString + "," + serverVersionString;
PreferencesManager.getPreferences().put(SKIP_VERSION, newSkipString);
}
} else {
MessageUtils.showMessage("IGV is up to date");
}
}
else {
if(Globals.VERSION.contains("3.0_beta") || Globals.VERSION.contains("snapshot")) {
HttpUtils.getInstance().getContentsAsString(new URL(Globals.getVersionURL())).trim();
}
}
} catch (Exception e) {
log.error("Error checking version", e);
} finally {
Globals.CONNECT_TIMEOUT = connectTimeout;
Globals.READ_TIMEOUT = readTimeout;
}
}
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(PreferencesManager.getPreferences().getAsBoolean(GENOME_SPACE_ENABLE));
return menu;
}
private JMenu createExtrasMenu() {
List<JComponent> menuItems = new ArrayList<JComponent>();
MenuAction menuAction = null;
// Preferences reset
menuAction = new ResetPreferencesAction("Reset Preferences", IGV.getInstance());
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 createGoogleMenu() {
// Dynamically name menu - dwm08
JMenu menu = new JMenu(OAuthUtils.authProvider);
final JMenuItem login = new JMenuItem("Login ... ");
login.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
try {
OAuthUtils.getInstance().openAuthorizationPage();
} catch (Exception ex) {
MessageUtils.showErrorMessage("Error fetching oAuth tokens. See log for details", ex);
log.error("Error fetching oAuth tokens", ex);
}
}
});
login.setEnabled(false);
menu.add(login);
final JMenuItem logout = new JMenuItem("Logout ");
logout.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
OAuthUtils.getInstance().logout();
}
});
logout.setEnabled(false);
menu.add(logout);
final JMenuItem loadReadset = new JMenuItem("Load Genomics ReadGroupSet... ");
loadReadset.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String readsetId = MessageUtils.showInputDialog("Enter ReadGroupSet ID (e.g. CMvnhpKTFhCjz9_25e_lCw): ");
if (readsetId != null) {
ResourceLocator locator = new ResourceLocator(readsetId);
locator.setName(readsetId);
locator.setType(Ga4ghAPIHelper.RESOURCE_TYPE);
locator.setAttribute("provider", Ga4ghAPIHelper.GA4GH_GOOGLE_PROVIDER);
IGV.getInstance().loadTracks(Arrays.asList(locator));
}
}
});
loadReadset.setEnabled(false);
menu.add(loadReadset);
menu.addMenuListener(new MenuListener() {
@Override
public void menuSelected(MenuEvent e) {
Runnable runnable = new Runnable() {
@Override
public void run() {
boolean loggedIn = OAuthUtils.getInstance().isLoggedIn();
if (loggedIn) {
login.setText(OAuthUtils.getInstance().getCurrentUserName());
} else {
login.setText("Login ...");
}
login.setEnabled(!loggedIn);
logout.setEnabled(loggedIn);
loadReadset.setEnabled(loggedIn);
}
};
LongRunningTask.submit(runnable);
}
@Override
public void menuDeselected(MenuEvent e) {
}
@Override
public void menuCanceled(MenuEvent e) {
}
});
return menu;
}
// public void enableRemoveGenomes() {
// if (removeImportedGenomeAction != null) {
// removeImportedGenomeAction.setEnabled(true);
// }
// }
public void resetSessionActions() {
if (filterTracksAction != null) {
filterTracksAction.resetTrackFilter();
}
}
public void setFilterMatchAll(boolean value) {
if (filterTracksAction != null) {
filterTracksAction.setFilterMatchAll(value);
}
}
public boolean isFilterMatchAll() {
if (filterTracksAction != null) {
return filterTracksAction.isFilterMatchAll();
}
return false;
}
public void setFilterShowAllTracks(boolean value) {
if (filterTracksAction != null) {
filterTracksAction.setFilterShowAllTracks(value);
}
}
public boolean isFilterShowAllTracks() {
if (filterTracksAction != null) {
return filterTracksAction.getShowAllTracksFilterCheckBox().isSelected();
}
return false;
}
public JMenu getViewMenu() {
return viewMenu;
}
final public void doExitApplication() {
try {
IGV.getInstance().saveStateForExit();
Frame mainFrame = IGV.getMainFrame();
PreferencesManager.getPreferences().setApplicationFrameBounds(mainFrame.getBounds());
// Hide and close the application
mainFrame.setVisible(false);
mainFrame.dispose();
} finally {
System.exit(0);
}
}
@ForTesting
static void destroyInstance() {
instance = null;
}
public void enableGoogleMenu(boolean aBoolean) {
googleMenu.setVisible(aBoolean);
}
@Override
public void receiveEvent(final Object event) {
if(event instanceof GenomeChangeEvent) {
UIUtilities.invokeOnEventThread(() -> encodeMenuItem.setVisible (EncodeFileBrowser.genomeSupported(((GenomeChangeEvent) event).genome.getId())));
}
}
}