/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.GridLayout; import java.awt.Point; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.Window; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.ClipboardOwner; import java.awt.datatransfer.DataFlavor; import java.awt.datatransfer.Transferable; import java.awt.dnd.DnDConstants; import java.awt.dnd.DropTargetDragEvent; import java.awt.dnd.DropTargetDropEvent; import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.InputEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.awt.geom.AffineTransform; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.beans.PropertyVetoException; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.lang.reflect.Field; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.ListIterator; import java.util.Locale; import java.util.Map; import java.util.Vector; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; import javax.swing.AbstractAction; import javax.swing.Action; import javax.swing.ActionMap; import javax.swing.Box; import javax.swing.BoxLayout; import javax.swing.DefaultDesktopManager; import javax.swing.DesktopManager; import javax.swing.InputMap; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; import javax.swing.JScrollPane; import javax.swing.JTextArea; import javax.swing.JTextField; import javax.swing.JTextPane; import javax.swing.KeyStroke; import javax.swing.SwingUtilities; import javax.swing.WindowConstants; import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; import javax.swing.text.JTextComponent; import org.stackoverflowusers.file.WindowsShortcut; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.bin.Jalview.ExitCode; import jalview.bin.argparser.Arg; import jalview.bin.groovy.JalviewObject; import jalview.bin.groovy.JalviewObjectI; import jalview.datamodel.Alignment; import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.ImageExporter.ImageWriterI; import jalview.gui.QuitHandler.QResponse; import jalview.io.BackupFiles; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.exceptions.ImageOutputException; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; import jalview.project.Jalview2XML; import jalview.structure.StructureSelectionManager; import jalview.urls.IdOrgSettings; import jalview.util.BrowserLauncher; import jalview.util.ChannelProperties; import jalview.util.ImageMaker.TYPE; import jalview.util.LaunchUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.ShortcutKeyMaskExWrapper; import jalview.util.UrlConstants; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.ParamManager; import jalview.ws.utils.UrlDownloadClient; /** * Jalview Desktop * * * @author $author$ * @version $Revision: 1.155 $ */ public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider, JalviewObjectI { private static final String CITATION; static { URL bg_logo_url = ChannelProperties.getImageURL( "bg_logo." + String.valueOf(SplashScreen.logoSize)); URL uod_logo_url = ChannelProperties.getImageURL( "uod_banner." + String.valueOf(SplashScreen.logoSize)); boolean logo = (bg_logo_url != null || uod_logo_url != null); StringBuilder sb = new StringBuilder(); sb.append( "

Jalview is free software released under GPLv3.

Development is managed by The Barton Group, University of Dundee, Scotland, UK."); if (logo) { sb.append("
"); } sb.append(bg_logo_url == null ? "" : "\"Barton"); sb.append(uod_logo_url == null ? "" : " \"University"); sb.append( "

For help, see www.jalview.org/faq and join discourse.jalview.org"); sb.append("

If you use Jalview, please cite:" + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" + "
Bioinformatics doi: 10.1093/bioinformatics/btp033"); CITATION = sb.toString(); } private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)"; private static int DEFAULT_MIN_WIDTH = 300; private static int DEFAULT_MIN_HEIGHT = 250; private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; public static HashMap savingFiles = new HashMap(); private static int DRAG_MODE = JDesktopPane.OUTLINE_DRAG_MODE; public static void setLiveDragMode(boolean b) { DRAG_MODE = b ? JDesktopPane.LIVE_DRAG_MODE : JDesktopPane.OUTLINE_DRAG_MODE; if (desktop != null) desktop.setDragMode(DRAG_MODE); } private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); public static boolean nosplash = false; /** * news reader - null if it was never started. */ private BlogReader jvnews = null; private File projectFile; /** * @param listener * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) */ public void addJalviewPropertyChangeListener( PropertyChangeListener listener) { changeSupport.addJalviewPropertyChangeListener(listener); } /** * @param propertyName * @param listener * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { changeSupport.addJalviewPropertyChangeListener(propertyName, listener); } /** * @param propertyName * @param listener * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { changeSupport.removeJalviewPropertyChangeListener(propertyName, listener); } /** Singleton Desktop instance */ public static Desktop instance; public static MyDesktopPane desktop; public static MyDesktopPane getDesktop() { // BH 2018 could use currentThread() here as a reference to a // Hashtable in JavaScript return desktop; } static int openFrameCount = 0; static final int xOffset = 30; static final int yOffset = 30; public static jalview.ws.jws1.Discoverer discoverer; public static Object[] jalviewClipboard; public static boolean internalCopy = false; static int fileLoadingCount = 0; class MyDesktopManager implements DesktopManager { private DesktopManager delegate; public MyDesktopManager(DesktopManager delegate) { this.delegate = delegate; } @Override public void activateFrame(JInternalFrame f) { try { delegate.activateFrame(f); } catch (NullPointerException npe) { Point p = getMousePosition(); instance.showPasteMenu(p.x, p.y); } } @Override public void beginDraggingFrame(JComponent f) { delegate.beginDraggingFrame(f); } @Override public void beginResizingFrame(JComponent f, int direction) { delegate.beginResizingFrame(f, direction); } @Override public void closeFrame(JInternalFrame f) { delegate.closeFrame(f); } @Override public void deactivateFrame(JInternalFrame f) { delegate.deactivateFrame(f); } @Override public void deiconifyFrame(JInternalFrame f) { delegate.deiconifyFrame(f); } @Override public void dragFrame(JComponent f, int newX, int newY) { if (newY < 0) { newY = 0; } delegate.dragFrame(f, newX, newY); } @Override public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); desktop.repaint(); } @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); desktop.repaint(); } @Override public void iconifyFrame(JInternalFrame f) { delegate.iconifyFrame(f); } @Override public void maximizeFrame(JInternalFrame f) { delegate.maximizeFrame(f); } @Override public void minimizeFrame(JInternalFrame f) { delegate.minimizeFrame(f); } @Override public void openFrame(JInternalFrame f) { delegate.openFrame(f); } @Override public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { if (newY < 0) { newY = 0; } delegate.resizeFrame(f, newX, newY, newWidth, newHeight); } @Override public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight); } // All other methods, simply delegate } /** * Creates a new Desktop object. */ public Desktop() { super(); /** * A note to implementors. It is ESSENTIAL that any activities that might * block are spawned off as threads rather than waited for during this * constructor. */ instance = this; doConfigureStructurePrefs(); setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION")); /** * Set taskbar "grouped windows" name for linux desktops (works in GNOME and * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not * officially documented or guaranteed to exist, so we access it via * reflection. There appear to be unfathomable criteria about what this * string can contain, and it if doesn't meet those criteria then "java" * (KDE) or "jalview-bin-Jalview" (GNOME) is used. "Jalview", "Jalview * Develop" and "Jalview Test" seem okay, but "Jalview non-release" does * not. The reflection access may generate a warning: WARNING: An illegal * reflective access operation has occurred WARNING: Illegal reflective * access by jalview.gui.Desktop () to field * sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided. */ if (Platform.isLinux()) { if (LaunchUtils.getJavaVersion() >= 11) { /* * Send this message to stderr as the warning that follows (due to * reflection) also goes to stderr. */ jalview.bin.Console.errPrintln( "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that."); } final String awtAppClassName = "awtAppClassName"; try { Toolkit xToolkit = Toolkit.getDefaultToolkit(); Field[] declaredFields = xToolkit.getClass().getDeclaredFields(); Field awtAppClassNameField = null; if (Arrays.stream(declaredFields) .anyMatch(f -> f.getName().equals(awtAppClassName))) { awtAppClassNameField = xToolkit.getClass() .getDeclaredField(awtAppClassName); } String title = ChannelProperties.getProperty("app_name"); if (awtAppClassNameField != null) { awtAppClassNameField.setAccessible(true); awtAppClassNameField.set(xToolkit, title); } else { jalview.bin.Console .debug("XToolkit: " + awtAppClassName + " not found"); } } catch (Exception e) { jalview.bin.Console.debug("Error setting " + awtAppClassName); jalview.bin.Console.trace(Cache.getStackTraceString(e)); } } setIconImages(ChannelProperties.getIconList()); // override quit handling when GUI OS close [X] button pressed this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); addWindowListener(new WindowAdapter() { @Override public void windowClosing(WindowEvent ev) { QuitHandler.QResponse ret = desktopQuit(true, true); // ui, disposeFlag } }); boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false); boolean showjconsole = Cache.getArgCacheDefault(Arg.JAVACONSOLE, "SHOW_JAVA_CONSOLE", false); // start dialogue queue for single dialogues startDialogQueue(); if (!Platform.isJS()) /** * Java only * * @j2sIgnore */ { Desktop.instance.acquireDialogQueue(); jconsole = new Console(this); jconsole.setHeader(Cache.getVersionDetailsForConsole()); showConsole(showjconsole); Desktop.instance.releaseDialogQueue(); } desktop = new MyDesktopPane(selmemusage); showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); // alternate config - have scrollbars - see notes in JAL-153 // JScrollPane sp = new JScrollPane(); // sp.getViewport().setView(desktop); // getContentPane().add(sp, BorderLayout.CENTER); // BH 2018 - just an experiment to try unclipped JInternalFrames. if (Platform.isJS()) { getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); } getContentPane().add(desktop, BorderLayout.CENTER); desktop.setDragMode(DRAG_MODE); // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised desktop.setDesktopManager(new MyDesktopManager( Platform.isJS() ? desktop.getDesktopManager() : new DefaultDesktopManager())); /* (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager( desktop.getDesktopManager()) : desktop.getDesktopManager()))); */ Rectangle dims = getLastKnownDimensions(""); if (dims != null) { setBounds(dims); } else { Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); int xPos = Math.max(5, (screenSize.width - 900) / 2); int yPos = Math.max(5, (screenSize.height - 650) / 2); setBounds(xPos, yPos, 900, 650); } if (!Platform.isJS()) /** * Java only * * @j2sIgnore */ { showNews.setVisible(false); experimentalFeatures.setSelected(showExperimental()); getIdentifiersOrgData(); checkURLLinks(); // Spawn a thread that shows the splashscreen if (!nosplash) { SwingUtilities.invokeLater(new Runnable() { @Override public void run() { new SplashScreen(true); } }); } // Thread off a new instance of the file chooser - this reduces the time // it takes to open it later on. new Thread(new Runnable() { @Override public void run() { jalview.bin.Console.debug("Filechooser init thread started."); String fileFormat = FileLoader.getUseDefaultFileFormat() ? Cache.getProperty("DEFAULT_FILE_FORMAT") : null; JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); jalview.bin.Console.debug("Filechooser init thread finished."); } }).start(); // Add the service change listener changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) { jalview.bin.Console .debug("Firing service changed event for " + evt.getNewValue()); JalviewServicesChanged(evt); } }); } this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); MouseAdapter ma; this.addMouseListener(ma = new MouseAdapter() { @Override public void mousePressed(MouseEvent evt) { if (evt.isPopupTrigger()) // Mac { showPasteMenu(evt.getX(), evt.getY()); } } @Override public void mouseReleased(MouseEvent evt) { if (evt.isPopupTrigger()) // Windows { showPasteMenu(evt.getX(), evt.getY()); } } }); desktop.addMouseListener(ma); if (Platform.isJS()) { // used for jalviewjsTest jalview.bin.Console.info("JALVIEWJS: CREATED DESKTOP"); } } /** * Answers true if user preferences to enable experimental features is True * (on), else false * * @return */ public boolean showExperimental() { String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, Boolean.FALSE.toString()); return Boolean.valueOf(experimental).booleanValue(); } public void doConfigureStructurePrefs() { // configure services StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(this); if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) { ssm.setAddTempFacAnnot( Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true)); ssm.setProcessSecondaryStructure( Cache.getDefault(Preferences.STRUCT_FROM_PDB, true)); // JAL-3915 - RNAView is no longer an option so this has no effect ssm.setSecStructServices( Cache.getDefault(Preferences.USE_RNAVIEW, false)); } else { ssm.setAddTempFacAnnot(false); ssm.setProcessSecondaryStructure(false); ssm.setSecStructServices(false); } } public void checkForNews() { final Desktop me = this; // Thread off the news reader, in case there are connection problems. new Thread(new Runnable() { @Override public void run() { jalview.bin.Console.debug("Starting news thread."); jvnews = new BlogReader(me); showNews.setVisible(true); jalview.bin.Console.debug("Completed news thread."); } }).start(); } public void getIdentifiersOrgData() { if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {// Thread off the identifiers fetcher new Thread(new Runnable() { @Override public void run() { jalview.bin.Console .debug("Downloading data from identifiers.org"); try { UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation()); } catch (IOException e) { jalview.bin.Console .debug("Exception downloading identifiers.org data" + e.getMessage()); } } }).start(); ; } } @Override protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); } void showNews(boolean visible) { jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news."); showNews.setSelected(visible); if (visible && !jvnews.isVisible()) { new Thread(new Runnable() { @Override public void run() { long now = System.currentTimeMillis(); Desktop.instance.setProgressBar( MessageManager.getString("status.refreshing_news"), now); jvnews.refreshNews(); Desktop.instance.setProgressBar(null, now); jvnews.showNews(); } }).start(); } } /** * recover the last known dimensions for a jalview window * * @param windowName * - empty string is desktop, all other windows have unique prefix * @return null or last known dimensions scaled to current geometry (if last * window geom was known) */ Rectangle getLastKnownDimensions(String windowName) { // TODO: lock aspect ratio for scaling desktop Bug #0058199 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); String x = Cache.getProperty(windowName + "SCREEN_X"); String y = Cache.getProperty(windowName + "SCREEN_Y"); String width = Cache.getProperty(windowName + "SCREEN_WIDTH"); String height = Cache.getProperty(windowName + "SCREEN_HEIGHT"); if ((x != null) && (y != null) && (width != null) && (height != null)) { int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer.parseInt(width), ih = Integer.parseInt(height); if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null) { // attempt #1 - try to cope with change in screen geometry - this // version doesn't preserve original jv aspect ratio. // take ratio of current screen size vs original screen size. double sw = ((1f * screenSize.width) / (1f * Integer .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH")))); double sh = ((1f * screenSize.height) / (1f * Integer .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT")))); // rescale the bounds depending upon the current screen geometry. ix = (int) (ix * sw); iw = (int) (iw * sw); iy = (int) (iy * sh); ih = (int) (ih * sh); if (ix >= screenSize.width) { jalview.bin.Console.debug( "Window geometry location recall error: shifting horizontal to within screenbounds."); ix = ix % screenSize.width; } if (iy >= screenSize.height) { jalview.bin.Console.debug( "Window geometry location recall error: shifting vertical to within screenbounds."); iy = iy % screenSize.height; } jalview.bin.Console.debug( "Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw + " height:" + ih); } // return dimensions for new instance return new Rectangle(ix, iy, iw, ih); } return null; } void showPasteMenu(int x, int y) { JPopupMenu popup = new JPopupMenu(); JMenuItem item = new JMenuItem( MessageManager.getString("label.paste_new_window")); item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { paste(); } }); popup.add(item); popup.show(this, x, y); } public void paste() { // quick patch for JAL-4150 - needs some more work and test coverage // TODO - unify below and AlignFrame.paste() // TODO - write tests and fix AlignFrame.paste() which doesn't track if // clipboard has come from a different alignment window than the one where // paste has been called! JAL-4151 if (Desktop.jalviewClipboard != null) { // The clipboard was filled from within Jalview, we must use the // sequences // And dataset from the copied alignment SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; // be doubly sure that we create *new* sequence objects. SequenceI[] sequences = new SequenceI[newseq.length]; for (int i = 0; i < newseq.length; i++) { sequences[i] = new Sequence(newseq[i]); } Alignment alignment = new Alignment(sequences); // dataset is inherited alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); AlignFrame af = new AlignFrame(alignment, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); String newtitle = new String("Copied sequences"); if (Desktop.jalviewClipboard[2] != null) { HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; af.viewport.setHiddenColumns(hc); } Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } else { try { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); Transferable contents = c.getContents(this); if (contents != null) { String file = (String) contents .getTransferData(DataFlavor.stringFlavor); FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE); new FileLoader().LoadFile(file, DataSourceType.PASTE, format); } } catch (Exception ex) { jalview.bin.Console.outPrintln( "Unable to paste alignment from system clipboard:\n" + ex); } } } /** * Adds and opens the given frame to the desktop * * @param frame * Frame to show * @param title * Visible Title * @param w * width * @param h * height */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, int w, int h) { addInternalFrame(frame, title, true, w, h, true, false); } /** * Add an internal frame to the Jalview desktop * * @param frame * Frame to show * @param title * Visible Title * @param makeVisible * When true, display frame immediately, otherwise, caller must call * setVisible themselves. * @param w * width * @param h * height */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, boolean makeVisible, int w, int h) { addInternalFrame(frame, title, makeVisible, w, h, true, false); } /** * Add an internal frame to the Jalview desktop and make it visible * * @param frame * Frame to show * @param title * Visible Title * @param w * width * @param h * height * @param resizable * Allow resize */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, int w, int h, boolean resizable) { addInternalFrame(frame, title, true, w, h, resizable, false); } /** * Add an internal frame to the Jalview desktop * * @param frame * Frame to show * @param title * Visible Title * @param makeVisible * When true, display frame immediately, otherwise, caller must call * setVisible themselves. * @param w * width * @param h * height * @param resizable * Allow resize * @param ignoreMinSize * Do not set the default minimum size for frame */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, boolean makeVisible, int w, int h, boolean resizable, boolean ignoreMinSize) { // TODO: allow callers to determine X and Y position of frame (eg. via // bounds object). // TODO: consider fixing method to update entries in the window submenu with // the current window title frame.setTitle(title); if (frame.getWidth() < 1 || frame.getHeight() < 1) { frame.setSize(w, h); } // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN // IF JALVIEW IS RUNNING HEADLESS // /////////////////////////////////////////////// if (instance == null || (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true"))) { return; } openFrameCount++; if (!ignoreMinSize) { frame.setMinimumSize( new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); // Set default dimension for Alignment Frame window. // The Alignment Frame window could be added from a number of places, // hence, // I did this here in order not to miss out on any Alignment frame. if (frame instanceof AlignFrame) { frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); } } frame.setVisible(makeVisible); frame.setClosable(true); frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); frame.setOpaque(Platform.isJS()); if (frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset); } /* * add an entry for the new frame in the Window menu (and remove it when the * frame is closed) */ final JMenuItem menuItem = new JMenuItem(title); frame.addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameActivated(InternalFrameEvent evt) { JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { if (itf instanceof AlignFrame) { Jalview.getInstance().setCurrentAlignFrame((AlignFrame) itf); } itf.requestFocus(); } } @Override public void internalFrameClosed(InternalFrameEvent evt) { PaintRefresher.RemoveComponent(frame); /* * defensive check to prevent frames being added half off the window */ if (openFrameCount > 0) { openFrameCount--; } /* * ensure no reference to alignFrame retained by menu item listener */ if (menuItem.getActionListeners().length > 0) { menuItem.removeActionListener(menuItem.getActionListeners()[0]); } windowMenu.remove(menuItem); } }); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { try { frame.setSelected(true); frame.setIcon(false); } catch (java.beans.PropertyVetoException ex) { } } }); setKeyBindings(frame); // Since the latest FlatLaf patch, we occasionally have problems showing // structureViewer frames... int tries = 3; boolean shown = false; Exception last = null; do { try { desktop.add(frame); shown = true; } catch (IllegalArgumentException iaex) { last = iaex; tries--; jalview.bin.Console.info("Squashed IllegalArgument Exception (" + tries + " left) for " + frame.getTitle(), iaex); try { Thread.sleep(5); } catch (InterruptedException iex) { } ; } } while (!shown && tries > 0); if (!shown) { jalview.bin.Console.error( "Serious Problem whilst showing window " + frame.getTitle(), last); } windowMenu.add(menuItem); frame.toFront(); try { frame.setSelected(true); frame.requestFocus(); } catch (java.beans.PropertyVetoException ve) { } catch (java.lang.ClassCastException cex) { jalview.bin.Console.warn( "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869", cex); } } /** * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close * the window * * @param frame */ private static void setKeyBindings(JInternalFrame frame) { @SuppressWarnings("serial") final Action closeAction = new AbstractAction() { @Override public void actionPerformed(ActionEvent e) { frame.dispose(); } }; /* * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action */ KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK); KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); InputMap inputMap = frame .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); String ctrlW = ctrlWKey.toString(); inputMap.put(ctrlWKey, ctrlW); inputMap.put(cmdWKey, ctrlW); ActionMap actionMap = frame.getActionMap(); actionMap.put(ctrlW, closeAction); } @Override public void lostOwnership(Clipboard clipboard, Transferable contents) { if (!internalCopy) { Desktop.jalviewClipboard = null; } internalCopy = false; } @Override public void dragEnter(DropTargetDragEvent evt) { } @Override public void dragExit(DropTargetEvent evt) { } @Override public void dragOver(DropTargetDragEvent evt) { } @Override public void dropActionChanged(DropTargetDragEvent evt) { } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ @Override public void drop(DropTargetDropEvent evt) { boolean success = true; // JAL-1552 - acceptDrop required before getTransferable call for // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); List files = new ArrayList<>(); List protocols = new ArrayList<>(); try { Desktop.transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { e.printStackTrace(); success = false; } if (files != null) { try { for (int i = 0; i < files.size(); i++) { // BH 2018 File or String Object file = files.get(i); String fileName = file.toString(); DataSourceType protocol = (protocols == null) ? DataSourceType.FILE : protocols.get(i); FileFormatI format = null; if (fileName.endsWith(".jar")) { format = FileFormat.Jalview; } else { format = new IdentifyFile().identify(file, protocol); } if (file instanceof File) { Platform.cacheFileData((File) file); } new FileLoader().LoadFile(null, file, protocol, format); } } catch (Exception ex) { success = false; } } evt.dropComplete(success); // need this to ensure input focus is properly // transfered to any new windows created } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { String fileFormat = FileLoader.getUseDefaultFileFormat() ? Cache.getProperty("DEFAULT_FILE_FORMAT") : null; JalviewFileChooser chooser = JalviewFileChooser.forRead( Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled()); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); chooser.setResponseHandler(0, () -> { File selectedFile = chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); FileFormatI format = chooser.getSelectedFormat(); /* * Call IdentifyFile to verify the file contains what its extension implies. * Skip this step for dynamically added file formats, because IdentifyFile does * not know how to recognise them. */ if (FileFormats.getInstance().isIdentifiable(format)) { try { format = new IdentifyFile().identify(selectedFile, DataSourceType.FILE); } catch (FileFormatException e) { // format = null; //?? } } new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format); }); chooser.showOpenDialog(this); } /** * Shows a dialog for input of a URL at which to retrieve alignment data * * @param viewport */ @Override public void inputURLMenuItem_actionPerformed(AlignViewport viewport) { // This construct allows us to have a wider textfield // for viewing JLabel label = new JLabel( MessageManager.getString("label.input_file_url")); JPanel panel = new JPanel(new GridLayout(2, 1)); panel.add(label); /* * the URL to fetch is input in Java: an editable combobox with history JS: * (pending JAL-3038) a plain text field */ JComponent history; String urlBase = "https://www."; if (Platform.isJS()) { history = new JTextField(urlBase, 35); } else /** * Java only * * @j2sIgnore */ { JComboBox asCombo = new JComboBox<>(); asCombo.setPreferredSize(new Dimension(400, 20)); asCombo.setEditable(true); asCombo.addItem(urlBase); String historyItems = Cache.getProperty("RECENT_URL"); if (historyItems != null) { for (String token : historyItems.split("\\t")) { asCombo.addItem(token); } } history = asCombo; } panel.add(history); Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; Runnable action = () -> { @SuppressWarnings("unchecked") String url = (history instanceof JTextField ? ((JTextField) history).getText() : ((JComboBox) history).getEditor().getItem() .toString().trim()); if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) { if (viewport != null) { new FileLoader().LoadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview); } else { new FileLoader().LoadFile(url, DataSourceType.URL, FileFormat.Jalview); } } else { FileFormatI format = null; try { format = new IdentifyFile().identify(url, DataSourceType.URL); } catch (FileFormatException e) { // TODO revise error handling, distinguish between // URL not found and response not valid } if (format == null) { String msg = MessageManager.formatMessage("label.couldnt_locate", url); JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE); return; } if (viewport != null) { new FileLoader().LoadFile(viewport, url, DataSourceType.URL, format); } else { new FileLoader().LoadFile(url, DataSourceType.URL, format); } } }; String dialogOption = MessageManager .getString("label.input_alignment_from_url"); JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action) .showInternalDialog(panel, dialogOption, JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, MessageManager.getString("action.ok")); } /** * Opens the CutAndPaste window for the user to paste an alignment in to * * @param viewPanel * - if not null, the pasted alignment is added to the current * alignment; if null, to a new alignment window */ @Override public void inputTextboxMenuItem_actionPerformed( AlignmentViewPanel viewPanel) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(viewPanel); Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500); } /* * Check with user and saving files before actually quitting */ public void desktopQuit() { desktopQuit(true, false); } /** * close everything, stash window geometries, and shut down all associated * threads/workers * * @param dispose * - sets the dispose on close flag - JVM may terminate when set * @param terminateJvm * - quit with prejudice - stops the JVM. */ public void quitTheDesktop(boolean dispose, boolean terminateJvm) { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight())); if (jconsole != null) { storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); jconsole.stopConsole(); } if (jvnews != null) { storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); } // Frames should all close automatically. Keeping external // viewers open should already be decided by user. closeAll_actionPerformed(null); if (dialogExecutor != null) { dialogExecutor.shutdownNow(); } if (groovyConsole != null) { // suppress a possible repeat prompt to save script groovyConsole.setDirty(false); // and tidy up if (((Window) groovyConsole.getFrame()) != null && ((Window) groovyConsole.getFrame()).isVisible()) { // console is visible -- FIXME JAL-4327 groovyConsole.exit(); } else { // console is not, so just let it dispose itself when we shutdown // we don't call groovyConsole.exit() because it calls the shutdown // handler with invokeAndWait() causing deadlock groovyConsole = null; } } if (terminateJvm) { // note that shutdown hook will not be run jalview.bin.Console.debug("Force Quit selected by user"); Runtime.getRuntime().halt(0); } jalview.bin.Console.debug("Quit selected by user"); if (dispose) { instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); // instance.dispose(); } } public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag) { final Runnable doDesktopQuit = () -> { // FIRST !! check for aborted quit if (QuitHandler.quitCancelled()) { jalview.bin.Console .debug("Quit was cancelled - Desktop aborting quit"); return; } // Proceed with quitting quitTheDesktop(disposeFlag, QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT); // and exit the JVM instance.quit(); }; return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit, QuitHandler.defaultCancelQuit); } /** * Exits the program and the JVM. * * Don't call this directly * * - use desktopQuit() above to tidy up first. * * - use closeDesktop() to shutdown Jalview without shutting down the JVM * */ @Override public void quit() { // this will run the shutdownHook but QuitHandler.getQuitResponse() should // not run a second time if gotQuitResponse flag has been set (i.e. user // confirmed quit of some kind). Jalview.exit("Desktop exiting.", ExitCode.OK); } private void storeLastKnownDimensions(String string, Rectangle jc) { jalview.bin.Console.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width + " height:" + jc.height); Cache.setProperty(string + "SCREEN_X", jc.x + ""); Cache.setProperty(string + "SCREEN_Y", jc.y + ""); Cache.setProperty(string + "SCREEN_WIDTH", jc.width + ""); Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + ""); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void aboutMenuItem_actionPerformed(ActionEvent e) { new Thread(new Runnable() { @Override public void run() { new SplashScreen(false); } }).start(); } /** * Returns the html text for the About screen, including any available version * number, build details, author details and citation reference, but without * the enclosing {@code html} tags * * @return */ public String getAboutMessage() { StringBuilder message = new StringBuilder(1024); message.append("
") .append("

Version: ") .append(Cache.getProperty("VERSION")).append("

") .append("Built: ") .append(Cache.getDefault("BUILD_DATE", "unknown")) .append(" from ").append(Cache.getBuildDetailsForSplash()) .append(""); String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking"); if (latestVersion.equals("Checking")) { // JBP removed this message for 2.11: May be reinstated in future version // message.append("
...Checking latest version...
"); } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) { boolean red = false; if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT) .indexOf("automated build") == -1) { red = true; // Displayed when code version and jnlp version do not match and code // version is not a development build message.append("
"); } message.append("
!! Version ") .append(Cache.getDefault("LATEST_VERSION", "..Checking..")) .append(" is available for download from ") .append(Cache.getDefault("www.jalview.org", "https://www.jalview.org")) .append(" !!"); if (red) { message.append("
"); } } message.append("
Authors: "); message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS)); message.append(CITATION); message.append("
"); return message.toString(); } /** * Action on requesting Help documentation */ @Override public void documentationMenuItem_actionPerformed() { try { if (Platform.isJS()) { BrowserLauncher.openURL("https://www.jalview.org/help.html"); } else /** * Java only * * @j2sIgnore */ { Help.showHelpWindow(); } } catch (Exception ex) { jalview.bin.Console .errPrintln("Error opening help: " + ex.getMessage()); } } @Override public void closeAll_actionPerformed(ActionEvent e) { // TODO show a progress bar while closing? JInternalFrame[] frames = desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { try { frames[i].setClosed(true); } catch (java.beans.PropertyVetoException ex) { } } Jalview.getInstance().setCurrentAlignFrame(null); jalview.bin.Console.info("ALL CLOSED"); /* * reset state of singleton objects as appropriate (clear down session state * when all windows are closed) */ StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(this); if (ssm != null) { ssm.resetAll(); } } public int structureViewersStillRunningCount() { int count = 0; JInternalFrame[] frames = desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { if (frames[i] != null && frames[i] instanceof JalviewStructureDisplayI) { if (((JalviewStructureDisplayI) frames[i]).stillRunning()) count++; } } return count; } @Override public void raiseRelated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(false, false); } @Override public void minimizeAssociated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(true, false); } void closeAssociatedWindows() { reorderAssociatedWindows(false, true); } /* * (non-Javadoc) * * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event. * ActionEvent) */ @Override protected void garbageCollect_actionPerformed(ActionEvent e) { // We simply collect the garbage jalview.bin.Console.debug("Collecting garbage..."); System.gc(); jalview.bin.Console.debug("Finished garbage collection."); } /* * (non-Javadoc) * * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event. * ActionEvent ) */ @Override protected void showMemusage_actionPerformed(ActionEvent e) { desktop.showMemoryUsage(showMemusage.isSelected()); } /* * (non-Javadoc) * * @see * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent * ) */ @Override protected void showConsole_actionPerformed(ActionEvent e) { showConsole(showConsole.isSelected()); } Console jconsole = null; /** * control whether the java console is visible or not * * @param selected */ void showConsole(boolean selected) { // TODO: decide if we should update properties file if (jconsole != null) // BH 2018 { showConsole.setSelected(selected); Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected).toString()); jconsole.setVisible(selected); } } void reorderAssociatedWindows(boolean minimize, boolean close) { JInternalFrame[] frames = desktop.getAllFrames(); if (frames == null || frames.length < 1) { return; } AlignmentViewport source = null, target = null; if (frames[0] instanceof AlignFrame) { source = ((AlignFrame) frames[0]).getCurrentView(); } else if (frames[0] instanceof TreePanel) { source = ((TreePanel) frames[0]).getViewPort(); } else if (frames[0] instanceof PCAPanel) { source = ((PCAPanel) frames[0]).av; } else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) { source = ((PairwiseAlignPanel) frames[0].getContentPane()).av; } if (source != null) { for (int i = 0; i < frames.length; i++) { target = null; if (frames[i] == null) { continue; } if (frames[i] instanceof AlignFrame) { target = ((AlignFrame) frames[i]).getCurrentView(); } else if (frames[i] instanceof TreePanel) { target = ((TreePanel) frames[i]).getViewPort(); } else if (frames[i] instanceof PCAPanel) { target = ((PCAPanel) frames[i]).av; } else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) { target = ((PairwiseAlignPanel) frames[i].getContentPane()).av; } if (source == target) { try { if (close) { frames[i].setClosed(true); } else { frames[i].setIcon(minimize); if (!minimize) { frames[i].toFront(); } } } catch (java.beans.PropertyVetoException ex) { } } } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override protected void preferences_actionPerformed(ActionEvent e) { Preferences.openPreferences(); } /** * Prompts the user to choose a file and then saves the Jalview state as a * Jalview project file */ @Override public void saveState_actionPerformed() { saveState_actionPerformed(false); } public void saveState_actionPerformed(boolean saveAs) { java.io.File projectFile = getProjectFile(); // autoSave indicates we already have a file and don't need to ask boolean autoSave = projectFile != null && !saveAs && BackupFiles.getEnabled(); // jalview.bin.Console.outPrintln("autoSave="+autoSave+", // projectFile='"+projectFile+"', // saveAs="+saveAs+", Backups // "+(BackupFiles.getEnabled()?"enabled":"disabled")); boolean approveSave = false; if (!autoSave) { JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { projectFile = chooser.getSelectedFile(); setProjectFile(projectFile); approveSave = true; } } if (approveSave || autoSave) { final Desktop me = this; final java.io.File chosenFile = projectFile; new Thread(new Runnable() { @Override public void run() { // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( "label.saving_jalview_project", new Object[] { chosenFile.getName() }), chosenFile.hashCode()); Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent()); // TODO catch and handle errors for savestate // TODO prevent user from messing with the Desktop whilst we're saving try { boolean doBackup = BackupFiles.getEnabled(); BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null; new Jalview2XML().saveState( doBackup ? backupfiles.getTempFile() : chosenFile); if (doBackup) { backupfiles.setWriteSuccess(true); backupfiles.rollBackupsAndRenameTempFile(); } } catch (OutOfMemoryError oom) { new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom); } catch (Exception ex) { jalview.bin.Console.error("Problems whilst trying to save to " + chosenFile.getName(), ex); JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", new Object[] { chosenFile.getName() }), MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, chosenFile.hashCode()); } }).start(); } } @Override public void saveAsState_actionPerformed(ActionEvent e) { saveState_actionPerformed(true); } protected void setProjectFile(File choice) { this.projectFile = choice; } public File getProjectFile() { return this.projectFile; } /** * Shows a file chooser dialog and tries to read in the selected file as a * Jalview project */ @Override public void loadState_actionPerformed() { final String[] suffix = new String[] { "jvp", "jar" }; final String[] desc = new String[] { "Jalview Project", "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), suffix, desc, "Jalview Project", true, BackupFiles.getEnabled()); // last two // booleans: // allFiles, // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); chooser.setResponseHandler(0, () -> { File selectedFile = chooser.getSelectedFile(); setProjectFile(selectedFile); String choice = selectedFile.getAbsolutePath(); Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); new Thread(new Runnable() { @Override public void run() { try { new Jalview2XML().loadJalviewAlign(selectedFile); } catch (OutOfMemoryError oom) { new OOMWarning("Whilst loading project from " + choice, oom); } catch (Exception ex) { jalview.bin.Console.error( "Problems whilst loading project from " + choice, ex); JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager.formatMessage( "label.error_whilst_loading_project_from", new Object[] { choice }), MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE); } } }, "Project Loader").start(); }); chooser.showOpenDialog(this); } @Override public void inputSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); } JPanel progressPanel; ArrayList fileLoadingPanels = new ArrayList<>(); public void startLoading(final Object fileName) { if (fileLoadingCount == 0) { fileLoadingPanels.add(addProgressPanel(MessageManager .formatMessage("label.loading_file", new Object[] { fileName }))); } fileLoadingCount++; } private JPanel addProgressPanel(String string) { if (progressPanel == null) { progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); } JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); progressBar.setIndeterminate(true); thisprogress.add(new JLabel(string), BorderLayout.WEST); thisprogress.add(progressBar, BorderLayout.CENTER); progressPanel.add(thisprogress); ((GridLayout) progressPanel.getLayout()).setRows( ((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; instance.validate(); return thisprogress; } int totalProgressCount = 0; private void removeProgressPanel(JPanel progbar) { if (progressPanel != null) { synchronized (progressPanel) { progressPanel.remove(progbar); GridLayout gl = (GridLayout) progressPanel.getLayout(); gl.setRows(gl.getRows() - 1); if (--totalProgressCount < 1) { this.getContentPane().remove(progressPanel); progressPanel = null; } } } validate(); } public void stopLoading() { fileLoadingCount--; if (fileLoadingCount < 1) { while (fileLoadingPanels.size() > 0) { removeProgressPanel(fileLoadingPanels.remove(0)); } fileLoadingPanels.clear(); fileLoadingCount = 0; } validate(); } public static int getViewCount(String alignmentId) { AlignmentViewport[] aps = getViewports(alignmentId); return (aps == null) ? 0 : aps.length; } /** * * @param alignmentId * - if null, all sets are returned * @return all AlignmentPanels concerning the alignmentId sequence set */ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { if (Desktop.desktop == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode return null; } List aps = new ArrayList<>(); AlignFrame[] frames = Desktop.getDesktopAlignFrames(); if (frames == null) { return null; } for (AlignFrame af : frames) { for (AlignmentPanel ap : af.alignPanels) { if (alignmentId == null || alignmentId.equals(ap.av.getSequenceSetId())) { aps.add(ap); } } } if (aps.size() == 0) { return null; } AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); return vap; } /** * get all the viewports on an alignment. * * @param sequenceSetId * unique alignment id (may be null - all viewports returned in that * case) * @return all viewports on the alignment bound to sequenceSetId */ public static AlignmentViewport[] getViewports(String sequenceSetId) { List viewp = new ArrayList<>(); if (desktop != null) { AlignFrame[] frames = Desktop.getDesktopAlignFrames(); for (AlignFrame afr : frames) { if (sequenceSetId == null || afr.getViewport().getSequenceSetId() .equals(sequenceSetId)) { if (afr.alignPanels != null) { for (AlignmentPanel ap : afr.alignPanels) { if (sequenceSetId == null || sequenceSetId.equals(ap.av.getSequenceSetId())) { viewp.add(ap.av); } } } else { viewp.add(afr.getViewport()); } } } if (viewp.size() > 0) { return viewp.toArray(new AlignmentViewport[viewp.size()]); } } return null; } /** * Explode the views in the given frame into separate AlignFrame * * @param af */ public static void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); if (size < 2) { return; } // FIXME: ideally should use UI interface API FeatureSettings viewFeatureSettings = (af.featureSettings != null && af.featureSettings.isOpen()) ? af.featureSettings : null; Rectangle fsBounds = af.getFeatureSettingsGeometry(); for (int i = 0; i < size; i++) { AlignmentPanel ap = af.alignPanels.get(i); AlignFrame newaf = new AlignFrame(ap); // transfer reference for existing feature settings to new alignFrame if (ap == af.alignPanel) { if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) { newaf.featureSettings = viewFeatureSettings; } newaf.setFeatureSettingsGeometry(fsBounds); } /* * Restore the view's last exploded frame geometry if known. Multiple views from * one exploded frame share and restore the same (frame) position and size. */ Rectangle geometry = ap.av.getExplodedGeometry(); if (geometry != null) { newaf.setBounds(geometry); } ap.av.setGatherViewsHere(false); addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); // and materialise a new feature settings dialog instance for the new // alignframe // (closes the old as if 'OK' was pressed) if (ap == af.alignPanel && newaf.featureSettings != null && newaf.featureSettings.isOpen() && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) { newaf.showFeatureSettingsUI(); } } af.featureSettings = null; af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); } /** * Gather expanded views (separate AlignFrame's) with the same sequence set * identifier back in to this frame as additional views, and close the * expanded views. Note the expanded frames may themselves have multiple * views. We take the lot. * * @param source */ public void gatherViews(AlignFrame source) { source.viewport.setGatherViewsHere(true); source.viewport.setExplodedGeometry(source.getBounds()); JInternalFrame[] frames = desktop.getAllFrames(); String viewId = source.viewport.getSequenceSetId(); for (int t = 0; t < frames.length; t++) { if (frames[t] instanceof AlignFrame && frames[t] != source) { AlignFrame af = (AlignFrame) frames[t]; boolean gatherThis = false; for (int a = 0; a < af.alignPanels.size(); a++) { AlignmentPanel ap = af.alignPanels.get(a); if (viewId.equals(ap.av.getSequenceSetId())) { gatherThis = true; ap.av.setGatherViewsHere(false); ap.av.setExplodedGeometry(af.getBounds()); source.addAlignmentPanel(ap, false); } } if (gatherThis) { if (af.featureSettings != null && af.featureSettings.isOpen()) { if (source.featureSettings == null) { // preserve the feature settings geometry for this frame source.featureSettings = af.featureSettings; source.setFeatureSettingsGeometry( af.getFeatureSettingsGeometry()); } else { // close it and forget af.featureSettings.close(); } } af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); } } } // refresh the feature setting UI for the source frame if it exists if (source.featureSettings != null && source.featureSettings.isOpen()) { source.showFeatureSettingsUI(); } } public JInternalFrame[] getAllFrames() { return desktop.getAllFrames(); } /** * Checks the given url to see if it gives a response indicating that the user * should be informed of a new questionnaire. * * @param url */ public void checkForQuestionnaire(String url) { UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url); // javax.swing.SwingUtilities.invokeLater(jvq); new Thread(jvq).start(); } public void checkURLLinks() { // Thread off the URL link checker addDialogThread(new Runnable() { @Override public void run() { if (Cache.getDefault("CHECKURLLINKS", true)) { // check what the actual links are - if it's just the default don't // bother with the warning List links = Preferences.sequenceUrlLinks .getLinksForMenu(); // only need to check links if there is one with a // SEQUENCE_ID which is not the default EMBL_EBI link ListIterator li = links.listIterator(); boolean check = false; List urls = new ArrayList<>(); while (li.hasNext()) { String link = li.next(); if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) { check = true; int barPos = link.indexOf("|"); String urlMsg = barPos == -1 ? link : link.substring(0, barPos) + ": " + link.substring(barPos + 1); urls.add(new JLabel(urlMsg)); } } if (!check) { return; } // ask user to check in case URL links use old style tokens // ($SEQUENCE_ID$ for sequence id _or_ accession id) JPanel msgPanel = new JPanel(); msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); msgPanel.add(Box.createVerticalGlue()); JLabel msg = new JLabel(MessageManager .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); JLabel msg2 = new JLabel(MessageManager .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); msgPanel.add(msg); for (JLabel url : urls) { msgPanel.add(url); } msgPanel.add(msg2); final JCheckBox jcb = new JCheckBox( MessageManager.getString("label.do_not_display_again")); jcb.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { // update Cache settings for "don't show this again" boolean showWarningAgain = !jcb.isSelected(); Cache.setProperty("CHECKURLLINKS", Boolean.valueOf(showWarningAgain).toString()); } }); msgPanel.add(jcb); JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, MessageManager .getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE); } } }); } /** * Proxy class for JDesktopPane which optionally displays the current memory * usage and highlights the desktop area with a red bar if free memory runs * low. * * @author AMW */ public class MyDesktopPane extends JDesktopPane implements Runnable { private static final float ONE_MB = 1048576f; boolean showMemoryUsage = false; Runtime runtime; java.text.NumberFormat df; float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage; public MyDesktopPane(boolean showMemoryUsage) { showMemoryUsage(showMemoryUsage); } public void showMemoryUsage(boolean showMemory) { this.showMemoryUsage = showMemory; if (showMemory) { Thread worker = new Thread(this); worker.start(); } repaint(); } public boolean isShowMemoryUsage() { return showMemoryUsage; } @Override public void run() { df = java.text.NumberFormat.getNumberInstance(); df.setMaximumFractionDigits(2); runtime = Runtime.getRuntime(); while (showMemoryUsage) { try { maxMemory = runtime.maxMemory() / ONE_MB; allocatedMemory = runtime.totalMemory() / ONE_MB; freeMemory = runtime.freeMemory() / ONE_MB; totalFreeMemory = freeMemory + (maxMemory - allocatedMemory); percentUsage = (totalFreeMemory / maxMemory) * 100; // if (percentUsage < 20) { // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, // Color.red); // instance.set.setBorder(border1); } repaint(); // sleep after showing usage Thread.sleep(3000); } catch (Exception ex) { ex.printStackTrace(); } } } @Override public void paintComponent(Graphics g) { if (showMemoryUsage && g != null && df != null) { if (percentUsage < 20) { g.setColor(Color.red); } FontMetrics fm = g.getFontMetrics(); if (fm != null) { g.drawString(MessageManager.formatMessage("label.memory_stats", new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }), 10, getHeight() - fm.getHeight()); } } // output debug scale message. Important for jalview.bin.HiDPISettingTest2 Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics()); } } /** * Accessor method to quickly get all the AlignmentFrames loaded. * * @return an array of AlignFrame, or null if none found */ @Override public AlignFrame[] getAlignFrames() { if (desktop == null) { return null; } JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) { return null; } List avp = new ArrayList<>(); // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { if (frames[i] instanceof AlignFrame) { avp.add((AlignFrame) frames[i]); } else if (frames[i] instanceof SplitFrame) { /* * Also check for a split frame containing an AlignFrame */ GSplitFrame sf = (GSplitFrame) frames[i]; if (sf.getTopFrame() instanceof AlignFrame) { avp.add((AlignFrame) sf.getTopFrame()); } if (sf.getBottomFrame() instanceof AlignFrame) { avp.add((AlignFrame) sf.getBottomFrame()); } } } if (avp.size() == 0) { return null; } AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]); return afs; } /** * static version */ public static AlignFrame[] getDesktopAlignFrames() { if (Jalview.isHeadlessMode()) { // Desktop.desktop is null in headless mode return Jalview.getInstance().getAlignFrames(); } if (instance != null && desktop != null) { return instance.getAlignFrames(); } return null; } /** * Returns an array of any AppJmol frames in the Desktop (or null if none). * * @return */ public GStructureViewer[] getJmols() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) { return null; } List avp = new ArrayList<>(); // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { if (frames[i] instanceof AppJmol) { GStructureViewer af = (GStructureViewer) frames[i]; avp.add(af); } } if (avp.size() == 0) { return null; } GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]); return afs; } /** * Add Groovy Support to Jalview */ @Override public void groovyShell_actionPerformed() { try { openGroovyConsole(); } catch (Exception ex) { jalview.bin.Console.error("Groovy Console creation failed.", ex); JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE); } } /** * Open the Groovy console */ void openGroovyConsole() { if (groovyConsole == null) { JalviewObjectI j = new JalviewObject(this); groovyConsole = new groovy.console.ui.Console(); groovyConsole.setVariable(JalviewObjectI.jalviewObjectName, j); groovyConsole.setVariable(JalviewObjectI.currentAlFrameName, getCurrentAlignFrame()); groovyConsole.run(); /* * We allow only one console at a time, so that AlignFrame menu option * 'Calculate | Run Groovy script' is unambiguous. Disable 'Groovy Console', and * enable 'Run script', when the console is opened, and the reverse when it is * closed */ Window window = (Window) groovyConsole.getFrame(); window.addWindowListener(new WindowAdapter() { @Override public void windowClosed(WindowEvent e) { /* * rebind CMD-Q from Groovy Console to Jalview Quit */ addQuitHandler(); enableExecuteGroovy(false); } }); } /* * show Groovy console window (after close and reopen) */ ((Window) groovyConsole.getFrame()).setVisible(true); /* * if we got this far, enable 'Run Groovy' in AlignFrame menus and disable * opening a second console */ enableExecuteGroovy(true); } /** * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this * binding when opened */ protected void addQuitHandler() { getRootPane() .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( KeyStroke .getKeyStroke(KeyEvent.VK_Q, jalview.util.ShortcutKeyMaskExWrapper .getMenuShortcutKeyMaskEx()), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @Override public void actionPerformed(ActionEvent e) { desktopQuit(); } }); } /** * Enable or disable 'Run Groovy script' in AlignFrame calculate menus * * @param enabled * true if Groovy console is open */ public void enableExecuteGroovy(boolean enabled) { /* * disable opening a second Groovy console (or re-enable when the console is * closed) */ groovyShell.setEnabled(!enabled); AlignFrame[] alignFrames = getDesktopAlignFrames(); if (alignFrames != null) { for (AlignFrame af : alignFrames) { af.setGroovyEnabled(enabled); } } } /** * Progress bars managed by the IProgressIndicator method. */ private Hashtable progressBars; private Hashtable progressBarHandlers; /* * (non-Javadoc) * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ @Override public void setProgressBar(String message, long id) { if (progressBars == null) { progressBars = new Hashtable<>(); progressBarHandlers = new Hashtable<>(); } if (progressBars.get(Long.valueOf(id)) != null) { JPanel panel = progressBars.remove(Long.valueOf(id)); if (progressBarHandlers.contains(Long.valueOf(id))) { progressBarHandlers.remove(Long.valueOf(id)); } removeProgressPanel(panel); } else { progressBars.put(Long.valueOf(id), addProgressPanel(message)); } } /* * (non-Javadoc) * * @see jalview.gui.IProgressIndicator#registerHandler(long, * jalview.gui.IProgressIndicatorHandler) */ @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { if (progressBarHandlers == null || !progressBars.containsKey(Long.valueOf(id))) { throw new Error(MessageManager.getString( "error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(Long.valueOf(id), handler); final JPanel progressPanel = progressBars.get(Long.valueOf(id)); if (handler.canCancel()) { JButton cancel = new JButton( MessageManager.getString("action.cancel")); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); us.setProgressBar(MessageManager .formatMessage("label.cancelled_params", new Object[] { ((JLabel) progressPanel.getComponent(0)).getText() }), id); } }); progressPanel.add(cancel, BorderLayout.EAST); } } /** * * @return true if any progress bars are still active */ @Override public boolean operationInProgress() { if (progressBars != null && progressBars.size() > 0) { return true; } return false; } /** * This will return the first AlignFrame holding the given viewport instance. * It will break if there are more than one AlignFrames viewing a particular * av. * * @param viewport * @return alignFrame for viewport */ public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { if (desktop != null) { AlignmentPanel[] aps = getAlignmentPanels( viewport.getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { if (aps[panel] != null && aps[panel].av == viewport) { return aps[panel].alignFrame; } } } return null; } public VamsasApplication getVamsasApplication() { // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS return null; } /** * flag set if jalview GUI is being operated programmatically */ private boolean inBatchMode = false; /** * check if jalview GUI is being operated programmatically * * @return inBatchMode */ public boolean isInBatchMode() { return inBatchMode; } /** * set flag if jalview GUI is being operated programmatically * * @param inBatchMode */ public void setInBatchMode(boolean inBatchMode) { this.inBatchMode = inBatchMode; } /** * start service discovery and wait till it is done */ public void startServiceDiscovery() { startServiceDiscovery(false); } /** * start service discovery threads - blocking or non-blocking * * @param blocking */ public void startServiceDiscovery(boolean blocking) { startServiceDiscovery(blocking, false); } /** * start service discovery threads * * @param blocking * - false means call returns immediately * @param ignore_SHOW_JWS2_SERVICES_preference * - when true JABA services are discovered regardless of user's JWS2 * discovery preference setting */ public void startServiceDiscovery(boolean blocking, boolean ignore_SHOW_JWS2_SERVICES_preference) { boolean alive = true; Thread t0 = null, t1 = null, t2 = null; // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release if (true) { // todo: changesupport handlers need to be transferred if (discoverer == null) { discoverer = new jalview.ws.jws1.Discoverer(); // register PCS handler for desktop. discoverer.addPropertyChangeListener(changeSupport); } // JAL-940 - disabled JWS1 service configuration - always start discoverer // until we phase out completely (t0 = new Thread(discoverer)).start(); } if (ignore_SHOW_JWS2_SERVICES_preference || Cache.getDefault("SHOW_JWS2_SERVICES", true)) { t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() .startDiscoverer(changeSupport); } Thread t3 = null; { // TODO: do rest service discovery } if (blocking) { while (alive) { try { Thread.sleep(15); } catch (Exception e) { } alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t3 != null && t3.isAlive()) || (t0 != null && t0.isAlive()); } } } /** * called to check if the service discovery process completed successfully. * * @param evt */ protected void JalviewServicesChanged(PropertyChangeEvent evt) { if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) { final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() .getErrorMessages(); if (ermsg != null) { if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) { if (serviceChangedDialog == null) { // only run if we aren't already displaying one of these. addDialogThread(serviceChangedDialog = new Runnable() { @Override public void run() { /* * JalviewDialog jd =new JalviewDialog() { * * @Override protected void cancelPressed() { // TODO Auto-generated method stub * * }@Override protected void okPressed() { // TODO Auto-generated method stub * * }@Override protected void raiseClosed() { // TODO Auto-generated method stub * * } }; jd.initDialogFrame(new JLabel("
" + * ermsg + * "
It may be that you have invalid JABA URLs in your web service preferences," * + " or mis-configured HTTP proxy settings.
" + * "Check the Connections and Web services tab of the" + * " Tools->Preferences dialog box to change them.
" ), * true, true, "Web Service Configuration Problem", 450, 400); * * jd.waitForInput(); */ JvOptionPane.showConfirmDialog(Desktop.desktop, new JLabel("
" + ermsg + "
" + "

It may be that you have invalid JABA URLs
in your web service preferences," + "
or as a command-line argument, or mis-configured HTTP proxy settings.

" + "

Check the Connections and Web services tab
of the" + " Tools->Preferences dialog box to change them.

"), "Web Service Configuration Problem", JvOptionPane.DEFAULT_OPTION, JvOptionPane.ERROR_MESSAGE); serviceChangedDialog = null; } }); } } else { jalview.bin.Console.error( "Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg); } } } } private Runnable serviceChangedDialog = null; /** * start a thread to open a URL in the configured browser. Pops up a warning * dialog to the user if there is an exception when calling out to the browser * to open the URL. * * @param url */ public static void showUrl(final String url) { if (url != null && !url.trim().equals("")) { jalview.bin.Console.info("Opening URL: " + url); showUrl(url, Desktop.instance); } else { jalview.bin.Console.warn("Ignoring attempt to show an empty URL."); } } /** * Like showUrl but allows progress handler to be specified * * @param url * @param progress * (null) or object implementing IProgressIndicator */ public static void showUrl(final String url, final IProgressIndicator progress) { new Thread(new Runnable() { @Override public void run() { try { if (progress != null) { progress.setProgressBar(MessageManager .formatMessage("status.opening_params", new Object[] { url }), this.hashCode()); } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (progress != null) { progress.setProgressBar(null, this.hashCode()); } } }).start(); } public static WsParamSetManager wsparamManager = null; public static ParamManager getUserParameterStore() { if (wsparamManager == null) { wsparamManager = new WsParamSetManager(); } return wsparamManager; } /** * static hyperlink handler proxy method for use by Jalview's internal windows * * @param e */ public static void hyperlinkUpdate(HyperlinkEvent e) { if (e.getEventType() == EventType.ACTIVATED) { String url = null; try { url = e.getURL().toString(); Desktop.showUrl(url); } catch (Exception x) { if (url != null) { jalview.bin.Console .error("Couldn't handle string " + url + " as a URL."); } // ignore any exceptions due to dud links. } } } /** * single thread that handles display of dialogs to user. */ ExecutorService dialogExecutor = Executors.newFixedThreadPool(3); /** * flag indicating if dialogExecutor should try to acquire a permit */ private volatile boolean dialogPause = true; /** * pause the queue */ private Semaphore block = new Semaphore(0); private static groovy.console.ui.Console groovyConsole; /** * add another dialog thread to the queue * * @param prompter */ public void addDialogThread(final Runnable prompter) { dialogExecutor.submit(new Runnable() { @Override public void run() { if (dialogPause) { acquireDialogQueue(); } if (instance == null) { return; } try { SwingUtilities.invokeAndWait(prompter); } catch (Exception q) { jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q); } } }); } private boolean dialogQueueStarted = false; public void startDialogQueue() { if (dialogQueueStarted) { return; } // set the flag so we don't pause waiting for another permit and semaphore // the current task to begin releaseDialogQueue(); dialogQueueStarted = true; } public void acquireDialogQueue() { try { block.acquire(); dialogPause = true; } catch (InterruptedException e) { jalview.bin.Console.debug("Interruption when acquiring DialogueQueue", e); } } public void releaseDialogQueue() { if (!dialogPause) { return; } block.release(); dialogPause = false; } /** * Outputs an image of the desktop to file in EPS format, after prompting the * user for choice of Text or Lineart character rendering (unless a preference * has been set). The file name is generated as * *
   * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
   * 
*/ @Override protected void snapShotWindow_actionPerformed(ActionEvent e) { // currently the menu option to do this is not shown invalidate(); int width = getWidth(); int height = getHeight(); File of = new File( "Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); ImageWriterI writer = new ImageWriterI() { @Override public void exportImage(Graphics g) throws Exception { paintAll(g); jalview.bin.Console.info("Successfully written snapshot to file " + of.getAbsolutePath()); } }; String title = "View of desktop"; ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title); try { exporter.doExport(of, this, width, height, title); } catch (ImageOutputException ioex) { jalview.bin.Console.error( "Unexpected error whilst writing Jalview desktop snapshot as EPS", ioex); } } /** * Explode the views in the given SplitFrame into separate SplitFrame windows. * This respects (remembers) any previous 'exploded geometry' i.e. the size * and location last time the view was expanded (if any). However it does not * remember the split pane divider location - this is set to match the * 'exploding' frame. * * @param sf */ public void explodeViews(SplitFrame sf) { AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame(); AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame(); List topPanels = oldTopFrame .getAlignPanels(); List bottomPanels = oldBottomFrame .getAlignPanels(); int viewCount = topPanels.size(); if (viewCount < 2) { return; } /* * Processing in reverse order works, forwards order leaves the first panels not * visible. I don't know why! */ for (int i = viewCount - 1; i >= 0; i--) { /* * Make new top and bottom frames. These take over the respective AlignmentPanel * objects, including their AlignmentViewports, so the cdna/protein * relationships between the viewports is carried over to the new split frames. * * explodedGeometry holds the (x, y) position of the previously exploded * SplitFrame, and the (width, height) of the AlignFrame component */ AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); AlignFrame newTopFrame = new AlignFrame(topPanel); newTopFrame.setSize(oldTopFrame.getSize()); newTopFrame.setVisible(true); Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) .getExplodedGeometry(); if (geometry != null) { newTopFrame.setSize(geometry.getSize()); } AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); AlignFrame newBottomFrame = new AlignFrame(bottomPanel); newBottomFrame.setSize(oldBottomFrame.getSize()); newBottomFrame.setVisible(true); geometry = ((AlignViewport) bottomPanel.getAlignViewport()) .getExplodedGeometry(); if (geometry != null) { newBottomFrame.setSize(geometry.getSize()); } topPanel.av.setGatherViewsHere(false); bottomPanel.av.setGatherViewsHere(false); JInternalFrame splitFrame = new SplitFrame(newTopFrame, newBottomFrame); if (geometry != null) { splitFrame.setLocation(geometry.getLocation()); } Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); } /* * Clear references to the panels (now relocated in the new SplitFrames) before * closing the old SplitFrame. */ topPanels.clear(); bottomPanels.clear(); sf.close(); } /** * Gather expanded split frames, sharing the same pairs of sequence set ids, * back into the given SplitFrame as additional views. Note that the gathered * frames may themselves have multiple views. * * @param source */ public void gatherViews(GSplitFrame source) { /* * special handling of explodedGeometry for a view within a SplitFrame: - it * holds the (x, y) position of the enclosing SplitFrame, and the (width, * height) of the AlignFrame component */ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); myBottomFrame.viewport .setExplodedGeometry(new Rectangle(source.getX(), source.getY(), myBottomFrame.getWidth(), myBottomFrame.getHeight())); myTopFrame.viewport.setGatherViewsHere(true); myBottomFrame.viewport.setGatherViewsHere(true); String topViewId = myTopFrame.viewport.getSequenceSetId(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); JInternalFrame[] frames = desktop.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof SplitFrame && frame != source) { SplitFrame sf = (SplitFrame) frame; AlignFrame topFrame = (AlignFrame) sf.getTopFrame(); AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame(); boolean gatherThis = false; for (int a = 0; a < topFrame.alignPanels.size(); a++) { AlignmentPanel topPanel = topFrame.alignPanels.get(a); AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a); if (topViewId.equals(topPanel.av.getSequenceSetId()) && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) { gatherThis = true; topPanel.av.setGatherViewsHere(false); bottomPanel.av.setGatherViewsHere(false); topPanel.av.setExplodedGeometry( new Rectangle(sf.getLocation(), topFrame.getSize())); bottomPanel.av.setExplodedGeometry( new Rectangle(sf.getLocation(), bottomFrame.getSize())); myTopFrame.addAlignmentPanel(topPanel, false); myBottomFrame.addAlignmentPanel(bottomPanel, false); } } if (gatherThis) { topFrame.getAlignPanels().clear(); bottomFrame.getAlignPanels().clear(); sf.close(); } } } /* * The dust settles...give focus to the tab we did this from. */ myTopFrame.setDisplayedView(myTopFrame.alignPanel); } public static groovy.console.ui.Console getGroovyConsole() { return groovyConsole; } /** * handles the payload of a drag and drop event. * * TODO refactor to desktop utilities class * * @param files * - Data source strings extracted from the drop event * @param protocols * - protocol for each data source extracted from the drop event * @param evt * - the drop event * @param t * - the payload from the drop event * @throws Exception */ public static void transferFromDropTarget(List files, List protocols, DropTargetDropEvent evt, Transferable t) throws Exception { DataFlavor uriListFlavor = new DataFlavor( "text/uri-list;class=java.lang.String"), urlFlavour = null; try { urlFlavour = new DataFlavor( "application/x-java-url; class=java.net.URL"); } catch (ClassNotFoundException cfe) { jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", cfe); } if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) { try { java.net.URL url = (URL) t.getTransferData(urlFlavour); // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099 // means url may be null. if (url != null) { protocols.add(DataSourceType.URL); files.add(url.toString()); jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1)); return; } else { if (Platform.isAMacAndNotJS()) { jalview.bin.Console.errPrintln( "Please ignore plist error - occurs due to problem with java 8 on OSX"); } } } catch (Throwable ex) { jalview.bin.Console.debug("URL drop handler failed.", ex); } } if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX jalview.bin.Console.debug("Drop handled as javaFileListFlavor"); for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { files.add(file); protocols.add(DataSourceType.FILE); } } else { // Unix like behaviour boolean added = false; String data = null; if (t.isDataFlavorSupported(uriListFlavor)) { jalview.bin.Console.debug("Drop handled as uriListFlavor"); // This is used by Unix drag system data = (String) t.getTransferData(uriListFlavor); } if (data == null) { // fallback to text: workaround - on OSX where there's a JVM bug jalview.bin.Console .debug("standard URIListFlavor failed. Trying text"); // try text fallback DataFlavor textDf = new DataFlavor( "text/plain;class=java.lang.String"); if (t.isDataFlavorSupported(textDf)) { data = (String) t.getTransferData(textDf); } jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data)); } if (data != null) { while (protocols.size() < files.size()) { jalview.bin.Console.debug("Adding missing FILE protocol for " + files.get(protocols.size())); protocols.add(DataSourceType.FILE); } for (java.util.StringTokenizer st = new java.util.StringTokenizer( data, "\r\n"); st.hasMoreTokens();) { added = true; String s = st.nextToken(); if (s.startsWith("#")) { // the line is a comment (as per the RFC 2483) continue; } java.net.URI uri = new java.net.URI(s); if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) { protocols.add(DataSourceType.URL); files.add(uri.toString()); } else { // otherwise preserve old behaviour: catch all for file objects java.io.File file = new java.io.File(uri); protocols.add(DataSourceType.FILE); files.add(file.toString()); } } } if (jalview.bin.Console.isDebugEnabled()) { if (data == null || !added) { if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) { jalview.bin.Console.debug( "Couldn't resolve drop data. Here are the supported flavors:"); for (DataFlavor fl : t.getTransferDataFlavors()) { jalview.bin.Console.debug( "Supported transfer dataflavor: " + fl.toString()); Object df = t.getTransferData(fl); if (df != null) { jalview.bin.Console.debug("Retrieves: " + df); } else { jalview.bin.Console.debug("Retrieved nothing"); } } } else { jalview.bin.Console .debug("Couldn't resolve dataflavor for drop: " + t.toString()); } } } } if (Platform.isWindowsAndNotJS()) { jalview.bin.Console .debug("Scanning dropped content for Windows Link Files"); // resolve any .lnk files in the file drop for (int f = 0; f < files.size(); f++) { String source = files.get(f).toString().toLowerCase(Locale.ROOT); if (protocols.get(f).equals(DataSourceType.FILE) && (source.endsWith(".lnk") || source.endsWith(".url") || source.endsWith(".site"))) { try { Object obj = files.get(f); File lf = (obj instanceof File ? (File) obj : new File((String) obj)); // process link file to get a URL jalview.bin.Console.debug("Found potential link file: " + lf); WindowsShortcut wscfile = new WindowsShortcut(lf); String fullname = wscfile.getRealFilename(); protocols.set(f, FormatAdapter.checkProtocol(fullname)); files.set(f, fullname); jalview.bin.Console.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f)); } catch (Exception ex) { jalview.bin.Console.error( "Couldn't parse " + files.get(f) + " as a link file.", ex); } } } } } /** * Sets the Preferences property for experimental features to True or False * depending on the state of the controlling menu item */ @Override protected void showExperimental_actionPerformed(boolean selected) { Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); } /** * Answers a (possibly empty) list of any structure viewer frames (currently * for either Jmol or Chimera) which are currently open. This may optionally * be restricted to viewers of a specified class, or viewers linked to a * specified alignment panel. * * @param apanel * if not null, only return viewers linked to this panel * @param structureViewerClass * if not null, only return viewers of this class * @return */ public List getStructureViewers( AlignmentPanel apanel, Class structureViewerClass) { List result = new ArrayList<>(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof StructureViewerBase) { if (structureViewerClass == null || structureViewerClass.isInstance(frame)) { if (apanel == null || ((StructureViewerBase) frame).isLinkedWith(apanel)) { result.add((StructureViewerBase) frame); } } } } return result; } public static final String debugScaleMessage = "Desktop graphics transform scale="; private static boolean debugScaleMessageDone = false; public static void debugScaleMessage(Graphics g) { if (debugScaleMessageDone) { return; } // output used by tests to check HiDPI scaling settings in action try { Graphics2D gg = (Graphics2D) g; if (gg != null) { AffineTransform t = gg.getTransform(); double scaleX = t.getScaleX(); double scaleY = t.getScaleY(); jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)"); jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)"); debugScaleMessageDone = true; } else { jalview.bin.Console.debug("Desktop graphics null"); } } catch (Exception e) { jalview.bin.Console.debug(Cache.getStackTraceString(e)); } } /** * closes the current instance window, but leaves the JVM running. Bypasses * any shutdown prompts, but does not set window dispose on close in case JVM * terminates. */ public static void closeDesktop() { if (Desktop.instance != null) { Desktop us = Desktop.instance; Desktop.instance.quitTheDesktop(false, false); // call dispose in a separate thread - try to avoid indirect deadlocks if (us != null) { new Thread(new Runnable() { @Override public void run() { ExecutorService dex = us.dialogExecutor; if (dex != null) { dex.shutdownNow(); us.dialogExecutor = null; us.block.drainPermits(); } us.dispose(); } }).start(); } } } /** * checks if any progress bars are being displayed in any of the windows * managed by the desktop * * @return */ public boolean operationsAreInProgress() { JInternalFrame[] frames = getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof IProgressIndicator) { if (((IProgressIndicator) frame).operationInProgress()) { return true; } } } return operationInProgress(); } /** * keep track of modal JvOptionPanes open as modal dialogs for AlignFrames. * The way the modal JInternalFrame is made means it cannot be a child of an * AlignFrame, so closing the AlignFrame might leave the modal open :( */ private static Map alignFrameModalMap = new HashMap<>(); protected static void addModal(AlignFrame af, JInternalFrame jif) { alignFrameModalMap.put(af, jif); } protected static void closeModal(AlignFrame af) { if (!alignFrameModalMap.containsKey(af)) { return; } JInternalFrame jif = alignFrameModalMap.get(af); if (jif != null) { try { jif.setClosed(true); } catch (PropertyVetoException e) { e.printStackTrace(); } } alignFrameModalMap.remove(af); } public void nonBlockingDialog(String title, String message, String button, int type, boolean scrollable, boolean modal) { nonBlockingDialog(title, message, null, button, type, scrollable, false, modal, -1); } public void nonBlockingDialog(String title, String message, String boxtext, String button, int type, boolean scrollable, boolean html, boolean modal, int timeout) { nonBlockingDialog(32, 2, title, message, boxtext, button, type, scrollable, html, modal, timeout); } public void nonBlockingDialog(int width, int height, String title, String message, String boxtext, String button, int type, boolean scrollable, boolean html, boolean modal, int timeout) { if (type < 0) { type = JvOptionPane.WARNING_MESSAGE; } JLabel jl = new JLabel(message); JTextComponent jtc = null; if (html) { JTextPane jtp = new JTextPane(); jtp.setContentType("text/html"); jtp.setEditable(false); jtp.setAutoscrolls(true); jtp.setText(boxtext); jtc = jtp; } else { JTextArea jta = new JTextArea(height, width); // jta.setLineWrap(true); jta.setEditable(false); jta.setWrapStyleWord(true); jta.setAutoscrolls(true); jta.setText(boxtext); jtc = jta; } JScrollPane jsp = scrollable ? new JScrollPane(jtc, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED) : null; JvOptionPane jvp = JvOptionPane.newOptionDialog(this); JPanel jp = new JPanel(); jp.setLayout(new BoxLayout(jp, BoxLayout.Y_AXIS)); if (message != null) { jl.setAlignmentX(Component.LEFT_ALIGNMENT); jp.add(jl); } if (boxtext != null) { if (scrollable) { jsp.setAlignmentX(Component.LEFT_ALIGNMENT); jp.add(jsp); } else { jtc.setAlignmentX(Component.LEFT_ALIGNMENT); jp.add(jtc); } } jvp.setResponseHandler(JOptionPane.YES_OPTION, () -> { }); jvp.setTimeout(timeout); JButton jb = new JButton(button); jvp.showDialogOnTopAsync(this, jp, title, JOptionPane.YES_OPTION, type, null, new Object[] { button }, button, modal, new JButton[] { jb }, false); } @Override public AlignFrame getCurrentAlignFrame() { return Jalview.getInstance().getCurrentAlignFrame(); } }