/* * 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 jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.StructureSelectionManagerProvider; import jalview.bin.ApplicationSingletonProvider; import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.gui.ImageExporter.ImageWriterI; 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.jbgui.GDesktop; 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.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.UrlConstants; import jalview.viewmodel.AlignmentViewport; import jalview.ws.jws1.Discoverer; import jalview.ws.params.ParamManager; import jalview.ws.utils.UrlDownloadClient; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.FontMetrics; import java.awt.Graphics; 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.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.net.URL; import java.util.ArrayList; import java.util.Hashtable; import java.util.List; import java.util.ListIterator; 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.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; import javax.swing.JTextField; import javax.swing.KeyStroke; import javax.swing.SwingUtilities; import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; import org.stackoverflowusers.file.WindowsShortcut; /** * Jalview Desktop * * * @author $author$ * @version $Revision: 1.155 $ */ @SuppressWarnings("serial") public class Desktop extends GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator, StructureSelectionManagerProvider, ApplicationSingletonI { private final static int DEFAULT_MIN_WIDTH = 300; private final static int DEFAULT_MIN_HEIGHT = 250; private final static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; private final static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; private final static String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); /** * news reader - null if it was never started. */ 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); } public static MyDesktopPane getDesktopPane() { return Desktop.getInstance().desktopPane; } public StructureSelectionManager getStructureSelectionManager() { return StructureSelectionManager .getStructureSelectionManager(this); } static int openFrameCount = 0; static final int xOffset = 30; static final int yOffset = 30; public Discoverer discoverer; public Object[] jalviewClipboard; public boolean internalCopy = false; private static int fileLoadingCount = 0; public JInternalFrame conservationSlider, PIDSlider; /** * just an instance (for testng, probably); no actual frames */ private boolean instanceOnly; 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(); 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); desktopPane.repaint(); } @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); desktopPane.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 } public MyDesktopPane desktopPane; /** * Answers an 'application scope' singleton instance of this class. Separate * SwingJS 'applets' running in the same browser page will each have a * distinct instance of Desktop. * * @return */ public static Desktop getInstance() { return (Desktop) ApplicationSingletonProvider .getInstance(Desktop.class); } /** * For testing. * * @param forInstance */ public Desktop(boolean forInstance) { instanceOnly = true; } /** * Private constructor enforces singleton pattern. It is called by reflection * from ApplicationSingletonProvider.getInstance(). */ @SuppressWarnings("unused") private Desktop() { /** * 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. */ if (!Platform.isJS()) { doVamsasClientCheck(); } doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", false); boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", false); desktopPane = new MyDesktopPane(selmemusage); showMemusage.setSelected(selmemusage); desktopPane.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(desktopPane, BorderLayout.CENTER); desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised desktopPane.setDesktopManager(new MyDesktopManager( (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager( desktopPane.getDesktopManager()) : desktopPane.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 */ { jconsole = new Console(this, showjconsole); // add essential build information jconsole.setHeader("Jalview Version: " + jalview.bin.Cache.getProperty("VERSION") + "\n" + "Jalview Installation: " + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") + "\n" + "Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n" + "Java version: " + System.getProperty("java.version") + "\n" + System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); showConsole(showjconsole); showNews.setVisible(false); experimentalFeatures.setSelected(showExperimental()); getIdentifiersOrgData(); checkURLLinks(); // Spawn a thread that shows the splashscreen SwingUtilities.invokeLater(new Runnable() { @Override public void run() { new SplashScreen(); } }); // 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() { Cache.log.debug("Filechooser init thread started."); String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); Cache.log.debug("Filechooser init thread finished."); } }).start(); // Add the service change listener changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) { Cache.log.debug("Firing service changed event for " + evt.getNewValue()); JalviewServicesChanged(evt); } }); } this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this)); this.addWindowListener(new WindowAdapter() { @Override public void windowClosing(WindowEvent evt) { quit(); } }); 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()); } } }); desktopPane.addMouseListener(ma); } /** * 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 = getStructureSelectionManager(); if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true)) { ssm.setAddTempFacAnnot(jalview.bin.Cache .getDefault(Preferences.ADD_TEMPFACT_ANN, true)); ssm.setProcessSecondaryStructure(jalview.bin.Cache .getDefault(Preferences.STRUCT_FROM_PDB, true)); ssm.setSecStructServices( jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true)); } 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() { Cache.log.debug("Starting news thread."); jvnews = new BlogReader(me); showNews.setVisible(true); Cache.log.debug("Completed news thread."); } }).start(); } public void getIdentifiersOrgData() { // Thread off the identifiers fetcher new Thread(new Runnable() { @Override public void run() { Cache.log.debug("Downloading data from identifiers.org"); // UrlDownloadClient client = new UrlDownloadClient(); try { UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation()); } catch (IOException e) { Cache.log.debug("Exception downloading identifiers.org data" + e.getMessage()); } } }).start(); } @Override protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); } protected void showNews(boolean visible) { Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); showNews.setSelected(visible); if (visible && !jvnews.isVisible()) { new Thread(new Runnable() { @Override public void run() { long now = System.currentTimeMillis(); setProgressBar( MessageManager.getString("status.refreshing_news"), now); jvnews.refreshNews(); 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 = jalview.bin.Cache.getProperty(windowName + "SCREEN_X"); String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y"); String width = jalview.bin.Cache .getProperty(windowName + "SCREEN_WIDTH"); String height = jalview.bin.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 (jalview.bin.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( jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH")))); double sh = ((1f * screenSize.height) / (1f * Integer.parseInt( jalview.bin.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); while (ix >= screenSize.width) { jalview.bin.Cache.log.debug( "Window geometry location recall error: shifting horizontal to within screenbounds."); ix -= screenSize.width; } while (iy >= screenSize.height) { jalview.bin.Cache.log.debug( "Window geometry location recall error: shifting vertical to within screenbounds."); iy -= screenSize.height; } jalview.bin.Cache.log.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; } private void doVamsasClientCheck() { if (Cache.vamsasJarsPresent()) { setupVamsasDisconnectedGui(); VamsasMenu.setVisible(true); final Desktop us = this; VamsasMenu.addMenuListener(new MenuListener() { // this listener remembers when the menu was first selected, and // doesn't rebuild the session list until it has been cleared and // reselected again. boolean refresh = true; @Override public void menuCanceled(MenuEvent e) { refresh = true; } @Override public void menuDeselected(MenuEvent e) { refresh = true; } @Override public void menuSelected(MenuEvent e) { if (refresh) { us.buildVamsasStMenu(); refresh = false; } } }); vamsasStart.setVisible(true); } } protected 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() { 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) { System.out.println( "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 (Desktop.getInstance().instanceOnly || Jalview.isHeadlessMode()) { 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) */ JMenuItem menuItem = new JMenuItem(title); frame.addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameActivated(InternalFrameEvent evt) { JInternalFrame itf = getDesktopPane().getSelectedFrame(); if (itf != null) { if (itf instanceof AlignFrame) { Jalview.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]); } Desktop.getInstance().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) { // System.err.println(ex.toString()); } } }); setKeyBindings(frame); getDesktopPane().add(frame); Desktop.getInstance().windowMenu.add(menuItem); frame.toFront(); try { frame.setSelected(true); frame.requestFocus(); } catch (java.beans.PropertyVetoException ve) { } catch (java.lang.ClassCastException cex) { Cache.log.warn( "Squashed a possible GUI implementation error. If you can recreate this, please look at http://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) { 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, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); 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.getInstance().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 = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); chooser.setResponseHandler(0, new Runnable() { @Override public void run() { 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 * Java: an editable combobox with history * JS: (pending JAL-3038) a plain text field */ JComponent history; String urlBase = "http://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 = new Runnable() { @Override public void run() { @SuppressWarnings("unchecked") String url = (history instanceof JTextField ? ((JTextField) history).getText() : ((JComboBox) history).getSelectedItem() .toString()); if (url.toLowerCase().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.getDesktopPane(), 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(getDesktopPane()) .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); } /* * Exit the program */ @Override public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); jalview.bin.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()); } if (dialogExecutor != null) { dialogExecutor.shutdownNow(); } closeAll_actionPerformed(null); if (groovyConsole != null) { // suppress a possible repeat prompt to save script groovyConsole.setDirty(false); groovyConsole.exit(); } System.exit(0); } private void storeLastKnownDimensions(String string, Rectangle jc) { jalview.bin.Cache.log.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width + " height:" + jc.height); jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + ""); jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + ""); jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + ""); jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + ""); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ @Override public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); // JvOptionPane.showInternalMessageDialog(Desktop.getDesktop(), // // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() { @Override public void run() { new SplashScreen(true); } }).start(); } public StringBuffer getAboutMessage(boolean shortv) { StringBuffer message = new StringBuffer(); message.append(""); if (shortv) { message.append("

Version: " + jalview.bin.Cache.getProperty("VERSION") + "

"); message.append("Last Updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + ""); } else { message.append("Version " + jalview.bin.Cache.getProperty("VERSION") + "; last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); } if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") .equals("Checking")) { message.append("
...Checking latest version...
"); } else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") .equals(jalview.bin.Cache.getProperty("VERSION"))) { boolean red = false; if (jalview.bin.Cache.getProperty("VERSION").toLowerCase() .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 " + jalview.bin.Cache.getDefault("LATEST_VERSION", "..Checking..") + " is available for download from " + jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org") + " !!"); if (red) { message.append("
"); } } message.append("
Authors: " + jalview.bin.Cache.getDefault( "AUTHORFNAMES", "The Jalview Authors (See AUTHORS file for current list)") + "

Development managed by The Barton Group, University of Dundee, Scotland, UK.
" + "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list" + "

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" + ""); return message; } /** * Action on requesting Help documentation */ @Override public void documentationMenuItem_actionPerformed() { try { if (Platform.isJS()) { BrowserLauncher.openURL("http://www.jalview.org/help.html"); } else /** * Java only * * @j2sIgnore */ { Help.showHelpWindow(); } } catch (Exception ex) { System.err.println("Error opening help: " + ex.getMessage()); } } @Override public void closeAll_actionPerformed(ActionEvent e) { if (desktopPane == null) { return; } // TODO show a progress bar while closing? JInternalFrame[] frames = desktopPane.getAllFrames(); for (int i = 0; i < frames.length; i++) { try { frames[i].setClosed(true); } catch (java.beans.PropertyVetoException ex) { } } Jalview.setCurrentAlignFrame(null); System.out.println("ALL CLOSED"); if (v_client != null) { // TODO clear binding to vamsas document objects on close_all } /* * reset state of singleton objects as appropriate (clear down session state * when all windows are closed) */ getStructureSelectionManager().resetAll(); } @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.Cache.log.debug("Collecting garbage..."); System.gc(); jalview.bin.Cache.log.debug("Finished garbage collection."); } /* * (non-Javadoc) * * @see * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent * ) */ @Override protected void showMemusage_actionPerformed(ActionEvent e) { getDesktopPane().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 = getDesktopPane().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) { new Preferences(); } /** * 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(); // System.out.println("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()); jalview.bin.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) { Cache.log.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, true); // last two booleans: allFiles, // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); chooser.setResponseHandler(0, new Runnable() { @Override public void run() { 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(choice); } catch (OutOfMemoryError oom) { new OOMWarning("Whilst loading project from " + choice, oom); } catch (Exception ex) { Cache.log.error( "Problems whilst loading project from " + choice, ex); JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "label.error_whilst_loading_project_from", new Object[] { choice }), MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE); } } }).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; 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; 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.getDesktopPane() == 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 = getAlignFrames(); 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 (getDesktopPane() != null) { AlignFrame[] frames = Desktop.getAlignFrames(); 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; } for (int i = 0; i < size; i++) { AlignmentPanel ap = af.alignPanels.get(i); AlignFrame newaf = new AlignFrame(ap); /* * 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); } 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 = 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) { af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); } } } } jalview.gui.VamsasApplication v_client = null; @Override public void vamsasImport_actionPerformed(ActionEvent e) { // TODO: JAL-3048 not needed for Jalview-JS if (v_client == null) { // Load and try to start a session. JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.open_saved_vamsas_session")); chooser.setToolTipText(MessageManager.getString( "label.select_vamsas_session_opened_as_new_vamsas_session")); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), JvOptionPane.ERROR_MESSAGE); } } } else { jalview.bin.Cache.log.error( "Implementation error - load session from a running session is not supported."); } } /** * import file into a new vamsas session (uses jalview.gui.VamsasApplication) * * @param file * @return true if import was a success and a session was started. */ public boolean vamsasImport(URL url) { // TODO: create progress bar if (v_client != null) { jalview.bin.Cache.log.error( "Implementation error - load session from a running session is not supported."); return false; } try { // copy the URL content to a temporary local file // TODO: be a bit cleverer here with nio (?!) File file = File.createTempFile("vdocfromurl", ".vdj"); FileOutputStream fos = new FileOutputStream(file); BufferedInputStream bis = new BufferedInputStream(url.openStream()); byte[] buffer = new byte[2048]; int ln; while ((ln = bis.read(buffer)) > -1) { fos.write(buffer, 0, ln); } bis.close(); fos.close(); v_client = new jalview.gui.VamsasApplication(this, file, url.toExternalForm()); } catch (Exception ex) { jalview.bin.Cache.log.error( "Failed to create new vamsas session from contents of URL " + url, ex); return false; } setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? return v_client.inSession(); } /** * import file into a new vamsas session (uses jalview.gui.VamsasApplication) * * @param file * @return true if import was a success and a session was started. */ public boolean vamsasImport(File file) { if (v_client != null) { jalview.bin.Cache.log.error( "Implementation error - load session from a running session is not supported."); return false; } setProgressBar(MessageManager.formatMessage( "status.importing_vamsas_session_from", new Object[] { file.getName() }), file.hashCode()); try { v_client = new jalview.gui.VamsasApplication(this, file, null); } catch (Exception ex) { setProgressBar(MessageManager.formatMessage( "status.importing_vamsas_session_from", new Object[] { file.getName() }), file.hashCode()); jalview.bin.Cache.log.error( "New vamsas session from existing session file failed:", ex); return false; } setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? setProgressBar(MessageManager.formatMessage( "status.importing_vamsas_session_from", new Object[] { file.getName() }), file.hashCode()); return v_client.inSession(); } public boolean joinVamsasSession(String mysesid) { if (v_client != null) { throw new Error(MessageManager .getString("error.try_join_vamsas_session_another")); } if (mysesid == null) { throw new Error( MessageManager.getString("error.invalid_vamsas_session_id")); } v_client = new VamsasApplication(this, mysesid); setupVamsasConnectedGui(); v_client.initial_update(); return (v_client.inSession()); } @Override public void vamsasStart_actionPerformed(ActionEvent e) { if (v_client == null) { // Start a session. // we just start a default session for moment. /* * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. * getProperty("LAST_DIRECTORY")); * * chooser.setFileView(new JalviewFileView()); * chooser.setDialogTitle("Load Vamsas file"); * chooser.setToolTipText("Import"); * * int value = chooser.showOpenDialog(this); * * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new * jalview.gui.VamsasApplication(this, chooser.getSelectedFile()); */ v_client = new VamsasApplication(this); setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? } else { // store current data in session. v_client.push_update(); // TODO: thread } } protected void setupVamsasConnectedGui() { vamsasStart.setText(MessageManager.getString("label.session_update")); vamsasSave.setVisible(true); vamsasStop.setVisible(true); vamsasImport.setVisible(false); // Document import to existing session is // not possible for vamsas-client-1.0. } protected void setupVamsasDisconnectedGui() { vamsasSave.setVisible(false); vamsasStop.setVisible(false); vamsasImport.setVisible(true); vamsasStart .setText(MessageManager.getString("label.new_vamsas_session")); } @Override public void vamsasStop_actionPerformed(ActionEvent e) { if (v_client != null) { v_client.end_session(); v_client = null; setupVamsasDisconnectedGui(); } } protected void buildVamsasStMenu() { if (v_client == null) { String[] sess = null; try { sess = VamsasApplication.getSessionList(); } catch (Exception e) { jalview.bin.Cache.log.warn("Problem getting current sessions list.", e); sess = null; } if (sess != null) { jalview.bin.Cache.log.debug( "Got current sessions list: " + sess.length + " entries."); VamsasStMenu.removeAll(); for (int i = 0; i < sess.length; i++) { JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); sessit.setToolTipText(MessageManager .formatMessage("label.connect_to_session", new Object[] { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; sessit.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { if (dsktp.v_client == null) { Thread rthr = new Thread(new Runnable() { @Override public void run() { dsktp.v_client = new VamsasApplication(dsktp, mysesid); dsktp.setupVamsasConnectedGui(); dsktp.v_client.initial_update(); } }); rthr.start(); } } }); VamsasStMenu.add(sessit); } // don't show an empty menu. VamsasStMenu.setVisible(sess.length > 0); } else { jalview.bin.Cache.log.debug("No current vamsas sessions."); VamsasStMenu.removeAll(); VamsasStMenu.setVisible(false); } } else { // Not interested in the content. Just hide ourselves. VamsasStMenu.setVisible(false); } } @Override public void vamsasSave_actionPerformed(ActionEvent e) { // TODO: JAL-3048 not needed for Jalview-JS if (v_client != null) { // TODO: VAMSAS DOCUMENT EXTENSION is VDJ JalviewFileChooser chooser = new JalviewFileChooser("vdj", "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.save_vamsas_document_archive")); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { java.io.File choice = chooser.getSelectedFile(); JPanel progpanel = addProgressPanel(MessageManager .formatMessage("label.saving_vamsas_doc", new Object[] { choice.getName() })); Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; try { v_client.vclient.storeDocument(choice); } catch (Error ex) { warnttl = "Serious Problem saving Vamsas Document"; warnmsg = ex.toString(); jalview.bin.Cache.log .error("Error Whilst saving document to " + choice, ex); } catch (Exception ex) { warnttl = "Problem saving Vamsas Document."; warnmsg = ex.toString(); jalview.bin.Cache.log.warn( "Exception Whilst saving document to " + choice, ex); } removeProgressPanel(progpanel); if (warnmsg != null) { JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } } } } JPanel vamUpdate = null; /** * hide vamsas user gui bits when a vamsas document event is being handled. * * @param b * true to hide gui, false to reveal gui */ public void setVamsasUpdate(boolean b) { Cache.log.debug("Setting gui for Vamsas update " + (b ? "in progress" : "finished")); if (vamUpdate != null) { this.removeProgressPanel(vamUpdate); } if (b) { vamUpdate = this.addProgressPanel( MessageManager.getString("label.updating_vamsas_session")); } vamsasStart.setVisible(!b); vamsasStop.setVisible(!b); vamsasSave.setVisible(!b); } public JInternalFrame[] getAllFrames() { return desktopPane.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(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(desktopPane, 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()); } } } } /** * Accessor method to quickly get all the AlignmentFrames loaded. * * @return an array of AlignFrame, or null if none found */ public static AlignFrame[] getAlignFrames() { if (Jalview.isHeadlessMode()) { // Desktop.getDesktop() is null in headless mode return new AlignFrame[] { Jalview.getCurrentAlignFrame() }; } JInternalFrame[] frames = Desktop.getDesktopPane().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; } /** * Returns an array of any AppJmol frames in the Desktop (or null if none). * * @return */ public GStructureViewer[] getJmols() { JInternalFrame[] frames = Desktop.getDesktopPane().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.Cache.log.error("Groovy Shell Creation failed.", ex); JvOptionPane.showInternalMessageDialog(desktopPane, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE); } } /** * Open the Groovy console */ private void openGroovyConsole() { if (groovyConsole == null) { groovyConsole = new groovy.ui.Console(); groovyConsole.setVariable("Jalview", this); 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, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @Override public void actionPerformed(ActionEvent e) { quit(); } }); } /** * 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 = getAlignFrames(); 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) { Platform.timeCheck("Desktop " + message, Platform.TIME_MARK); if (progressBars == null) { progressBars = new Hashtable<>(); progressBarHandlers = new Hashtable<>(); } if (progressBars.get(new Long(id)) != null) { JPanel panel = progressBars.remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { progressBarHandlers.remove(new Long(id)); } removeProgressPanel(panel); } else { progressBars.put(new Long(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(new Long(id))) { throw new Error(MessageManager.getString( "error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = progressBars.get(new Long(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 (getDesktopPane() != 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() { return v_client; } /** * 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; } public void startServiceDiscovery() { startServiceDiscovery(false); } public void startServiceDiscovery(boolean blocking) { 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 = Discoverer.getInstance(); // register PCS handler for getDesktop(). discoverer.addPropertyChangeListener(changeSupport); } // JAL-940 - disabled JWS1 service configuration - always start discoverer // until we phase out completely (t0 = new Thread(discoverer)).start(); } if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { t2 = jalview.ws.jws2.Jws2Discoverer.getInstance() .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.getInstance() .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.getDesktopPane(), 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 { Cache.log.error( "Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg); } } } } 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) { showUrl(url, Desktop.getInstance()); } /** * 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()); } BrowserLauncher.openURL(url); } catch (Exception ex) { JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), 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(); } private WsParamSetManager wsparamManager = null; public static ParamManager getUserParameterStore() { Desktop d = Desktop.getInstance(); if (d.wsparamManager == null) { d.wsparamManager = new WsParamSetManager(); } return d.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) { if (Cache.log != null) { Cache.log.error("Couldn't handle string " + url + " as a URL."); } else { System.err.println( "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.newSingleThreadExecutor(); /** * flag indicating if dialogExecutor should try to acquire a permit */ volatile boolean dialogPause = true; /** * pause the queue */ java.util.concurrent.Semaphore block = new Semaphore(0); private groovy.ui.Console groovyConsole; public StructureViewer lastTargetedView; /** * 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) { try { block.acquire(); } catch (InterruptedException x) { } } if (instanceOnly) { return; } try { SwingUtilities.invokeAndWait(prompter); } catch (Exception q) { Cache.log.warn("Unexpected Exception in dialog thread.", q); } } }); } public void startDialogQueue() { // set the flag so we don't pause waiting for another permit and semaphore // the current task to begin dialogPause = false; block.release(); } /** * 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); Cache.log.info("Successfully written snapshot to file " + of.getAbsolutePath()); } }; String title = "View of desktop"; ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title); exporter.doExport(of, this, width, height, title); } /** * 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 = desktopPane.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.ui.Console getGroovyConsole() { return Desktop.getInstance().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 */ @SuppressWarnings("unchecked") public static void transferFromDropTarget(List files, List protocols, DropTargetDropEvent evt, Transferable t) throws Exception { // BH 2018 changed List to List to allow for File from SwingJS // DataFlavor[] flavors = t.getTransferDataFlavors(); // for (int i = 0; i < flavors.length; i++) { // if (flavors[i].isFlavorJavaFileListType()) { // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); // List list = (List) t.getTransferData(flavors[i]); // for (int j = 0; j < list.size(); j++) { // File file = (File) list.get(j); // byte[] data = getDroppedFileBytes(file); // fileName.setText(file.getName() + " - " + data.length + " " + // evt.getLocation()); // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent(); // target.setText(new String(data)); // } // dtde.dropComplete(true); // return; // } // 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) { Cache.log.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()); Cache.log.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1)); return; } else { if (Platform.isAMacAndNotJS()) { System.err.println( "Please ignore plist error - occurs due to problem with java 8 on OSX"); } } } catch (Throwable ex) { Cache.log.debug("URL drop handler failed.", ex); } } if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX Cache.log.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)) { Cache.log.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 Cache.log.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); } Cache.log.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data)); } if (data != null) { while (protocols.size() < files.size()) { Cache.log.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().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 (Cache.log.isDebugEnabled()) { if (data == null || !added) { if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) { Cache.log.debug( "Couldn't resolve drop data. Here are the supported flavors:"); for (DataFlavor fl : t.getTransferDataFlavors()) { Cache.log.debug( "Supported transfer dataflavor: " + fl.toString()); Object df = t.getTransferData(fl); if (df != null) { Cache.log.debug("Retrieves: " + df); } else { Cache.log.debug("Retrieved nothing"); } } } else { Cache.log.debug("Couldn't resolve dataflavor for drop: " + t.toString()); } } } } if (Platform.isWindowsAndNotJS()) { Cache.log.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(); 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 Cache.log.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); Cache.log.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f)); } catch (Exception ex) { Cache.log.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 = 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; } }