/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * 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 . */ package jalview.gui; import jalview.bin.Cache; import jalview.io.*; import jalview.ws.params.ParamManager; import java.awt.*; import java.awt.datatransfer.*; import java.awt.dnd.*; import java.awt.event.*; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.File; import java.io.FileOutputStream; import java.io.InputStream; import java.lang.reflect.Constructor; import java.net.URL; import java.net.URLConnection; import java.nio.channels.ReadableByteChannel; import java.util.*; import javax.swing.*; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; /** * Jalview Desktop * * * @author $author$ * @version $Revision$ */ public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator { private class JalviewChangeSupport implements PropertyChangeListener { public void propertyChange(PropertyChangeEvent evt) { // Handle change events - most are simply routed to other sources changeSupport.firePropertyChange(evt); } /** * change listeners are notified of changes to resources so they can update * their state. E.g. - the 'services' property notifies when the available * set of web service endpoints have changed. */ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( this); /** * @param propertyName * @param listener * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { changeSupport.addPropertyChangeListener(propertyName, listener); } /** * @param listener * @see java.beans.PropertyChangeSupport#addPropertyChangeListener( * java.beans.PropertyChangeListener) */ public void addJalviewPropertyChangeListener( PropertyChangeListener listener) { changeSupport.addPropertyChangeListener(listener); } /* * @param propertyName * * @param oldValue * * @param newValue * * @see * java.beans.PropertyChangeSupport#firePropertyChange(java.lang.String, * java.lang.Object, java.lang.Object) public void firePropertyChange(String * propertyName, Object oldValue, Object newValue) { * changeSupport.firePropertyChange(propertyName, oldValue, newValue); } */ /** * @param propertyName * @param listener * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { changeSupport.removePropertyChangeListener(propertyName, listener); } } private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); /** * @param listener * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) */ public void addJalviewPropertyChangeListener( PropertyChangeListener listener) { changeSupport.addJalviewPropertyChangeListener(listener); } /** * @param propertyName * @param listener * @see jalview.gui.Desktop.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.Desktop.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; 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; } public void activateFrame(JInternalFrame f) { try { delegate.activateFrame(f); } catch (NullPointerException npe) { Point p = getMousePosition(); instance.showPasteMenu(p.x, p.y); } } public void beginDraggingFrame(JComponent f) { delegate.beginDraggingFrame(f); } public void beginResizingFrame(JComponent f, int direction) { delegate.beginResizingFrame(f, direction); } public void closeFrame(JInternalFrame f) { delegate.closeFrame(f); } public void deactivateFrame(JInternalFrame f) { delegate.deactivateFrame(f); } public void deiconifyFrame(JInternalFrame f) { delegate.deiconifyFrame(f); } public void dragFrame(JComponent f, int newX, int newY) { delegate.dragFrame(f, newX, newY); } public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); } public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); } public void iconifyFrame(JInternalFrame f) { delegate.iconifyFrame(f); } public void maximizeFrame(JInternalFrame f) { delegate.maximizeFrame(f); } public void minimizeFrame(JInternalFrame f) { delegate.minimizeFrame(f); } public void openFrame(JInternalFrame f) { delegate.openFrame(f); } public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { delegate.resizeFrame(f, newX, newY, newWidth, newHeight); } 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() { /** * 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; doVamsasClientCheck(); doGroovyCheck(); 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); desktop = new MyDesktopPane(selmemusage); showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); getContentPane().add(desktop, BorderLayout.CENTER); desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); // This line prevents Windows Look&Feel resizing all new windows to maximum // if previous window was maximised desktop.setDesktopManager(new MyDesktopManager( new DefaultDesktopManager())); Rectangle dims = getLastKnownDimensions(""); if (dims != null) { setBounds(dims); } else { Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); setBounds((int) (screenSize.width - 900) / 2, (int) (screenSize.height - 650) / 2, 900, 650); } jconsole = new Console(this, showjconsole); // add essential build information jconsole.setHeader("Jalview Desktop " + jalview.bin.Cache.getProperty("VERSION") + "\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); this.addWindowListener(new WindowAdapter() { public void windowClosing(WindowEvent evt) { quit(); } }); this.addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent evt) { if (SwingUtilities.isRightMouseButton(evt)) { showPasteMenu(evt.getX(), evt.getY()); } } }); this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); // Spawn a thread that shows the splashscreen SwingUtilities.invokeLater(new Runnable() { public void run() { new SplashScreen(); } }); // displayed. // Thread off a new instance of the file chooser - this reduces the time it // takes to open it later on. new Thread(new Runnable() { public void run() { Cache.log.debug("Filechooser init thread started."); JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.READABLE_FNAMES, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); Cache.log.debug("Filechooser init thread finished."); } }).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 (jalview.bin.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; public void menuCanceled(MenuEvent e) { refresh = true; } public void menuDeselected(MenuEvent e) { refresh = true; } public void menuSelected(MenuEvent e) { if (refresh) { us.buildVamsasStMenu(); refresh = false; } } }); vamsasStart.setVisible(true); } } void showPasteMenu(int x, int y) { JPopupMenu popup = new JPopupMenu(); JMenuItem item = new JMenuItem("Paste To New Window"); item.addActionListener(new ActionListener() { 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); String format = new IdentifyFile().Identify(file, FormatAdapter.PASTE); new FileLoader().LoadFile(file, FormatAdapter.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 * DOCUMENT ME! * @param title * DOCUMENT ME! * @param w * DOCUMENT ME! * @param h * DOCUMENT ME! */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, int w, int h) { addInternalFrame(frame, title, w, h, true); } /** * DOCUMENT ME! * * @param frame * DOCUMENT ME! * @param title * DOCUMENT ME! * @param w * DOCUMENT ME! * @param h * DOCUMENT ME! * @param resizable * DOCUMENT ME! */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, int w, int h, boolean resizable) { // 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 (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) { return; } openFrameCount++; frame.setVisible(true); frame.setClosable(true); frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); frame.setFrameIcon(null); if (frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset); } final JMenuItem menuItem = new JMenuItem(title); frame .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameActivated( javax.swing.event.InternalFrameEvent evt) { JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); } } public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { PaintRefresher.RemoveComponent(frame); openFrameCount--; windowMenu.remove(menuItem); JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); } System.gc(); }; }); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { try { frame.setSelected(true); frame.setIcon(false); } catch (java.beans.PropertyVetoException ex) { } } }); windowMenu.add(menuItem); desktop.add(frame); frame.toFront(); try { frame.setSelected(true); frame.requestFocus(); } catch (java.beans.PropertyVetoException ve) { } } public void lostOwnership(Clipboard clipboard, Transferable contents) { if (!internalCopy) { Desktop.jalviewClipboard = null; } internalCopy = false; } public void dragEnter(DropTargetDragEvent evt) { } public void dragExit(DropTargetEvent evt) { } public void dragOver(DropTargetDragEvent evt) { } public void dropActionChanged(DropTargetDragEvent evt) { } /** * DOCUMENT ME! * * @param evt * DOCUMENT ME! */ public void drop(DropTargetDropEvent evt) { Transferable t = evt.getTransferable(); java.util.List files = null; java.util.List protocols = null; try { DataFlavor uriListFlavor = new DataFlavor( "text/uri-list;class=java.lang.String"); if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); files = (java.util.List) t .getTransferData(DataFlavor.javaFileListFlavor); } else if (t.isDataFlavorSupported(uriListFlavor)) { // This is used by Unix drag system evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); String data = (String) t.getTransferData(uriListFlavor); files = new java.util.ArrayList(1); protocols = new java.util.ArrayList(1); for (java.util.StringTokenizer st = new java.util.StringTokenizer( data, "\r\n"); st.hasMoreTokens();) { 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(FormatAdapter.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(FormatAdapter.FILE); files.add(file.toString()); } } } } catch (Exception e) { } if (files != null) { try { for (int i = 0; i < files.size(); i++) { String file = files.get(i).toString(); String protocol = (protocols == null) ? FormatAdapter.FILE : (String) protocols.get(i); String format = null; if (file.endsWith(".jar")) { format = "Jalview"; } else { format = new IdentifyFile().Identify(file, protocol); } new FileLoader().LoadFile(file, protocol, format); } } catch (Exception ex) { } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache .getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.READABLE_FNAMES, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Open local file"); chooser.setToolTipText("Open"); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); String format = null; if (chooser.getSelectedFormat().equals("Jalview")) { format = "Jalview"; } else { format = new IdentifyFile().Identify(choice, FormatAdapter.FILE); } if (viewport != null) { new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format); } else { new FileLoader().LoadFile(choice, FormatAdapter.FILE, format); } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void inputURLMenuItem_actionPerformed(AlignViewport viewport) { // This construct allows us to have a wider textfield // for viewing JLabel label = new JLabel("Enter URL of Input File"); final JComboBox history = new JComboBox(); JPanel panel = new JPanel(new GridLayout(2, 1)); panel.add(label); panel.add(history); history.setPreferredSize(new Dimension(400, 20)); history.setEditable(true); history.addItem("http://www."); String historyItems = jalview.bin.Cache.getProperty("RECENT_URL"); StringTokenizer st; if (historyItems != null) { st = new StringTokenizer(historyItems, "\t"); while (st.hasMoreTokens()) { history.addItem(st.nextElement()); } } int reply = JOptionPane.showInternalConfirmDialog(desktop, panel, "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION); if (reply != JOptionPane.OK_OPTION) { return; } String url = history.getSelectedItem().toString(); if (url.toLowerCase().endsWith(".jar")) { if (viewport != null) { new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview"); } else { new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview"); } } else { String format = new IdentifyFile().Identify(url, FormatAdapter.URL); if (format.equals("URL NOT FOUND")) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't locate " + url, "URL not found", JOptionPane.WARNING_MESSAGE); return; } if (viewport != null) { new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format); } else { new FileLoader().LoadFile(url, FormatAdapter.URL, format); } } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(viewport); Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); } /* * Exit the program */ 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(); } 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! */ public void aboutMenuItem_actionPerformed(ActionEvent e) { StringBuffer message = new StringBuffer("Jalview version " + jalview.bin.Cache.getProperty("VERSION") + "; last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( jalview.bin.Cache.getProperty("VERSION"))) { message .append("\n\n!! Jalview version " + jalview.bin.Cache.getProperty("LATEST_VERSION") + " is available for download from http://www.jalview.org !!\n"); } // TODO: update this text for each release or centrally store it for lite // and application message .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton." + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n" + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n" + "\nIf you use Jalview, please cite:" + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench" + "\nBioinformatics doi: 10.1093/bioinformatics/btp033"); JOptionPane.showInternalMessageDialog(Desktop.desktop, message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void documentationMenuItem_actionPerformed(ActionEvent e) { try { ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); javax.help.HelpBroker hb = hs.createHelpBroker(); hb.setCurrentID("home"); hb.setDisplayed(true); } catch (Exception ex) { } } public void closeAll_actionPerformed(ActionEvent e) { JInternalFrame[] frames = desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) { try { frames[i].setClosed(true); } catch (java.beans.PropertyVetoException ex) { } } System.out.println("ALL CLOSED"); if (v_client != null) { // TODO clear binding to vamsas document objects on close_all } } public void raiseRelated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(false, false); } 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) */ 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 * ) */ protected void showMemusage_actionPerformed(ActionEvent e) { desktop.showMemoryUsage(showMemusage.isSelected()); } /* * (non-Javadoc) * * @see * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent * ) */ 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) { showConsole.setSelected(selected); // TODO: decide if we should update properties file 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; } AlignViewport 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! */ protected void preferences_actionPerformed(ActionEvent e) { new Preferences(); } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void saveState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache .getProperty("LAST_DIRECTORY"), new String[] { "jar" }, new String[] { "Jalview Project" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save State"); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { java.io.File choice = chooser.getSelectedFile(); setProgressBar("Saving jalview project " + choice.getName(), choice.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); // TODO catch and handle errors for savestate try { new Jalview2XML().SaveState(choice); } catch (OutOfMemoryError oom) { new OOMWarning("Whilst saving current state to "+choice.getName(), oom); } catch (Exception ex) { Cache.log.error("Problems whilst trying to save to "+choice.getName(),ex); JOptionPane.showMessageDialog(this, "Error whilst saving current state to "+choice.getName(), "Couldn't save project", JOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } } /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ public void loadState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache .getProperty("LAST_DIRECTORY"), new String[] { "jar" }, new String[] { "Jalview Project" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Restore state"); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { final String choice = chooser.getSelectedFile().getAbsolutePath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); new Thread(new Runnable() { public void run() { setProgressBar("loading jalview project " + choice, choice.hashCode()); 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); JOptionPane.showMessageDialog(Desktop.desktop, "Error whilst loading project from "+choice, "Couldn't load project", JOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } }).start(); } } public void inputSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); } JPanel progressPanel; public void startLoading(final String fileName) { if (fileLoadingCount == 0) { addProgressPanel("Loading File: " + fileName + " "); } fileLoadingCount++; } private JProgressBar addProgressPanel(String string) { if (progressPanel == null) { progressPanel = new JPanel(new BorderLayout()); totalProgressCount = 0; } JProgressBar progressBar = new JProgressBar(); progressBar.setIndeterminate(true); progressPanel.add(new JLabel(string), BorderLayout.WEST); progressPanel.add(progressBar, BorderLayout.CENTER); instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); totalProgressCount++; validate(); return progressBar; } int totalProgressCount = 0; private void removeProgressPanel(JProgressBar progbar) { if (progressPanel != null) { progressPanel.remove(progbar); if (--totalProgressCount < 1) { this.getContentPane().remove(progressPanel); progressPanel = null; } } validate(); } public void stopLoading() { fileLoadingCount--; if (fileLoadingCount < 1) { if (progressPanel != null) { this.getContentPane().remove(progressPanel); progressPanel = null; } fileLoadingCount = 0; } validate(); } public static int getViewCount(String viewId) { AlignViewport[] aps = getViewports(viewId); return (aps == null) ? 0 : aps.length; } /** * * @param viewId * @return all AlignmentPanels concerning the viewId sequence set */ public static AlignmentPanel[] getAlignmentPanels(String viewId) { int count = 0; if (Desktop.desktop == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode return null; } JInternalFrame[] frames = Desktop.desktop.getAllFrames(); ArrayList aps = new ArrayList(); for (int t = 0; t < frames.length; t++) { if (frames[t] instanceof AlignFrame) { AlignFrame af = (AlignFrame) frames[t]; for (int a = 0; a < af.alignPanels.size(); a++) { if (viewId .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av .getSequenceSetId())) { aps.add(af.alignPanels.elementAt(a)); } } } } if (aps.size() == 0) { return null; } AlignmentPanel[] vap = new AlignmentPanel[aps.size()]; for (int t = 0; t < vap.length; t++) { vap[t] = (AlignmentPanel) aps.get(t); } return vap; } /** * get all the viewports on an alignment. * * @param sequenceSetId * unique alignment id * @return all viewports on the alignment bound to sequenceSetId */ public static AlignViewport[] getViewports(String sequenceSetId) { Vector viewp = new Vector(); if (desktop != null) { javax.swing.JInternalFrame[] frames = instance.getAllFrames(); for (int t = 0; t < frames.length; t++) { if (frames[t] instanceof AlignFrame) { AlignFrame afr = ((AlignFrame) frames[t]); if (afr.getViewport().getSequenceSetId().equals(sequenceSetId)) { if (afr.alignPanels != null) { for (int a = 0; a < afr.alignPanels.size(); a++) { if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels .elementAt(a)).av.getSequenceSetId())) { viewp.addElement(((AlignmentPanel) afr.alignPanels .elementAt(a)).av); } } } else { viewp.addElement(((AlignFrame) frames[t]).getViewport()); } } } } if (viewp.size() > 0) { AlignViewport[] vp = new AlignViewport[viewp.size()]; viewp.copyInto(vp); return vp; } } return null; } public void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); if (size < 2) { return; } for (int i = 0; i < size; i++) { AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i); AlignFrame newaf = new AlignFrame(ap); if (ap.av.explodedPosition != null && !ap.av.explodedPosition.equals(af.getBounds())) { newaf.setBounds(ap.av.explodedPosition); } ap.av.gatherViewsHere = false; addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); } public void gatherViews(AlignFrame source) { source.viewport.gatherViewsHere = true; source.viewport.explodedPosition = source.getBounds(); JInternalFrame[] frames = desktop.getAllFrames(); String viewId = source.viewport.sequenceSetID; 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 = (AlignmentPanel) af.alignPanels.elementAt(a); if (viewId.equals(ap.av.getSequenceSetId())) { gatherThis = true; ap.av.gatherViewsHere = false; ap.av.explodedPosition = af.getBounds(); source.addAlignmentPanel(ap, false); } } if (gatherThis) { af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); } } } } jalview.gui.VamsasApplication v_client = null; public void vamsasImport_actionPerformed(ActionEvent e) { 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("Open a saved VAMSAS session"); chooser .setToolTipText("select a vamsas session to be opened as a new vamsas session."); int value = chooser.showOpenDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't import '" + fle + "' as a new vamsas session.", "Vamsas Document Import Failed", JOptionPane.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("Importing VAMSAS session from " + file.getName(), file .hashCode()); try { v_client = new jalview.gui.VamsasApplication(this, file, null); } catch (Exception ex) { setProgressBar("Importing VAMSAS session from " + 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("Importing VAMSAS session from " + file.getName(), file .hashCode()); return v_client.inSession(); } public boolean joinVamsasSession(String mysesid) { if (v_client != null) { throw new Error( "Trying to join a vamsas session when another is already connected."); } if (mysesid == null) { throw new Error("Invalid vamsas session id."); } v_client = new VamsasApplication(this, mysesid); setupVamsasConnectedGui(); v_client.initial_update(); return (v_client.inSession()); } 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("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("New Vamsas Session"); } 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("Connect to session " + sess[i]); final Desktop dsktp = this; final String mysesid = sess[i]; sessit.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { if (dsktp.v_client == null) { Thread rthr = new Thread(new Runnable() { 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); } } public void vamsasSave_actionPerformed(ActionEvent e) { if (v_client != null) { JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache .getProperty("LAST_DIRECTORY"), new String[] { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ new String[] { "Vamsas Document" }, "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save Vamsas Document Archive"); int value = chooser.showSaveDialog(this); if (value == JalviewFileChooser.APPROVE_OPTION) { java.io.File choice = chooser.getSelectedFile(); JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to " + choice.getName()); jalview.bin.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) { JOptionPane.showInternalMessageDialog(Desktop.desktop, warnmsg, warnttl, JOptionPane.ERROR_MESSAGE); } } } } JProgressBar 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) { jalview.bin.Cache.log.debug("Setting gui for Vamsas update " + (b ? "in progress" : "finished")); if (vamUpdate != null) { this.removeProgressPanel(vamUpdate); } if (b) { vamUpdate = this.addProgressPanel("Updating vamsas session"); } vamsasStart.setVisible(!b); vamsasStop.setVisible(!b); vamsasSave.setVisible(!b); } 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(); } /** * 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 { 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 showMemoryUsage) { this.showMemoryUsage = showMemoryUsage; if (showMemoryUsage) { Thread worker = new Thread(this); worker.start(); } } public boolean isShowMemoryUsage() { return showMemoryUsage; } public void run() { df = java.text.NumberFormat.getNumberInstance(); df.setMaximumFractionDigits(2); runtime = Runtime.getRuntime(); while (showMemoryUsage) { try { maxMemory = runtime.maxMemory() / 1048576f; allocatedMemory = runtime.totalMemory() / 1048576f; freeMemory = runtime.freeMemory() / 1048576f; 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(); } } } 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("Total Free Memory: " + df.format(totalFreeMemory) + "MB; Max Memory: " + df.format(maxMemory) + "MB; " + df.format(percentUsage) + "%", 10, getHeight() - fm.getHeight()); } } } } protected JMenuItem groovyShell; public void doGroovyCheck() { if (jalview.bin.Cache.groovyJarsPresent()) { groovyShell = new JMenuItem(); groovyShell.setText("Groovy Console..."); groovyShell.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { groovyShell_actionPerformed(e); } }); toolsMenu.add(groovyShell); groovyShell.setVisible(true); } } /** * Accessor method to quickly get all the AlignmentFrames loaded. */ public static AlignFrame[] getAlignframes() { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) { return null; } Vector avp = new Vector(); try { // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { if (frames[i] instanceof AlignFrame) { AlignFrame af = (AlignFrame) frames[i]; avp.addElement(af); } } } catch (Exception ex) { ex.printStackTrace(); } if (avp.size() == 0) { return null; } AlignFrame afs[] = new AlignFrame[avp.size()]; for (int i = 0, j = avp.size(); i < j; i++) { afs[i] = (AlignFrame) avp.elementAt(i); } avp.clear(); return afs; } /** * Add Groovy Support to Jalview */ public void groovyShell_actionPerformed(ActionEvent e) { // use reflection to avoid creating compilation dependency. if (!jalview.bin.Cache.groovyJarsPresent()) { throw new Error( "Implementation Error. Cannot create groovyShell without Groovy on the classpath!"); } try { Class gcClass = Desktop.class.getClassLoader().loadClass( "groovy.ui.Console"); Constructor gccons = gcClass.getConstructor(null); java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class }); java.lang.reflect.Method run = gcClass.getMethod("run", null); Object gc = gccons.newInstance(null); setvar.invoke(gc, new Object[] { "Jalview", this }); run.invoke(gc, null); } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); JOptionPane .showInternalMessageDialog( Desktop.desktop, "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed", JOptionPane.ERROR_MESSAGE); } } /** * Progress bars managed by the IProgressIndicator method. */ private Hashtable progressBars, progressBarHandlers; /* * (non-Javadoc) * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ public void setProgressBar(String message, long id) { if (progressBars == null) { progressBars = new Hashtable(); progressBarHandlers = new Hashtable(); } if (progressBars.get(new Long(id)) != null) { JProgressBar progressPanel = (JProgressBar) progressBars .remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { progressBarHandlers.remove(new Long(id)); } removeProgressPanel(progressPanel); } else { progressBars.put(new Long(id), addProgressPanel(message)); } } /* * (non-Javadoc) * * @see jalview.gui.IProgressIndicator#registerHandler(long, * jalview.gui.IProgressIndicatorHandler) */ public void registerHandler(final long id, final IProgressIndicatorHandler handler) { if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { throw new Error( "call setProgressBar before registering the progress bar's handler."); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { JButton cancel = new JButton("Cancel"); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); us.setProgressBar("Cancelled " + ((JLabel) progressPanel.getComponent(0)).getText(), id); } }); progressPanel.add(cancel, BorderLayout.EAST); } } /** * This will return the first AlignFrame viewing AlignViewport av. It will * break if there are more than one AlignFrames viewing a particular av. This * * @param av * @return alignFrame for av */ public static AlignFrame getAlignFrameFor(AlignViewport av) { if (desktop != null) { AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { if (aps[panel] != null && aps[panel].av == av) { 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; // todo: changesupport handlers need to be transferred if (discoverer == null) { discoverer = new jalview.ws.jws1.Discoverer(); // register PCS handler for desktop. discoverer.addPropertyChangeListener(changeSupport); } if (Cache.getDefault("SHOW_JWS1_SERVICES", true)) { (t0 = new Thread(discoverer)).start(); } try { if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) { // EnfinEnvision web service menu entries are rebuild every time the // menu is shown, so no changeSupport events are needed. jalview.ws.EnfinEnvision2OneWay.getInstance(); (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance())) .start(); } } catch (Exception e) { Cache.log .info( "Exception when trying to launch Envision2 workflow discovery.", e); Cache.log.info(e.getStackTrace()); } if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { jalview.ws.jws2.Jws2Discoverer.getDiscoverer() .addPropertyChangeListener(changeSupport); (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer())) .start(); } if (blocking) { while (alive) { try { Thread.sleep(15); } catch (Exception e) { } alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t0 != null && t0.isAlive()); } } } /** * 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) { new Thread(new Runnable() { public void run() { try { jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { JOptionPane .showInternalMessageDialog( Desktop.desktop, "Unixers: Couldn't find default web browser." + "\nAdd the full path to your browser in Preferences.", "Web browser not found", JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } }).start(); } public static WsParamSetManager wsparamManager = null; public static ParamManager getUserParameterStore() { if (wsparamManager==null) { wsparamManager = new WsParamSetManager(); } return wsparamManager; } }