X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=b35495fe88c7acd2c54945f604e93373ea8990ab;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=45a03faf204715afdcb1c8d435983cf971acf0fb;hpb=cca1d315fd19ddcc7c67a5aba91dafa98be097cf;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
old mode 100755
new mode 100644
index 45a03fa..3f3950c
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,889 +1,2900 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import jalview.io.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
-import java.util.*;
-
-import javax.swing.*;
-
+import jalview.bin.Cache;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.ws.params.ParamManager;
+
+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.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.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Semaphore;
+
+import javax.swing.DefaultDesktopManager;
+import javax.swing.DesktopManager;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JProgressBar;
+import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkEvent.EventType;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
 
 /**
- * DOCUMENT ME!
- *
+ * Jalview Desktop
+ * 
+ * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.155 $
  */
-public class Desktop extends jalview.jbgui.GDesktop
-    implements DropTargetListener, ClipboardOwner
+public class Desktop extends jalview.jbgui.GDesktop implements
+        DropTargetListener, ClipboardOwner, IProgressIndicator,
+        jalview.api.StructureSelectionManagerProvider
 {
-    /** DOCUMENT ME!! */
-    public static Desktop instance;
-    public static JDesktopPane desktop;
-    static int openFrameCount = 0;
-    static final int xOffset = 30;
-    static final int yOffset = 30;
-    public static jalview.ws.Discoverer discoverer;
-
-    public static Object [] jalviewClipboard;
-    public static boolean internalCopy = false;
 
-    static int fileLoadingCount= 0;
+  private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
-    /**
-     * Creates a new Desktop object.
-     */
-    public Desktop()
-    {
-        instance = this;
-        doVamsasClientCheck();
-        Image image = null;
+  /**
+   * news reader - null if it was never started.
+   */
+  private BlogReader jvnews = null;
 
-        try
-        {
-            java.net.URL url = getClass().getResource("/images/logo.gif");
+  private File projectFile;
 
-            if (url != null)
-            {
-                image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+  /**
+   * @param listener
+   * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+   */
+  public void addJalviewPropertyChangeListener(
+          PropertyChangeListener listener)
+  {
+    changeSupport.addJalviewPropertyChangeListener(listener);
+  }
 
-                MediaTracker mt = new MediaTracker(this);
-                mt.addImage(image, 0);
-                mt.waitForID(0);
-                setIconImage(image);
-            }
-        }
-        catch (Exception ex)
-        {
-        }
+  /**
+   * @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);
+  }
 
-        setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
-        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-        desktop = new JDesktopPane();
-        desktop.setBackground(Color.white);
-        getContentPane().setLayout(new BorderLayout());
-        getContentPane().add(desktop, BorderLayout.CENTER);
-        desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+  /**
+   * @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);
+  }
 
-        // This line prevents Windows Look&Feel resizing all new windows to maximum
-        // if previous window was maximised
-        desktop.setDesktopManager(new DefaultDesktopManager());
+  /** Singleton Desktop instance */
+  public static Desktop instance;
 
-        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-        String x = jalview.bin.Cache.getProperty("SCREEN_X");
-        String y = jalview.bin.Cache.getProperty("SCREEN_Y");
-        String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
-        String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
+  public static MyDesktopPane desktop;
 
-        if ((x != null) && (y != null) && (width != null) && (height != null))
-        {
-            setBounds(Integer.parseInt(x), Integer.parseInt(y),
-                Integer.parseInt(width), Integer.parseInt(height));
-        }
-        else
-        {
-            setBounds((int) (screenSize.width - 900) / 2,
-                (int) (screenSize.height - 650) / 2, 900, 650);
-        }
+  static int openFrameCount = 0;
 
-        this.addWindowListener(new WindowAdapter()
-            {
-                public void windowClosing(WindowEvent evt)
-                {
-                    quit();
-                }
-            });
+  static final int xOffset = 30;
 
-        this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+  static final int yOffset = 30;
 
-        /////////Add a splashscreen on startup
-        /////////Add a splashscreen on startup
-        JInternalFrame frame = new JInternalFrame();
+  public static jalview.ws.jws1.Discoverer discoverer;
 
-        SplashScreen splash = new SplashScreen(frame, image);
-        frame.setContentPane(splash);
-        frame.setLayer(JLayeredPane.PALETTE_LAYER);
-        frame.setLocation((int) ((getWidth() - 750) / 2),
-            (int) ((getHeight() - 160) / 2));
+  public static Object[] jalviewClipboard;
 
-        addInternalFrame(frame, "", 750, 160, false);
+  public static boolean internalCopy = false;
 
-        discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
-    }
+  static int fileLoadingCount = 0;
 
-    private void doVamsasClientCheck() {
-      if (jalview.bin.Cache.vamsasJarsPresent()) {
-        VamsasMenu.setVisible(true);
-        vamsasLoad.setVisible(true);
-      }
+  class MyDesktopManager implements DesktopManager
+  {
 
-    }
+    private DesktopManager delegate;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @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)
+    public MyDesktopManager(DesktopManager delegate)
     {
-        addInternalFrame(frame, title, w, h, true);
+      this.delegate = delegate;
     }
 
-    /**
-     * 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)
+    public void activateFrame(JInternalFrame f)
     {
-
-      frame.setTitle(title);
-      if(frame.getWidth()<1 || frame.getHeight()<1)
+      try
       {
-        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"))
+        delegate.activateFrame(f);
+      } catch (NullPointerException npe)
       {
-        return;
+        Point p = getMousePosition();
+        instance.showPasteMenu(p.x, p.y);
       }
-
-
-        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();
-                }
-                ;
-            });
-
-        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)
+    public void beginDraggingFrame(JComponent f)
     {
-        Transferable t = evt.getTransferable();
-        java.util.List files = 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);
-            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);
-              java.io.File file = new java.io.File(uri);
-              files.add(file);
-            }
-          }
-        }
-        catch (Exception e)
-        {      }
-
-        if (files != null)
-        {
-          try
-          {
-            for (int i = 0; i < files.size(); i++)
-            {
-              String file = files.get(i).toString();
-              String protocol = FormatAdapter.FILE;
-              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)
-          {      }
-        }
+      delegate.beginDraggingFrame(f);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+    public void beginResizingFrame(JComponent f, int direction)
     {
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
-                    "LAST_DIRECTORY"),
-                new String[]
-                {
-                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-                    "jar"
-                },
-                new String[]
-                {
-                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-                }, 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);
-        }
+      delegate.beginResizingFrame(f, direction);
     }
 
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+    public void closeFrame(JInternalFrame f)
     {
-      // 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);
-        }
+      delegate.closeFrame(f);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+    public void deactivateFrame(JInternalFrame f)
     {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput(viewport);
-        Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+      delegate.deactivateFrame(f);
     }
 
-    /*
-     * Exit the program
-     */
-    public void quit()
+    public void deiconifyFrame(JInternalFrame f)
     {
-        jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
-        jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
-        jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
-        jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
-        System.exit(0);
+      delegate.deiconifyFrame(f);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void aboutMenuItem_actionPerformed(ActionEvent e)
+    public void dragFrame(JComponent f, int newX, int newY)
     {
-      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")))
+      if (newY < 0)
       {
-        message.append("\n\n!! Jalview version "
-                       + jalview.bin.Cache.getProperty("LATEST_VERSION")
-                       + " is available for download from http://www.jalview.org !!\n");
-
+        newY = 0;
       }
-
-      message.append( "\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
-            "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
-            "\nFor all issues relating to Jalview, email help@jalview.org" +
-            "\n\nIf  you use JalView, please cite:" +
-            "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
-            "\nBioinformatics,  2004 20;426-7.");
-
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-
-           message.toString(), "About Jalview",
-            JOptionPane.INFORMATION_MESSAGE);
+      delegate.dragFrame(f, newX, newY);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void documentationMenuItem_actionPerformed(ActionEvent e)
+    public void endDraggingFrame(JComponent f)
     {
-        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)
-        {     }
+      delegate.endDraggingFrame(f);
     }
 
-    public void closeAll_actionPerformed(ActionEvent e)
+    public void endResizingFrame(JComponent f)
     {
-      JInternalFrame [] frames = desktop.getAllFrames();
-      for(int i=0; i<frames.length; i++)
-      {
-        try{
-        frames[i].setClosed(true);
-      }catch(java.beans.PropertyVetoException ex){}
-      }
+      delegate.endResizingFrame(f);
     }
 
-    public void raiseRelated_actionPerformed(ActionEvent e)
+    public void iconifyFrame(JInternalFrame f)
     {
-      reorderAssociatedWindows(false, false);
+      delegate.iconifyFrame(f);
     }
 
-    public void minimizeAssociated_actionPerformed(ActionEvent e)
+    public void maximizeFrame(JInternalFrame f)
     {
-      reorderAssociatedWindows(true, false);
+      delegate.maximizeFrame(f);
     }
 
-    void closeAssociatedWindows()
+    public void minimizeFrame(JInternalFrame f)
     {
-      reorderAssociatedWindows(false, true);
+      delegate.minimizeFrame(f);
     }
 
-    void reorderAssociatedWindows(boolean minimize, boolean close)
+    public void openFrame(JInternalFrame f)
     {
-      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;
-
+      delegate.openFrame(f);
+    }
 
-      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();
-                }
-              }
+    public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+            int newHeight)
+    {
+      Rectangle b = desktop.getBounds();
+      if (newY < 0)
+      {
+        newY = 0;
+      }
+      delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+    }
 
-            }
-            catch (java.beans.PropertyVetoException ex)
-            {       }
-          }
-        }
+    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()
+  {
     /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
+     * 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.
      */
-    protected void preferences_actionPerformed(ActionEvent e)
+    instance = this;
+    doVamsasClientCheck();
+    doGroovyCheck();
+    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);
+    desktop = new MyDesktopPane(selmemusage);
+    showMemusage.setSelected(selmemusage);
+    desktop.setBackground(Color.white);
+    getContentPane().setLayout(new BorderLayout());
+    // alternate config - have scrollbars - see notes in JAL-153
+    // JScrollPane sp = new JScrollPane();
+    // sp.getViewport().setView(desktop);
+    // getContentPane().add(sp, BorderLayout.CENTER);
+    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)
     {
-        new Preferences();
+      setBounds(dims);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveState_actionPerformed(ActionEvent e)
+    else
     {
-        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();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-            new Jalview2XML().SaveState(choice);
-        }
+      Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+      setBounds((screenSize.width - 900) / 2,
+              (screenSize.height - 650) / 2, 900, 650);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadState_actionPerformed(ActionEvent e)
+    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);
+
+    this.addWindowListener(new WindowAdapter()
     {
-        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);
+      public void windowClosing(WindowEvent evt)
+      {
+        quit();
+      }
+    });
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+    MouseAdapter ma;
+    this.addMouseListener(ma = new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (SwingUtilities.isRightMouseButton(evt))
         {
-            String choice = chooser.getSelectedFile().getAbsolutePath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
-            new Jalview2XML().LoadJalviewAlign(choice);
+          showPasteMenu(evt.getX(), evt.getY());
         }
-    }
+      }
+    });
+    desktop.addMouseListener(ma);
 
-  /*  public void vamsasLoad_actionPerformed(ActionEvent e)
+    this.addFocusListener(new FocusListener()
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-          getProperty("LAST_DIRECTORY"));
 
-      chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle("Load Vamsas file");
-      chooser.setToolTipText("Import");
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        // TODO Auto-generated method stub
 
-      int value = chooser.showOpenDialog(this);
+      }
 
-      if (value == JalviewFileChooser.APPROVE_OPTION)
+      @Override
+      public void focusGained(FocusEvent e)
+      {
+        Cache.log.debug("Relaying windows after focus gain");
+        // make sure that we sort windows properly after we gain focus
+        instance.relayerWindows();
+      }
+    });
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    // Spawn a thread that shows the splashscreen
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
       {
-        jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
-        vs.load(
-            chooser.getSelectedFile().getAbsolutePath()
-            );
+        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();
+    // 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);
+              }
 
-    public void inputSequence_actionPerformed(ActionEvent e)
+            });
+  }
+
+  public void doConfigureStructurePrefs()
+  {
+    // configure services
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(this);
+    if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
     {
-      new SequenceFetcher(null);
+      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);
+    }
+  }
 
-    JPanel progressPanel;
-
-    public void startLoading(final String fileName)
+  public void checkForNews()
+  {
+    final Desktop me = this;
+    // Thread off the news reader, in case there are connection problems.
+    addDialogThread(new Runnable()
     {
-      if (fileLoadingCount == 0)
+      @Override
+      public void run()
       {
-        progressPanel = new JPanel(new BorderLayout());
-        JProgressBar progressBar = new JProgressBar();
-        progressBar.setIndeterminate(true);
+        Cache.log.debug("Starting news thread.");
 
-        progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
-                          BorderLayout.WEST);
+        jvnews = new BlogReader(me);
+        showNews.setVisible(true);
+        Cache.log.debug("Completed news thread.");
+      }
+    });
+  }
 
-        progressPanel.add(progressBar, BorderLayout.CENTER);
+  protected void showNews_actionPerformed(ActionEvent e)
+  {
+    showNews(showNews.isSelected());
+  }
 
-        instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+  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 instance = System.currentTimeMillis();
+            Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), instance);
+            jvnews.refreshNews();
+            Desktop.instance.setProgressBar(null, instance);
+            jvnews.showNews();
+          }
+        }).start();
       }
-      fileLoadingCount++;
-      validate();
     }
-
-    public void stopLoading()
+  }
+
+  /**
+   * 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))
     {
-      fileLoadingCount--;
-      if (fileLoadingCount < 1)
+      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)
       {
-        if(progressPanel!=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)
         {
-          this.getContentPane().remove(progressPanel);
-          progressPanel = null;
+          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;
         }
-        fileLoadingCount = 0;
+        jalview.bin.Cache.log.debug("Got last known dimensions for "
+                + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+                + " height:" + ih);
       }
-      validate();
+      // return dimensions for new instance
+      return new Rectangle(ix, iy, iw, ih);
     }
+    return null;
+  }
 
-    public static int getViewCount(String viewId)
+  private void doVamsasClientCheck()
+  {
+    if (jalview.bin.Cache.vamsasJarsPresent())
     {
-      int count = 0;
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-      for (int t = 0; t < frames.length; t++)
+      setupVamsasDisconnectedGui();
+      VamsasMenu.setVisible(true);
+      final Desktop us = this;
+      VamsasMenu.addMenuListener(new MenuListener()
       {
-        if (frames[t] instanceof AlignFrame)
+        // 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)
         {
-          AlignFrame af = (AlignFrame) frames[t];
-          for(int a=0; a<af.alignPanels.size(); a++)
+          if (refresh)
           {
-            if(viewId.equals(
-                ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )
-                )
-            count ++;
+            us.buildVamsasStMenu();
+            refresh = false;
           }
         }
+      });
+      vamsasStart.setVisible(true);
+    }
+  }
+
+  void showPasteMenu(int x, int y)
+  {
+    JPopupMenu popup = new JPopupMenu();
+    JMenuItem item = new JMenuItem(
+            MessageManager.getString("label.paste_new_window"));
+    item.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent evt)
+      {
+        paste();
       }
+    });
 
-      return count;
-    }
+    popup.add(item);
+    popup.show(this, x, y);
+  }
 
-    public void explodeViews(AlignFrame af)
+  public void paste()
+  {
+    try
     {
-      int size = af.alignPanels.size();
-      if(size<2)
-        return;
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
 
-      for(int i=0; i<size; i++)
+      if (contents != null)
       {
-        AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
-        AlignFrame newaf = new AlignFrame(ap);
-        if(ap.av.explodedPosition!=null)
-          newaf.setBounds(ap.av.explodedPosition);
+        String file = (String) contents
+                .getTransferData(DataFlavor.stringFlavor);
+
+        String format = new IdentifyFile().Identify(file,
+                FormatAdapter.PASTE);
 
-        ap.av.gatherViewsHere = false;
+        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
 
-        addInternalFrame(newaf, af.getTitle(),
-                         AlignFrame.DEFAULT_WIDTH,
-                         AlignFrame.DEFAULT_HEIGHT);
       }
+    } 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);
+  }
+
+
+  /**
+   * 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);
+  }
+
+  /**
+   * 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);
+  }
+
+  /**
+   * 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
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, boolean makeVisible,
+          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 (instance == null
+            || (System.getProperty("java.awt.headless") != null && System
+                    .getProperty("java.awt.headless").equals("true")))
+    {
+      return;
+    }
 
-      af.alignPanels.clear();
-      af.closeMenuItem_actionPerformed(true);
+    openFrameCount++;
 
-    }
+    frame.setVisible(makeVisible);
+    frame.setClosable(true);
+    frame.setResizable(resizable);
+    frame.setMaximizable(resizable);
+    frame.setIconifiable(resizable);
+    frame.setFrameIcon(null);
 
-    public void gatherViews(AlignFrame source)
+    if (frame.getX() < 1 && frame.getY() < 1)
     {
-      source.viewport.gatherViewsHere = true;
-      source.viewport.explodedPosition = source.getBounds();
-      JInternalFrame[] frames = desktop.getAllFrames();
-      String viewId = source.viewport.sequenceSetID;
+      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)
+        {
+
+        }
+      }
+    });
+    menuItem.addMouseListener(new MouseListener()
+    {
+
+      @Override
+      public void mouseReleased(MouseEvent e)
+      {
+      }
+
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+      }
+
+      @Override
+      public void mouseExited(MouseEvent e)
+      {
+        try
+        {
+          frame.setSelected(false);
+        } catch (PropertyVetoException e1)
+        {
+        }
+      }
+
+      @Override
+      public void mouseEntered(MouseEvent e)
+      {
+        try
+        {
+          frame.setSelected(true);
+        } catch (PropertyVetoException e1)
+        {
+        }
+      }
+
+      @Override
+      public void mouseClicked(MouseEvent e)
+      {
+
+      }
+    });
+
+    windowMenu.add(menuItem);
+
+    desktop.add(frame);
+    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);
+    }
+  }
+
+  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)
+  {
+    boolean success = true;
+    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)
+    {
+      success = false;
+    }
+
+    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)
+      {
+        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!
+   */
+  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(MessageManager
+            .getString("label.open_local_file"));
+    chooser.setToolTipText(MessageManager.getString("action.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() != null
+              && 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(
+            MessageManager.getString("label.input_file_url"));
+    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,
+            MessageManager.getString("label.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,
+                MessageManager.formatMessage("label.couldnt_locate", new String[]{url}), MessageManager.getString("label.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,
+            MessageManager.getString("label.cut_paste_alignmen_file"),
+            true, 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();
+    }
+    if (jvnews != null)
+    {
+      storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+
+    }
+    if (dialogExecutor != null)
+    {
+      dialogExecutor.shutdownNow();
+    }
+
+    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 = getAboutMessage(false);
+    // JOptionPane.showInternalMessageDialog(Desktop.desktop,
+    //
+    // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+    new Thread(new Runnable()
+    {
+      public void run()
+      {
+        new SplashScreen(true);
+      }
+    }).start();
+  }
+
+  public StringBuffer getAboutMessage(boolean shortv)
+  {
+    StringBuffer message = new StringBuffer();
+    message.append("<html>");
+    if (shortv)
+    {
+      message.append("<h1><strong>Version: "
+              + jalview.bin.Cache.getProperty("VERSION")
+              + "</strong></h1>");
+      message.append("<strong>Last Updated: <em>"
+              + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+              + "</em></strong>");
+
+    }
+    else
+    {
+
+      message.append("<strong>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("<br>...Checking latest version...</br>");
+    }
+    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("<div style=\"color: #FF0000;font-style: bold;\">");
+      }
+
+      message.append("<br>!! 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("</div>");
+      }
+    }
+    message.append("<br>Authors:  "
+            + jalview.bin.Cache
+                    .getDefault(
+                            "AUTHORFNAMES",
+                            "The Jalview Authors (See AUTHORS file for current list)")
+            + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+            + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+            + "<br><br>If  you use Jalview, please cite:"
+            + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+            + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+            + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
+            + "</html>");
+    return message;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void documentationMenuItem_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      Help.showHelpWindow();
+    } 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[]
+            { "jvp" }, new String[]
+            { "Jalview Project" }, "Jalview Project");
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      final Desktop me = this;
+      final java.io.File choice = chooser.getSelectedFile();
+      setProjectFile(choice);
+
+      // TODO or move inside the new Thread?
+      saveChimeraSessions(choice.getAbsolutePath());
+
+      new Thread(new Runnable()
+      {
+        public void run()
+        {
+
+          setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new String[]{choice.getName()}),
+                  choice.hashCode());
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                  choice.getParent());
+          // TODO catch and handle errors for savestate
+          // TODO prevent user from messing with the Desktop whilst we're saving
+          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(
+                    me,
+                    MessageManager.formatMessage("label.error_whilst_saving_current_state_to", new String[]{ choice.getName()}),
+                    MessageManager.getString("label.couldnt_save_project"),
+                    JOptionPane.WARNING_MESSAGE);
+          }
+          setProgressBar(null, choice.hashCode());
+        }
+      }).start();
+    }
+  }
+
+  /**
+   * Request any open, linked Chimera sessions to save their state.
+   * 
+   * @param jalviewProjectFilename
+   *          the filename of the Jalview project; Chimera session files should
+   *          be given distinct, but obviously related, names.
+   */
+  public void saveChimeraSessions(String jalviewProjectFilename)
+  {
+    int i = 0;
+    for (JInternalFrame frame : getAllFrames())
+    {
+      if (frame instanceof ChimeraViewFrame)
+      {
+        /*
+         * Construct a filename for the Chimera session by append _chimera<n>.py
+         * to the Jalview project file name.
+         */
+        String chimeraPath = jalviewProjectFilename + "_chimera_" + i
+                + ".py";
+        ((ChimeraViewFrame) frame).saveSession(chimeraPath);
+        i++;
+      }
+    }
+  }
+
+  private void setProjectFile(File choice)
+  {
+    this.projectFile = choice;
+  }
+
+  public File getProjectFile()
+  {
+    return this.projectFile;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void loadState_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            { "jvp", "jar" }, new String[]
+            { "Jalview Project", "Jalview Project (old)" },
+            "Jalview Project");
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      final File selectedFile = chooser.getSelectedFile();
+      setProjectFile(selectedFile);
+      final String choice = selectedFile.getAbsolutePath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+      new Thread(new Runnable()
+      {
+        public void run()
+        {
+          setProgressBar(MessageManager.formatMessage("label.loading_jalview_project", new String[]{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,
+            		MessageManager.formatMessage("label.error_whilst_loading_project_from", new String[]{choice}),
+                    MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE);
+          }
+          setProgressBar(null, choice.hashCode());
+        }
+      }).start();
+    }
+  }
+
+  public void inputSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(this);
+  }
+
+  JPanel progressPanel;
+
+  ArrayList<JPanel> fileLoadingPanels = new ArrayList<JPanel>();
+
+  public void startLoading(final String fileName)
+  {
+    if (fileLoadingCount == 0)
+    {
+      fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName})));
+    }
+    fileLoadingCount++;
+  }
+
+  private JPanel addProgressPanel(String string)
+  {
+    if (progressPanel == null)
+    {
+      progressPanel = new JPanel(new GridLayout(1, 1));
+      totalProgressCount = 0;
+      instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+    }
+    JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
+    JProgressBar progressBar = new JProgressBar();
+    progressBar.setIndeterminate(true);
+
+    thisprogress.add(new JLabel(string), BorderLayout.WEST);
+
+    thisprogress.add(progressBar, BorderLayout.CENTER);
+    progressPanel.add(thisprogress);
+    ((GridLayout) progressPanel.getLayout())
+            .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
+    ++totalProgressCount;
+    instance.validate();
+    return thisprogress;
+  }
+
+  int totalProgressCount = 0;
+
+  private void removeProgressPanel(JPanel progbar)
+  {
+    if (progressPanel != null)
+    {
+      synchronized (progressPanel)
+      {
+        progressPanel.remove(progbar);
+        GridLayout gl = (GridLayout) progressPanel.getLayout();
+        gl.setRows(gl.getRows() - 1);
+        if (--totalProgressCount < 1)
+        {
+          this.getContentPane().remove(progressPanel);
+          progressPanel = null;
+        }
+      }
+    }
+    validate();
+  }
+
+  public void stopLoading()
+  {
+    fileLoadingCount--;
+    if (fileLoadingCount < 1)
+    {
+      while (fileLoadingPanels.size() > 0)
+      {
+        removeProgressPanel(fileLoadingPanels.remove(0));
+      }
+      fileLoadingPanels.clear();
+      fileLoadingCount = 0;
+    }
+    validate();
+  }
+
+  public static int getViewCount(String alignmentId)
+  {
+    AlignViewport[] aps = getViewports(alignmentId);
+    return (aps == null) ? 0 : aps.length;
+  }
+
+  /**
+   * 
+   * @param alignmentId
+   * @return all AlignmentPanels concerning the alignmentId sequence set
+   */
+  public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
+  {
+    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 (alignmentId.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 && frames[t] != source)
+        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.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 = (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(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()))
+        {
+          JOptionPane
+                  .showInternalMessageDialog(
+                          Desktop.desktop,
+                          MessageManager.formatMessage(
+                                  "label.couldnt_import_as_vamsas_session",
+                                  new String[]
+                                  { fle }),
+                          MessageManager
+                                  .getString("label.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(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{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 String[]{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 String[]{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());
+  }
+
+  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"));
+  }
+
+  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++)
         {
-          AlignFrame af = (AlignFrame) frames[t];
-          boolean gatherThis = false;
-          for (int a = 0; a < af.alignPanels.size(); a++)
+          JMenuItem sessit = new JMenuItem();
+          sessit.setText(sess[i]);
+          sessit.setToolTipText(MessageManager.formatMessage(
+                  "label.connect_to_session", new String[]
+                  { sess[i] }));
+          final Desktop dsktp = this;
+          final String mysesid = sess[i];
+          sessit.addActionListener(new ActionListener()
           {
-            AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
-            if (viewId.equals(ap.av.getSequenceSetId()))
+
+            public void actionPerformed(ActionEvent e)
             {
-              gatherThis = true;
-              ap.av.gatherViewsHere = false;
-              ap.av.explodedPosition = af.getBounds();
-              source.addAlignmentPanel(ap, false);
-            }
-          }
+              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(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 String[]{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);
+        }
+      }
+    }
+  }
+
+  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)
+  {
+    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(MessageManager.getString("label.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);
 
-          if (gatherThis)
+          percentUsage = (totalFreeMemory / maxMemory) * 100;
+
+          // if (percentUsage < 20)
           {
-            af.alignPanels.clear();
-            af.closeMenuItem_actionPerformed(true);
+            // 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(MessageManager.formatMessage(
+                  "label.memory_stats",
+                  new String[]
+                  { df.format(totalFreeMemory), df.format(maxMemory),
+                      df.format(percentUsage) }), 10,
+                  getHeight() - fm.getHeight());
+        }
+      }
+    }
+  }
+
+  /**
+   * fixes stacking order after a modal dialog to ensure windows that should be
+   * on top actually are
+   */
+  public void relayerWindows()
+  {
+
+  }
+
+  protected JMenuItem groovyShell;
+
+  public void doGroovyCheck()
+  {
+    if (jalview.bin.Cache.groovyJarsPresent())
+    {
+      groovyShell = new JMenuItem();
+      groovyShell.setText(MessageManager.getString("label.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;
+  }
+
+  public GStructureViewer[] getJmols()
+  {
+    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 AppJmol)
+        {
+          GStructureViewer af = (GStructureViewer) frames[i];
+          avp.addElement(af);
+        }
+      }
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+    if (avp.size() == 0)
+    {
+      return null;
+    }
+    GStructureViewer afs[] = new GStructureViewer[avp.size()];
+    for (int i = 0, j = avp.size(); i < j; i++)
+    {
+      afs[i] = (GStructureViewer) 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(MessageManager.getString("error.implementation_error_cannot_create_groovyshell"));
+    }
+    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,
+
+                      MessageManager.getString("label.couldnt_create_groovy_shell"),
+                      MessageManager.getString("label.groovy_support_failed"),
+                      JOptionPane.ERROR_MESSAGE);
+    }
+  }
+
+  /**
+   * Progress bars managed by the IProgressIndicator method.
+   */
+  private Hashtable<Long, JPanel> progressBars;
+
+  private Hashtable<Long, IProgressIndicatorHandler> 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<Long, JPanel>();
+      progressBarHandlers = new Hashtable<Long, IProgressIndicatorHandler>();
+    }
 
+    if (progressBars.get(new Long(id)) != null)
+    {
+      JPanel progressPanel = 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(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()
+      {
 
-    jalview.gui.VamsasClient v_client=null;
-    public void vamsasLoad_actionPerformed(ActionEvent e)
+        public void actionPerformed(ActionEvent e)
+        {
+          handler.cancelActivity(id);
+          us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((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 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;
+    // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
+    if (true)
     {
-      if (v_client==null) {
-        // Start a session.
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-            getProperty("LAST_DIRECTORY"));
+      // todo: changesupport handlers need to be transferred
+      if (discoverer == null)
+      {
+        discoverer = new jalview.ws.jws1.Discoverer();
+        // register PCS handler for desktop.
+        discoverer.addPropertyChangeListener(changeSupport);
+      }
+      // JAL-940 - disabled JWS1 service configuration - always start discoverer
+      // until we phase out completely
+      (t0 = new Thread(discoverer)).start();
+    }
 
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Load Vamsas file");
-        chooser.setToolTipText("Import");
+    // ENFIN services are EOLed as of Jalview 2.8.1 release
+    if (false)
+    {
+      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());
+      }
+    }
 
-        int value = chooser.showOpenDialog(this);
+    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    {
+      if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
+      {
+        jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
+      }
+      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
+              changeSupport);
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+    }
+    Thread t3 = null;
+    {
+      // TODO: do rest service discovery
+    }
+    if (blocking)
+    {
+      while (alive)
+      {
+        try
+        {
+          Thread.sleep(15);
+        } catch (Exception e)
         {
-          v_client = new jalview.gui.VamsasClient(this,
-              chooser.getSelectedFile());
-          this.vamsasLoad.setText("Session Update");
-          this.vamsasStop.setVisible(true);
-          v_client.initial_update();
-          v_client.startWatcher();
         }
-      } else {
-        // store current data in session.
-        v_client.push_update();
+        alive = (t1 != null && t1.isAlive())
+                || (t2 != null && t2.isAlive())
+                || (t3 != null && t3.isAlive())
+                || (t0 != null && t0.isAlive());
       }
     }
-    public void vamsasStop_actionPerformed(ActionEvent e) {
-      if (v_client!=null) {
-        v_client.end_session();
-        v_client=null;
-        this.vamsasStop.setVisible(false);
-        this.vamsasLoad.setText("Start Vamsas Session...");
+  }
+
+  /**
+   * called to check if the service discovery process completed successfully.
+   * 
+   * @param evt
+   */
+  protected void JalviewServicesChanged(PropertyChangeEvent evt)
+  {
+    if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+    {
+      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+              .getErrorMessages();
+      if (ermsg != null)
+      {
+        if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
+        {
+          if (serviceChangedDialog == null)
+          {
+            // only run if we aren't already displaying one of these.
+            addDialogThread(serviceChangedDialog = new Runnable()
+            {
+              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("<html><table width=\"450\"><tr><td>" + ermsg +
+                 * "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
+                 * + " or mis-configured HTTP proxy settings.<br/>" +
+                 * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
+                 * +
+                 * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
+                 * ), true, true, "Web Service Configuration Problem", 450,
+                 * 400);
+                 * 
+                 * jd.waitForInput();
+                 */
+                JOptionPane
+                        .showConfirmDialog(
+                                Desktop.desktop,
+                                new JLabel(
+                                        "<html><table width=\"450\"><tr><td>"
+                                                + ermsg
+                                                + "</td></tr></table>"
+                                                + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+                                                + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+                                                + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+                                                + " Tools->Preferences dialog box to change them.</p></html>"),
+                                "Web Service Configuration Problem",
+                                JOptionPane.DEFAULT_OPTION,
+                                JOptionPane.ERROR_MESSAGE);
+                serviceChangedDialog = null;
+
+              }
+            });
+          }
+        }
+        else
+        {
+          Cache.log
+                  .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+                          + ermsg);
+        }
       }
     }
-    /**
-     * 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"));
-      vamsasLoad.setVisible(!b);
-      vamsasStop.setVisible(!b);
+  }
+
+  private Runnable serviceChangedDialog = null;
+
+  /**
+   * start a thread to open a URL in the configured browser. Pops up a warning
+   * dialog to the user if there is an exception when calling out to the browser
+   * to open the URL.
+   * 
+   * @param url
+   */
+  public static void showUrl(final String url)
+  {
+    showUrl(url, Desktop.instance);
+  }
+
+  /**
+   * 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()
+    {
+      public void run()
+      {
+        try
+        {
+          if (progress != null)
+          {
+            progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new String[]{url}), this.hashCode());
+          }
+          jalview.util.BrowserLauncher.openURL(url);
+        } catch (Exception ex)
+        {
+          JOptionPane
+                  .showInternalMessageDialog(
+                          Desktop.desktop,
+                          MessageManager.getString("label.web_browser_not_found_unix"),
+                          MessageManager.getString("label.web_browser_not_found"),
+                          JOptionPane.WARNING_MESSAGE);
+
+          ex.printStackTrace();
+        }
+        if (progress != null)
+        {
+          progress.setProgressBar(null, this.hashCode());
+        }
+      }
+    }).start();
+  }
 
+  public static WsParamSetManager wsparamManager = null;
+
+  public static ParamManager getUserParameterStore()
+  {
+    if (wsparamManager == null)
+    {
+      wsparamManager = new WsParamSetManager();
     }
+    return wsparamManager;
+  }
+
+  /**
+   * static hyperlink handler proxy method for use by Jalview's internal windows
+   * 
+   * @param e
+   */
+  public static void hyperlinkUpdate(HyperlinkEvent e)
+  {
+    if (e.getEventType() == EventType.ACTIVATED)
+    {
+      String url = null;
+      try
+      {
+        url = e.getURL().toString();
+        Desktop.showUrl(url);
+      } catch (Exception x)
+      {
+        if (url != null)
+        {
+          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
+   */
+  private volatile boolean dialogPause = true;
+
+  /**
+   * pause the queue
+   */
+  private java.util.concurrent.Semaphore block = new Semaphore(0);
+
+  /**
+   * add another dialog thread to the queue
+   * 
+   * @param prompter
+   */
+  public void addDialogThread(final Runnable prompter)
+  {
+    dialogExecutor.submit(new Runnable()
+    {
+      public void run()
+      {
+        if (dialogPause)
+        {
+          try
+          {
+            block.acquire();
+          } catch (InterruptedException x)
+          {
+          }
+          ;
+        }
+        if (instance == null)
+        {
+          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();
+  }
+  @Override
+  protected void snapShotWindow_actionPerformed(ActionEvent e)
+  {
+    invalidate();
+    File of;
+    ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
+            "View of Desktop", getWidth(), getHeight(), of = new File(
+                    "Jalview_snapshot" + System.currentTimeMillis()
+                            + ".eps"), "View of desktop");
+    try {
+      paintAll(im.getGraphics());
+      im.writeImage();
+    } catch (Exception q)
+    {
+      Cache.log.error("Couldn't write snapshot to "+of.getAbsolutePath(),q);
+      return;
+    }
+    Cache.log.info("Successfully written snapshot to file "+of.getAbsolutePath());
+  }
 }
-