X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=6910f280a01abe4a38249c4ceaf7a08179bba7d5;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=fca0accbe61c5a69c438cbbae5ef0c4bfa52eead;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index fca0acc..6910f28 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,382 +1,2246 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* 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.
-*
-* 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
-*/
-
-package jalview.gui;
-
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.datamodel.*;
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.dnd.*;
-import javax.swing.*;
-import java.awt.datatransfer.*;
-import jalview.bin.Cache;
-
-
-public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
-{
-  public static JDesktopPane desktop;
-  static int openFrameCount = 0;
-  static final int xOffset = 30, yOffset = 30;
-
-  public Desktop()
-  {
-    Image image =null;
-    try{
-      java.net.URL url = getClass().getResource("/images/logo.gif");
-      if(url!=null)
-      {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        mt.waitForID(0);
-        setIconImage(image);
-      }
-
-    }catch(Exception ex){}
-
-    setTitle("Jalview 2005");
-    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    desktop = new JDesktopPane();
-    desktop.setBackground(Color.white);
-    setContentPane(desktop);
-    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 DefaultDesktopManager() );
-
-
-    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");
-
-    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);
-
-this.addWindowListener(new WindowAdapter()
-{
-public void windowClosing(WindowEvent evt)
-{
- 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() + "");
-}
-});
-setVisible(true);
-
-this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
-
-/////////Add a splashscreen on startup
-   /////////Add a splashscreen on startup
-    JInternalFrame frame = new JInternalFrame();
-
-    SplashScreen splash = new SplashScreen(frame, image);
-    frame.setContentPane(splash);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    addInternalFrame(frame, "", 750,160, false);
-    frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
-  }
-  public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
-  {
-    addInternalFrame(frame, title, w, h, true);
-  }
-
-  public static void addInternalFrame(final JInternalFrame frame, String title,
-                                      int w,
-                                      int h,
-                                      boolean resizable )
-  {
-   desktop.add(frame);
-   openFrameCount++;
-   try {
-       frame.setSelected(true);
-   } catch (java.beans.PropertyVetoException e) {}
-   frame.setTitle(title);
-   frame.setSize(w,h);
-   frame.setClosable(true);
-   frame.setResizable(resizable);
-   frame.setMaximizable(resizable);
-   frame.setIconifiable(resizable);
-   frame.setFrameIcon(null);
-   frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
-   frame.toFront();
-   final JMenuItem menuItem = new JMenuItem(title);
-   frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-   {
-     public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-     {
-       openFrameCount--;
-       windowMenu.remove(menuItem);
-     };
-   });
-
-   menuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        try{  frame.setSelected(true);   frame.setIcon(false); }
-        catch(java.beans.PropertyVetoException ex){};
-      }
-    });
-
-   frame.setVisible(true);
-   windowMenu.add(menuItem);
- }
-
- public void dragEnter(DropTargetDragEvent evt){}
- public void dragExit(DropTargetEvent evt){}
- public void dragOver(DropTargetDragEvent evt){}
- public void dropActionChanged(DropTargetDragEvent evt){}
- public void drop(DropTargetDropEvent evt)
-{
-   Transferable t = evt.getTransferable();
-   if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
-     return;
-
-   evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-   try{
-     java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
-
-     for (int i = 0; i < files.size(); i++)
-     {
-       String file = files.get(i).toString();
-       String protocol = "File";
-       if(file.endsWith(".jar"))
-                Jalview2XML.LoadJalviewAlign(file);
-      else
-      {
-        String format = jalview.io.IdentifyFile.Identify(file, protocol);
-        LoadFile(file, protocol, format);
-      }
-     }
-
-   }catch(Exception ex){ex.printStackTrace();}
-  }
-
-
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
- {
-   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());
-     if(chooser.getSelectedFormat().equals("Jalview"))
-     {
-       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");
-       Jalview2XML.LoadJalviewAlign(choice);
-     }
-     else
-     {
-       String format = IdentifyFile.Identify(choice, "File");
-       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
-       LoadFile(choice, "File", format);
-     }
-   }
- }
-
- public void LoadFile(String file, String protocol,  String format)
- {
-   LoadingThread loader = new LoadingThread(file, protocol, format);
-   loader.start();
- }
-
- class LoadingThread extends Thread
- {
-   String file, protocol, format;
-
-   public LoadingThread(String file, String protocol,  String format)
-   {
-     this.file = file;
-     this.protocol = protocol;
-     this.format = format;
-   }
-   public void run()
-   {
-     SequenceI [] sequences = null;
-
-     if (FormatAdapter.formats.contains(format))
-         sequences = FormatAdapter.readFile(file, protocol, format);
-
-     if (sequences != null && sequences.length>0)
-     {
-       AlignFrame af = new AlignFrame(new Alignment(sequences));
-       addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
-       af.currentFileFormat = format;
-       af.statusBar.setText("Successfully loaded file " + file);
-       try{
-           af.setMaximum(Preferences.showFullscreen);
-       }catch(Exception ex){}
-
-     }
-     else
-       JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"
-                            + "Formats currently supported are\n"
-                            + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
-                            ,"Error loading file",
-                                     JOptionPane.WARNING_MESSAGE);
-
-   }
- }
-
-
- public void inputURLMenuItem_actionPerformed(ActionEvent e)
- {
-   String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
-                                            "Input alignment from URL",
-                                            JOptionPane.QUESTION_MESSAGE,
-                                            null, null,
-                                            "http://www.").toString();
-   if (url == null)
-     return;
-
-   String format = IdentifyFile.Identify(url, "URL");
-
-   if (format.equals("URL NOT FOUND"))
-   {
-     JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
-                                   "URL not found",
-                                   JOptionPane.WARNING_MESSAGE);
-     return;
-   }
-
-    LoadFile(url, "URL", format);
- }
-
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
- {
-   CutAndPasteTransfer cap = new CutAndPasteTransfer();
-   cap.setForInput();
-   Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
- }
-
-/*
-* Exit the program
-*/
- public void quit_actionPerformed(ActionEvent e)
- {
-   if(jalview.bin.Jalview.applet!=null)
-     jalview.bin.Jalview.applet.destroy();
-    else
-      System.exit(0);
- }
-
-
-
- public void aboutMenuItem_actionPerformed(ActionEvent e)
- {
-   JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                         "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE
-                                       +"\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 12;426-7.",
-                                         "About Jalview",
-                                         JOptionPane.INFORMATION_MESSAGE);
- }
-
- public void documentationMenuItem_actionPerformed(ActionEvent e)
- {
-   try
-   {
-      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-      java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
-      javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
-
-      javax.help.HelpBroker hb = hs.createHelpBroker();
-      hb.setLocation(new Point(200, 50));
-      hb.setSize(new Dimension(800,700));
-      hb.setCurrentID("home");
-      hb.setDisplayed(true);
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
- }
-
- protected void preferences_actionPerformed(ActionEvent e)
- {
-   Preferences pref = new Preferences();
- }
-
- public void saveState_actionPerformed(ActionEvent e)
- {
-   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-       getProperty("LAST_DIRECTORY"),
-       new String[]
-       {"jar"}, new String[]{"Jalview Project"}, "Jalview Project");
-
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Save State");
-   int value = chooser.showSaveDialog(this);
-   if (value == JalviewFileChooser.APPROVE_OPTION)
-   {
-     java.io.File choice = chooser.getSelectedFile();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-     Jalview2XML.SaveState(choice);
-   }
-
- }
-
-
- public void loadState_actionPerformed(ActionEvent e)
- {
-   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-       new String[]{"jar"}, new String[]{"Jalview Project"}, "Jalview Project");
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Restore state");
-   int value = chooser.showOpenDialog(this);
-   if(value == JalviewFileChooser.APPROVE_OPTION)
-   {
-     String choice =  chooser.getSelectedFile().getAbsolutePath();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
-     Jalview2XML.LoadJalviewAlign(choice);
-   }
- }
-}
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import jalview.bin.Cache;
+import jalview.io.*;
+import jalview.ws.params.ParamManager;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import java.awt.event.*;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
+import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.net.URLConnection;
+import java.nio.channels.ReadableByteChannel;
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+/**
+ * Jalview Desktop
+ * 
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop extends jalview.jbgui.GDesktop implements
+        DropTargetListener, ClipboardOwner, IProgressIndicator
+{
+
+  private class JalviewChangeSupport implements PropertyChangeListener
+  {
+    public void propertyChange(PropertyChangeEvent evt)
+    {
+      // Handle change events - most are simply routed to other sources
+      changeSupport.firePropertyChange(evt);
+    }
+
+    /**
+     * change listeners are notified of changes to resources so they can update
+     * their state. E.g. - the 'services' property notifies when the available
+     * set of web service endpoints have changed.
+     */
+    private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+            this);
+
+    /**
+     * @param propertyName
+     * @param listener
+     * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.lang.String,
+     *      java.beans.PropertyChangeListener)
+     */
+    public void addJalviewPropertyChangeListener(String propertyName,
+            PropertyChangeListener listener)
+    {
+      changeSupport.addPropertyChangeListener(propertyName, listener);
+    }
+
+    /**
+     * @param listener
+     * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(
+     *      java.beans.PropertyChangeListener)
+     */
+    public void addJalviewPropertyChangeListener(
+            PropertyChangeListener listener)
+    {
+      changeSupport.addPropertyChangeListener(listener);
+    }
+
+    /*
+     * @param propertyName
+     * 
+     * @param oldValue
+     * 
+     * @param newValue
+     * 
+     * @see
+     * java.beans.PropertyChangeSupport#firePropertyChange(java.lang.String,
+     * java.lang.Object, java.lang.Object) public void firePropertyChange(String
+     * propertyName, Object oldValue, Object newValue) {
+     * changeSupport.firePropertyChange(propertyName, oldValue, newValue); }
+     */
+
+    /**
+     * @param propertyName
+     * @param listener
+     * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.lang.String,
+     *      java.beans.PropertyChangeListener)
+     */
+    public void removeJalviewPropertyChangeListener(String propertyName,
+            PropertyChangeListener listener)
+    {
+      changeSupport.removePropertyChangeListener(propertyName, listener);
+    }
+
+  }
+
+  private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
+
+  /**
+   * @param listener
+   * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+   */
+  public void addJalviewPropertyChangeListener(
+          PropertyChangeListener listener)
+  {
+    changeSupport.addJalviewPropertyChangeListener(listener);
+  }
+
+  /**
+   * @param propertyName
+   * @param listener
+   * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
+   *      java.beans.PropertyChangeListener)
+   */
+  public void addJalviewPropertyChangeListener(String propertyName,
+          PropertyChangeListener listener)
+  {
+    changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
+  }
+
+  /**
+   * @param propertyName
+   * @param listener
+   * @see jalview.gui.Desktop.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
+   *      java.beans.PropertyChangeListener)
+   */
+  public void removeJalviewPropertyChangeListener(String propertyName,
+          PropertyChangeListener listener)
+  {
+    changeSupport.removeJalviewPropertyChangeListener(propertyName,
+            listener);
+  }
+
+  /** Singleton Desktop instance */
+  public static Desktop instance;
+
+  public static MyDesktopPane desktop;
+
+  static int openFrameCount = 0;
+
+  static final int xOffset = 30;
+
+  static final int yOffset = 30;
+
+  public static jalview.ws.jws1.Discoverer discoverer;
+
+  public static Object[] jalviewClipboard;
+
+  public static boolean internalCopy = false;
+
+  static int fileLoadingCount = 0;
+
+  class MyDesktopManager implements DesktopManager
+  {
+
+    private DesktopManager delegate;
+
+    public MyDesktopManager(DesktopManager delegate)
+    {
+      this.delegate = delegate;
+    }
+
+    public void activateFrame(JInternalFrame f)
+    {
+      try
+      {
+        delegate.activateFrame(f);
+      } catch (NullPointerException npe)
+      {
+        Point p = getMousePosition();
+        instance.showPasteMenu(p.x, p.y);
+      }
+    }
+
+    public void beginDraggingFrame(JComponent f)
+    {
+      delegate.beginDraggingFrame(f);
+    }
+
+    public void beginResizingFrame(JComponent f, int direction)
+    {
+      delegate.beginResizingFrame(f, direction);
+    }
+
+    public void closeFrame(JInternalFrame f)
+    {
+      delegate.closeFrame(f);
+    }
+
+    public void deactivateFrame(JInternalFrame f)
+    {
+      delegate.deactivateFrame(f);
+    }
+
+    public void deiconifyFrame(JInternalFrame f)
+    {
+      delegate.deiconifyFrame(f);
+    }
+
+    public void dragFrame(JComponent f, int newX, int newY)
+    {
+      delegate.dragFrame(f, newX, newY);
+    }
+
+    public void endDraggingFrame(JComponent f)
+    {
+      delegate.endDraggingFrame(f);
+    }
+
+    public void endResizingFrame(JComponent f)
+    {
+      delegate.endResizingFrame(f);
+    }
+
+    public void iconifyFrame(JInternalFrame f)
+    {
+      delegate.iconifyFrame(f);
+    }
+
+    public void maximizeFrame(JInternalFrame f)
+    {
+      delegate.maximizeFrame(f);
+    }
+
+    public void minimizeFrame(JInternalFrame f)
+    {
+      delegate.minimizeFrame(f);
+    }
+
+    public void openFrame(JInternalFrame f)
+    {
+      delegate.openFrame(f);
+    }
+
+    public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+            int newHeight)
+    {
+      delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+    }
+
+    public void setBoundsForFrame(JComponent f, int newX, int newY,
+            int newWidth, int newHeight)
+    {
+      delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
+    }
+
+    // All other methods, simply delegate
+
+  }
+
+  /**
+   * Creates a new Desktop object.
+   */
+  public Desktop()
+  {
+    /**
+     * A note to implementors. It is ESSENTIAL that any activities that might
+     * block are spawned off as threads rather than waited for during this
+     * constructor.
+     */
+    instance = this;
+    doVamsasClientCheck();
+    doGroovyCheck();
+
+    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+    boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
+            false);
+    boolean showjconsole = jalview.bin.Cache.getDefault(
+            "SHOW_JAVA_CONSOLE", false);
+    desktop = new MyDesktopPane(selmemusage);
+    showMemusage.setSelected(selmemusage);
+    desktop.setBackground(Color.white);
+    getContentPane().setLayout(new BorderLayout());
+    getContentPane().add(desktop, BorderLayout.CENTER);
+    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
+    // This line prevents Windows Look&Feel resizing all new windows to maximum
+    // if previous window was maximised
+    desktop.setDesktopManager(new MyDesktopManager(
+            new DefaultDesktopManager()));
+    Rectangle dims = getLastKnownDimensions("");
+    if (dims != null)
+    {
+      setBounds(dims);
+    }
+    else
+    {
+      Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+      setBounds((int) (screenSize.width - 900) / 2,
+              (int) (screenSize.height - 650) / 2, 900, 650);
+    }
+    jconsole = new Console(this, showjconsole);
+    // add essential build information
+    jconsole.setHeader("Jalview Desktop "
+            + jalview.bin.Cache.getProperty("VERSION") + "\n"
+            + "Build Date: "
+            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+            + "Java version: " + System.getProperty("java.version") + "\n"
+            + System.getProperty("os.arch") + " "
+            + System.getProperty("os.name") + " "
+            + System.getProperty("os.version"));
+
+    showConsole(showjconsole);
+
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        quit();
+      }
+    });
+
+    this.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (SwingUtilities.isRightMouseButton(evt))
+        {
+          showPasteMenu(evt.getX(), evt.getY());
+        }
+      }
+    });
+
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    // Spawn a thread that shows the splashscreen
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        new SplashScreen();
+      }
+    });
+
+    // displayed.
+    // Thread off a new instance of the file chooser - this reduces the time it
+    // takes to open it later on.
+    new Thread(new Runnable()
+    {
+      public void run()
+      {
+        Cache.log.debug("Filechooser init thread started.");
+        JalviewFileChooser chooser = new JalviewFileChooser(
+                jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+                jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
+                jalview.io.AppletFormatAdapter.READABLE_FNAMES,
+                jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+        Cache.log.debug("Filechooser init thread finished.");
+      }
+    }).start();
+  }
+
+  /**
+   * recover the last known dimensions for a jalview window
+   * 
+   * @param windowName
+   *          - empty string is desktop, all other windows have unique prefix
+   * @return null or last known dimensions scaled to current geometry (if last
+   *         window geom was known)
+   */
+  Rectangle getLastKnownDimensions(String windowName)
+  {
+    // TODO: lock aspect ratio for scaling desktop Bug #0058199
+    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+    String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
+    String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
+    String width = jalview.bin.Cache.getProperty(windowName
+            + "SCREEN_WIDTH");
+    String height = jalview.bin.Cache.getProperty(windowName
+            + "SCREEN_HEIGHT");
+    if ((x != null) && (y != null) && (width != null) && (height != null))
+    {
+      int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
+              .parseInt(width), ih = Integer.parseInt(height);
+      if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+      {
+        // attempt #1 - try to cope with change in screen geometry - this
+        // version doesn't preserve original jv aspect ratio.
+        // take ratio of current screen size vs original screen size.
+        double sw = ((1f * screenSize.width) / (1f * Integer
+                .parseInt(jalview.bin.Cache
+                        .getProperty("SCREENGEOMETRY_WIDTH"))));
+        double sh = ((1f * screenSize.height) / (1f * Integer
+                .parseInt(jalview.bin.Cache
+                        .getProperty("SCREENGEOMETRY_HEIGHT"))));
+        // rescale the bounds depending upon the current screen geometry.
+        ix = (int) (ix * sw);
+        iw = (int) (iw * sw);
+        iy = (int) (iy * sh);
+        ih = (int) (ih * sh);
+        while (ix>=screenSize.width) {
+          jalview.bin.Cache.log.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+          ix-=screenSize.width;
+        }
+        while (iy>=screenSize.height) {
+          jalview.bin.Cache.log.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+                    iy-=screenSize.height;
+        }
+        jalview.bin.Cache.log.debug("Got last known dimensions for "
+                + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+                + " height:" + ih);
+      }
+      // return dimensions for new instance
+      return new Rectangle(ix, iy, iw, ih);
+    }
+    return null;
+  }
+
+  private void doVamsasClientCheck()
+  {
+    if (jalview.bin.Cache.vamsasJarsPresent())
+    {
+      setupVamsasDisconnectedGui();
+      VamsasMenu.setVisible(true);
+      final Desktop us = this;
+      VamsasMenu.addMenuListener(new MenuListener()
+      {
+        // this listener remembers when the menu was first selected, and
+        // doesn't rebuild the session list until it has been cleared and
+        // reselected again.
+        boolean refresh = true;
+
+        public void menuCanceled(MenuEvent e)
+        {
+          refresh = true;
+        }
+
+        public void menuDeselected(MenuEvent e)
+        {
+          refresh = true;
+        }
+
+        public void menuSelected(MenuEvent e)
+        {
+          if (refresh)
+          {
+            us.buildVamsasStMenu();
+            refresh = false;
+          }
+        }
+      });
+      vamsasStart.setVisible(true);
+    }
+  }
+
+  void showPasteMenu(int x, int y)
+  {
+    JPopupMenu popup = new JPopupMenu();
+    JMenuItem item = new JMenuItem("Paste To New Window");
+    item.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent evt)
+      {
+        paste();
+      }
+    });
+
+    popup.add(item);
+    popup.show(this, x, y);
+  }
+
+  public void paste()
+  {
+    try
+    {
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
+
+      if (contents != null)
+      {
+        String file = (String) contents
+                .getTransferData(DataFlavor.stringFlavor);
+
+        String format = new IdentifyFile().Identify(file,
+                FormatAdapter.PASTE);
+
+        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
+
+      }
+    } catch (Exception ex)
+    {
+      System.out
+              .println("Unable to paste alignment from system clipboard:\n"
+                      + ex);
+    }
+  }
+
+  /**
+   * Adds and opens the given frame to the desktop
+   * 
+   * @param frame
+   *          DOCUMENT ME!
+   * @param title
+   *          DOCUMENT ME!
+   * @param w
+   *          DOCUMENT ME!
+   * @param h
+   *          DOCUMENT ME!
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, int w, int h)
+  {
+    addInternalFrame(frame, title, w, h, true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param frame
+   *          DOCUMENT ME!
+   * @param title
+   *          DOCUMENT ME!
+   * @param w
+   *          DOCUMENT ME!
+   * @param h
+   *          DOCUMENT ME!
+   * @param resizable
+   *          DOCUMENT ME!
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, int w, int h,
+          boolean resizable)
+  {
+
+    // TODO: allow callers to determine X and Y position of frame (eg. via
+    // bounds object).
+    // TODO: consider fixing method to update entries in the window submenu with
+    // the current window title
+
+    frame.setTitle(title);
+    if (frame.getWidth() < 1 || frame.getHeight() < 1)
+    {
+      frame.setSize(w, h);
+    }
+    // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
+    // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
+    // IF JALVIEW IS RUNNING HEADLESS
+    // ///////////////////////////////////////////////
+    if (System.getProperty("java.awt.headless") != null
+            && System.getProperty("java.awt.headless").equals("true"))
+    {
+      return;
+    }
+
+    openFrameCount++;
+
+    frame.setVisible(true);
+    frame.setClosable(true);
+    frame.setResizable(resizable);
+    frame.setMaximizable(resizable);
+    frame.setIconifiable(resizable);
+    frame.setFrameIcon(null);
+
+    if (frame.getX() < 1 && frame.getY() < 1)
+    {
+      frame.setLocation(xOffset * openFrameCount, yOffset
+              * ((openFrameCount - 1) % 10) + yOffset);
+    }
+
+    final JMenuItem menuItem = new JMenuItem(title);
+    frame
+            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+              public void internalFrameActivated(
+                      javax.swing.event.InternalFrameEvent evt)
+              {
+                JInternalFrame itf = desktop.getSelectedFrame();
+                if (itf != null)
+                {
+                  itf.requestFocus();
+                }
+
+              }
+
+              public void internalFrameClosed(
+                      javax.swing.event.InternalFrameEvent evt)
+              {
+                PaintRefresher.RemoveComponent(frame);
+                openFrameCount--;
+                windowMenu.remove(menuItem);
+                JInternalFrame itf = desktop.getSelectedFrame();
+                if (itf != null)
+                {
+                  itf.requestFocus();
+                }
+                System.gc();
+              };
+            });
+
+    menuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          frame.setSelected(true);
+          frame.setIcon(false);
+        } catch (java.beans.PropertyVetoException ex)
+        {
+
+        }
+      }
+    });
+
+    windowMenu.add(menuItem);
+
+    desktop.add(frame);
+    frame.toFront();
+    try
+    {
+      frame.setSelected(true);
+      frame.requestFocus();
+    } catch (java.beans.PropertyVetoException ve)
+    {
+    }
+  }
+
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    if (!internalCopy)
+    {
+      Desktop.jalviewClipboard = null;
+    }
+
+    internalCopy = false;
+  }
+
+  public void dragEnter(DropTargetDragEvent evt)
+  {
+  }
+
+  public void dragExit(DropTargetEvent evt)
+  {
+  }
+
+  public void dragOver(DropTargetDragEvent evt)
+  {
+  }
+
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  public void drop(DropTargetDropEvent evt)
+  {
+    Transferable t = evt.getTransferable();
+    java.util.List files = null;
+    java.util.List protocols = null;
+
+    try
+    {
+      DataFlavor uriListFlavor = new DataFlavor(
+              "text/uri-list;class=java.lang.String");
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+      {
+        // Works on Windows and MacOSX
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        files = (java.util.List) t
+                .getTransferData(DataFlavor.javaFileListFlavor);
+      }
+      else if (t.isDataFlavorSupported(uriListFlavor))
+      {
+        // This is used by Unix drag system
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        String data = (String) t.getTransferData(uriListFlavor);
+        files = new java.util.ArrayList(1);
+        protocols = new java.util.ArrayList(1);
+        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+                data, "\r\n"); st.hasMoreTokens();)
+        {
+          String s = st.nextToken();
+          if (s.startsWith("#"))
+          {
+            // the line is a comment (as per the RFC 2483)
+            continue;
+          }
+          java.net.URI uri = new java.net.URI(s);
+          if (uri.getScheme().toLowerCase().startsWith("http"))
+          {
+            protocols.add(FormatAdapter.URL);
+            files.add(uri.toString());
+          }
+          else
+          {
+            // otherwise preserve old behaviour: catch all for file objects
+            java.io.File file = new java.io.File(uri);
+            protocols.add(FormatAdapter.FILE);
+            files.add(file.toString());
+          }
+        }
+      }
+    } catch (Exception e)
+    {
+    }
+
+    if (files != null)
+    {
+      try
+      {
+        for (int i = 0; i < files.size(); i++)
+        {
+          String file = files.get(i).toString();
+          String protocol = (protocols == null) ? FormatAdapter.FILE
+                  : (String) protocols.get(i);
+          String format = null;
+
+          if (file.endsWith(".jar"))
+          {
+            format = "Jalview";
+
+          }
+          else
+          {
+            format = new IdentifyFile().Identify(file, protocol);
+          }
+
+          new FileLoader().LoadFile(file, protocol, format);
+
+        }
+      } catch (Exception ex)
+      {
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"),
+            jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
+            jalview.io.AppletFormatAdapter.READABLE_FNAMES,
+            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Open local file");
+    chooser.setToolTipText("Open");
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
+
+      String format = null;
+      if (chooser.getSelectedFormat().equals("Jalview"))
+      {
+        format = "Jalview";
+      }
+      else
+      {
+        format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
+      }
+
+      if (viewport != null)
+      {
+        new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
+                format);
+      }
+      else
+      {
+        new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+  {
+    // This construct allows us to have a wider textfield
+    // for viewing
+    JLabel label = new JLabel("Enter URL of Input File");
+    final JComboBox history = new JComboBox();
+
+    JPanel panel = new JPanel(new GridLayout(2, 1));
+    panel.add(label);
+    panel.add(history);
+    history.setPreferredSize(new Dimension(400, 20));
+    history.setEditable(true);
+    history.addItem("http://www.");
+
+    String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+    StringTokenizer st;
+
+    if (historyItems != null)
+    {
+      st = new StringTokenizer(historyItems, "\t");
+
+      while (st.hasMoreTokens())
+      {
+        history.addItem(st.nextElement());
+      }
+    }
+
+    int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+            "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
+
+    if (reply != JOptionPane.OK_OPTION)
+    {
+      return;
+    }
+
+    String url = history.getSelectedItem().toString();
+
+    if (url.toLowerCase().endsWith(".jar"))
+    {
+      if (viewport != null)
+      {
+        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
+                "Jalview");
+      }
+      else
+      {
+        new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+      }
+    }
+    else
+    {
+      String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+
+      if (format.equals("URL NOT FOUND"))
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Couldn't locate " + url, "URL not found",
+                JOptionPane.WARNING_MESSAGE);
+
+        return;
+      }
+
+      if (viewport != null)
+      {
+        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+      }
+      else
+      {
+        new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(viewport);
+    Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+  }
+
+  /*
+   * Exit the program
+   */
+  public void quit()
+  {
+    Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+    jalview.bin.Cache
+            .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+    jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
+            + "");
+    storeLastKnownDimensions("", new Rectangle(getBounds().x,
+            getBounds().y, getWidth(), getHeight()));
+
+    if (jconsole != null)
+    {
+      storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+      jconsole.stopConsole();
+    }
+    System.exit(0);
+  }
+
+  private void storeLastKnownDimensions(String string, Rectangle jc)
+  {
+    jalview.bin.Cache.log.debug("Storing last known dimensions for "
+            + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+            + " height:" + jc.height);
+
+    jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
+    jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+    jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+    jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void aboutMenuItem_actionPerformed(ActionEvent e)
+  {
+    StringBuffer message = new StringBuffer("Jalview version "
+            + jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
+            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+
+    if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
+            jalview.bin.Cache.getProperty("VERSION")))
+    {
+      message
+              .append("\n\n!! Jalview version "
+                      + jalview.bin.Cache.getProperty("LATEST_VERSION")
+                      + " is available for download from http://www.jalview.org !!\n");
+
+    }
+    // TODO: update this text for each release or centrally store it for lite
+    // and application
+    message
+            .append("\nAuthors:  Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n    David Martin & Geoff Barton."
+                    + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
+                    + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
+                    + "\nIf  you use Jalview, please cite:"
+                    + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+                    + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+                    + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
+    JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+    message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void documentationMenuItem_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+      java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+      javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+      javax.help.HelpBroker hb = hs.createHelpBroker();
+      hb.setCurrentID("home");
+      hb.setDisplayed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public void closeAll_actionPerformed(ActionEvent e)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    for (int i = 0; i < frames.length; i++)
+    {
+      try
+      {
+        frames[i].setClosed(true);
+      } catch (java.beans.PropertyVetoException ex)
+      {
+      }
+    }
+    System.out.println("ALL CLOSED");
+    if (v_client != null)
+    {
+      // TODO clear binding to vamsas document objects on close_all
+
+    }
+  }
+
+  public void raiseRelated_actionPerformed(ActionEvent e)
+  {
+    reorderAssociatedWindows(false, false);
+  }
+
+  public void minimizeAssociated_actionPerformed(ActionEvent e)
+  {
+    reorderAssociatedWindows(true, false);
+  }
+
+  void closeAssociatedWindows()
+  {
+    reorderAssociatedWindows(false, true);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+   * ActionEvent)
+   */
+  protected void garbageCollect_actionPerformed(ActionEvent e)
+  {
+    // We simply collect the garbage
+    jalview.bin.Cache.log.debug("Collecting garbage...");
+    System.gc();
+    jalview.bin.Cache.log.debug("Finished garbage collection.");
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
+   * )
+   */
+  protected void showMemusage_actionPerformed(ActionEvent e)
+  {
+    desktop.showMemoryUsage(showMemusage.isSelected());
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
+   * )
+   */
+  protected void showConsole_actionPerformed(ActionEvent e)
+  {
+    showConsole(showConsole.isSelected());
+  }
+
+  Console jconsole = null;
+
+  /**
+   * control whether the java console is visible or not
+   * 
+   * @param selected
+   */
+  void showConsole(boolean selected)
+  {
+    showConsole.setSelected(selected);
+    // TODO: decide if we should update properties file
+    Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
+            .toString());
+    jconsole.setVisible(selected);
+  }
+
+  void reorderAssociatedWindows(boolean minimize, boolean close)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    if (frames == null || frames.length < 1)
+    {
+      return;
+    }
+
+    AlignViewport source = null, target = null;
+    if (frames[0] instanceof AlignFrame)
+    {
+      source = ((AlignFrame) frames[0]).getCurrentView();
+    }
+    else if (frames[0] instanceof TreePanel)
+    {
+      source = ((TreePanel) frames[0]).getViewPort();
+    }
+    else if (frames[0] instanceof PCAPanel)
+    {
+      source = ((PCAPanel) frames[0]).av;
+    }
+    else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+    {
+      source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
+    }
+
+    if (source != null)
+    {
+      for (int i = 0; i < frames.length; i++)
+      {
+        target = null;
+        if (frames[i] == null)
+        {
+          continue;
+        }
+        if (frames[i] instanceof AlignFrame)
+        {
+          target = ((AlignFrame) frames[i]).getCurrentView();
+        }
+        else if (frames[i] instanceof TreePanel)
+        {
+          target = ((TreePanel) frames[i]).getViewPort();
+        }
+        else if (frames[i] instanceof PCAPanel)
+        {
+          target = ((PCAPanel) frames[i]).av;
+        }
+        else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+        {
+          target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
+        }
+
+        if (source == target)
+        {
+          try
+          {
+            if (close)
+            {
+              frames[i].setClosed(true);
+            }
+            else
+            {
+              frames[i].setIcon(minimize);
+              if (!minimize)
+              {
+                frames[i].toFront();
+              }
+            }
+
+          } catch (java.beans.PropertyVetoException ex)
+          {
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
+    new Preferences();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void saveState_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "jar" }, new String[]
+    { "Jalview Project" }, "Jalview Project");
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Save State");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      java.io.File choice = chooser.getSelectedFile();
+      setProgressBar("Saving jalview project "
+              + choice.getName(), choice.hashCode());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+      // TODO catch and handle errors for savestate
+      try {
+        new Jalview2XML().SaveState(choice);
+      } catch (OutOfMemoryError oom)
+      {
+        new OOMWarning("Whilst saving current state to "+choice.getName(), oom);
+      }
+      catch (Exception ex)
+      {
+        Cache.log.error("Problems whilst trying to save to "+choice.getName(),ex);
+        JOptionPane.showMessageDialog(this, "Error whilst saving current state to "+choice.getName(), "Couldn't save project", JOptionPane.WARNING_MESSAGE);
+      }
+      setProgressBar(null, choice.hashCode());
+      
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void loadState_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+            .getProperty("LAST_DIRECTORY"), new String[]
+    { "jar" }, new String[]
+    { "Jalview Project" }, "Jalview Project");
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Restore state");
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      final String choice = chooser.getSelectedFile().getAbsolutePath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
+      new Thread(new Runnable() {
+        public void run() {
+          setProgressBar("loading jalview project "
+              + choice, choice.hashCode());
+          try {
+      new Jalview2XML().LoadJalviewAlign(choice); } 
+      catch (OutOfMemoryError oom)
+      {
+        new OOMWarning("Whilst loading project from "+choice, oom);
+      }
+      catch (Exception ex)
+      {
+        Cache.log.error("Problems whilst loading project from "+choice,ex);
+        JOptionPane.showMessageDialog(Desktop.desktop, "Error whilst loading project from "+choice, "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+      }
+      setProgressBar(null, choice.hashCode());
+        }
+      }).start();
+    }
+  }
+
+  public void inputSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(this);
+  }
+
+  JPanel progressPanel;
+
+  public void startLoading(final String fileName)
+  {
+    if (fileLoadingCount == 0)
+    {
+      addProgressPanel("Loading File: " + fileName + "   ");
+
+    }
+    fileLoadingCount++;
+  }
+
+  private JProgressBar addProgressPanel(String string)
+  {
+    if (progressPanel == null)
+    {
+      progressPanel = new JPanel(new BorderLayout());
+      totalProgressCount = 0;
+    }
+    JProgressBar progressBar = new JProgressBar();
+    progressBar.setIndeterminate(true);
+
+    progressPanel.add(new JLabel(string), BorderLayout.WEST);
+
+    progressPanel.add(progressBar, BorderLayout.CENTER);
+
+    instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+    totalProgressCount++;
+    validate();
+    return progressBar;
+  }
+
+  int totalProgressCount = 0;
+
+  private void removeProgressPanel(JProgressBar progbar)
+  {
+    if (progressPanel != null)
+    {
+      progressPanel.remove(progbar);
+      if (--totalProgressCount < 1)
+      {
+        this.getContentPane().remove(progressPanel);
+        progressPanel = null;
+      }
+    }
+    validate();
+  }
+
+  public void stopLoading()
+  {
+    fileLoadingCount--;
+    if (fileLoadingCount < 1)
+    {
+      if (progressPanel != null)
+      {
+        this.getContentPane().remove(progressPanel);
+        progressPanel = null;
+      }
+      fileLoadingCount = 0;
+    }
+    validate();
+  }
+
+  public static int getViewCount(String viewId)
+  {
+    AlignViewport[] aps = getViewports(viewId);
+    return (aps == null) ? 0 : aps.length;
+  }
+
+  /**
+   * 
+   * @param viewId
+   * @return all AlignmentPanels concerning the viewId sequence set
+   */
+  public static AlignmentPanel[] getAlignmentPanels(String viewId)
+  {
+    int count = 0;
+    if (Desktop.desktop == null)
+    {
+      // no frames created and in headless mode
+      // TODO: verify that frames are recoverable when in headless mode
+      return null;
+    }
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    ArrayList aps = new ArrayList();
+    for (int t = 0; t < frames.length; t++)
+    {
+      if (frames[t] instanceof AlignFrame)
+      {
+        AlignFrame af = (AlignFrame) frames[t];
+        for (int a = 0; a < af.alignPanels.size(); a++)
+        {
+          if (viewId
+                  .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
+                          .getSequenceSetId()))
+          {
+            aps.add(af.alignPanels.elementAt(a));
+          }
+        }
+      }
+    }
+    if (aps.size() == 0)
+    {
+      return null;
+    }
+    AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
+    for (int t = 0; t < vap.length; t++)
+    {
+      vap[t] = (AlignmentPanel) aps.get(t);
+    }
+    return vap;
+  }
+
+  /**
+   * get all the viewports on an alignment.
+   * 
+   * @param sequenceSetId
+   *          unique alignment id
+   * @return all viewports on the alignment bound to sequenceSetId
+   */
+  public static AlignViewport[] getViewports(String sequenceSetId)
+  {
+    Vector viewp = new Vector();
+    if (desktop != null)
+    {
+      javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+
+      for (int t = 0; t < frames.length; t++)
+      {
+        if (frames[t] instanceof AlignFrame)
+        {
+          AlignFrame afr = ((AlignFrame) frames[t]);
+          if (afr.getViewport().getSequenceSetId().equals(sequenceSetId))
+          {
+            if (afr.alignPanels != null)
+            {
+              for (int a = 0; a < afr.alignPanels.size(); a++)
+              {
+                if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels
+                        .elementAt(a)).av.getSequenceSetId()))
+                {
+                  viewp.addElement(((AlignmentPanel) afr.alignPanels
+                          .elementAt(a)).av);
+                }
+              }
+            }
+            else
+            {
+              viewp.addElement(((AlignFrame) frames[t]).getViewport());
+            }
+          }
+        }
+      }
+      if (viewp.size() > 0)
+      {
+        AlignViewport[] vp = new AlignViewport[viewp.size()];
+        viewp.copyInto(vp);
+        return vp;
+      }
+    }
+    return null;
+  }
+
+  public void explodeViews(AlignFrame af)
+  {
+    int size = af.alignPanels.size();
+    if (size < 2)
+    {
+      return;
+    }
+
+    for (int i = 0; i < size; i++)
+    {
+      AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
+      AlignFrame newaf = new AlignFrame(ap);
+      if (ap.av.explodedPosition != null
+              && !ap.av.explodedPosition.equals(af.getBounds()))
+      {
+        newaf.setBounds(ap.av.explodedPosition);
+      }
+
+      ap.av.gatherViewsHere = false;
+
+      addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
+    }
+
+    af.alignPanels.clear();
+    af.closeMenuItem_actionPerformed(true);
+
+  }
+
+  public void gatherViews(AlignFrame source)
+  {
+    source.viewport.gatherViewsHere = true;
+    source.viewport.explodedPosition = source.getBounds();
+    JInternalFrame[] frames = desktop.getAllFrames();
+    String viewId = source.viewport.sequenceSetID;
+
+    for (int t = 0; t < frames.length; t++)
+    {
+      if (frames[t] instanceof AlignFrame && frames[t] != source)
+      {
+        AlignFrame af = (AlignFrame) frames[t];
+        boolean gatherThis = false;
+        for (int a = 0; a < af.alignPanels.size(); a++)
+        {
+          AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+          if (viewId.equals(ap.av.getSequenceSetId()))
+          {
+            gatherThis = true;
+            ap.av.gatherViewsHere = false;
+            ap.av.explodedPosition = af.getBounds();
+            source.addAlignmentPanel(ap, false);
+          }
+        }
+
+        if (gatherThis)
+        {
+          af.alignPanels.clear();
+          af.closeMenuItem_actionPerformed(true);
+        }
+      }
+    }
+
+  }
+
+  jalview.gui.VamsasApplication v_client = null;
+
+  public void vamsasImport_actionPerformed(ActionEvent e)
+  {
+    if (v_client == null)
+    {
+      // Load and try to start a session.
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+              .getProperty("LAST_DIRECTORY"));
+
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Open a saved VAMSAS session");
+      chooser
+              .setToolTipText("select a vamsas session to be opened as a new vamsas session.");
+
+      int value = chooser.showOpenDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        String fle = chooser.getSelectedFile().toString();
+        if (!vamsasImport(chooser.getSelectedFile()))
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Couldn't import '" + fle + "' as a new vamsas session.",
+                  "Vamsas Document Import Failed",
+                  JOptionPane.ERROR_MESSAGE);
+        }
+      }
+    }
+    else
+    {
+      jalview.bin.Cache.log
+              .error("Implementation error - load session from a running session is not supported.");
+    }
+  }
+
+  /**
+   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+   * 
+   * @param file
+   * @return true if import was a success and a session was started.
+   */
+  public boolean vamsasImport(URL url)
+  {
+    // TODO: create progress bar
+    if (v_client != null)
+    {
+
+      jalview.bin.Cache.log
+              .error("Implementation error - load session from a running session is not supported.");
+      return false;
+    }
+
+    try
+    {
+      // copy the URL content to a temporary local file
+      // TODO: be a bit cleverer here with nio (?!)
+      File file = File.createTempFile("vdocfromurl", ".vdj");
+      FileOutputStream fos = new FileOutputStream(file);
+      BufferedInputStream bis = new BufferedInputStream(url.openStream());
+      byte[] buffer = new byte[2048];
+      int ln;
+      while ((ln = bis.read(buffer)) > -1)
+      {
+        fos.write(buffer, 0, ln);
+      }
+      bis.close();
+      fos.close();
+      v_client = new jalview.gui.VamsasApplication(this, file, url
+              .toExternalForm());
+    } catch (Exception ex)
+    {
+      jalview.bin.Cache.log.error(
+              "Failed to create new vamsas session from contents of URL "
+                      + url, ex);
+      return false;
+    }
+    setupVamsasConnectedGui();
+    v_client.initial_update(); // TODO: thread ?
+    return v_client.inSession();
+  }
+
+  /**
+   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+   * 
+   * @param file
+   * @return true if import was a success and a session was started.
+   */
+  public boolean vamsasImport(File file)
+  {
+    if (v_client != null)
+    {
+
+      jalview.bin.Cache.log
+              .error("Implementation error - load session from a running session is not supported.");
+      return false;
+    }
+
+    setProgressBar("Importing VAMSAS session from " + file.getName(), file
+            .hashCode());
+    try
+    {
+      v_client = new jalview.gui.VamsasApplication(this, file, null);
+    } catch (Exception ex)
+    {
+      setProgressBar("Importing VAMSAS session from " + file.getName(),
+              file.hashCode());
+      jalview.bin.Cache.log.error(
+              "New vamsas session from existing session file failed:", ex);
+      return false;
+    }
+    setupVamsasConnectedGui();
+    v_client.initial_update(); // TODO: thread ?
+    setProgressBar("Importing VAMSAS session from " + file.getName(), file
+            .hashCode());
+    return v_client.inSession();
+  }
+
+  public boolean joinVamsasSession(String mysesid)
+  {
+    if (v_client != null)
+    {
+      throw new Error(
+              "Trying to join a vamsas session when another is already connected.");
+    }
+    if (mysesid == null)
+    {
+      throw new Error("Invalid vamsas session id.");
+    }
+    v_client = new VamsasApplication(this, mysesid);
+    setupVamsasConnectedGui();
+    v_client.initial_update();
+    return (v_client.inSession());
+  }
+
+  public void vamsasStart_actionPerformed(ActionEvent e)
+  {
+    if (v_client == null)
+    {
+      // Start a session.
+      // we just start a default session for moment.
+      /*
+       * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+       * getProperty("LAST_DIRECTORY"));
+       * 
+       * chooser.setFileView(new JalviewFileView());
+       * chooser.setDialogTitle("Load Vamsas file");
+       * chooser.setToolTipText("Import");
+       * 
+       * int value = chooser.showOpenDialog(this);
+       * 
+       * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
+       * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
+       */
+      v_client = new VamsasApplication(this);
+      setupVamsasConnectedGui();
+      v_client.initial_update(); // TODO: thread ?
+    }
+    else
+    {
+      // store current data in session.
+      v_client.push_update(); // TODO: thread
+    }
+  }
+
+  protected void setupVamsasConnectedGui()
+  {
+    vamsasStart.setText("Session Update");
+    vamsasSave.setVisible(true);
+    vamsasStop.setVisible(true);
+    vamsasImport.setVisible(false); // Document import to existing session is
+    // not possible for vamsas-client-1.0.
+  }
+
+  protected void setupVamsasDisconnectedGui()
+  {
+    vamsasSave.setVisible(false);
+    vamsasStop.setVisible(false);
+    vamsasImport.setVisible(true);
+    vamsasStart.setText("New Vamsas Session");
+  }
+
+  public void vamsasStop_actionPerformed(ActionEvent e)
+  {
+    if (v_client != null)
+    {
+      v_client.end_session();
+      v_client = null;
+      setupVamsasDisconnectedGui();
+    }
+  }
+
+  protected void buildVamsasStMenu()
+  {
+    if (v_client == null)
+    {
+      String[] sess = null;
+      try
+      {
+        sess = VamsasApplication.getSessionList();
+      } catch (Exception e)
+      {
+        jalview.bin.Cache.log.warn(
+                "Problem getting current sessions list.", e);
+        sess = null;
+      }
+      if (sess != null)
+      {
+        jalview.bin.Cache.log.debug("Got current sessions list: "
+                + sess.length + " entries.");
+        VamsasStMenu.removeAll();
+        for (int i = 0; i < sess.length; i++)
+        {
+          JMenuItem sessit = new JMenuItem();
+          sessit.setText(sess[i]);
+          sessit.setToolTipText("Connect to session " + sess[i]);
+          final Desktop dsktp = this;
+          final String mysesid = sess[i];
+          sessit.addActionListener(new ActionListener()
+          {
+
+            public void actionPerformed(ActionEvent e)
+            {
+              if (dsktp.v_client == null)
+              {
+                Thread rthr = new Thread(new Runnable()
+                {
+
+                  public void run()
+                  {
+                    dsktp.v_client = new VamsasApplication(dsktp, mysesid);
+                    dsktp.setupVamsasConnectedGui();
+                    dsktp.v_client.initial_update();
+                  }
+
+                });
+                rthr.start();
+              }
+            };
+          });
+          VamsasStMenu.add(sessit);
+        }
+        // don't show an empty menu.
+        VamsasStMenu.setVisible(sess.length > 0);
+
+      }
+      else
+      {
+        jalview.bin.Cache.log.debug("No current vamsas sessions.");
+        VamsasStMenu.removeAll();
+        VamsasStMenu.setVisible(false);
+      }
+    }
+    else
+    {
+      // Not interested in the content. Just hide ourselves.
+      VamsasStMenu.setVisible(false);
+    }
+  }
+
+  public void vamsasSave_actionPerformed(ActionEvent e)
+  {
+    if (v_client != null)
+    {
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+              .getProperty("LAST_DIRECTORY"), new String[]
+      { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+              new String[]
+              { "Vamsas Document" }, "Vamsas Document");
+
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Save Vamsas Document Archive");
+
+      int value = chooser.showSaveDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        java.io.File choice = chooser.getSelectedFile();
+        JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to "
+                + choice.getName());
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+        String warnmsg = null;
+        String warnttl = null;
+        try
+        {
+          v_client.vclient.storeDocument(choice);
+        } catch (Error ex)
+        {
+          warnttl = "Serious Problem saving Vamsas Document";
+          warnmsg = ex.toString();
+          jalview.bin.Cache.log.error("Error Whilst saving document to "
+                  + choice, ex);
+
+        } catch (Exception ex)
+        {
+          warnttl = "Problem saving Vamsas Document.";
+          warnmsg = ex.toString();
+          jalview.bin.Cache.log.warn("Exception Whilst saving document to "
+                  + choice, ex);
+
+        }
+        removeProgressPanel(progpanel);
+        if (warnmsg != null)
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+          warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+        }
+      }
+    }
+  }
+
+  JProgressBar vamUpdate = null;
+
+  /**
+   * hide vamsas user gui bits when a vamsas document event is being handled.
+   * 
+   * @param b
+   *          true to hide gui, false to reveal gui
+   */
+  public void setVamsasUpdate(boolean b)
+  {
+    jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+            + (b ? "in progress" : "finished"));
+
+    if (vamUpdate != null)
+    {
+      this.removeProgressPanel(vamUpdate);
+    }
+    if (b)
+    {
+      vamUpdate = this.addProgressPanel("Updating vamsas session");
+    }
+    vamsasStart.setVisible(!b);
+    vamsasStop.setVisible(!b);
+    vamsasSave.setVisible(!b);
+  }
+
+  public JInternalFrame[] getAllFrames()
+  {
+    return desktop.getAllFrames();
+  }
+
+  /**
+   * Checks the given url to see if it gives a response indicating that the user
+   * should be informed of a new questionnaire.
+   * 
+   * @param url
+   */
+  public void checkForQuestionnaire(String url)
+  {
+    UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
+    // javax.swing.SwingUtilities.invokeLater(jvq);
+    new Thread(jvq).start();
+  }
+
+  /**
+   * Proxy class for JDesktopPane which optionally displays the current memory
+   * usage and highlights the desktop area with a red bar if free memory runs
+   * low.
+   * 
+   * @author AMW
+   */
+  public class MyDesktopPane extends JDesktopPane implements Runnable
+  {
+
+    boolean showMemoryUsage = false;
+
+    Runtime runtime;
+
+    java.text.NumberFormat df;
+
+    float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+            percentUsage;
+
+    public MyDesktopPane(boolean showMemoryUsage)
+    {
+      showMemoryUsage(showMemoryUsage);
+    }
+
+    public void showMemoryUsage(boolean showMemoryUsage)
+    {
+      this.showMemoryUsage = showMemoryUsage;
+      if (showMemoryUsage)
+      {
+        Thread worker = new Thread(this);
+        worker.start();
+      }
+    }
+
+    public boolean isShowMemoryUsage()
+    {
+      return showMemoryUsage;
+    }
+
+    public void run()
+    {
+      df = java.text.NumberFormat.getNumberInstance();
+      df.setMaximumFractionDigits(2);
+      runtime = Runtime.getRuntime();
+
+      while (showMemoryUsage)
+      {
+        try
+        {
+          maxMemory = runtime.maxMemory() / 1048576f;
+          allocatedMemory = runtime.totalMemory() / 1048576f;
+          freeMemory = runtime.freeMemory() / 1048576f;
+          totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
+
+          percentUsage = (totalFreeMemory / maxMemory) * 100;
+
+          // if (percentUsage < 20)
+          {
+            // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
+            // Color.red);
+            // instance.set.setBorder(border1);
+          }
+          repaint();
+          // sleep after showing usage
+          Thread.sleep(3000);
+        } catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+    }
+
+    public void paintComponent(Graphics g)
+    {
+      if (showMemoryUsage && g != null && df != null)
+      {
+        if (percentUsage < 20)
+          g.setColor(Color.red);
+        FontMetrics fm = g.getFontMetrics();
+        if (fm != null)
+        {
+          g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+                  + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
+                  + df.format(percentUsage) + "%", 10, getHeight()
+                  - fm.getHeight());
+        }
+      }
+    }
+
+  }
+
+  protected JMenuItem groovyShell;
+
+  public void doGroovyCheck()
+  {
+    if (jalview.bin.Cache.groovyJarsPresent())
+    {
+      groovyShell = new JMenuItem();
+      groovyShell.setText("Groovy Console...");
+      groovyShell.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          groovyShell_actionPerformed(e);
+        }
+      });
+      toolsMenu.add(groovyShell);
+      groovyShell.setVisible(true);
+    }
+  }
+
+  /**
+   * Accessor method to quickly get all the AlignmentFrames loaded.
+   */
+  public static AlignFrame[] getAlignframes()
+  {
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+    if (frames == null)
+    {
+      return null;
+    }
+    Vector avp = new Vector();
+    try
+    {
+      // REVERSE ORDER
+      for (int i = frames.length - 1; i > -1; i--)
+      {
+        if (frames[i] instanceof AlignFrame)
+        {
+          AlignFrame af = (AlignFrame) frames[i];
+          avp.addElement(af);
+        }
+      }
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+    if (avp.size() == 0)
+    {
+      return null;
+    }
+    AlignFrame afs[] = new AlignFrame[avp.size()];
+    for (int i = 0, j = avp.size(); i < j; i++)
+    {
+      afs[i] = (AlignFrame) avp.elementAt(i);
+    }
+    avp.clear();
+    return afs;
+  }
+
+  /**
+   * Add Groovy Support to Jalview
+   */
+  public void groovyShell_actionPerformed(ActionEvent e)
+  {
+    // use reflection to avoid creating compilation dependency.
+    if (!jalview.bin.Cache.groovyJarsPresent())
+    {
+      throw new Error(
+              "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+    }
+    try
+    {
+      Class gcClass = Desktop.class.getClassLoader().loadClass(
+              "groovy.ui.Console");
+      Constructor gccons = gcClass.getConstructor(null);
+      java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
+              new Class[]
+              { String.class, Object.class });
+      java.lang.reflect.Method run = gcClass.getMethod("run", null);
+      Object gc = gccons.newInstance(null);
+      setvar.invoke(gc, new Object[]
+      { "Jalview", this });
+      run.invoke(gc, null);
+    } catch (Exception ex)
+    {
+      jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+
+                      "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
+                      "Jalview Groovy Support Failed",
+                      JOptionPane.ERROR_MESSAGE);
+    }
+  }
+
+  /**
+   * Progress bars managed by the IProgressIndicator method.
+   */
+  private Hashtable progressBars, progressBarHandlers;
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+   */
+  public void setProgressBar(String message, long id)
+  {
+    if (progressBars == null)
+    {
+      progressBars = new Hashtable();
+      progressBarHandlers = new Hashtable();
+    }
+
+    if (progressBars.get(new Long(id)) != null)
+    {
+      JProgressBar progressPanel = (JProgressBar) progressBars
+              .remove(new Long(id));
+      if (progressBarHandlers.contains(new Long(id)))
+      {
+        progressBarHandlers.remove(new Long(id));
+      }
+      removeProgressPanel(progressPanel);
+    }
+    else
+    {
+      progressBars.put(new Long(id), addProgressPanel(message));
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.gui.IProgressIndicator#registerHandler(long,
+   * jalview.gui.IProgressIndicatorHandler)
+   */
+  public void registerHandler(final long id,
+          final IProgressIndicatorHandler handler)
+  {
+    if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+    {
+      throw new Error(
+              "call setProgressBar before registering the progress bar's handler.");
+    }
+    progressBarHandlers.put(new Long(id), handler);
+    final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+    if (handler.canCancel())
+    {
+      JButton cancel = new JButton("Cancel");
+      final IProgressIndicator us = this;
+      cancel.addActionListener(new ActionListener()
+      {
+
+        public void actionPerformed(ActionEvent e)
+        {
+          handler.cancelActivity(id);
+          us.setProgressBar("Cancelled "
+                  + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+        }
+      });
+      progressPanel.add(cancel, BorderLayout.EAST);
+    }
+  }
+
+  /**
+   * This will return the first AlignFrame viewing AlignViewport av. It will
+   * break if there are more than one AlignFrames viewing a particular av. This
+   * 
+   * @param av
+   * @return alignFrame for av
+   */
+  public static AlignFrame getAlignFrameFor(AlignViewport av)
+  {
+    if (desktop != null)
+    {
+      AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
+      for (int panel = 0; aps != null && panel < aps.length; panel++)
+      {
+        if (aps[panel] != null && aps[panel].av == av)
+        {
+          return aps[panel].alignFrame;
+        }
+      }
+    }
+    return null;
+  }
+
+  public VamsasApplication getVamsasApplication()
+  {
+    return v_client;
+
+  }
+  /**
+   * flag set if jalview GUI is being operated programmatically
+   */
+  private boolean inBatchMode=false;
+
+  /**
+   * check if jalview GUI is being operated programmatically
+   * @return inBatchMode
+   */
+  public boolean isInBatchMode()
+  {
+    return inBatchMode;
+  }
+
+  /**
+   * set flag if jalview GUI is being operated programmatically
+   * @param inBatchMode 
+   */
+  public void setInBatchMode(boolean inBatchMode)
+  {
+    this.inBatchMode = inBatchMode;
+  }
+
+
+  public void startServiceDiscovery()
+  {
+    startServiceDiscovery(false);
+  }
+
+  public void startServiceDiscovery(boolean blocking)
+  {
+    boolean alive = true;
+    Thread t0 = null, t1 = null, t2 = null;
+
+    // todo: changesupport handlers need to be transferred
+    if (discoverer == null)
+    {
+      discoverer = new jalview.ws.jws1.Discoverer();
+      // register PCS handler for desktop.
+      discoverer.addPropertyChangeListener(changeSupport);
+    }
+    if (Cache.getDefault("SHOW_JWS1_SERVICES", true))
+    {
+      (t0 = new Thread(discoverer)).start();
+    }
+
+    try
+    {
+      if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+      {
+        // EnfinEnvision web service menu entries are rebuild every time the
+        // menu is shown, so no changeSupport events are needed.
+        jalview.ws.EnfinEnvision2OneWay.getInstance();
+        (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
+                .start();
+      }
+    } catch (Exception e)
+    {
+      Cache.log
+              .info(
+                      "Exception when trying to launch Envision2 workflow discovery.",
+                      e);
+      Cache.log.info(e.getStackTrace());
+    }
+    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    {
+      jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+              .addPropertyChangeListener(changeSupport);
+      (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()))
+              .start();
+    }
+    if (blocking)
+    {
+      while (alive)
+      {
+        try
+        {
+          Thread.sleep(15);
+        } catch (Exception e)
+        {
+        }
+        alive = (t1 != null && t1.isAlive())
+                || (t2 != null && t2.isAlive())
+                || (t0 != null && t0.isAlive());
+      }
+    }
+  }
+
+  /**
+   * start a thread to open a URL in the configured browser. Pops up a warning dialog to the user if there is an exception when calling out to the browser to open the URL.
+   * @param url
+   */
+  public static void showUrl(final String url)
+  {
+    new Thread(new Runnable() {
+      public void run() {
+        try {
+          jalview.util.BrowserLauncher.openURL(url);
+        } catch (Exception ex)
+        {    
+          JOptionPane
+                  .showInternalMessageDialog(
+                          Desktop.desktop,
+                          "Unixers: Couldn't find default web browser."
+                                  + "\nAdd the full path to your browser in Preferences.",
+                          "Web browser not found", JOptionPane.WARNING_MESSAGE);
+
+          ex.printStackTrace();
+        }
+      }
+    }).start();    
+  }
+
+  public static WsParamSetManager wsparamManager = null;
+  public static ParamManager getUserParameterStore()
+  {
+    if (wsparamManager==null)
+    {
+      wsparamManager = new WsParamSetManager();
+    }
+    return wsparamManager;
+  }
+
+}