X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=262a9becfa450a194e9a3f3a5684c917a23cfa45;hb=dbbd8851fe0e30aa9606657b5f4eb41e0db21563;hp=464ec5965f196dbaf6d40ba6a38ddb049d5315d0;hpb=90bd6677b1f44a0608dcccde1ff59632cc9a54a1;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 464ec59..262a9be 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,264 +1,1417 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
-
-package jalview.gui;
-
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.datamodel.*;
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-
-
-public class Desktop extends jalview.jbgui.GDesktop
-{
-  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("/BartonGroupBanner.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);
-    setVisible(true);
-    desktop = new JDesktopPane();
-    setContentPane(desktop);
-    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
-    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    int width = 1200, height = 800;
-    if(screenSize.getWidth()<width)
-      width = screenSize.width;
-    if(screenSize.getHeight()<height)
-      height = screenSize.height;
-
-    setBounds( (int)(screenSize.width-width)/2,
-               (int)(screenSize.height-height)/2,
-              width ,
-              height);
-
-
-   /////////Add a splashscreen on startup
-    JInternalFrame frame = new JInternalFrame();
-
-    SplashScreen splash = new SplashScreen(frame, image);
-    frame.setContentPane(splash);
-    desktop.add(frame);
-    frame.setVisible(true);
-    openFrameCount++;
-    try
-    {
-      frame.setSelected(true);
-    }
-    catch (java.beans.PropertyVetoException e)
-    {}
-    frame.setResizable(true);
-    frame.setSize(845, 200);
-    frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));
-    frame.setClosable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-    frame.setFrameIcon(null);
-
-  }
-
-  public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
-  {
-   desktop.add(frame);
-   frame.setVisible(true);
-   openFrameCount++;
-   try {
-       frame.setSelected(true);
-   } catch (java.beans.PropertyVetoException e) {}
-   frame.setTitle(title);
-   frame.setResizable(true);
-   frame.setSize(w,h);
-   frame.setClosable(true);
-   frame.setMaximizable(true);
-   frame.setIconifiable(true);
-   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){};
-      }
-    });
-
-   windowMenu.add(menuItem);
- }
-
-
-
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
- {
-   JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
-   chooser.setDialogTitle("Open local file");
-   chooser.setToolTipText("Open");
-   int value = chooser.showOpenDialog(this);
-   if(value == JFileChooser.APPROVE_OPTION)
-   {
-     String choice =  chooser.getSelectedFile().getPath();
-     jalview.bin.Cache.LAST_DIRECTORY = choice;
-     String format = IdentifyFile.Identify(choice, "File");
-     LoadFile(choice, "File", format);
-   }
- }
-
- public void LoadFile(String file, String protocol,  String format)
- {
-   SequenceI [] sequences = null;
-
-   if (FormatProperties.contains(format))
-       sequences = FormatAdapter.read(file, protocol, format);
-
-   if (sequences != null)
-   {
-     AlignFrame af = new AlignFrame(new Alignment(sequences));
-     addInternalFrame(af, file, 700, 500);
-     af.statusBar.setText("Successfully loaded file " + file);
-
-
-   }
-   else
-     JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"
-                          + "Formats currently supported are\n"
-                          + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"
-                          ,"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);
-   if (url == null)
-     return;
-
-   String format = IdentifyFile.Identify(url, "URL");
-
-   System.out.println(format +" format");
-   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(true);
-   int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
-                                       JOptionPane.YES_NO_CANCEL_OPTION,
-                                       JOptionPane.PLAIN_MESSAGE,
-                                       null,
-                                       new Object[]{"Accept", "Cancel", }, null);
-
-
-  if(accept == JOptionPane.YES_OPTION)
-  {
-    String format = IdentifyFile.Identify(cap.getText(), "Paste");
-    SequenceI [] sequences = null;
-
-    if (FormatProperties.contains( format ))
-      sequences = FormatAdapter.read(cap.getText(), "Paste", format);
-
-
-      if(sequences!=null)
-      {
-        AlignFrame af = new AlignFrame(new Alignment(sequences));
-        addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
-        af.statusBar.setText("Successfully pasted alignment file");
-      }
-      else
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
-                                      +"Formats currently supported are\n"
-                                      +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
-                                      "Error parsing text", JOptionPane.WARNING_MESSAGE);
-
-   }
- }
-
-/*
-* 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"
-                                       +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
-                                       +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
-                                       +"\nIf  you use JalView, please cite:  \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
-                                         "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();
-   }
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.io.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import java.awt.event.*;
+import java.lang.reflect.Constructor;
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop
+    extends jalview.jbgui.GDesktop implements DropTargetListener,
+    ClipboardOwner, IProgressIndicator
+{
+  /** DOCUMENT ME!! */
+  public static Desktop instance;
+
+  //Need to decide if the Memory Usage is to be included in
+  //Next release or not.
+  public static MyDesktopPane desktop;
+  // 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;
+
+  /**
+   * 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);
+    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 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)
+      {
+        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
+    new SplashScreen();     
+
+
+
+    discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+  }
+
+  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);
+    }
+  }
+
+  /**
+   * 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)
+  {
+    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)
+  {
+
+    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;
+
+    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)
+      {}
+    }
+  }
+
+  /**
+   * 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()
+  {
+    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);
+  }
+
+  /**
+   * 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");
+
+    }
+
+    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);
+  }
+
+  /**
+   * 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");
+
+  }
+
+  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)
+   * @see jalview.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());
+  }
+
+  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();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+      new Jalview2XML().SaveState(choice);
+    }
+  }
+
+  /**
+   * 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)
+    {
+      String choice = chooser.getSelectedFile().getAbsolutePath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
+      new Jalview2XML().LoadJalviewAlign(choice);
+    }
+  }
+
+  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)
+  {
+    int count = 0;
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    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())
+              )
+          {
+            count++;
+          }
+        }
+      }
+    }
+
+    return count;
+  }
+
+  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)
+      {
+        try {
+          v_client = new jalview.gui.VamsasApplication(this,
+                                                chooser.getSelectedFile());
+        } catch (Exception ex)
+        {
+          jalview.bin.Cache.log.error("New vamsas session from existing session file failed:",ex);
+          return;
+        }
+        setupVamsasConnectedGui();
+        v_client.initial_update(); // TODO: thread ?
+      }
+    }else {
+      jalview.bin.Cache.log.error("Implementation error - load session from a running session is not supported.");
+    }
+  }
+
+  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();
+          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);
+            
+          }
+          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
+        {
+          Thread.sleep(3000);
+          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();
+
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+    }
+
+    public void paintComponent(Graphics g)
+    {
+      if(showMemoryUsage)
+      {
+        if (percentUsage < 20)
+          g.setColor(Color.red);
+
+        g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+                     + "MB; Max Memory: " + df.format(maxMemory)
+                     + "MB; " + df.format(percentUsage) + "%", 10,
+                     getHeight() - g.getFontMetrics().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;
+  /* (non-Javadoc)
+   * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+   */
+  public void setProgressBar(String message, long id)
+  {
+    if(progressBars == null)
+    {
+      progressBars = new Hashtable();
+    }
+
+    if(progressBars.get( new Long(id) )!=null)
+    {
+      JProgressBar progressPanel = (JProgressBar)progressBars.remove( new Long(id) );
+       removeProgressPanel(progressPanel);
+    } else {
+      progressBars.put(new Long(id), addProgressPanel(message));
+    }
+  }
+}