X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=a0b93fbc55815e3b952e160038b35488ed6deaed;hb=12e7f97678ce85b0238f987d5f4eaf18512a0b94;hp=0f77b9df36534a00334cfb302e39fc316ad34e43;hpb=5951e3b0b9faea1c8b54914cb64ff3a08ba27cb6;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 0f77b9d..a0b93fb 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -24,862 +24,1549 @@ 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
+public class Desktop extends jalview.jbgui.GDesktop implements
+        DropTargetListener, ClipboardOwner, IProgressIndicator
 {
-    /** DOCUMENT ME!! */
-    public static Desktop instance;
-    public static JDesktopPane desktop;
-    static int openFrameCount = 0;
-    static final int xOffset = 30;
-    static final int yOffset = 30;
-    public static jalview.ws.Discoverer discoverer;
+  /** 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 Object[] jalviewClipboard;
 
-    static int fileLoadingCount= 0;
+  public static boolean internalCopy = false;
 
+  static int fileLoadingCount = 0;
+
+  /**
+   * Creates a new Desktop object.
+   */
+  public Desktop()
+  {
     /**
-     * Creates a new Desktop object.
+     * 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.
      */
-    public Desktop()
+    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
     {
-        instance = this;
-        doVamsasClientCheck();
-        Image image = null;
+      setBounds((int) (screenSize.width - 900) / 2,
+              (int) (screenSize.height - 650) / 2, 900, 650);
+    }
 
-        try
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        quit();
+      }
+    });
+
+    this.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent evt)
+      {
+        if (SwingUtilities.isRightMouseButton(evt))
         {
-            java.net.URL url = getClass().getResource("/images/logo.gif");
+          showPasteMenu(evt.getX(), evt.getY());
+        }
+      }
+    });
 
-            if (url != null)
-            {
-                image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    // Spawn a thread that shows the splashscreen
+    new SplashScreen();
 
-                MediaTracker mt = new MediaTracker(this);
-                mt.addImage(image, 0);
-                mt.waitForID(0);
-                setIconImage(image);
-            }
-        }
-        catch (Exception ex)
+    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;
         }
 
-        setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
-        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-        desktop = new JDesktopPane();
-        desktop.setBackground(Color.white);
-        getContentPane().setLayout(new BorderLayout());
-        getContentPane().add(desktop, BorderLayout.CENTER);
-        desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
-        // 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))
+        public void menuDeselected(MenuEvent e)
         {
-            setBounds(Integer.parseInt(x), Integer.parseInt(y),
-                Integer.parseInt(width), Integer.parseInt(height));
+          refresh = true;
         }
-        else
+
+        public void menuSelected(MenuEvent e)
         {
-            setBounds((int) (screenSize.width - 900) / 2,
-                (int) (screenSize.height - 650) / 2, 900, 650);
+          if (refresh)
+          {
+            us.buildVamsasStMenu();
+            refresh = false;
+          }
         }
+      });
+      vamsasStart.setVisible(true);
+    }
+  }
 
-        this.addWindowListener(new WindowAdapter()
-            {
-                public void windowClosing(WindowEvent evt)
-                {
-                    quit();
-                }
-            });
+  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();
+      }
+    });
 
-        this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    popup.add(item);
+    popup.show(this, x, y);
+  }
 
-        /////////Add a splashscreen on startup
-        /////////Add a splashscreen on startup
-        JInternalFrame frame = new JInternalFrame();
+  public void paste()
+  {
+    try
+    {
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
 
-        SplashScreen splash = new SplashScreen(frame, image);
-        frame.setContentPane(splash);
-        frame.setLayer(JLayeredPane.PALETTE_LAYER);
-        frame.setLocation((int) ((getWidth() - 750) / 2),
-            (int) ((getHeight() - 160) / 2));
+      if (contents != null)
+      {
+        String file = (String) contents
+                .getTransferData(DataFlavor.stringFlavor);
 
-        addInternalFrame(frame, "", 750, 160, false);
+        String format = new IdentifyFile().Identify(file,
+                FormatAdapter.PASTE);
 
-        discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
-    }
+        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
 
-    private void doVamsasClientCheck() {
-      if (jalview.bin.Cache.vamsasJarsPresent()) {
-        VamsasMenu.setVisible(true);
-        vamsasLoad.setVisible(true);
       }
-
+    } 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)
+  }
+
+  /**
+   * 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)
+  {
+
+    // 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)
     {
-        addInternalFrame(frame, title, w, h, true);
+      frame.setSize(w, h);
     }
-
-    /**
-     * 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)
+    // 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;
+    }
 
-      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++;
+    openFrameCount++;
 
-        frame.setVisible(true);
-        frame.setClosable(true);
-        frame.setResizable(resizable);
-        frame.setMaximizable(resizable);
-        frame.setIconifiable(resizable);
-        frame.setFrameIcon(null);
+    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);
-       }
+    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()
+    final JMenuItem menuItem = new JMenuItem(title);
+    frame
+            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
             {
-              public void internalFrameActivated(javax.swing.event.
-                                                 InternalFrameEvent evt)
+              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)
+              public void internalFrameClosed(
+                      javax.swing.event.InternalFrameEvent evt)
+              {
+                PaintRefresher.RemoveComponent(frame);
+                openFrameCount--;
+                windowMenu.remove(menuItem);
+                JInternalFrame itf = desktop.getSelectedFrame();
+                if (itf != null)
                 {
-                    PaintRefresher.RemoveComponent(frame);
-                    openFrameCount--;
-                    windowMenu.remove(menuItem);
-                    JInternalFrame itf = desktop.getSelectedFrame();
-                       if (itf != null)
-                        itf.requestFocus();
+                  itf.requestFocus();
                 }
-                ;
+                System.gc();
+              };
             });
 
-        menuItem.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    try
-                    {
-                        frame.setSelected(true);
-                        frame.setIcon(false);
-                    }
-                    catch (java.beans.PropertyVetoException ex)
-                    {
-
-                    }
-                }
-            });
+    menuItem.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)
-        {   }
+    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)
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    if (!internalCopy)
     {
       Desktop.jalviewClipboard = null;
     }
 
-    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)
+    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
     {
-        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();)
         {
-          DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
-          if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+          String s = st.nextToken();
+          if (s.startsWith("#"))
           {
-            //Works on Windows and MacOSX
-            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-            files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+            // the line is a comment (as per the RFC 2483)
+            continue;
           }
-          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);
-            }
-          }
+          java.net.URI uri = new java.net.URI(s);
+          java.io.File file = new java.io.File(uri);
+          files.add(file);
         }
-        catch (Exception e)
-        {      }
+      }
+    } catch (Exception e)
+    {
+    }
 
-        if (files != null)
+    if (files != null)
+    {
+      try
+      {
+        for (int i = 0; i < files.size(); i++)
         {
-          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";
+          String file = files.get(i).toString();
+          String protocol = FormatAdapter.FILE;
+          String format = null;
 
-              }
-              else
-              {
-                format = new IdentifyFile().Identify(file,
-                                                          protocol);
-              }
+          if (file.endsWith(".jar"))
+          {
+            format = "Jalview";
 
+          }
+          else
+          {
+            format = new IdentifyFile().Identify(file, protocol);
+          }
 
-              new FileLoader().LoadFile(file, protocol, format);
+          new FileLoader().LoadFile(file, protocol, format);
 
-            }
-          }
-          catch (Exception ex)
-          {      }
         }
+      } 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());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+      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)
     {
-        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"));
+      st = new StringTokenizer(historyItems, "\t");
 
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Open local file");
-        chooser.setToolTipText("Open");
+      while (st.hasMoreTokens())
+      {
+        history.addItem(st.nextElement());
+      }
+    }
 
-        int value = chooser.showOpenDialog(this);
+    int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+            "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            String choice = chooser.getSelectedFile().getPath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
+    if (reply != JOptionPane.OK_OPTION)
+    {
+      return;
+    }
 
-            String format = null;
-            if (chooser.getSelectedFormat().equals("Jalview"))
-            {
-                format = "Jalview";
-            }
-            else
-            {
-                format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
-            }
+    String url = history.getSelectedItem().toString();
 
-            if (viewport != null)
-              new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
-            else
-              new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
-        }
+    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;
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+      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")))
     {
-      // 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();
+      message
+              .append("\n\n!! Jalview version "
+                      + jalview.bin.Cache.getProperty("LATEST_VERSION")
+                      + " is available for download from http://www.jalview.org !!\n");
 
-      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.");
+    }
+    // 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:"
+                    + "\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)
+    {
+    }
+  }
 
-      String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+  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)
+   * 
+   * @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;
+    }
 
-      StringTokenizer st;
+    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 (historyItems != null)
+    if (source != null)
+    {
+      for (int i = 0; i < frames.length; i++)
       {
-        st = new StringTokenizer(historyItems, "\t");
-
-        while (st.hasMoreTokens())
+        target = null;
+        if (frames[i] == null)
         {
-          history.addItem(st.nextElement());
+          continue;
         }
-      }
-
-       int reply = JOptionPane.showInternalConfirmDialog(desktop,
-          panel, "Input Alignment From URL",
-          JOptionPane.OK_CANCEL_OPTION );
-
-
-        if (reply != JOptionPane.OK_OPTION )
+        if (frames[i] instanceof AlignFrame)
         {
-            return;
+          target = ((AlignFrame) frames[i]).getCurrentView();
         }
-
-        String url = history.getSelectedItem().toString();
-
-        if (url.toLowerCase().endsWith(".jar"))
+        else if (frames[i] instanceof TreePanel)
         {
-          if (viewport != null)
-            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
-          else
-            new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+          target = ((TreePanel) frames[i]).getViewPort();
+        }
+        else if (frames[i] instanceof PCAPanel)
+        {
+          target = ((PCAPanel) frames[i]).av;
         }
-        else
+        else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
         {
-          String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+          target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
+        }
 
-          if (format.equals("URL NOT FOUND"))
+        if (source == target)
+        {
+          try
           {
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                  "Couldn't locate " + url,
-                                                  "URL not found",
-                                                  JOptionPane.WARNING_MESSAGE);
+            if (close)
+            {
+              frames[i].setClosed(true);
+            }
+            else
+            {
+              frames[i].setIcon(minimize);
+              if (!minimize)
+              {
+                frames[i].toFront();
+              }
+            }
 
-            return;
+          } catch (java.beans.PropertyVetoException ex)
+          {
           }
-
-          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)
+  }
+
+  /**
+   * 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)
     {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput(viewport);
-        Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+      java.io.File choice = chooser.getSelectedFile();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+      new Jalview2XML().SaveState(choice);
     }
-
-    /*
-     * Exit the program
-     */
-    public void quit()
+  }
+
+  /**
+   * 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)
     {
-        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);
+      String choice = chooser.getSelectedFile().getAbsolutePath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+              .getSelectedFile().getParent());
+      new Jalview2XML().LoadJalviewAlign(choice);
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void aboutMenuItem_actionPerformed(ActionEvent e)
+  public void inputSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(this);
+  }
+
+  JPanel progressPanel;
+
+  public void startLoading(final String fileName)
+  {
+    if (fileLoadingCount == 0)
     {
-      StringBuffer message = new StringBuffer("JalView version " +
-                                              jalview.bin.Cache.getProperty(
-          "VERSION") +
-                                              "; last updated: " +
-                                              jalview.bin.
-                                              Cache.getDefault("BUILD_DATE", "unknown"));
+      addProgressPanel("Loading File: " + fileName + "   ");
 
-      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");
+    }
+    fileLoadingCount++;
+  }
 
-      }
+  private JProgressBar addProgressPanel(String string)
+  {
+    if (progressPanel == null)
+    {
+      progressPanel = new JPanel(new BorderLayout());
+      totalProgressCount = 0;
+    }
+    JProgressBar progressBar = new JProgressBar();
+    progressBar.setIndeterminate(true);
 
-      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.");
+    progressPanel.add(new JLabel(string), BorderLayout.WEST);
 
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+    progressPanel.add(progressBar, BorderLayout.CENTER);
 
-           message.toString(), "About Jalview",
-            JOptionPane.INFORMATION_MESSAGE);
-    }
+    instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+    totalProgressCount++;
+    validate();
+    return progressBar;
+  }
 
-    /**
-     * 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);
+  int totalProgressCount = 0;
 
-            javax.help.HelpBroker hb = hs.createHelpBroker();
-            hb.setCurrentID("home");
-            hb.setDisplayed(true);
-        }
-        catch (Exception ex)
-        {     }
+  private void removeProgressPanel(JProgressBar progbar)
+  {
+    if (progressPanel != null)
+    {
+      progressPanel.remove(progbar);
+      if (--totalProgressCount < 1)
+      {
+        this.getContentPane().remove(progressPanel);
+        progressPanel = null;
+      }
     }
+    validate();
+  }
 
-    public void closeAll_actionPerformed(ActionEvent e)
+  public void stopLoading()
+  {
+    fileLoadingCount--;
+    if (fileLoadingCount < 1)
     {
-      JInternalFrame [] frames = desktop.getAllFrames();
-      for(int i=0; i<frames.length; i++)
+      if (progressPanel != null)
       {
-        try{
-        frames[i].setClosed(true);
-      }catch(java.beans.PropertyVetoException ex){}
+        this.getContentPane().remove(progressPanel);
+        progressPanel = null;
       }
+      fileLoadingCount = 0;
     }
-
-    public void raiseRelated_actionPerformed(ActionEvent e)
+    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;
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    ArrayList aps = new ArrayList();
+    for (int t = 0; t < frames.length; t++)
     {
-      reorderAssociatedWindows(false, false);
+      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));
+          }
+        }
+      }
     }
-
-    public void minimizeAssociated_actionPerformed(ActionEvent e)
+    if (aps.size()==0)
     {
-      reorderAssociatedWindows(true, false);
+      return null;
     }
-
-    void closeAssociatedWindows()
+    AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
+    for (int t=0;t<vap.length;t++)
     {
-      reorderAssociatedWindows(false, true);
+      vap[t] = (AlignmentPanel) aps.get(t);
     }
-
-    void reorderAssociatedWindows(boolean minimize, boolean close)
+    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)
     {
-      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++)
+      javax.swing.JInternalFrame[] frames = instance.getAllFrames();
+  
+      for (int t = 0; t < frames.length; t++)
+      {
+        if (frames[t] instanceof AlignFrame)
         {
-          target = null;
-          if(frames[i]==null)
+          AlignFrame afr = ((AlignFrame) frames[t]);
+          if (afr.getViewport().getSequenceSetId()
+                  .equals(sequenceSetId))
           {
-            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 (afr.alignPanels!=null)
             {
-              if (close)
-                frames[i].setClosed(true);
-              else
+              for (int a = 0; a < afr.alignPanels.size(); a++)
               {
-                frames[i].setIcon(minimize);
-                if (!minimize)
+                if (sequenceSetId
+                        .equals(((AlignmentPanel) afr.alignPanels.elementAt(a)).av
+                                .getSequenceSetId()))
                 {
-                  frames[i].toFront();
+                  viewp.addElement(((AlignmentPanel)afr.alignPanels.elementAt(a)).av);
                 }
               }
-
+            } else {
+              viewp.addElement(((AlignFrame) frames[t]).getViewport());
             }
-            catch (java.beans.PropertyVetoException ex)
-            {       }
           }
         }
+      }
+      if (viewp.size() > 0)
+      {
+        AlignViewport[] vp = new AlignViewport[viewp.size()];
+        viewp.copyInto(vp);
+        return vp;
+      }
     }
+    return null;
+  }
 
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void preferences_actionPerformed(ActionEvent e)
+  public void explodeViews(AlignFrame af)
+  {
+    int size = af.alignPanels.size();
+    if (size < 2)
     {
-        new Preferences();
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveState_actionPerformed(ActionEvent e)
+    for (int i = 0; i < size; i++)
     {
-        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");
+      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);
+      }
 
-        int value = chooser.showSaveDialog(this);
+      ap.av.gatherViewsHere = false;
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            java.io.File choice = chooser.getSelectedFile();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-            new Jalview2XML().SaveState(choice);
-        }
+      addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
     }
 
-    /**
-     * 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");
+    af.alignPanels.clear();
+    af.closeMenuItem_actionPerformed(true);
+
+  }
 
-        int value = chooser.showOpenDialog(this);
+  public void gatherViews(AlignFrame source)
+  {
+    source.viewport.gatherViewsHere = true;
+    source.viewport.explodedPosition = source.getBounds();
+    JInternalFrame[] frames = desktop.getAllFrames();
+    String viewId = source.viewport.sequenceSetID;
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+    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++)
         {
-            String choice = chooser.getSelectedFile().getAbsolutePath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
-            new Jalview2XML().LoadJalviewAlign(choice);
+          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);
         }
+      }
     }
 
-  /*  public void vamsasLoad_actionPerformed(ActionEvent e)
+  }
+
+  jalview.gui.VamsasApplication v_client = null;
+
+  public void vamsasImport_actionPerformed(ActionEvent e)
+  {
+    if (v_client == null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-          getProperty("LAST_DIRECTORY"));
+      // Load and try to start a session.
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+              .getProperty("LAST_DIRECTORY"));
 
       chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle("Load Vamsas file");
-      chooser.setToolTipText("Import");
+      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)
       {
-        jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
-        vs.load(
-            chooser.getSelectedFile().getAbsolutePath()
-            );
+        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 ?
       }
-
-    }*/
-
-
-    public void inputSequence_actionPerformed(ActionEvent e)
+    }
+    else
     {
-      new SequenceFetcher(null);
+      jalview.bin.Cache.log
+              .error("Implementation error - load session from a running session is not supported.");
     }
+  }
 
-    JPanel progressPanel;
+  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();
+    }
+  }
 
-    public void startLoading(final String fileName)
+  protected void buildVamsasStMenu()
+  {
+    if (v_client == null)
     {
-      if (fileLoadingCount == 0)
+      String[] sess = null;
+      try
+      {
+        sess = VamsasApplication.getSessionList();
+      } catch (Exception e)
       {
-        progressPanel = new JPanel(new BorderLayout());
-        JProgressBar progressBar = new JProgressBar();
-        progressBar.setIndeterminate(true);
+        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()
+          {
 
-        progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
-                          BorderLayout.WEST);
+            public void actionPerformed(ActionEvent e)
+            {
+              if (dsktp.v_client == null)
+              {
+                Thread rthr = new Thread(new Runnable()
+                {
 
-        progressPanel.add(progressBar, BorderLayout.CENTER);
+                  public void run()
+                  {
+                    dsktp.v_client = new VamsasApplication(dsktp, mysesid);
+                    dsktp.setupVamsasConnectedGui();
+                    dsktp.v_client.initial_update();
+                  }
 
-        instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
-      }
-      fileLoadingCount++;
-      validate();
-    }
+                });
+                rthr.start();
+              }
+            };
+          });
+          VamsasStMenu.add(sessit);
+        }
+        // don't show an empty menu.
+        VamsasStMenu.setVisible(sess.length > 0);
 
-    public void stopLoading()
-    {
-      fileLoadingCount--;
-      if (fileLoadingCount < 1)
+      }
+      else
       {
-        if(progressPanel!=null)
-        {
-          this.getContentPane().remove(progressPanel);
-          progressPanel = null;
-        }
-        fileLoadingCount = 0;
+        jalview.bin.Cache.log.debug("No current vamsas sessions.");
+        VamsasStMenu.removeAll();
+        VamsasStMenu.setVisible(false);
       }
-      validate();
     }
+    else
+    {
+      // Not interested in the content. Just hide ourselves.
+      VamsasStMenu.setVisible(false);
+    }
+  }
 
-    public static int getViewCount(String viewId)
+  public void vamsasSave_actionPerformed(ActionEvent e)
+  {
+    if (v_client != null)
     {
-      int count = 0;
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-      for (int t = 0; t < frames.length; t++)
+      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)
       {
-        if (frames[t] instanceof AlignFrame)
+        java.io.File choice = chooser.getSelectedFile();
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+        String warnmsg = null;
+        String warnttl = null;
+        try
         {
-          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 ++;
-          }
+          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,
 
-      return count;
+          warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+        }
+      }
     }
-
-    public void explodeViews(AlignFrame af)
+  }
+
+  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)
     {
-      int size = af.alignPanels.size();
-      if(size<2)
-        return;
+      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);
+    }
 
-      for(int i=0; i<size; i++)
+    public void showMemoryUsage(boolean showMemoryUsage)
+    {
+      this.showMemoryUsage = showMemoryUsage;
+      if (showMemoryUsage)
       {
-        AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
-        AlignFrame newaf = new AlignFrame(ap);
-        if(ap.av.explodedPosition!=null)
-          newaf.setBounds(ap.av.explodedPosition);
-
-        ap.av.gatherViewsHere = false;
-
-        addInternalFrame(newaf, af.getTitle(),
-                         AlignFrame.DEFAULT_WIDTH,
-                         AlignFrame.DEFAULT_HEIGHT);
+        Thread worker = new Thread(this);
+        worker.start();
       }
+    }
 
-      af.alignPanels.clear();
-      af.closeMenuItem_actionPerformed(true);
-
+    public boolean isShowMemoryUsage()
+    {
+      return showMemoryUsage;
     }
 
-    public void gatherViews(AlignFrame source)
+    public void run()
     {
-      source.viewport.gatherViewsHere = true;
-      source.viewport.explodedPosition = source.getBounds();
-      JInternalFrame[] frames = desktop.getAllFrames();
-      String viewId = source.viewport.sequenceSetID;
+      df = java.text.NumberFormat.getNumberInstance();
+      df.setMaximumFractionDigits(2);
+      runtime = Runtime.getRuntime();
 
-      for (int t = 0; t < frames.length; t++)
+      while (showMemoryUsage)
       {
-        if (frames[t] instanceof AlignFrame && frames[t] != source)
+        try
         {
-          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);
-            }
-          }
+          Thread.sleep(3000);
+          maxMemory = runtime.maxMemory() / 1048576f;
+          allocatedMemory = runtime.totalMemory() / 1048576f;
+          freeMemory = runtime.freeMemory() / 1048576f;
+          totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
+
+          percentUsage = (totalFreeMemory / maxMemory) * 100;
 
-          if (gatherThis)
+          // if (percentUsage < 20)
           {
-            af.alignPanels.clear();
-            af.closeMenuItem_actionPerformed(true);
+            // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
+            // Color.red);
+            // instance.set.setBorder(border1);
           }
+          repaint();
+
+        } catch (Exception ex)
+        {
+          ex.printStackTrace();
         }
       }
-
     }
 
-    jalview.gui.VamsasClient v_client=null;
-    public void vamsasLoad_actionPerformed(ActionEvent e)
+    public void paintComponent(Graphics g)
     {
-      if (v_client==null) {
-        // Start a session.
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-            getProperty("LAST_DIRECTORY"));
+      if (showMemoryUsage)
+      {
+        if (percentUsage < 20)
+          g.setColor(Color.red);
 
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Load Vamsas file");
-        chooser.setToolTipText("Import");
+        g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+                + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
+                + df.format(percentUsage) + "%", 10, getHeight()
+                - g.getFontMetrics().getHeight());
+      }
+    }
+
+  }
 
-        int value = chooser.showOpenDialog(this);
+  protected JMenuItem groovyShell;
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+  public void doGroovyCheck()
+  {
+    if (jalview.bin.Cache.groovyJarsPresent())
+    {
+      groovyShell = new JMenuItem();
+      groovyShell.setText("Groovy Console...");
+      groovyShell.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
         {
-          v_client = new jalview.gui.VamsasClient(this,
-              chooser.getSelectedFile());
-          this.vamsasLoad.setText("Session Update");
-          this.vamsasStop.setVisible(true);
-          v_client.initial_update();
-          v_client.startWatcher();
+          groovyShell_actionPerformed(e);
         }
-      } else {
-        // store current data in session.
-        v_client.push_update();
-      }
+      });
+      toolsMenu.add(groovyShell);
+      groovyShell.setVisible(true);
     }
-    public void vamsasStop_actionPerformed(ActionEvent e) {
-      if (v_client!=null) {
-        v_client.end_session();
-        v_client=null;
-        this.vamsasStop.setVisible(false);
-        this.vamsasLoad.setText("Start Vamsas Session...");
+  }
+
+  /**
+   * 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();
     }
-    /**
-     * hide vamsas user gui bits when a vamsas document event is being handled.
-     * @param b true to hide gui, false to reveal gui
-     */
-    public void setVamsasUpdate(boolean b) {
-      jalview.bin.Cache.log.debug("Setting gui for Vamsas update "+(b ? "in progress" : "finished"));
-      vamsasLoad.setVisible(!b);
-      vamsasStop.setVisible(!b);
-
+    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));
+    }
+  }
+
+  /**
+   * 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;
+  }
 }
-