X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=263eb1876260d2a832528d2ea99538b57a157335;hb=495723ac6f2a30ba8d7f5e65b0723e2ba8f121e1;hp=6d8f125cb19acd2d6b4706502ca87475be634e78;hpb=9961a60fb0e1ab87e60dc301485b00d058abf9e5;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6d8f125..263eb18 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -23,674 +23,764 @@ 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.*;
 
-
 /**
  * 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
 {
-    /** DOCUMENT ME!! */
-    public static Desktop instance;
-    public static JDesktopPane desktop;
-    static int openFrameCount = 0;
-    static final int xOffset = 30;
-    static final int yOffset = 30;
-    public static jalview.ws.Discoverer discoverer;
-
-    public static Object [] jalviewClipboard;
-    public static boolean internalCopy = false;
-
-    static int fileLoadingCount= 0;
-
-    /**
-     * Creates a new Desktop object.
-     */
-    public Desktop()
-    {
-        instance = this;
-        doVamsasClientCheck();
-        Image image = null;
+  /** DOCUMENT ME!! */
+  public static Desktop instance;
 
-        try
-        {
-            java.net.URL url = getClass().getResource("/images/logo.gif");
+  //Need to decide if the Memory Usage is to be included in
+  //Next release or not.
+ // public static MyDesktopPane desktop;
+   public static JDesktopPane desktop;
 
-            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)
-        {
-        }
+  static int openFrameCount = 0;
+  static final int xOffset = 30;
+  static final int yOffset = 30;
+  public static jalview.ws.Discoverer discoverer;
 
-        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))
-        {
-            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);
-        }
+  public static Object[] jalviewClipboard;
+  public static boolean internalCopy = false;
 
-        this.addWindowListener(new WindowAdapter()
-            {
-                public void windowClosing(WindowEvent evt)
-                {
-                    quit();
-                }
-            });
+  static int fileLoadingCount = 0;
 
-        this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+  /**
+   * Creates a new Desktop object.
+   */
+  public Desktop()
+  {
+    instance = this;
+    doVamsasClientCheck();
+    doGroovyCheck();
 
-        /////////Add a splashscreen on startup
-        /////////Add a splashscreen on startup
-        JInternalFrame frame = new JInternalFrame();
 
-        SplashScreen splash = new SplashScreen(frame, image);
-        frame.setContentPane(splash);
-        frame.setLayer(JLayeredPane.PALETTE_LAYER);
-        frame.setLocation((int) ((getWidth() - 750) / 2),
-            (int) ((getHeight() - 160) / 2));
+    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 
-        addInternalFrame(frame, "", 750, 160, false);
+    desktop = new JDesktopPane();
+    desktop.setBackground(Color.white);
+    getContentPane().setLayout(new BorderLayout());
+    getContentPane().add(desktop, BorderLayout.CENTER);
+    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
 
-        discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
-    }
+    // This line prevents Windows Look&Feel resizing all new windows to maximum
+    // if previous window was maximised
+    desktop.setDesktopManager(new DefaultDesktopManager());
 
-    private void doVamsasClientCheck() {
-      if (jalview.bin.Cache.vamsasJarsPresent()) {
-        VamsasMenu.setVisible(true);
-        vamsasLoad.setVisible(true);
-      }
+    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));
     }
-
-    /**
-     * 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)
+    else
     {
-        addInternalFrame(frame, title, w, h, true);
+      setBounds( (int) (screenSize.width - 900) / 2,
+                (int) (screenSize.height - 650) / 2, 900, 650);
     }
 
-    /**
-     * 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.addWindowListener(new WindowAdapter()
     {
-
-      frame.setTitle(title);
-      if(frame.getWidth()<1 || frame.getHeight()<1)
+      public void windowClosing(WindowEvent evt)
       {
-        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;
+        quit();
       }
+    });
 
+    this.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            if(SwingUtilities.isRightMouseButton(evt))
+            {
+              showPasteMenu(evt.getX(), evt.getY());
+            }
+          }
+        });
 
-        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);
-       }
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
-        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();
+    /////////Add a splashscreen on startup
+    /////////Add a splashscreen on startup
+    new SplashScreen();
 
-              }
 
+    discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+  }
 
-                public void internalFrameClosed(
-                    javax.swing.event.InternalFrameEvent evt)
-                {
-                    PaintRefresher.RemoveComponent(frame);
-                    openFrameCount--;
-                    windowMenu.remove(menuItem);
-                    JInternalFrame itf = desktop.getSelectedFrame();
-                       if (itf != null)
-                        itf.requestFocus();
-                }
-                ;
-            });
-
-        menuItem.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    try
-                    {
-                        frame.setSelected(true);
-                        frame.setIcon(false);
-                    }
-                    catch (java.beans.PropertyVetoException ex)
-                    {
-
-                    }
-                }
-            });
-
-        windowMenu.add(menuItem);
-
-        desktop.add(frame);
-        frame.toFront();
-        try{
-          frame.setSelected(true);
-          frame.requestFocus();
-        }catch(java.beans.PropertyVetoException ve)
-        {   }
+  private void doVamsasClientCheck()
+  {
+    if (jalview.bin.Cache.vamsasJarsPresent())
+    {
+      VamsasMenu.setVisible(true);
+      vamsasLoad.setVisible(true);
     }
+  }
 
-    public void lostOwnership(Clipboard clipboard, Transferable contents)
+  void showPasteMenu(int x, int y)
+  {
+    JPopupMenu popup = new JPopupMenu();
+    JMenuItem item = new JMenuItem("Paste To New Window");
+    item.addActionListener(new ActionListener()
     {
-      if (!internalCopy)
-        Desktop.jalviewClipboard = null;
+      public void actionPerformed(ActionEvent evt)
+      {
+        paste();
+      }
+    });
 
-      internalCopy = false;
-    }
+    popup.add(item);
+    popup.show(this, x, y);
+  }
 
-    public void dragEnter(DropTargetDragEvent evt)
-    {}
+  public void paste()
+  {
+    try
+    {
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
 
-    public void dragExit(DropTargetEvent evt)
-    {}
+      if (contents != null)
+      {
+        String file = (String) contents
+            .getTransferData(DataFlavor.stringFlavor);
 
-    public void dragOver(DropTargetDragEvent evt)
-    {}
+        String format = new IdentifyFile().Identify(file,
+                                                    FormatAdapter.PASTE);
 
-    public void dropActionChanged(DropTargetDragEvent evt)
-    {}
+        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void drop(DropTargetDropEvent evt)
+      }
+    }
+    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)
     {
-        Transferable t = evt.getTransferable();
-        java.util.List files = null;
+      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;
+    }
 
-        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;
-              }
+    openFrameCount++;
 
-              java.net.URI uri = new java.net.URI(s);
-              java.io.File file = new java.io.File(uri);
-              files.add(file);
-            }
-          }
-        }
-        catch (Exception e)
-        {      }
+    frame.setVisible(true);
+    frame.setClosable(true);
+    frame.setResizable(resizable);
+    frame.setMaximizable(resizable);
+    frame.setIconifiable(resizable);
+    frame.setFrameIcon(null);
 
-        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 (frame.getX() < 1 && frame.getY() < 1)
+    {
+      frame.setLocation(xOffset * openFrameCount,
+                        yOffset * ( (openFrameCount - 1) % 10) + yOffset);
+    }
 
-              if (file.endsWith(".jar"))
-              {
-                format = "Jalview";
+    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();
+        }
 
-              }
-              else
-              {
-                format = new IdentifyFile().Identify(file,
-                                                          protocol);
-              }
+      }
 
+      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();
+      }
+      ;
+    });
 
-              new FileLoader().LoadFile(file, protocol, format);
+    menuItem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          frame.setSelected(true);
+          frame.setIcon(false);
+        }
+        catch (java.beans.PropertyVetoException 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"),
-                new String[]
-                {
-                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-                    "jar"
-                },
-                new String[]
-                {
-                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-                }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Open local file");
-        chooser.setToolTipText("Open");
-
-        int value = chooser.showOpenDialog(this);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            String choice = chooser.getSelectedFile().getPath();
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
+    windowMenu.add(menuItem);
 
-            String format = null;
-            if (chooser.getSelectedFormat().equals("Jalview"))
-            {
-                format = "Jalview";
-            }
-            else
-            {
-                format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
-            }
+    desktop.add(frame);
+    frame.toFront();
+    try
+    {
+      frame.setSelected(true);
+      frame.requestFocus();
+    }
+    catch (java.beans.PropertyVetoException ve)
+    {}
+  }
 
-            if (viewport != null)
-              new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
-            else
-              new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
-        }
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    if (!internalCopy)
+    {
+      Desktop.jalviewClipboard = null;
     }
 
+    internalCopy = false;
+  }
 
+  public void dragEnter(DropTargetDragEvent evt)
+  {}
 
-    /**
-     * 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();
+  public void dragExit(DropTargetEvent evt)
+  {}
 
-      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.");
+  public void dragOver(DropTargetDragEvent evt)
+  {}
 
-      String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {}
 
-      StringTokenizer st;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void drop(DropTargetDropEvent evt)
+  {
+    Transferable t = evt.getTransferable();
+    java.util.List files = null;
 
-      if (historyItems != null)
+    try
+    {
+      DataFlavor uriListFlavor = new DataFlavor(
+          "text/uri-list;class=java.lang.String");
+      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
       {
-        st = new StringTokenizer(historyItems, "\t");
-
-        while (st.hasMoreTokens())
+        //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(); )
         {
-          history.addItem(st.nextElement());
+          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)
+    {}
 
-       int reply = JOptionPane.showInternalConfirmDialog(desktop,
-          panel, "Input Alignment From URL",
-          JOptionPane.OK_CANCEL_OPTION );
-
-
-        if (reply != JOptionPane.OK_OPTION )
+    if (files != null)
+    {
+      try
+      {
+        for (int i = 0; i < files.size(); i++)
         {
-            return;
-        }
+          String file = files.get(i).toString();
+          String protocol = FormatAdapter.FILE;
+          String format = null;
 
-        String url = history.getSelectedItem().toString();
+          if (file.endsWith(".jar"))
+          {
+            format = "Jalview";
 
-        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;
+            format = new IdentifyFile().Identify(file,
+                                                 protocol);
           }
 
-          if (viewport != null)
-            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
-          else
-            new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+          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"),
+        new String[]
+        {
+        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+        "jar"
+    },
+        new String[]
+        {
+        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+    }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Open local file");
+    chooser.setToolTipText("Open");
+
+    int value = chooser.showOpenDialog(this);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput(viewport);
-        Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+      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);
 
-    /*
-     * Exit the program
-     */
-    public void quit()
+    if (reply != JOptionPane.OK_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);
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void aboutMenuItem_actionPerformed(ActionEvent e)
+    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
     {
-      StringBuffer message = new StringBuffer("JalView version " +
-                                              jalview.bin.Cache.getProperty(
-          "VERSION") +
-                                              "; last updated: " +
-                                              jalview.bin.
-                                              Cache.getDefault("BUILD_DATE", "unknown"));
+      String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
 
-      if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
-          jalview.bin.Cache.getProperty("VERSION")))
+      if (format.equals("URL NOT FOUND"))
       {
-        message.append("\n\n!! Jalview version "
-                       + jalview.bin.Cache.getProperty("LATEST_VERSION")
-                       + " is available for download from http://www.jalview.org !!\n");
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              "Couldn't locate " + url,
+                                              "URL not found",
+                                              JOptionPane.WARNING_MESSAGE);
 
+        return;
       }
 
-      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,
+      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.toString(), "About Jalview",
-            JOptionPane.INFORMATION_MESSAGE);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void documentationMenuItem_actionPerformed(ActionEvent e)
+    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
     {
-        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);
+      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)
-        {     }
+      javax.help.HelpBroker hb = hs.createHelpBroker();
+      hb.setCurrentID("home");
+      hb.setDisplayed(true);
     }
+    catch (Exception ex)
+    {}
+  }
 
-    public void closeAll_actionPerformed(ActionEvent e)
+  public void closeAll_actionPerformed(ActionEvent e)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    for (int i = 0; i < frames.length; i++)
     {
-      JInternalFrame [] frames = desktop.getAllFrames();
-      for(int i=0; i<frames.length; i++)
+      try
       {
-        try{
         frames[i].setClosed(true);
-      }catch(java.beans.PropertyVetoException ex){}
       }
+      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);
+  }
 
-    public void raiseRelated_actionPerformed(ActionEvent e)
+  void closeAssociatedWindows()
+  {
+    reorderAssociatedWindows(false, true);
+  }
+
+  void reorderAssociatedWindows(boolean minimize, boolean close)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    if (frames == null || frames.length < 1)
     {
-      reorderAssociatedWindows(false, false);
+      return;
     }
 
-    public void minimizeAssociated_actionPerformed(ActionEvent e)
+    AlignViewport source = null, target = null;
+    if (frames[0] instanceof AlignFrame)
     {
-      reorderAssociatedWindows(true, false);
+      source = ( (AlignFrame) frames[0]).getCurrentView();
     }
-
-    void closeAssociatedWindows()
+    else if (frames[0] instanceof TreePanel)
     {
-      reorderAssociatedWindows(false, true);
+      source = ( (TreePanel) frames[0]).getViewPort();
     }
-
-    void reorderAssociatedWindows(boolean minimize, boolean close)
+    else if (frames[0] instanceof PCAPanel)
     {
-      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;
+      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 != null)
-        for (int i = 0; i < frames.length; i++)
+        if (source == target)
         {
-          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
           {
-            try
+            if (close)
+            {
+              frames[i].setClosed(true);
+            }
+            else
             {
-              if (close)
-                frames[i].setClosed(true);
-              else
+              frames[i].setIcon(minimize);
+              if (!minimize)
               {
-                frames[i].setIcon(minimize);
-                if (!minimize)
-                {
-                  frames[i].toFront();
-                }
+                frames[i].toFront();
               }
-
             }
-            catch (java.beans.PropertyVetoException ex)
-            {       }
+
           }
+          catch (java.beans.PropertyVetoException ex)
+          {}
         }
+      }
     }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void preferences_actionPerformed(ActionEvent e)
+  }
+
+  /**
+   * 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)
     {
-        new Preferences();
+      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 saveState_actionPerformed(ActionEvent e)
+  }
+
+  /**
+   * 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)
     {
-        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);
-        }
+      String choice = chooser.getSelectedFile().getAbsolutePath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                    chooser.getSelectedFile().getParent());
+      new Jalview2XML().LoadJalviewAlign(choice);
     }
+  }
 
   /*  public void vamsasLoad_actionPerformed(ActionEvent e)
     {
@@ -714,184 +804,362 @@ public class Desktop extends jalview.jbgui.GDesktop
     }*/
 
 
-    public void inputSequence_actionPerformed(ActionEvent e)
-    {
-      new SequenceFetcher(null);
-    }
+  public void inputSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(null);
+  }
 
-    JPanel progressPanel;
+  JPanel progressPanel;
 
-    public void startLoading(final String fileName)
+  public void startLoading(final String fileName)
+  {
+    if (fileLoadingCount == 0)
     {
-      if (fileLoadingCount == 0)
-      {
-        progressPanel = new JPanel(new BorderLayout());
-        JProgressBar progressBar = new JProgressBar();
-        progressBar.setIndeterminate(true);
+      progressPanel = new JPanel(new BorderLayout());
+      JProgressBar progressBar = new JProgressBar();
+      progressBar.setIndeterminate(true);
 
-        progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
-                          BorderLayout.WEST);
+      progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
+                        BorderLayout.WEST);
 
-        progressPanel.add(progressBar, BorderLayout.CENTER);
+      progressPanel.add(progressBar, BorderLayout.CENTER);
 
-        instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
-      }
-      fileLoadingCount++;
-      validate();
+      instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
     }
-
-    public void stopLoading()
+    fileLoadingCount++;
+    validate();
+  }
+
+  public void stopLoading()
+  {
+    fileLoadingCount--;
+    if (fileLoadingCount < 1)
     {
-      fileLoadingCount--;
-      if (fileLoadingCount < 1)
+      if (progressPanel != null)
       {
-        if(progressPanel!=null)
-        {
-          this.getContentPane().remove(progressPanel);
-          progressPanel = null;
-        }
-        fileLoadingCount = 0;
+        this.getContentPane().remove(progressPanel);
+        progressPanel = null;
       }
-      validate();
+      fileLoadingCount = 0;
     }
-
-    public static int getViewCount(String viewId)
+    validate();
+  }
+
+  public static int getViewCount(String viewId)
+  {
+    int count = 0;
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    for (int t = 0; t < frames.length; t++)
     {
-      int count = 0;
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-      for (int t = 0; t < frames.length; t++)
+      if (frames[t] instanceof AlignFrame)
       {
-        if (frames[t] instanceof AlignFrame)
+        AlignFrame af = (AlignFrame) frames[t];
+        for (int a = 0; a < af.alignPanels.size(); a++)
         {
-          AlignFrame af = (AlignFrame) frames[t];
-          for(int a=0; a<af.alignPanels.size(); a++)
+          if (viewId.equals(
+              ( (AlignmentPanel) af.alignPanels.elementAt(a)).av.
+              getSequenceSetId())
+              )
           {
-            if(viewId.equals(
-                ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )
-                )
-            count ++;
+            count++;
           }
         }
       }
-
-      return count;
     }
 
-    public void explodeViews(AlignFrame af)
+    return count;
+  }
+
+  public void explodeViews(AlignFrame af)
+  {
+    int size = af.alignPanels.size();
+    if (size < 2)
     {
-      int size = af.alignPanels.size();
-      if(size<2)
-        return;
+      return;
+    }
 
-      for(int i=0; i<size; i++)
+    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()))
       {
-        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);
+        newaf.setBounds(ap.av.explodedPosition);
       }
 
-      af.alignPanels.clear();
-      af.closeMenuItem_actionPerformed(true);
+      ap.av.gatherViewsHere = false;
 
+      addInternalFrame(newaf, af.getTitle(),
+                       AlignFrame.DEFAULT_WIDTH,
+                       AlignFrame.DEFAULT_HEIGHT);
     }
 
-    public void gatherViews(AlignFrame source)
-    {
-      source.viewport.gatherViewsHere = true;
-      source.viewport.explodedPosition = source.getBounds();
-      JInternalFrame[] frames = desktop.getAllFrames();
-      String viewId = source.viewport.sequenceSetID;
+    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++)
+    for (int t = 0; t < frames.length; t++)
+    {
+      if (frames[t] instanceof AlignFrame && frames[t] != source)
       {
-        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++)
         {
-          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()))
           {
-            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);
-            }
+            gatherThis = true;
+            ap.av.gatherViewsHere = false;
+            ap.av.explodedPosition = af.getBounds();
+            source.addAlignmentPanel(ap, false);
           }
+        }
 
-          if (gatherThis)
-          {
-            af.alignPanels.clear();
-            af.closeMenuItem_actionPerformed(true);
-          }
+        if (gatherThis)
+        {
+          af.alignPanels.clear();
+          af.closeMenuItem_actionPerformed(true);
         }
       }
+    }
+
+  }
+
+  jalview.gui.VamsasClient v_client = null;
+  public void vamsasLoad_actionPerformed(ActionEvent e)
+  {
+    if (v_client == null)
+    {
+      // 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");
+
+      int value = chooser.showOpenDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        v_client = new jalview.gui.VamsasClient(this,
+                                                chooser.getSelectedFile());
+        this.vamsasLoad.setText("Session Update");
+        this.vamsasStop.setVisible(true);
+        v_client.initial_update();
+        v_client.startWatcher();
+      }
+    }
+    else
+    {
+      // store current data in session.
+      v_client.push_update();
+    }
+  }
+
+  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...");
+    }
+  }
+
+  /**
+   * 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);
+
+  }
+
+  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);
+  }
+
+  /*DISABLED
+   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();
+      }
     }
 
-    jalview.gui.VamsasClient v_client=null;
-    public void vamsasLoad_actionPerformed(ActionEvent e)
+    public void run()
     {
-      if (v_client==null) {
-        // Start a session.
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-            getProperty("LAST_DIRECTORY"));
+      df = java.text.NumberFormat.getNumberInstance();
+      df.setMaximumFractionDigits(2);
+      runtime = Runtime.getRuntime();
 
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Load Vamsas file");
-        chooser.setToolTipText("Import");
+      while (showMemoryUsage)
+      {
+        try
+        {
+          Thread.sleep(3000);
+          maxMemory = runtime.maxMemory() / 1048576f;
+          allocatedMemory = runtime.totalMemory() / 1048576f;
+          freeMemory = runtime.freeMemory() / 1048576f;
+          totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
 
-        int value = chooser.showOpenDialog(this);
+          percentUsage = (totalFreeMemory / maxMemory) * 100;
+
+        //  if (percentUsage < 20)
+          {
+            //   border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red);
+            //    instance.set.setBorder(border1);
+          }
+          repaint();
 
-        if (value == JalviewFileChooser.APPROVE_OPTION)
+        }
+        catch (Exception ex)
         {
-          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();
+          ex.printStackTrace();
         }
-      } else {
-        // store current data in session.
-        v_client.push_update();
       }
     }
-    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...");
+
+    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());
       }
     }
-    /**
-     * 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);
-
+  }*/
+  protected JMenuItem groovyShell;
+  public void doGroovyCheck() {
+    if (jalview.bin.Cache.groovyJarsPresent())
+    {
+      groovyShell = new JMenuItem();
+      groovyShell.setText("Groovy Shell...");
+      groovyShell.addActionListener(new ActionListener()
+      {
+          public void actionPerformed(ActionEvent e) {
+              groovyShell_actionPerformed(e);
+          }
+      });
+      toolsMenu.add(groovyShell);
+      groovyShell.setVisible(true);
     }
-    /**
-     * 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);
+  }
+  /**
+   * Accessor method to quickly get all the AlignmentFrames
+   * loaded.
+   */
+  protected 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);
+    }
+  }
 }
-