X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9b1bef3047dae85856bf6f1ea5f656445b41b590;hb=1a56a24b084eadd78387eabf71dc7114e356bd00;hp=efa283cb1bc0e45188f2e683b7a60a52c4fc1db5;hpb=577f505f54fe343e89f581461e780ea8308c20ec;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index efa283c..9b1bef3 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,348 +1,804 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
-
-package jalview.gui;
-
-import jalview.gui.*;
-import jalview.io.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-
-
-public class Desktop extends jalview.jbgui.GDesktop
-{
-  public static JDesktopPane desktop;
-  static int openFrameCount = 0;
-  static final int xOffset = 30, yOffset = 30;
-
-  public Desktop()
-  {
-    Image image =null;
-    try{
-      java.net.URL url = getClass().getResource("/images/BartonGroupBanner.gif");
-      if(url!=null)
-      {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        mt.waitForID(0);
-        setIconImage(image);
-      }
-
-    }catch(Exception ex){}
-
-    setTitle("Jalview 2005");
-    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    setVisible(true);
-    desktop = new JDesktopPane();
-    setContentPane(desktop);
-    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
-    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    int width = 900, height = 650;
-    if(screenSize.getWidth()<width)
-      width = screenSize.width;
-    if(screenSize.getHeight()<height)
-      height = screenSize.height;
-
-    setBounds( (int)(screenSize.width-width)/2,
-               (int)(screenSize.height-height)/2,
-              width ,
-              height);
-
-
-   /////////Add a splashscreen on startup
-    JInternalFrame frame = new JInternalFrame();
-
-    SplashScreen splash = new SplashScreen(frame, image);
-    frame.setContentPane(splash);
-    desktop.add(frame);
-    frame.setVisible(true);
-    openFrameCount++;
-    try
-    {
-      frame.setSelected(true);
-    }
-    catch (java.beans.PropertyVetoException e)
-    {}
-    frame.setResizable(true);
-    frame.setSize(845, 200);
-    frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));
-    frame.setClosable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-    frame.setFrameIcon(null);
-
-  }
-
-  public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
-  {
-   desktop.add(frame);
-   frame.setVisible(true);
-   openFrameCount++;
-   try {
-       frame.setSelected(true);
-   } catch (java.beans.PropertyVetoException e) {}
-   frame.setTitle(title);
-   frame.setResizable(true);
-   frame.setSize(w,h);
-   frame.setClosable(true);
-   frame.setMaximizable(true);
-   frame.setIconifiable(true);
-   frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
-   frame.toFront();
-   final JMenuItem menuItem = new JMenuItem(title);
-   frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-                                   { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-                                     {
-                                       openFrameCount--;
-                                       windowMenu.remove(menuItem);
-                                     };
-                                   });
-
-   menuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        try{  frame.setSelected(true);   frame.setIcon(false); }
-        catch(java.beans.PropertyVetoException ex){};
-      }
-    });
-
-   windowMenu.add(menuItem);
- }
-
-
-
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
- {
-   JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Open local file");
-   chooser.setToolTipText("Open");
-   int value = chooser.showOpenDialog(this);
-   if(value == JFileChooser.APPROVE_OPTION)
-   {
-     String choice =  chooser.getSelectedFile().getPath();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-     String format = IdentifyFile.Identify(choice, "File");
-     LoadFile(choice, "File", format);
-   }
- }
-
- public void LoadFile(String file, String protocol,  String format)
- {
-   SequenceI [] sequences = null;
-
-   if (FormatProperties.contains(format))
-       sequences = FormatAdapter.read(file, protocol, format);
-
-   if (sequences != null)
-   {
-     AlignFrame af = new AlignFrame(new Alignment(sequences));
-     addInternalFrame(af, file, 700, 500);
-     af.statusBar.setText("Successfully loaded file " + file);
-
-
-   }
-   else
-     JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"
-                          + "Formats currently supported are\n"
-                          + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"
-                          ,"Error loading file",
-                                   JOptionPane.WARNING_MESSAGE);
-
- }
-
- public void inputURLMenuItem_actionPerformed(ActionEvent e)
- {
-   String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
-                                            "Input alignment from URL",
-                                            JOptionPane.QUESTION_MESSAGE);
-   if (url == null)
-     return;
-
-   String format = IdentifyFile.Identify(url, "URL");
-
-   System.out.println(format +" format");
-   if (format.equals("URL NOT FOUND"))
-   {
-     JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
-                                   "URL not found",
-                                   JOptionPane.WARNING_MESSAGE);
-     return;
-   }
-
-    LoadFile(url, "URL", format);
- }
-
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
- {
-   CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
-   int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",
-                                       JOptionPane.YES_NO_CANCEL_OPTION,
-                                       JOptionPane.PLAIN_MESSAGE,
-                                       null,
-                                       new Object[]{"Accept", "Cancel", }, null);
-
-
-  if(accept == JOptionPane.YES_OPTION)
-  {
-    String format = IdentifyFile.Identify(cap.getText(), "Paste");
-    SequenceI [] sequences = null;
-
-    if (FormatProperties.contains( format ))
-      sequences = FormatAdapter.read(cap.getText(), "Paste", format);
-
-
-      if(sequences!=null)
-      {
-        AlignFrame af = new AlignFrame(new Alignment(sequences));
-        addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);
-        af.statusBar.setText("Successfully pasted alignment file");
-      }
-      else
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
-                                      +"Formats currently supported are\n"
-                                      +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",
-                                      "Error parsing text", JOptionPane.WARNING_MESSAGE);
-
-   }
- }
-
-/*
-* Exit the program
-*/
- public void quit_actionPerformed(ActionEvent e)
- {
-   if(jalview.bin.Jalview.applet!=null)
-     jalview.bin.Jalview.applet.destroy();
-    else
-      System.exit(0);
- }
-
-
-
- public void aboutMenuItem_actionPerformed(ActionEvent e)
- {
-   JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                         "JalView 2005"
-                                       +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
-                                       +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
-                                       +"\nIf  you use JalView, please cite:  \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
-                                         "About Jalview",
-                                         JOptionPane.INFORMATION_MESSAGE);
- }
-
- public void documentationMenuItem_actionPerformed(ActionEvent e)
- {
-   try
-   {
-      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-      java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
-      javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
-
-      javax.help.HelpBroker hb = hs.createHelpBroker();
-      hb.setLocation(new Point(200, 50));
-      hb.setSize(new Dimension(800,700));
-      hb.setCurrentID("home");
-      hb.setDisplayed(true);
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
- }
-
- static JInternalFrame conservationSlider;
- static JInternalFrame PIDSlider;
- public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
- {
-   SliderPanel sp = null;
-
-   if(conservationSlider == null)
-   {
-     sp = new SliderPanel(ap, 30, true, cs);
-     conservationSlider = new JInternalFrame();
-     conservationSlider.setContentPane(sp);
-     conservationSlider.setResizable(false);
-     addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);
-     conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-                  {
-                    public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)
-                    {
-                      conservationSlider = null;
-                    }
-                  });
-   }
-   else
-   {
-       conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");
-       sp = (SliderPanel)conservationSlider.getContentPane();
-       sp.cs = cs;
-   }
-
-   if(ap.av.alignment.getGroups()!=null)
-     sp.setAllGroupsCheckEnabled( true );
-   else
-     sp.setAllGroupsCheckEnabled( false);
-
-   return sp.getValue();
-
- }
-
- public static void hideConservationSlider()
- {
-  try{
-    conservationSlider.setClosed(true);
-    conservationSlider = null;
-  }catch(Exception ex){}
-}
-
-
- public static void hidePIDSlider()
- {
-   try{
-     PIDSlider.setClosed(true);
-     PIDSlider = null;
-   }catch(Exception ex){}
- }
-
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)
- {
-   SliderPanel pid = null;
-   if(PIDSlider == null)
-   {
-     pid = new SliderPanel(ap, 50, false, cs);
-     PIDSlider = new JInternalFrame();
-     PIDSlider.setContentPane(pid);
-     PIDSlider.setResizable(false);
-     addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);
-   }
-   else
-   {
-       PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");
-       pid = (SliderPanel)PIDSlider.getContentPane();
-       pid.cs = cs;
-   }
-
-   if (ap.av.alignment.getGroups() != null)
-     pid.setAllGroupsCheckEnabled(true);
-   else
-     pid.setAllGroupsCheckEnabled(false);
-
-
-   return pid.getValue();
-
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.io.*;
+
+import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import java.awt.event.*;
+import java.util.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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;
+
+    static int fileLoadingCount= 0;
+
+    /**
+     * Creates a new Desktop object.
+     */
+    public Desktop()
+    {
+        instance = this;
+        doVamsasClientCheck();
+        Image image = null;
+
+        try
+        {
+            java.net.URL url = getClass().getResource("/images/logo.gif");
+
+            if (url != null)
+            {
+                image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+
+                MediaTracker mt = new MediaTracker(this);
+                mt.addImage(image, 0);
+                mt.waitForID(0);
+                setIconImage(image);
+            }
+        }
+        catch (Exception ex)
+        {
+        }
+
+        setTitle("Jalview "+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);
+        }
+
+        this.addWindowListener(new WindowAdapter()
+            {
+                public void windowClosing(WindowEvent evt)
+                {
+                    quit();
+                }
+            });
+
+        this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+
+        /////////Add a splashscreen on startup
+        /////////Add a splashscreen on startup
+        JInternalFrame frame = new JInternalFrame();
+
+        SplashScreen splash = new SplashScreen(frame, image);
+        frame.setContentPane(splash);
+        frame.setLayer(JLayeredPane.PALETTE_LAYER);
+        frame.setLocation((int) ((getWidth() - 750) / 2),
+            (int) ((getHeight() - 160) / 2));
+
+        addInternalFrame(frame, "", 750, 160, false);
+
+        discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+    }
+
+    private void doVamsasClientCheck() {
+      if (jalview.bin.Cache.vamsasJarsPresent()) {
+        VamsasMenu.setVisible(true);
+        vamsasLoad.setVisible(true);
+      }
+
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param frame DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     * @param w DOCUMENT ME!
+     * @param h DOCUMENT ME!
+     */
+    public static synchronized void addInternalFrame(final JInternalFrame frame,
+        String title, int w, int h)
+    {
+        addInternalFrame(frame, title, w, h, true);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param frame DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     * @param w DOCUMENT ME!
+     * @param h DOCUMENT ME!
+     * @param resizable DOCUMENT ME!
+     */
+    public static synchronized void addInternalFrame(final JInternalFrame frame,
+        String title, int w, int h, boolean resizable)
+    {
+
+      frame.setTitle(title);
+      if(frame.getWidth()<1 || frame.getHeight()<1)
+      {
+        frame.setSize(w, h);
+      }
+      // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
+      // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
+      // IF JALVIEW IS RUNNING HEADLESS
+      /////////////////////////////////////////////////
+      if (System.getProperty("java.awt.headless") != null
+          && System.getProperty("java.awt.headless").equals("true"))
+      {
+        return;
+      }
+
+
+        openFrameCount++;
+
+        frame.setVisible(true);
+        frame.setClosable(true);
+        frame.setResizable(resizable);
+        frame.setMaximizable(resizable);
+        frame.setIconifiable(resizable);
+        frame.setFrameIcon(null);
+
+        if (frame.getX()<1 && frame.getY()<1)
+       {
+         frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
+       }
+
+        final JMenuItem menuItem = new JMenuItem(title);
+        frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+            {
+              public void internalFrameActivated(javax.swing.event.
+                                                 InternalFrameEvent evt)
+              {
+                JInternalFrame itf = desktop.getSelectedFrame();
+                if (itf != null)
+                  itf.requestFocus();
+
+              }
+
+                public void internalFrameClosed(
+                    javax.swing.event.InternalFrameEvent evt)
+                {
+                    openFrameCount--;
+                    windowMenu.remove(menuItem);
+                    JInternalFrame itf = desktop.getSelectedFrame();
+                       if (itf != null)
+                        itf.requestFocus();
+                }
+                ;
+            });
+
+        menuItem.addActionListener(new ActionListener()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    try
+                    {
+                        frame.setSelected(true);
+                        frame.setIcon(false);
+                    }
+                    catch (java.beans.PropertyVetoException ex)
+                    {
+
+                    }
+                }
+            });
+
+        windowMenu.add(menuItem);
+
+        desktop.add(frame);
+        frame.toFront();
+        try{
+          frame.setSelected(true);
+          frame.requestFocus();
+        }catch(java.beans.PropertyVetoException ve)
+        {}
+    }
+
+    public void lostOwnership(Clipboard clipboard, Transferable contents)
+    {
+      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)
+    {
+        Transferable t = evt.getTransferable();
+        java.util.List files = null;
+
+        try
+        {
+          DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
+          if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+          {
+            //Works on Windows and MacOSX
+            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+            files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
+          }
+          else if (t.isDataFlavorSupported(uriListFlavor))
+          {
+            // This is used by Unix drag system
+            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+            String data = (String) t.getTransferData(uriListFlavor);
+            files = new java.util.ArrayList(1);
+            for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+                data,
+                "\r\n");
+                 st.hasMoreTokens(); )
+            {
+              String s = st.nextToken();
+              if (s.startsWith("#"))
+              {
+                // the line is a comment (as per the RFC 2483)
+                continue;
+              }
+
+              java.net.URI uri = new java.net.URI(s);
+              java.io.File file = new java.io.File(uri);
+              files.add(file);
+            }
+          }
+        }
+        catch (Exception e)
+        {
+          e.printStackTrace();
+        }
+
+        if (files != null)
+        {
+          try
+          {
+            for (int i = 0; i < files.size(); i++)
+            {
+              String file = files.get(i).toString();
+              String protocol = FormatAdapter.FILE;
+              String format = null;
+
+              if (file.endsWith(".jar"))
+              {
+                format = "Jalview";
+
+              }
+              else
+              {
+                format = new IdentifyFile().Identify(file,
+                                                          protocol);
+              }
+
+
+              new FileLoader().LoadFile(file, protocol, format);
+
+            }
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
+        }
+    }
+
+    /**
+     * 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());
+
+            String format = null;
+            if (chooser.getSelectedFormat().equals("Jalview"))
+            {
+                format = "Jalview";
+            }
+            else
+            {
+                format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
+            }
+
+            if (viewport != null)
+              new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+            else
+              new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+        }
+    }
+
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+    {
+      // This construct allows us to have a wider textfield
+      // for viewing
+      JLabel label = new JLabel("Enter URL of Input File");
+      final JComboBox history = new JComboBox();
+
+      JPanel panel = new JPanel(new GridLayout(2,1));
+      panel.add(label);
+      panel.add(history);
+      history.setPreferredSize(new Dimension(400,20));
+      history.setEditable(true);
+      history.addItem("http://www.");
+
+      String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+
+      StringTokenizer st;
+
+      if (historyItems != null)
+      {
+        st = new StringTokenizer(historyItems, "\t");
+
+        while (st.hasMoreTokens())
+        {
+          history.addItem(st.nextElement());
+        }
+      }
+
+       int reply = JOptionPane.showInternalConfirmDialog(desktop,
+          panel, "Input Alignment From URL",
+          JOptionPane.OK_CANCEL_OPTION );
+
+
+        if (reply != JOptionPane.OK_OPTION )
+        {
+            return;
+        }
+
+        String url = history.getSelectedItem().toString();
+
+        if (url.toLowerCase().endsWith(".jar"))
+        {
+          if (viewport != null)
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+          else
+            new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+        }
+        else
+        {
+          String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+
+          if (format.equals("URL NOT FOUND"))
+          {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                  "Couldn't locate " + url,
+                                                  "URL not found",
+                                                  JOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+
+          if (viewport != null)
+            new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+          else
+            new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
+    {
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
+        cap.setForInput(viewport);
+        Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+    }
+
+    /*
+     * Exit the program
+     */
+    public void quit()
+    {
+        jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
+        jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
+        jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
+        jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
+        System.exit(0);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void aboutMenuItem_actionPerformed(ActionEvent e)
+    {
+      StringBuffer message = new StringBuffer("JalView version " +
+                                              jalview.bin.Cache.getProperty(
+          "VERSION") +
+                                              "; last updated: " +
+                                              jalview.bin.
+                                              Cache.getDefault("BUILD_DATE", "unknown"));
+
+      if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
+          jalview.bin.Cache.getProperty("VERSION")))
+      {
+        message.append("\n\n!! Jalview version "
+                       + jalview.bin.Cache.getProperty("LATEST_VERSION")
+                       + " is available for download from http://www.jalview.org !!\n");
+
+      }
+
+      message.append( "\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
+            "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
+            "\nFor all issues relating to Jalview, email help@jalview.org" +
+            "\n\nIf  you use JalView, please cite:" +
+            "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
+            "\nBioinformatics,  2004 20;426-7.");
+
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+           message.toString(), "About Jalview",
+            JOptionPane.INFORMATION_MESSAGE);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void documentationMenuItem_actionPerformed(ActionEvent e)
+    {
+        try
+        {
+            ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+            java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+            javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+            javax.help.HelpBroker hb = hs.createHelpBroker();
+            hb.setCurrentID("home");
+            hb.setDisplayed(true);
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void preferences_actionPerformed(ActionEvent e)
+    {
+        new Preferences();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveState_actionPerformed(ActionEvent e)
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "jar" },
+                new String[] { "Jalview Project" }, "Jalview Project");
+
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save State");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            java.io.File choice = chooser.getSelectedFile();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+            new Jalview2XML().SaveState(choice);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void loadState_actionPerformed(ActionEvent e)
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "jar" },
+                new String[] { "Jalview Project" }, "Jalview Project");
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Restore state");
+
+        int value = chooser.showOpenDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            String choice = chooser.getSelectedFile().getAbsolutePath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+            new Jalview2XML().LoadJalviewAlign(choice);
+        }
+    }
+
+  /*  public void vamsasLoad_actionPerformed(ActionEvent e)
+    {
+      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)
+      {
+        jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+        vs.load(
+            chooser.getSelectedFile().getAbsolutePath()
+            );
+      }
+
+    }*/
+
+
+    public void inputSequence_actionPerformed(ActionEvent e)
+    {
+      new SequenceFetcher(null);
+    }
+
+    JPanel progressPanel;
+
+    public void startLoading(final String fileName)
+    {
+      if (fileLoadingCount == 0)
+      {
+        progressPanel = new JPanel(new BorderLayout());
+        JProgressBar progressBar = new JProgressBar();
+        progressBar.setIndeterminate(true);
+
+        progressPanel.add(new JLabel("Loading File: " + fileName + "   "),
+                          BorderLayout.WEST);
+
+        progressPanel.add(progressBar, BorderLayout.CENTER);
+
+        instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+      }
+      fileLoadingCount++;
+      validate();
+    }
+
+    public void stopLoading()
+    {
+      fileLoadingCount--;
+      if (fileLoadingCount < 1)
+      {
+        if(progressPanel!=null)
+        {
+          this.getContentPane().remove(progressPanel);
+          progressPanel = null;
+        }
+        fileLoadingCount = 0;
+      }
+      validate();
+    }
+
+    public static int getViewCount(String viewId)
+    {
+      int count = 0;
+      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+      for (int t = 0; t < frames.length; t++)
+      {
+        if (frames[t] instanceof AlignFrame)
+        {
+          AlignFrame af = (AlignFrame) frames[t];
+          for(int a=0; a<af.alignPanels.size(); a++)
+          {
+            if(viewId.equals(
+                ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )
+                )
+            count ++;
+          }
+        }
+      }
+
+      return count;
+    }
+
+    public void explodeViews(AlignFrame af)
+    {
+      int size = af.alignPanels.size();
+      if(size<2)
+        return;
+
+      for(int i=0; i<size; i++)
+      {
+        AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
+        AlignFrame newaf = new AlignFrame(ap);
+        if(ap.av.explodedPosition!=null)
+          newaf.setBounds(ap.av.explodedPosition);
+
+        ap.av.gatherViewsHere = false;
+
+        addInternalFrame(newaf, af.getTitle(),
+                         AlignFrame.DEFAULT_WIDTH,
+                         AlignFrame.DEFAULT_HEIGHT);
+      }
+
+      af.alignPanels.clear();
+      af.closeMenuItem_actionPerformed(null);
+
+    }
+
+    public void gatherViews(AlignFrame source)
+    {
+      source.viewport.gatherViewsHere = true;
+      source.viewport.explodedPosition = source.getBounds();
+      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+      String viewId = source.viewport.sequenceSetID;
+
+      for (int t = 0; t < frames.length; t++)
+      {
+        if (frames[t] instanceof AlignFrame && frames[t] != source)
+        {
+          AlignFrame af = (AlignFrame) frames[t];
+          boolean gatherThis = false;
+          for (int a = 0; a < af.alignPanels.size(); a++)
+          {
+            AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+            if (viewId.equals(ap.av.getSequenceSetId()))
+            {
+              gatherThis = true;
+              ap.av.gatherViewsHere = false;
+              ap.av.explodedPosition = af.getBounds();
+              source.addAlignmentPanel(ap, false);
+            }
+          }
+
+          if (gatherThis)
+          {
+            af.alignPanels.clear();
+            af.closeMenuItem_actionPerformed(null);
+          }
+        }
+      }
+
+    }
+
+    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);
+
+    }
+}
+