X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9d58c7badef5f205da54936e314b68d820a49115;hb=174230b4233d9ce80f94527768d2cd2f76da11ab;hp=05486468880ba3346b0493cd433f1073ab66deea;hpb=b618755c67d798ace34ebd6d0f384e913e8574c9;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 0548646..9d58c7b 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,401 +1,669 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.gui.*;
 import jalview.io.*;
-import jalview.datamodel.*;
-import javax.swing.*;
+
 import java.awt.*;
-import java.awt.event.*;
+import java.awt.datatransfer.*;
 import java.awt.dnd.*;
+import java.awt.event.*;
+import java.util.*;
+
 import javax.swing.*;
-import java.awt.datatransfer.*;
-import jalview.bin.Cache;
 
 
-public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop extends jalview.jbgui.GDesktop
+    implements DropTargetListener, ClipboardOwner
 {
-  public static JDesktopPane desktop;
-  static int openFrameCount = 0;
-  static final int xOffset = 30, yOffset = 30;
-
-  public Desktop()
-  {
-    Image image =null;
-    try{
-      java.net.URL url = getClass().getResource("/images/logo.gif");
-      if(url!=null)
+    /** 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;
+
+        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.
+
+    }
+
+    /**
+     * 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"))
       {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        mt.waitForID(0);
-        setIconImage(image);
+        return;
       }
 
-    }catch(Exception ex){}
 
-    setTitle("Jalview 2005");
-    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    desktop = new JDesktopPane();
-    desktop.setBackground(Color.white);
-    setContentPane(desktop);
-    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+        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)
+    {}
 
-    // This line prevents Windows Look&Feel resizing all new windows to maximum
-    // if previous window was maximised
-    desktop.setDesktopManager( new DefaultDesktopManager() );
+    public void dragExit(DropTargetEvent evt)
+    {}
 
+    public void dragOver(DropTargetDragEvent evt)
+    {}
 
-    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");
+    public void dropActionChanged(DropTargetDragEvent evt)
+    {}
 
-    if(x!=null && y!=null && width!=null && height!=null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void drop(DropTargetDropEvent evt)
     {
-      setBounds( Integer.parseInt(x), Integer.parseInt(y),
-                 Integer.parseInt(width), Integer.parseInt(height));
+        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();
+          }
+        }
     }
-    else
-      setBounds( (int)(screenSize.width-900)/2,
-           (int)(screenSize.height-650)/2,
-          900 ,
-          650);
 
-this.addWindowListener(new WindowAdapter()
-{
-public void windowClosing(WindowEvent evt)
-{
- jalview.bin.Cache.setProperty("SCREEN_X",
-                               getBounds().x + "");
- jalview.bin.Cache.setProperty("SCREEN_Y",
-                               getBounds().y + "");
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
-}
-});
-setVisible(true);
-
-this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
-
-/////////Add a splashscreen on startup
-   /////////Add a splashscreen on startup
-    JInternalFrame frame = new JInternalFrame();
-
-    SplashScreen splash = new SplashScreen(frame, image);
-    frame.setContentPane(splash);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    addInternalFrame(frame, "", 750,160, false);
-    frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));
-  }
-  public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
-  {
-    addInternalFrame(frame, title, w, h, true);
-  }
-
-  public static void addInternalFrame(final JInternalFrame frame, String title,
-                                      int w,
-                                      int h,
-                                      boolean resizable )
-  {
-   desktop.add(frame);
-   openFrameCount++;
-   try {
-       frame.setSelected(true);
-   } catch (java.beans.PropertyVetoException e) {}
-   frame.setTitle(title);
-   frame.setSize(w,h);
-   frame.setClosable(true);
-   frame.setResizable(resizable);
-   frame.setMaximizable(resizable);
-   frame.setIconifiable(resizable);
-   frame.setFrameIcon(null);
-   frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);
-   frame.toFront();
-   final JMenuItem menuItem = new JMenuItem(title);
-   frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-   {
-     public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
-     {
-       openFrameCount--;
-       windowMenu.remove(menuItem);
-     };
-   });
-
-   menuItem.addActionListener(new ActionListener()
+    /**
+     * 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)
     {
-      public void actionPerformed(ActionEvent e)
+      // 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)
       {
-        try{  frame.setSelected(true);   frame.setIcon(false); }
-        catch(java.beans.PropertyVetoException ex){};
+        st = new StringTokenizer(historyItems, "\t");
+
+        while (st.hasMoreTokens())
+        {
+          history.addItem(st.nextElement());
+        }
       }
-    });
 
-   frame.setVisible(true);
-   windowMenu.add(menuItem);
- }
+       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);
+    }
 
- public void dragEnter(DropTargetDragEvent evt){}
- public void dragExit(DropTargetEvent evt){}
- public void dragOver(DropTargetDragEvent evt){}
- public void dropActionChanged(DropTargetDragEvent evt){}
- public void drop(DropTargetDropEvent evt)
-{
-   Transferable t = evt.getTransferable();
-   if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
-     return;
-
-   evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-   try{
-     java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
-
-     for (int i = 0; i < files.size(); i++)
-     {
-       String file = files.get(i).toString();
-       String protocol = "File";
-       if(file.endsWith(".jar"))
-                Jalview2XML.LoadJalviewAlign(file);
-      else
+    /*
+     * 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")))
       {
-        String format = jalview.io.IdentifyFile.Identify(file, protocol);
-        LoadFile(file, protocol, format);
+        message.append("\n\n!! Jalview version "
+                       + jalview.bin.Cache.getProperty("LATEST_VERSION")
+                       + " is available for download from http://www.jalview.org !!\n");
+
       }
-     }
-
-   }catch(Exception ex){ex.printStackTrace();}
-  }
-
-
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
- {
-   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-       new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
-       new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}
-       ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Open local file");
-   chooser.setToolTipText("Open");
-   int value = chooser.showOpenDialog(this);
-   if(value == JalviewFileChooser.APPROVE_OPTION)
-   {
-     String choice =  chooser.getSelectedFile().getPath();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
-     if(chooser.getSelectedFormat().equals("Jalview"))
-     {
-       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");
-       Jalview2XML.LoadJalviewAlign(choice);
-     }
-     else
-     {
-       String format = IdentifyFile.Identify(choice, "File");
-       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
-       LoadFile(choice, "File", format);
-     }
-   }
- }
-
- public void LoadFile(String file, String protocol,  String format)
- {
-   LoadingThread loader = new LoadingThread(file, protocol, format);
-   loader.start();
- }
-
- class LoadingThread extends Thread
- {
-   String file, protocol, format;
-
-   public LoadingThread(String file, String protocol,  String format)
-   {
-     this.file = file;
-     this.protocol = protocol;
-     this.format = format;
-   }
-   public void run()
-   {
-     SequenceI [] sequences = null;
-
-     if (FormatAdapter.formats.contains(format))
-         sequences = FormatAdapter.readFile(file, protocol, format);
-
-     if (sequences != null && sequences.length>0)
-     {
-       AlignFrame af = new AlignFrame(new Alignment(sequences));
-       addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
-       af.currentFileFormat = format;
-       af.statusBar.setText("Successfully loaded file " + file);
-       try{
-           af.setMaximum(Preferences.showFullscreen);
-       }catch(Exception ex){}
-
-     }
-     else
-       JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"
-                            + "Formats currently supported are\n"
-                            + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!
-                            ,"Error loading file",
-                                     JOptionPane.WARNING_MESSAGE);
-
-   }
- }
-
-
- public void inputURLMenuItem_actionPerformed(ActionEvent e)
- {
-   String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",
-                                            "Input alignment from URL",
-                                            JOptionPane.QUESTION_MESSAGE,
-                                            null, null,
-                                            "http://www.").toString();
-   if (url == null)
-     return;
-
-   String format = IdentifyFile.Identify(url, "URL");
-
-   if (format.equals("URL NOT FOUND"))
-   {
-     JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,
-                                   "URL not found",
-                                   JOptionPane.WARNING_MESSAGE);
-     return;
-   }
-
-    LoadFile(url, "URL", format);
- }
-
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
- {
-   CutAndPasteTransfer cap = new CutAndPasteTransfer();
-   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 (FormatAdapter.formats.contains( format ))
-      sequences = FormatAdapter.readFile(cap.getText(), "Paste", format);
-
-
-      if(sequences!=null)
+
+      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)
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences));
-        af.currentFileFormat = format;
-        addInternalFrame(af, "Cut & Paste input - "+format,
-                         AlignFrame.NEW_WINDOW_WIDTH,
-                         AlignFrame.NEW_WINDOW_HEIGHT);
-        af.statusBar.setText("Successfully pasted alignment file");
+        jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+        vs.load(
+            chooser.getSelectedFile().getAbsolutePath()
+            );
       }
-      else
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"
-                                      +"Formats currently supported are\n"
-                                      +"Fasta, MSF, Clustal, BLC, PIR, MSP, and 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 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE
-                                       +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."
-                                       +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."
-                                       +"\nIf  you use JalView, please cite:"
-                                       +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""
-                                       +"\nBioinformatics,  2004 12;426-7.",
-                                         "About Jalview",
-                                         JOptionPane.INFORMATION_MESSAGE);
- }
-
- public void documentationMenuItem_actionPerformed(ActionEvent e)
- {
-   try
-   {
-      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-      java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");
-      javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);
-
-      javax.help.HelpBroker hb = hs.createHelpBroker();
-      hb.setLocation(new Point(200, 50));
-      hb.setSize(new Dimension(800,700));
-      hb.setCurrentID("home");
-      hb.setDisplayed(true);
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
- }
-
- protected void preferences_actionPerformed(ActionEvent e)
- {
-   Preferences pref = new Preferences();
- }
-
- public void saveState_actionPerformed(ActionEvent e)
- {
-   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-       getProperty("LAST_DIRECTORY"),
-       new String[]
-       {"jar"}, new String[]{"Jalview Project"}, "Jalview Project");
-
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Save State");
-   int value = chooser.showSaveDialog(this);
-   if (value == JalviewFileChooser.APPROVE_OPTION)
-   {
-     java.io.File choice = chooser.getSelectedFile();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-     Jalview2XML.SaveState(choice);
-   }
-
- }
-
-
- public void loadState_actionPerformed(ActionEvent e)
- {
-   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-       new String[]{"jar"}, new String[]{"Jalview Project"}, "Jalview Project");
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Restore state");
-   int value = chooser.showOpenDialog(this);
-   if(value == JalviewFileChooser.APPROVE_OPTION)
-   {
-     String choice =  chooser.getSelectedFile().getAbsolutePath();
-     jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
-     Jalview2XML.LoadJalviewAlign(choice);
-   }
- }
-}
 
+    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();
+    }
+
+}