X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=2a1979e518621c7f53e675901da0019c8df86f37;hb=0a5c25233b642021bec70224aff9d405b70a3f72;hp=95c08a148a6f746c599a3dad56a20f1b7764a753;hpb=1d123ffc99d3e9fb14dd1440adcd8d60a938722f;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 95c08a1..2a1979e 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,60 +1,72 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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 javax.swing.*;
-import java.awt.datatransfer.*;
-import jalview.bin.Cache;
 
+import jalview.datamodel.*;
+import jalview.io.*;
 
-public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener
+public class Desktop
+    extends jalview.jbgui.GDesktop implements DropTargetListener
 {
   public static JDesktopPane desktop;
   static int openFrameCount = 0;
-  static final int xOffset = 30, yOffset = 30;
+  static final int xOffset = 30;
+  static final int yOffset = 30;
 
   public Desktop()
   {
-    Image image =null;
-    try{
+    Image image = null;
+
+    try
+    {
       java.net.URL url = getClass().getResource("/images/logo.gif");
-      if(url!=null)
+
+      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){}
+    }
+    catch (Exception ex)
+    {
+    }
 
     setTitle("Jalview 2005");
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
     desktop = new JDesktopPane();
- //   desktop.setBackground(Color.white);
+    desktop.setBackground(Color.white);
     setContentPane(desktop);
     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() );
-
+    desktop.setDesktopManager(new DefaultDesktopManager());
 
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
     String x = jalview.bin.Cache.getProperty("SCREEN_X");
@@ -62,288 +74,397 @@ public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListene
     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)
+    if ( (x != null) && (y != null) && (width != null) && (height != null))
     {
-      setBounds( Integer.parseInt(x), Integer.parseInt(y),
-                 Integer.parseInt(width), Integer.parseInt(height));
+      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);
+    {
+      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.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent evt)
+      {
+        quit();
+      }
+    });
+    setVisible(true);
 
-this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
-/////////Add a splashscreen on startup
-   /////////Add a splashscreen on startup
+    /////////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));
+    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)
+
+  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 )
+  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()
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        try{  frame.setSelected(true);   frame.setIcon(false); }
-        catch(java.beans.PropertyVetoException ex){};
+        try
+        {
+          frame.setSelected(true);
+          frame.setIcon(false);
+        }
+        catch (java.beans.PropertyVetoException ex)
+        {
+        }
+
+        ;
       }
     });
 
-   frame.setVisible(true);
-   windowMenu.add(menuItem);
- }
+    frame.setVisible(true);
+    windowMenu.add(menuItem);
+  }
 
- 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";
-       String format = jalview.io.IdentifyFile.Identify(file, protocol);
-       LoadFile(file, protocol, format);
-     }
-
-   }catch(Exception ex){ex.printStackTrace();}
+  public void dragEnter(DropTargetDragEvent evt)
+  {
   }
 
+  public void dragExit(DropTargetEvent evt)
+  {
+  }
 
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
- {
-   JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-       new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");
-   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", choice);
-     String format = IdentifyFile.Identify(choice, "File");
-     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.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 or PFAM" // JBPNote - message should be generated through FormatAdapter!
-                            ,"Error loading file",
-                                     JOptionPane.WARNING_MESSAGE);
-
-   }
- }
-
-
- public void inputURLMenuItem_actionPerformed(ActionEvent e)
- {
-   JOptionPane op = new JOptionPane();
-
-   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;
-   }
+  public void dragOver(DropTargetDragEvent evt)
+  {
+  }
 
-    LoadFile(url, "URL", format);
- }
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {
+  }
 
- 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);
+  public void drop(DropTargetDropEvent evt)
+  {
+    Transferable t = evt.getTransferable();
 
+    if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+    {
+      return;
+    }
 
-  if(accept == JOptionPane.YES_OPTION)
-  {
-    String format = IdentifyFile.Identify(cap.getText(), "Paste");
-    SequenceI [] sequences = null;
+    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 
-    if (FormatAdapter.formats.contains( format ))
-      sequences = FormatAdapter.readFile(cap.getText(), "Paste", format);
+    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
+        {
+          String format = jalview.io.IdentifyFile.Identify(file,
+              protocol);
+          LoadFile(file, protocol, format);
+        }
+      }
+    }
+    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(sequences!=null)
+      if (chooser.getSelectedFormat().equals("Jalview"))
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences));
-        addInternalFrame(af, "Cut & Paste input - "+format,
-                         AlignFrame.NEW_WINDOW_WIDTH,
-                         AlignFrame.NEW_WINDOW_HEIGHT);
-        af.statusBar.setText("Successfully pasted alignment file");
+        jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");
+        Jalview2XML.LoadJalviewAlign(choice);
       }
       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);
+      {
+        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();
+  }
 
-/*
-* Exit the program
-*/
- public void quit_actionPerformed(ActionEvent e)
- {
-   if(jalview.bin.Jalview.applet!=null)
-     jalview.bin.Jalview.applet.destroy();
+  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();
+    cap.setForInput();
+    Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+  }
+
+  /*
+   * Exit the program
+   */
+  public void quit()
+  {
+    if (jalview.bin.Jalview.applet != null)
+    {
+      jalview.bin.Jalview.applet.destroy();
+    }
     else
+    {
+      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);
- }
-
-
-
- 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
-   {
+    }
+  }
+
+  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." +
+                                          "\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 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);
+      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.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();
- }
+    }
+    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);
+    }
+  }
+
+  class LoadingThread
+      extends Thread
+  {
+    String file;
+    String protocol;
+    String 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);
+      }
+    }
+  }
+}