X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=d5182df040fd7efbf39394636355b815545b4c00;hb=1ee8b306b296ea2724e128f66486675bdaac7a3d;hp=4156fa2b3de8acfcfd0bbe6e6be1b2b5f925b63c;hpb=f0c4c7517ae29233a1afbfefdb1a104917f996ee;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 4156fa2..d5182df 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,246 +1,607 @@
-/********************
- * 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 jalview.io.*;
+
 import java.awt.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
 import java.awt.event.*;
 
+import javax.swing.*;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 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 boolean splashScreenVisible = false;
-
-  public Desktop()
-  {
-    Image image =null;
-    try{
-      java.net.URL url = getClass().getResource("/BartonGroupBanner.gif");
-      if(url!=null)
+    /** DOCUMENT ME!! */
+    public static JDesktopPane desktop;
+    static int openFrameCount = 0;
+    static final int xOffset = 30;
+    static final int yOffset = 30;
+
+    /**
+     * Creates a new Desktop object.
+     */
+    public Desktop()
+    {
+        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 2005");
+        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+        desktop = new JDesktopPane();
+        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());
+
+        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);
+        addInternalFrame(frame, "", 750, 160, false);
+        frame.setLocation((int) ((getWidth() - 750) / 2),
+            (int) ((getHeight() - 160) / 2));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param frame DOCUMENT ME!
+     * @param title DOCUMENT ME!
+     * @param w DOCUMENT ME!
+     * @param h DOCUMENT ME!
+     */
+    public static 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 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()
+            {
+                public void actionPerformed(ActionEvent e)
+                {
+                    try
+                    {
+                        frame.setSelected(true);
+                        frame.setIcon(false);
+                    }
+                    catch (java.beans.PropertyVetoException ex)
+                    {
+                    }
+
+                    ;
+                }
+            });
+
+        frame.setVisible(true);
+        windowMenu.add(menuItem);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dragEnter(DropTargetDragEvent evt)
+    {
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dragExit(DropTargetEvent evt)
+    {
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dragOver(DropTargetDragEvent evt)
+    {
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void dropActionChanged(DropTargetDragEvent evt)
+    {
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    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 = null;
+
+                if (file.endsWith(".jar"))
+                {
+                  format = "Jalview";
+
+                }
+                else
+                {
+                    format = jalview.io.IdentifyFile.Identify(file,
+                            protocol);
+                }
+                LoadFile(file, protocol, format);
+            }
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    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());
+
+            String format = null;
+            if (chooser.getSelectedFormat().equals("Jalview"))
+            {
+              format = "Jalview";
+            }
+            else
+            {
+                format = IdentifyFile.Identify(choice, "File");
+            }
+
+            jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+            LoadFile(choice, "File", format);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     * @param protocol DOCUMENT ME!
+     * @param format DOCUMENT ME!
+     */
+    public void LoadFile(String file, String protocol, String format)
+    {
+        LoadingThread loader = new LoadingThread(file, protocol, format);
+        loader.start();
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param file DOCUMENT ME!
+     * @param protocol DOCUMENT ME!
+     * @param format DOCUMENT ME!
+     */
+    public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format)
+    {
+        LoadingThread loader = new LoadingThread(file, protocol, format);
+        loader.start();
+
+        while (loader.isAlive())
+        {
+          try
+          {
+            Thread.sleep(50);
+          }
+          catch (Exception ex)
+          {}
+        }
+
+      return loader.af;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    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;
+        }
+
+        if (url.trim().toLowerCase().endsWith(".jar"))
+        {
+               jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
+               Jalview2XML.LoadJalviewAlign(url);
+        }
+        else
+        {
+
+          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);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    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()
+    {
+        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 2005 version " +
+                                              jalview.bin.Cache.getProperty(
+          "VERSION") +
+                                              "; last updated: " +
+                                              jalview.bin.
+                                              Cache.getProperty("BUILD_DATE"));
+
+      if (!jalview.bin.Cache.getProperty("jalview.version").equals(
+          jalview.bin.Cache.getProperty("VERSION")))
       {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        mt.waitForID(0);
-        setIconImage(image);
-      }
+        message.append("\n\n!! Jalview version "
+                       + jalview.bin.Cache.getProperty("jalview.version")
+                       + " is available for download from http://www.jalview.org !!\n");
 
-    }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();
-    setBounds( (int)(screenSize.getWidth()-1200)/2,
-               (int)(screenSize.getHeight()-800)/2,
-              1200 ,
-              800);
-
-
-   /////////Add a splashscreen on startup
-    JInternalFrame frame = new JInternalFrame();
-
-    SplashScreen splash = new SplashScreen(frame, image);
-    frame.setContentPane(splash);
-    addInternalFrame(frame, "",845,200);
-    splashScreenVisible = true;
-
-    frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));
-    frame.setClosable(false);
-    frame.setIconifiable(false);
-    frame.setMaximizable(false);
-    frame.setFrameIcon(null);
-    splashScreenVisible = false;
-
-  }
-
-  public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)
-  {
-   if(!splashScreenVisible)
-      frame.setVisible(true); //necessary as of 1.3
-   desktop.add(frame);
-   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.LAST_DIRECTORY);
-   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.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(this,  "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(this,"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(this,"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, 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(this, "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)
- {
-   this.setVisible(false);
-   System.exit(0);
- }
-
-
- protected void colourIndexMenuItem_actionPerformed(ActionEvent e)
- {
-   ColourKey colourKey = new ColourKey(null);
-   addInternalFrame(colourKey, "Colour scheme key", 400, 320);
- }
-
-
- public void aboutMenuItem_actionPerformed(ActionEvent e)
- {
-   JOptionPane.showInternalMessageDialog(desktop,
-                                         "JalView 2005"
-                                       +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse and 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{
-     jalview.util.BrowserLauncher.openURL("http://jalview.org/documentation.html");
-   }catch(Exception ex){}
- }
-
 
+      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 12;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.setLocation(new Point(200, 50));
+            hb.setSize(new Dimension(800, 700));
+            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());
+            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());
+            Jalview2XML.LoadJalviewAlign(choice);
+        }
+    }
+
+    class LoadingThread extends Thread
+    {
+        String file;
+        String protocol;
+        String format;
+        AlignFrame af;
+
+        public LoadingThread(String file, String protocol, String format)
+        {
+            this.file = file;
+            this.protocol = protocol;
+            this.format = format;
+        }
+
+        public void run()
+        {
+            SequenceI[] sequences = null;
+
+            if(format.equalsIgnoreCase("Jalview"))
+            {
+              Jalview2XML.LoadJalviewAlign(file);
+            }
+            else
+            {
+              if (FormatAdapter.formats.contains(format))
+              {
+                sequences = FormatAdapter.readFile(file, protocol, format);
+              }
+
+              if ( (sequences != null) && (sequences.length > 0))
+              {
+                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);
+              }
+            }
+        }
+    }
 }