X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=ed968f89b942ea534c9daaeede74e8dc890e8ddb;hb=ccc0d91abe38690088a6050faba8ef66cde1f271;hp=163e297c9475ff21bf323cc8670b13f31c43bcc5;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 163e297..ed968f8 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,752 +1,1393 @@
-/*
- * 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;
-
-        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"))
-      {
-        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;
-      af.closeMenuItem_actionPerformed(null);
-
-      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;
-
-        PaintRefresher.Register(ap.seqPanel.seqCanvas, ap.av.getSequenceSetId());
-        PaintRefresher.Register(ap.idPanel.idCanvas, ap.av.getSequenceSetId());
-        PaintRefresher.Register(ap, ap.av.getSequenceSetId());
-
-
-        newaf.viewport = ap.av;
-        addInternalFrame(newaf, af.getTitle(),
-                         AlignFrame.DEFAULT_WIDTH,
-                         AlignFrame.DEFAULT_HEIGHT);
-      }
-
-    }
-
-    public void gatherViews(AlignFrame source)
-    {
-      source.viewport.gatherViewsHere = true;
-      source.viewport.explodedPosition = source.getBounds();
-      JInternalFrame[] frames = Desktop.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);
-            }
-          }
-          if (gatherThis)
-            af.closeMenuItem_actionPerformed(null);
-        }
-      }
-
-    }
-
-
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * 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.lang.reflect.Constructor;
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Desktop
+    extends jalview.jbgui.GDesktop implements DropTargetListener,
+    ClipboardOwner
+{
+  /** DOCUMENT ME!! */
+  public static Desktop instance;
+
+  //Need to decide if the Memory Usage is to be included in
+  //Next release or not.
+  public static MyDesktopPane desktop;
+  // public static JDesktopPane desktop;
+
+
+  static int openFrameCount = 0;
+  static final int xOffset = 30;
+  static final int yOffset = 30;
+  public static jalview.ws.Discoverer discoverer;
+
+  public static Object[] jalviewClipboard;
+  public static boolean internalCopy = false;
+
+  static int fileLoadingCount = 0;
+
+  /**
+   * Creates a new Desktop object.
+   */
+  public Desktop()
+  {
+    /**
+     * A note to implementors. It is ESSENTIAL that any 
+     * activities that might block are spawned off as threads rather 
+     * than waited for during this constructor.
+     */
+    instance = this;
+    doVamsasClientCheck();
+    doGroovyCheck();
+
+
+    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+    boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",false);
+    desktop = new MyDesktopPane(selmemusage);
+    showMemusage.setSelected(selmemusage);
+    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.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            if(SwingUtilities.isRightMouseButton(evt))
+            {
+              showPasteMenu(evt.getX(), evt.getY());
+            }
+          }
+        });
+
+
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+    // Spawn a thread that shows the splashscreen
+    new SplashScreen();     
+
+
+
+    discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+  }
+
+  private void doVamsasClientCheck()
+  {
+    if (jalview.bin.Cache.vamsasJarsPresent())
+    {
+      setupVamsasDisconnectedGui();
+      VamsasMenu.setVisible(true);
+      final Desktop us = this;
+      VamsasMenu.addMenuListener(new MenuListener() {
+        // this listener remembers when the menu was first selected, and
+        // doesn't rebuild the session list until it has been cleared and
+        // reselected again.
+        boolean refresh=true;
+        public void menuCanceled(MenuEvent e)
+        {
+          refresh=true;
+        }
+
+        public void menuDeselected(MenuEvent e)
+        {
+          refresh = true;
+        }
+
+        public void menuSelected(MenuEvent e)
+        {
+          if (refresh)
+          {
+            us.buildVamsasStMenu();
+            refresh=false;
+          }
+        }
+      });
+      vamsasStart.setVisible(true);
+    }
+  }
+
+  void showPasteMenu(int x, int y)
+  {
+    JPopupMenu popup = new JPopupMenu();
+    JMenuItem item = new JMenuItem("Paste To New Window");
+    item.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent evt)
+      {
+        paste();
+      }
+    });
+
+    popup.add(item);
+    popup.show(this, x, y);
+  }
+
+  public void paste()
+  {
+    try
+    {
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
+
+      if (contents != null)
+      {
+        String file = (String) contents
+            .getTransferData(DataFlavor.stringFlavor);
+
+        String format = new IdentifyFile().Identify(file,
+                                                    FormatAdapter.PASTE);
+
+        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
+
+      }
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Unable to paste alignment from system clipboard:\n"
+                         + ex);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param frame DOCUMENT ME!
+   * @param title DOCUMENT ME!
+   * @param w DOCUMENT ME!
+   * @param h DOCUMENT ME!
+   */
+  public static synchronized void addInternalFrame(final JInternalFrame frame,
+      String title, int w, int h)
+  {
+    addInternalFrame(frame, title, w, h, true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param frame DOCUMENT ME!
+   * @param title DOCUMENT ME!
+   * @param w DOCUMENT ME!
+   * @param h DOCUMENT ME!
+   * @param resizable DOCUMENT ME!
+   */
+  public static synchronized void addInternalFrame(final JInternalFrame frame,
+      String title, int w, int h, boolean resizable)
+  {
+
+    frame.setTitle(title);
+    if (frame.getWidth() < 1 || frame.getHeight() < 1)
+    {
+      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)
+      {
+        PaintRefresher.RemoveComponent(frame);
+        openFrameCount--;
+        windowMenu.remove(menuItem);
+        JInternalFrame itf = desktop.getSelectedFrame();
+        if (itf != null)
+        {
+          itf.requestFocus();
+        }
+        System.gc();
+      }
+      ;
+    });
+
+    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)
+  {
+    if (!internalCopy)
+    {
+      Desktop.jalviewClipboard = null;
+    }
+
+    internalCopy = false;
+  }
+
+  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)
+    {}
+
+    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)
+      {}
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"),
+            jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
+            jalview.io.AppletFormatAdapter.READABLE_FNAMES, 
+            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)
+    {}
+  }
+
+  public void closeAll_actionPerformed(ActionEvent e)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    for (int i = 0; i < frames.length; i++)
+    {
+      try
+      {
+        frames[i].setClosed(true);
+      }
+      catch (java.beans.PropertyVetoException ex)
+      {}
+    }
+    System.out.println("ALL CLOSED");
+
+  }
+
+  public void raiseRelated_actionPerformed(ActionEvent e)
+  {
+    reorderAssociatedWindows(false, false);
+  }
+
+  public void minimizeAssociated_actionPerformed(ActionEvent e)
+  {
+    reorderAssociatedWindows(true, false);
+  }
+
+  void closeAssociatedWindows()
+  {
+    reorderAssociatedWindows(false, true);
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void garbageCollect_actionPerformed(ActionEvent e)
+  {
+    // We simply collect the garbage
+    jalview.bin.Cache.log.debug("Collecting garbage...");
+    System.gc();
+    jalview.bin.Cache.log.debug("Finished garbage collection.");
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+   */
+  protected void showMemusage_actionPerformed(ActionEvent e)
+  {
+    desktop.showMemoryUsage(showMemusage.isSelected());
+  }
+
+  void reorderAssociatedWindows(boolean minimize, boolean close)
+  {
+    JInternalFrame[] frames = desktop.getAllFrames();
+    if (frames == null || frames.length < 1)
+    {
+      return;
+    }
+
+    AlignViewport source = null, target = null;
+    if (frames[0] instanceof AlignFrame)
+    {
+      source = ( (AlignFrame) frames[0]).getCurrentView();
+    }
+    else if (frames[0] instanceof TreePanel)
+    {
+      source = ( (TreePanel) frames[0]).getViewPort();
+    }
+    else if (frames[0] instanceof PCAPanel)
+    {
+      source = ( (PCAPanel) frames[0]).av;
+    }
+    else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+    {
+      source = ( (PairwiseAlignPanel) frames[0].getContentPane()).av;
+    }
+
+    if (source != null)
+    {
+      for (int i = 0; i < frames.length; i++)
+      {
+        target = null;
+        if (frames[i] == null)
+        {
+          continue;
+        }
+        if (frames[i] instanceof AlignFrame)
+        {
+          target = ( (AlignFrame) frames[i]).getCurrentView();
+        }
+        else if (frames[i] instanceof TreePanel)
+        {
+          target = ( (TreePanel) frames[i]).getViewPort();
+        }
+        else if (frames[i] instanceof PCAPanel)
+        {
+          target = ( (PCAPanel) frames[i]).av;
+        }
+        else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+        {
+          target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
+        }
+
+        if (source == target)
+        {
+          try
+          {
+            if (close)
+            {
+              frames[i].setClosed(true);
+            }
+            else
+            {
+              frames[i].setIcon(minimize);
+              if (!minimize)
+              {
+                frames[i].toFront();
+              }
+            }
+
+          }
+          catch (java.beans.PropertyVetoException ex)
+          {}
+        }
+      }
+    }
+  }
+  /**
+   * 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 inputSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(null);
+  }
+
+  JPanel progressPanel;
+
+  public void startLoading(final String fileName)
+  {
+    if (fileLoadingCount == 0)
+    {
+      addProgressPanel("Loading File: " + fileName + "   ");
+      
+    }
+    fileLoadingCount++;
+  }
+  private JProgressBar addProgressPanel(String string)
+  {
+    if (progressPanel==null)
+    {
+      progressPanel = new JPanel(new BorderLayout());
+      totalProgressCount=0;
+    }
+    JProgressBar progressBar = new JProgressBar();
+    progressBar.setIndeterminate(true);
+
+    progressPanel.add(new JLabel(string),
+                      BorderLayout.WEST);
+
+    progressPanel.add(progressBar, BorderLayout.CENTER);
+
+    instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+    totalProgressCount++;
+    validate();
+    return progressBar;
+  }
+  int totalProgressCount=0;
+  private void removeProgressPanel(JProgressBar progbar)
+  {
+    if (progressPanel!=null)
+    {
+      progressPanel.remove(progbar);
+      if (--totalProgressCount<1)
+      {
+        this.getContentPane().remove(progressPanel);
+        progressPanel = null;
+      }
+    }
+    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 &&
+          !ap.av.explodedPosition.equals(af.getBounds()))
+      {
+        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(true);
+
+  }
+
+  public void gatherViews(AlignFrame source)
+  {
+    source.viewport.gatherViewsHere = true;
+    source.viewport.explodedPosition = source.getBounds();
+    JInternalFrame[] frames = desktop.getAllFrames();
+    String viewId = source.viewport.sequenceSetID;
+
+    for (int t = 0; t < frames.length; t++)
+    {
+      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(true);
+        }
+      }
+    }
+
+  }
+
+  jalview.gui.VamsasApplication v_client = null;
+  public void vamsasImport_actionPerformed(ActionEvent e)
+  {
+    if (v_client==null)
+    {
+      // Load and try to start a session.
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+          getProperty("LAST_DIRECTORY"));
+
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle("Open a saved VAMSAS session");
+      chooser.setToolTipText("select a vamsas session to be opened as a new vamsas session.");
+
+      int value = chooser.showOpenDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        try {
+          v_client = new jalview.gui.VamsasApplication(this,
+                                                chooser.getSelectedFile());
+        } catch (Exception ex)
+        {
+          jalview.bin.Cache.log.error("New vamsas session from existing session file failed:",ex);
+          return;
+        }
+        setupVamsasConnectedGui();
+        v_client.initial_update(); // TODO: thread ?
+      }
+    }else {
+      jalview.bin.Cache.log.error("Implementation error - load session from a running session is not supported.");
+    }
+  }
+
+  public void vamsasStart_actionPerformed(ActionEvent e)
+  {
+    if (v_client == null)
+    {
+      // Start a session.
+      // we just start a default session for moment.
+      /*
+      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.VamsasApplication(this,
+                                                chooser.getSelectedFile());
+                                                *
+                                                */
+      v_client = new VamsasApplication(this);
+      setupVamsasConnectedGui();
+      v_client.initial_update(); // TODO: thread ?
+    }
+    else
+    {
+      // store current data in session.
+      v_client.push_update(); // TODO: thread
+    }
+  }
+
+  protected void setupVamsasConnectedGui()
+  {
+    vamsasStart.setText("Session Update");
+    vamsasSave.setVisible(true);
+    vamsasStop.setVisible(true);
+    vamsasImport.setVisible(false); // Document import to existing session is not possible for vamsas-client-1.0.
+  }
+  protected void setupVamsasDisconnectedGui()
+  {
+    vamsasSave.setVisible(false);
+    vamsasStop.setVisible(false);
+    vamsasImport.setVisible(true);
+    vamsasStart.setText("New Vamsas Session...");
+  }
+
+  public void vamsasStop_actionPerformed(ActionEvent e)
+  {
+    if (v_client != null)
+    {
+      v_client.end_session();
+      v_client = null;
+      setupVamsasDisconnectedGui();
+    }
+  }
+  protected void buildVamsasStMenu()
+  {
+    if (v_client == null)
+    {
+      String[] sess = null;
+      try
+      {
+        sess = VamsasApplication.getSessionList();
+      } catch (Exception e)
+      {
+        jalview.bin.Cache.log.warn(
+                "Problem getting current sessions list.", e);
+        sess = null;
+      }
+      if (sess != null)
+      {
+        jalview.bin.Cache.log.debug("Got current sessions list: "
+                + sess.length + " entries.");
+        VamsasStMenu.removeAll();
+        for (int i = 0; i < sess.length; i++)
+        {
+          JMenuItem sessit = new JMenuItem();
+          sessit.setText(sess[i]);
+          sessit.setToolTipText("Connect to session " + sess[i]);
+          final Desktop dsktp = this;
+          final String mysesid = sess[i];
+          sessit.addActionListener(new ActionListener()
+          {
+
+            public void actionPerformed(ActionEvent e)
+            {
+              if (dsktp.v_client == null)
+              {
+                Thread rthr = new Thread(new Runnable() {
+
+                  public void run()
+                  {
+                    dsktp.v_client = new VamsasApplication(dsktp, mysesid);
+                    dsktp.setupVamsasConnectedGui();
+                    dsktp.v_client.initial_update();
+                  }
+                  
+                });
+                rthr.start();
+              }
+            };
+          });
+          VamsasStMenu.add(sessit);
+        }
+        // don't show an empty menu.
+        VamsasStMenu.setVisible(sess.length>0);
+        
+      }
+      else
+      {
+        jalview.bin.Cache.log.debug("No current vamsas sessions.");
+        VamsasStMenu.removeAll();
+        VamsasStMenu.setVisible(false);
+      }
+    } else {
+      // Not interested in the content. Just hide ourselves.
+      VamsasStMenu.setVisible(false);
+    }
+  }
+  public void vamsasSave_actionPerformed(ActionEvent e)
+  {
+    if (v_client != null)
+    {
+      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+            getProperty(
+                "LAST_DIRECTORY"), new String[]
+            {"vdj"}, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+            new String[]
+            {"Vamsas Document"}, "Vamsas Document");
+
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save Vamsas Document Archive");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+          java.io.File choice = chooser.getSelectedFile();
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+          String warnmsg=null;
+          String warnttl=null;
+          try {
+            v_client.vclient.storeDocument(choice);
+          }
+          catch (Error ex)
+          {
+            warnttl = "Serious Problem saving Vamsas Document";
+            warnmsg = ex.toString();
+            jalview.bin.Cache.log.error("Error Whilst saving document to "+choice,ex);
+            
+          }
+          catch (Exception ex)
+          {
+            warnttl = "Problem saving Vamsas Document.";
+            warnmsg = ex.toString();
+            jalview.bin.Cache.log.warn("Exception Whilst saving document to "+choice,ex);
+            
+          }
+          if (warnmsg!=null)
+          {
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+                  warnmsg, warnttl,
+                  JOptionPane.ERROR_MESSAGE);
+          }
+        }
+    }
+  }
+  JProgressBar vamUpdate = null;
+  /**
+   * 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"));
+    
+    if (vamUpdate!=null)
+    {
+      this.removeProgressPanel(vamUpdate);
+    }
+    if (b)
+    {
+      vamUpdate = this.addProgressPanel("Updating vamsas session");
+    }
+    vamsasStart.setVisible(!b);
+    vamsasStop.setVisible(!b);
+    vamsasSave.setVisible(!b);
+  }
+
+  public JInternalFrame[] getAllFrames()
+  {
+    return desktop.getAllFrames();
+  }
+
+
+  /**
+   * Checks the given url to see if it gives a response indicating that
+   * the user should be informed of a new questionnaire.
+   * @param url
+   */
+  public void checkForQuestionnaire(String url)
+  {
+    UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
+    //javax.swing.SwingUtilities.invokeLater(jvq);
+    new Thread(jvq).start();
+  }
+  /**
+   * Proxy class for JDesktopPane which optionally 
+   * displays the current memory usage and highlights 
+   * the desktop area with a red bar if free memory runs low.
+   * @author AMW
+   */
+  public class  MyDesktopPane extends JDesktopPane implements Runnable
+  {
+    
+    boolean showMemoryUsage = false;
+    Runtime runtime;
+    java.text.NumberFormat df;
+
+    float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+
+    public MyDesktopPane(boolean showMemoryUsage)
+    {
+      showMemoryUsage(showMemoryUsage);
+    }
+
+    public void showMemoryUsage(boolean showMemoryUsage)
+    {
+      this.showMemoryUsage = showMemoryUsage;
+      if (showMemoryUsage)
+      {
+        Thread worker = new Thread(this);
+        worker.start();
+      }
+    }
+    public boolean isShowMemoryUsage()
+    {
+      return showMemoryUsage;
+    }
+    public void run()
+    {
+      df = java.text.NumberFormat.getNumberInstance();
+      df.setMaximumFractionDigits(2);
+      runtime = Runtime.getRuntime();
+
+      while (showMemoryUsage)
+      {
+        try
+        {
+          Thread.sleep(3000);
+          maxMemory = runtime.maxMemory() / 1048576f;
+          allocatedMemory = runtime.totalMemory() / 1048576f;
+          freeMemory = runtime.freeMemory() / 1048576f;
+          totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
+
+          percentUsage = (totalFreeMemory / maxMemory) * 100;
+
+        //  if (percentUsage < 20)
+          {
+            //   border1 = BorderFactory.createMatteBorder(12, 12, 12, 12, Color.red);
+            //    instance.set.setBorder(border1);
+          }
+          repaint();
+
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+    }
+
+    public void paintComponent(Graphics g)
+    {
+      if(showMemoryUsage)
+      {
+        if (percentUsage < 20)
+          g.setColor(Color.red);
+
+        g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+                     + "MB; Max Memory: " + df.format(maxMemory)
+                     + "MB; " + df.format(percentUsage) + "%", 10,
+                     getHeight() - g.getFontMetrics().getHeight());
+      }
+    }
+
+    
+    
+  }
+  protected JMenuItem groovyShell;
+  public void doGroovyCheck() {
+    if (jalview.bin.Cache.groovyJarsPresent())
+    {
+      groovyShell = new JMenuItem();
+      groovyShell.setText("Groovy Console...");
+      groovyShell.addActionListener(new ActionListener()
+      {
+          public void actionPerformed(ActionEvent e) {
+              groovyShell_actionPerformed(e);
+          }
+      });
+      toolsMenu.add(groovyShell);
+      groovyShell.setVisible(true);
+    }
+  }
+  /**
+   * Accessor method to quickly get all the AlignmentFrames
+   * loaded.
+   */
+  public static AlignFrame[] getAlignframes() {
+    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+    if (frames == null)
+    {
+      return null;
+      }
+      Vector avp=new Vector();
+      try
+      {
+          //REVERSE ORDER
+          for (int i = frames.length - 1; i > -1; i--)
+          {
+              if (frames[i] instanceof AlignFrame)
+              {
+                  AlignFrame af = (AlignFrame) frames[i];
+                  avp.addElement(af);
+              }
+          }
+      }
+      catch (Exception ex)
+      {
+          ex.printStackTrace();
+      }
+      if (avp.size()==0)
+      {
+          return null;
+      }
+      AlignFrame afs[] = new AlignFrame[avp.size()];
+      for (int i=0,j=avp.size(); i<j; i++) {
+          afs[i] = (AlignFrame) avp.elementAt(i);
+      }
+      avp.clear();
+      return afs;
+  }
+
+  /**
+    * Add Groovy Support to Jalview
+    */
+  public void groovyShell_actionPerformed(ActionEvent e) {
+    // use reflection to avoid creating compilation dependency.
+    if (!jalview.bin.Cache.groovyJarsPresent())
+    {
+      throw new Error("Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+    }
+    try {
+    Class gcClass = Desktop.class.getClassLoader().loadClass("groovy.ui.Console");
+    Constructor gccons = gcClass.getConstructor(null);
+    java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", new Class[] { String.class, Object.class} );
+    java.lang.reflect.Method run = gcClass.getMethod("run", null);
+    Object gc = gccons.newInstance(null);
+    setvar.invoke(gc, new Object[] { "Jalview", this});
+    run.invoke(gc, null);
+    }
+    catch (Exception ex)
+    {
+      jalview.bin.Cache.log.error("Groovy Shell Creation failed.",ex);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+
+              "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.", "Jalview Groovy Support Failed",
+              JOptionPane.ERROR_MESSAGE);
+    }
+  }
+}