X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=7a972a181f18dcec6eb94a7246231abc35d396e4;hb=de87ceaadf42025516d3201bb8f1ba1ea1776fd1;hp=4cdf84c2b92a04b9ff2eac233dd7bc3c0ad5e8d9;hpb=06b8ab919b9d65007873fdf1d357ffbb7b10b1b0;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 4cdf84c..7a972a1 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,30 +1,38 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3 of the License, or (at your option) any later version.
  * 
- * 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
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.io.*;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.InputStream;
 import java.lang.reflect.Constructor;
+import java.net.URL;
+import java.net.URLConnection;
+import java.nio.channels.ReadableByteChannel;
 import java.util.*;
 
 import javax.swing.*;
@@ -81,6 +89,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
     boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
             false);
+    boolean showjconsole = jalview.bin.Cache.getDefault(
+            "SHOW_JAVA_CONSOLE", false);
     desktop = new MyDesktopPane(selmemusage);
     showMemusage.setSelected(selmemusage);
     desktop.setBackground(Color.white);
@@ -92,22 +102,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // 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))
+    Rectangle dims = getLastKnownDimensions("");
+    if (dims != null)
     {
-      setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer
-              .parseInt(width), Integer.parseInt(height));
+      setBounds(dims);
     }
     else
     {
+      Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
       setBounds((int) (screenSize.width - 900) / 2,
               (int) (screenSize.height - 650) / 2, 900, 650);
     }
+    jconsole = new Console(this, showjconsole);
+    // add essential build information
+    jconsole.setHeader("Jalview Desktop "
+            + jalview.bin.Cache.getProperty("VERSION") + "\n"
+            + "Build Date: "
+            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+            + "Java version: " + System.getProperty("java.version") + "\n"
+            + System.getProperty("os.arch") + " "
+            + System.getProperty("os.name") + " "
+            + System.getProperty("os.version"));
+
+    showConsole(showjconsole);
 
     this.addWindowListener(new WindowAdapter()
     {
@@ -130,10 +147,79 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
     // Spawn a thread that shows the splashscreen
-    new SplashScreen();
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        new SplashScreen();
+      }
+    });
 
     discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is
-                                              // displayed.
+    // displayed.
+    // Thread off a new instance of the file chooser - this reduces the time it
+    // takes to open it later on.
+    new Thread(new Runnable()
+    {
+      public void run()
+      {
+        Cache.log.debug("Filechooser init thread started.");
+        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"));
+        Cache.log.debug("Filechooser init thread finished.");
+      }
+    }).start();
+  }
+
+  /**
+   * recover the last known dimensions for a jalview window
+   * 
+   * @param windowName
+   *          - empty string is desktop, all other windows have unique prefix
+   * @return null or last known dimensions scaled to current geometry (if last
+   *         window geom was known)
+   */
+  Rectangle getLastKnownDimensions(String windowName)
+  {
+    // TODO: lock aspect ratio for scaling desktop Bug #0058199
+    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+    String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
+    String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
+    String width = jalview.bin.Cache.getProperty(windowName
+            + "SCREEN_WIDTH");
+    String height = jalview.bin.Cache.getProperty(windowName
+            + "SCREEN_HEIGHT");
+    if ((x != null) && (y != null) && (width != null) && (height != null))
+    {
+      int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
+              .parseInt(width), ih = Integer.parseInt(height);
+      if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+      {
+        // attempt #1 - try to cope with change in screen geometry - this
+        // version doesn't preserve original jv aspect ratio.
+        // take ratio of current screen size vs original screen size.
+        double sw = ((1f * screenSize.width) / (1f * Integer
+                .parseInt(jalview.bin.Cache
+                        .getProperty("SCREENGEOMETRY_WIDTH"))));
+        double sh = ((1f * screenSize.height) / (1f * Integer
+                .parseInt(jalview.bin.Cache
+                        .getProperty("SCREENGEOMETRY_HEIGHT"))));
+        // rescale the bounds depending upon the current screen geometry.
+        ix = (int) (ix * sw);
+        iw = (int) (iw * sw);
+        iy = (int) (iy * sh);
+        ih = (int) (ih * sh);
+        jalview.bin.Cache.log.debug("Got last known dimensions for "
+                + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+                + " height:" + ih);
+      }
+      // return dimensions for new instance
+      return new Rectangle(ix, iy, iw, ih);
+    }
+    return null;
   }
 
   private void doVamsasClientCheck()
@@ -216,16 +302,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Adds and opens the given frame to the desktop
    * 
    * @param frame
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param title
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param w
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param h
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, int w, int h)
@@ -237,21 +323,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param frame
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param title
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param w
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param h
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param resizable
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, int w, int h,
           boolean resizable)
   {
 
+    // TODO: allow callers to determine X and Y position of frame (eg. via
+    // bounds object).
     // TODO: consider fixing method to update entries in the window submenu with
     // the current window title
 
@@ -373,12 +461,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param evt
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void drop(DropTargetDropEvent evt)
   {
     Transferable t = evt.getTransferable();
     java.util.List files = null;
+    java.util.List protocols = null;
 
     try
     {
@@ -397,6 +486,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
         String data = (String) t.getTransferData(uriListFlavor);
         files = new java.util.ArrayList(1);
+        protocols = new java.util.ArrayList(1);
         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
                 data, "\r\n"); st.hasMoreTokens();)
         {
@@ -406,10 +496,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             // 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);
+          if (uri.getScheme().toLowerCase().startsWith("http"))
+          {
+            protocols.add(FormatAdapter.URL);
+            files.add(uri.toString());
+          }
+          else
+          {
+            // otherwise preserve old behaviour: catch all for file objects
+            java.io.File file = new java.io.File(uri);
+            protocols.add(FormatAdapter.FILE);
+            files.add(file.toString());
+          }
         }
       }
     } catch (Exception e)
@@ -423,7 +522,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         for (int i = 0; i < files.size(); i++)
         {
           String file = files.get(i).toString();
-          String protocol = FormatAdapter.FILE;
+          String protocol = (protocols == null) ? FormatAdapter.FILE
+                  : (String) protocols.get(i);
           String format = null;
 
           if (file.endsWith(".jar"))
@@ -449,7 +549,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
@@ -497,7 +597,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
   {
@@ -577,7 +677,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
   {
@@ -591,18 +691,39 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   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() + "");
+    Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+    jalview.bin.Cache
+            .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+    jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
+            + "");
+    storeLastKnownDimensions("", new Rectangle(getBounds().x,
+            getBounds().y, getWidth(), getHeight()));
+
+    if (jconsole != null)
+    {
+      storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+      jconsole.stopConsole();
+    }
     System.exit(0);
   }
 
+  private void storeLastKnownDimensions(String string, Rectangle jc)
+  {
+    jalview.bin.Cache.log.debug("Storing last known dimensions for "
+            + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+            + " height:" + jc.height);
+
+    jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
+    jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+    jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+    jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void aboutMenuItem_actionPerformed(ActionEvent e)
   {
@@ -627,8 +748,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                     + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
                     + "\nIf  you use Jalview, please cite:"
                     + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
-            + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-            + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
+                    + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+                    + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
     JOptionPane.showInternalMessageDialog(Desktop.desktop,
 
     message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
@@ -638,7 +759,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void documentationMenuItem_actionPerformed(ActionEvent e)
   {
@@ -669,10 +790,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
     System.out.println("ALL CLOSED");
-    if (v_client!=null)
+    if (v_client != null)
     {
       // TODO clear binding to vamsas document objects on close_all
-      
+
     }
   }
 
@@ -694,7 +815,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.ActionEvent)
+   * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
+   * ActionEvent)
    */
   protected void garbageCollect_actionPerformed(ActionEvent e)
   {
@@ -707,13 +829,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent)
+   * @see
+   * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
+   * )
    */
   protected void showMemusage_actionPerformed(ActionEvent e)
   {
     desktop.showMemoryUsage(showMemusage.isSelected());
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
+   * )
+   */
+  protected void showConsole_actionPerformed(ActionEvent e)
+  {
+    showConsole(showConsole.isSelected());
+  }
+
+  Console jconsole = null;
+
+  /**
+   * control whether the java console is visible or not
+   * 
+   * @param selected
+   */
+  void showConsole(boolean selected)
+  {
+    showConsole.setSelected(selected);
+    // TODO: decide if we should update properties file
+    Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
+            .toString());
+    jconsole.setVisible(selected);
+  }
+
   void reorderAssociatedWindows(boolean minimize, boolean close)
   {
     JInternalFrame[] frames = desktop.getAllFrames();
@@ -795,7 +947,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void preferences_actionPerformed(ActionEvent e)
   {
@@ -806,7 +958,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void saveState_actionPerformed(ActionEvent e)
   {
@@ -823,8 +975,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       java.io.File choice = chooser.getSelectedFile();
+      JProgressBar progpanel = addProgressPanel("Saving jalview project "
+              + choice.getName());
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+      // TODO catch and handle errors for savestate
       new Jalview2XML().SaveState(choice);
+      removeProgressPanel(progpanel);
+
     }
   }
 
@@ -832,7 +989,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void loadState_actionPerformed(ActionEvent e)
   {
@@ -848,9 +1005,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getAbsolutePath();
+      setProgressBar("loading jalview project "
+              + chooser.getSelectedFile().getName(), choice.hashCode());
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
       new Jalview2XML().LoadJalviewAlign(choice);
+      setProgressBar(null, choice.hashCode());
     }
   }
 
@@ -925,8 +1085,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public static int getViewCount(String viewId)
   {
     AlignViewport[] aps = getViewports(viewId);
-    return (aps==null) ? 0 : aps.length;
+    return (aps == null) ? 0 : aps.length;
   }
+
   /**
    * 
    * @param viewId
@@ -935,6 +1096,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public static AlignmentPanel[] getAlignmentPanels(String viewId)
   {
     int count = 0;
+    if (Desktop.desktop == null)
+    {
+      // no frames created and in headless mode
+      // TODO: verify that frames are recoverable when in headless mode
+      return null;
+    }
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     ArrayList aps = new ArrayList();
     for (int t = 0; t < frames.length; t++)
@@ -953,20 +1120,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
       }
     }
-    if (aps.size()==0)
+    if (aps.size() == 0)
     {
       return null;
     }
     AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
-    for (int t=0;t<vap.length;t++)
+    for (int t = 0; t < vap.length; t++)
     {
       vap[t] = (AlignmentPanel) aps.get(t);
     }
     return vap;
   }
+
   /**
    * get all the viewports on an alignment.
-   * @param sequenceSetId unique alignment id
+   * 
+   * @param sequenceSetId
+   *          unique alignment id
    * @return all viewports on the alignment bound to sequenceSetId
    */
   public static AlignViewport[] getViewports(String sequenceSetId)
@@ -975,27 +1145,28 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (desktop != null)
     {
       javax.swing.JInternalFrame[] frames = instance.getAllFrames();
-  
+
       for (int t = 0; t < frames.length; t++)
       {
         if (frames[t] instanceof AlignFrame)
         {
           AlignFrame afr = ((AlignFrame) frames[t]);
-          if (afr.getViewport().getSequenceSetId()
-                  .equals(sequenceSetId))
+          if (afr.getViewport().getSequenceSetId().equals(sequenceSetId))
           {
-            if (afr.alignPanels!=null)
+            if (afr.alignPanels != null)
             {
               for (int a = 0; a < afr.alignPanels.size(); a++)
               {
-                if (sequenceSetId
-                        .equals(((AlignmentPanel) afr.alignPanels.elementAt(a)).av
-                                .getSequenceSetId()))
+                if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels
+                        .elementAt(a)).av.getSequenceSetId()))
                 {
-                  viewp.addElement(((AlignmentPanel)afr.alignPanels.elementAt(a)).av);
+                  viewp.addElement(((AlignmentPanel) afr.alignPanels
+                          .elementAt(a)).av);
                 }
               }
-            } else {
+            }
+            else
+            {
               viewp.addElement(((AlignFrame) frames[t]).getViewport());
             }
           }
@@ -1094,19 +1265,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
-        try
-        {
-          v_client = new jalview.gui.VamsasApplication(this, chooser
-                  .getSelectedFile());
-        } catch (Exception ex)
+        String fle = chooser.getSelectedFile().toString();
+        if (!vamsasImport(chooser.getSelectedFile()))
         {
-          jalview.bin.Cache.log.error(
-                  "New vamsas session from existing session file failed:",
-                  ex);
-          return;
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Couldn't import '" + fle + "' as a new vamsas session.",
+                  "Vamsas Document Import Failed",
+                  JOptionPane.ERROR_MESSAGE);
         }
-        setupVamsasConnectedGui();
-        v_client.initial_update(); // TODO: thread ?
       }
     }
     else
@@ -1116,6 +1282,105 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
   }
 
+  /**
+   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+   * 
+   * @param file
+   * @return true if import was a success and a session was started.
+   */
+  public boolean vamsasImport(URL url)
+  {
+    // TODO: create progress bar
+    if (v_client != null)
+    {
+
+      jalview.bin.Cache.log
+              .error("Implementation error - load session from a running session is not supported.");
+      return false;
+    }
+
+    try
+    {
+      // copy the URL content to a temporary local file
+      // TODO: be a bit cleverer here with nio (?!)
+      File file = File.createTempFile("vdocfromurl", ".vdj");
+      FileOutputStream fos = new FileOutputStream(file);
+      BufferedInputStream bis = new BufferedInputStream(url.openStream());
+      byte[] buffer = new byte[2048];
+      int ln;
+      while ((ln = bis.read(buffer)) > -1)
+      {
+        fos.write(buffer, 0, ln);
+      }
+      bis.close();
+      fos.close();
+      v_client = new jalview.gui.VamsasApplication(this, file, url
+              .toExternalForm());
+    } catch (Exception ex)
+    {
+      jalview.bin.Cache.log.error(
+              "Failed to create new vamsas session from contents of URL "
+                      + url, ex);
+      return false;
+    }
+    setupVamsasConnectedGui();
+    v_client.initial_update(); // TODO: thread ?
+    return v_client.inSession();
+  }
+
+  /**
+   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+   * 
+   * @param file
+   * @return true if import was a success and a session was started.
+   */
+  public boolean vamsasImport(File file)
+  {
+    if (v_client != null)
+    {
+
+      jalview.bin.Cache.log
+              .error("Implementation error - load session from a running session is not supported.");
+      return false;
+    }
+
+    setProgressBar("Importing VAMSAS session from " + file.getName(), file
+            .hashCode());
+    try
+    {
+      v_client = new jalview.gui.VamsasApplication(this, file, null);
+    } catch (Exception ex)
+    {
+      setProgressBar("Importing VAMSAS session from " + file.getName(),
+              file.hashCode());
+      jalview.bin.Cache.log.error(
+              "New vamsas session from existing session file failed:", ex);
+      return false;
+    }
+    setupVamsasConnectedGui();
+    v_client.initial_update(); // TODO: thread ?
+    setProgressBar("Importing VAMSAS session from " + file.getName(), file
+            .hashCode());
+    return v_client.inSession();
+  }
+
+  public boolean joinVamsasSession(String mysesid)
+  {
+    if (v_client != null)
+    {
+      throw new Error(
+              "Trying to join a vamsas session when another is already connected.");
+    }
+    if (mysesid == null)
+    {
+      throw new Error("Invalid vamsas session id.");
+    }
+    v_client = new VamsasApplication(this, mysesid);
+    setupVamsasConnectedGui();
+    v_client.initial_update();
+    return (v_client.inSession());
+  }
+
   public void vamsasStart_actionPerformed(ActionEvent e)
   {
     if (v_client == null)
@@ -1134,7 +1399,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
        * 
        * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
        * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
-       * 
        */
       v_client = new VamsasApplication(this);
       setupVamsasConnectedGui();
@@ -1153,7 +1417,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     vamsasSave.setVisible(true);
     vamsasStop.setVisible(true);
     vamsasImport.setVisible(false); // Document import to existing session is
-                                    // not possible for vamsas-client-1.0.
+    // not possible for vamsas-client-1.0.
   }
 
   protected void setupVamsasDisconnectedGui()
@@ -1260,6 +1524,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         java.io.File choice = chooser.getSelectedFile();
+        JProgressBar progpanel = addProgressPanel("Saving VAMSAS Document to "
+                + choice.getName());
         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
         String warnmsg = null;
         String warnttl = null;
@@ -1281,6 +1547,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                   + choice, ex);
 
         }
+        removeProgressPanel(progpanel);
         if (warnmsg != null)
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -1297,7 +1564,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * hide vamsas user gui bits when a vamsas document event is being handled.
    * 
    * @param b
-   *                true to hide gui, false to reveal gui
+   *          true to hide gui, false to reveal gui
    */
   public void setVamsasUpdate(boolean b)
   {
@@ -1384,7 +1651,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         try
         {
-          Thread.sleep(3000);
           maxMemory = runtime.maxMemory() / 1048576f;
           allocatedMemory = runtime.totalMemory() / 1048576f;
           freeMemory = runtime.freeMemory() / 1048576f;
@@ -1399,7 +1665,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             // instance.set.setBorder(border1);
           }
           repaint();
-
+          // sleep after showing usage
+          Thread.sleep(3000);
         } catch (Exception ex)
         {
           ex.printStackTrace();
@@ -1409,15 +1676,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     public void paintComponent(Graphics g)
     {
-      if (showMemoryUsage)
+      if (showMemoryUsage && g != null)
       {
         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());
+        FontMetrics fm = g.getFontMetrics();
+        if (fm != null)
+        {
+          g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
+                  + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
+                  + df.format(percentUsage) + "%", 10, getHeight()
+                  - fm.getHeight());
+        }
       }
     }
 
@@ -1544,7 +1814,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               .remove(new Long(id));
       if (progressBarHandlers.contains(new Long(id)))
       {
-          progressBarHandlers.remove(new Long(id));
+        progressBarHandlers.remove(new Long(id));
       }
       removeProgressPanel(progressPanel);
     }
@@ -1553,32 +1823,41 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       progressBars.put(new Long(id), addProgressPanel(message));
     }
   }
-  /* (non-Javadoc)
-   * @see jalview.gui.IProgressIndicator#registerHandler(long, jalview.gui.IProgressIndicatorHandler)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.gui.IProgressIndicator#registerHandler(long,
+   * jalview.gui.IProgressIndicatorHandler)
    */
-  public void registerHandler(final long id, final IProgressIndicatorHandler handler)
+  public void registerHandler(final long id,
+          final IProgressIndicatorHandler handler)
   {
-    if (progressBarHandlers==null || !progressBars.contains(new Long(id)))
+    if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
     {
-      throw new Error("call setProgressBar before registering the progress bar's handler.");
+      throw new Error(
+              "call setProgressBar before registering the progress bar's handler.");
     }
     progressBarHandlers.put(new Long(id), handler);
     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
     if (handler.canCancel())
     {
       JButton cancel = new JButton("Cancel");
-      final IProgressIndicator us=this;
-      cancel.addActionListener(new ActionListener() {
+      final IProgressIndicator us = this;
+      cancel.addActionListener(new ActionListener()
+      {
 
         public void actionPerformed(ActionEvent e)
         {
           handler.cancelActivity(id);
-          us.setProgressBar("Cancelled "+((JLabel)progressPanel.getComponent(0)).getText(), id);
+          us.setProgressBar("Cancelled "
+                  + ((JLabel) progressPanel.getComponent(0)).getText(), id);
         }
       });
       progressPanel.add(cancel, BorderLayout.EAST);
     }
   }
+
   /**
    * This will return the first AlignFrame viewing AlignViewport av. It will
    * break if there are more than one AlignFrames viewing a particular av. This
@@ -1591,12 +1870,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (desktop != null)
     {
       AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
-      for (int panel=0;aps!=null && panel<aps.length;panel++)
-        { if (aps[panel]!=null && aps[panel].av==av) {
+      for (int panel = 0; aps != null && panel < aps.length; panel++)
+      {
+        if (aps[panel] != null && aps[panel].av == av)
+        {
           return aps[panel].alignFrame;
         }
-        }
+      }
     }
     return null;
   }
+
+  public VamsasApplication getVamsasApplication()
+  {
+    return v_client;
+
+  }
 }