X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=ec9974ca73b1b6733c0450bcdfcc2a4f9e3faefb;hb=cf25e4f4f7d2cb2a7847a01d7cbe52003b46bf54;hp=4cdf84c2b92a04b9ff2eac233dd7bc3c0ad5e8d9;hpb=06b8ab919b9d65007873fdf1d357ffbb7b10b1b0;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 4cdf84c..ec9974c 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,30 +1,41 @@
 /*
- * 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 2.6)
+ * 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 jalview.ws.params.ParamManager;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
 import java.awt.dnd.*;
 import java.awt.event.*;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+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.*;
@@ -32,7 +43,8 @@ import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
 /**
- * DOCUMENT ME!
+ * Jalview Desktop
+ * 
  * 
  * @author $author$
  * @version $Revision$
@@ -40,22 +52,122 @@ import javax.swing.event.MenuListener;
 public class Desktop extends jalview.jbgui.GDesktop implements
         DropTargetListener, ClipboardOwner, IProgressIndicator
 {
-  /** DOCUMENT ME!! */
+
+  private class JalviewChangeSupport implements PropertyChangeListener
+  {
+    public void propertyChange(PropertyChangeEvent evt)
+    {
+      // Handle change events - most are simply routed to other sources
+      changeSupport.firePropertyChange(evt);
+    }
+
+    /**
+     * change listeners are notified of changes to resources so they can update
+     * their state. E.g. - the 'services' property notifies when the available
+     * set of web service endpoints have changed.
+     */
+    private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+            this);
+
+    /**
+     * @param propertyName
+     * @param listener
+     * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.lang.String,
+     *      java.beans.PropertyChangeListener)
+     */
+    public void addJalviewPropertyChangeListener(String propertyName,
+            PropertyChangeListener listener)
+    {
+      changeSupport.addPropertyChangeListener(propertyName, listener);
+    }
+
+    /**
+     * @param listener
+     * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
+     */
+    public void addJalviewPropertyChangeListener(
+            PropertyChangeListener listener)
+    {
+      changeSupport.addPropertyChangeListener(listener);
+    }
+
+    /*
+     * @param propertyName
+     * 
+     * @param oldValue
+     * 
+     * @param newValue
+     * 
+     * @see
+     * java.beans.PropertyChangeSupport#firePropertyChange(java.lang.String,
+     * java.lang.Object, java.lang.Object) public void firePropertyChange(String
+     * propertyName, Object oldValue, Object newValue) {
+     * changeSupport.firePropertyChange(propertyName, oldValue, newValue); }
+     */
+
+    /**
+     * @param propertyName
+     * @param listener
+     * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.lang.String,
+     *      java.beans.PropertyChangeListener)
+     */
+    public void removeJalviewPropertyChangeListener(String propertyName,
+            PropertyChangeListener listener)
+    {
+      changeSupport.removePropertyChangeListener(propertyName, listener);
+    }
+
+  }
+
+  private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
+
+  /**
+   * @param listener
+   * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
+   */
+  public void addJalviewPropertyChangeListener(
+          PropertyChangeListener listener)
+  {
+    changeSupport.addJalviewPropertyChangeListener(listener);
+  }
+
+  /**
+   * @param propertyName
+   * @param listener
+   * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
+   *      java.beans.PropertyChangeListener)
+   */
+  public void addJalviewPropertyChangeListener(String propertyName,
+          PropertyChangeListener listener)
+  {
+    changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
+  }
+
+  /**
+   * @param propertyName
+   * @param listener
+   * @see jalview.gui.Desktop.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
+   *      java.beans.PropertyChangeListener)
+   */
+  public void removeJalviewPropertyChangeListener(String propertyName,
+          PropertyChangeListener listener)
+  {
+    changeSupport.removeJalviewPropertyChangeListener(propertyName,
+            listener);
+  }
+
+  /** Singleton Desktop instance */
   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 jalview.ws.jws1.Discoverer discoverer;
 
   public static Object[] jalviewClipboard;
 
@@ -63,6 +175,104 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   static int fileLoadingCount = 0;
 
+  class MyDesktopManager implements DesktopManager
+  {
+
+    private DesktopManager delegate;
+
+    public MyDesktopManager(DesktopManager delegate)
+    {
+      this.delegate = delegate;
+    }
+
+    public void activateFrame(JInternalFrame f)
+    {
+      try
+      {
+        delegate.activateFrame(f);
+      } catch (NullPointerException npe)
+      {
+        Point p = getMousePosition();
+        instance.showPasteMenu(p.x, p.y);
+      }
+    }
+
+    public void beginDraggingFrame(JComponent f)
+    {
+      delegate.beginDraggingFrame(f);
+    }
+
+    public void beginResizingFrame(JComponent f, int direction)
+    {
+      delegate.beginResizingFrame(f, direction);
+    }
+
+    public void closeFrame(JInternalFrame f)
+    {
+      delegate.closeFrame(f);
+    }
+
+    public void deactivateFrame(JInternalFrame f)
+    {
+      delegate.deactivateFrame(f);
+    }
+
+    public void deiconifyFrame(JInternalFrame f)
+    {
+      delegate.deiconifyFrame(f);
+    }
+
+    public void dragFrame(JComponent f, int newX, int newY)
+    {
+      delegate.dragFrame(f, newX, newY);
+    }
+
+    public void endDraggingFrame(JComponent f)
+    {
+      delegate.endDraggingFrame(f);
+    }
+
+    public void endResizingFrame(JComponent f)
+    {
+      delegate.endResizingFrame(f);
+    }
+
+    public void iconifyFrame(JInternalFrame f)
+    {
+      delegate.iconifyFrame(f);
+    }
+
+    public void maximizeFrame(JInternalFrame f)
+    {
+      delegate.maximizeFrame(f);
+    }
+
+    public void minimizeFrame(JInternalFrame f)
+    {
+      delegate.minimizeFrame(f);
+    }
+
+    public void openFrame(JInternalFrame f)
+    {
+      delegate.openFrame(f);
+    }
+
+    public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+            int newHeight)
+    {
+      delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
+    }
+
+    public void setBoundsForFrame(JComponent f, int newX, int newY,
+            int newWidth, int newHeight)
+    {
+      delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
+    }
+
+    // All other methods, simply delegate
+
+  }
+
   /**
    * Creates a new Desktop object.
    */
@@ -81,6 +291,8 @@ 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);
@@ -90,24 +302,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     // 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))
+    desktop.setDesktopManager(new MyDesktopManager(
+            new DefaultDesktopManager()));
+    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 +349,90 @@ 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);
+        while (ix >= screenSize.width)
+        {
+          jalview.bin.Cache.log
+                  .debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+          ix -= screenSize.width;
+        }
+        while (iy >= screenSize.height)
+        {
+          jalview.bin.Cache.log
+                  .debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+          iy -= screenSize.height;
+        }
+        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 +515,16 @@ 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 +536,23 @@ 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
 
@@ -286,34 +587,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
 
     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();
-                }
+    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();
-              };
-            });
+      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()
     {
@@ -373,12 +673,13 @@ 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 +698,7 @@ 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 +708,19 @@ 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 +734,8 @@ 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"))
@@ -449,12 +761,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"),
+    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"));
@@ -497,7 +809,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
   {
@@ -577,7 +889,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
   {
@@ -591,18 +903,39 @@ 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)
   {
@@ -613,20 +946,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     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("\n\n!! Jalview version "
+              + jalview.bin.Cache.getProperty("LATEST_VERSION")
+              + " is available for download from http://www.jalview.org !!\n");
 
     }
     // TODO: update this text for each release or centrally store it for lite
     // and application
-    message
-            .append("\nAuthors:  Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n    David Martin & Geoff Barton."
-                    + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
-                    + "\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)"
+    message.append("\nAuthors:  Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,\n    David Martin & Geoff Barton."
+            + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
+            + "\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");
     JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -638,7 +969,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void documentationMenuItem_actionPerformed(ActionEvent e)
   {
@@ -669,10 +1000,10 @@ 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 +1025,8 @@ 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 +1039,43 @@ 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 +1157,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void preferences_actionPerformed(ActionEvent e)
   {
@@ -806,14 +1168,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          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");
+    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");
@@ -823,8 +1185,28 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       java.io.File choice = chooser.getSelectedFile();
+      setProgressBar("Saving jalview project " + choice.getName(),
+              choice.hashCode());
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-      new Jalview2XML().SaveState(choice);
+      // TODO catch and handle errors for savestate
+      try
+      {
+        new Jalview2XML().SaveState(choice);
+      } catch (OutOfMemoryError oom)
+      {
+        new OOMWarning(
+                "Whilst saving current state to " + choice.getName(), oom);
+      } catch (Exception ex)
+      {
+        Cache.log
+                .error("Problems whilst trying to save to "
+                        + choice.getName(), ex);
+        JOptionPane.showMessageDialog(this,
+                "Error whilst saving current state to " + choice.getName(),
+                "Couldn't save project", JOptionPane.WARNING_MESSAGE);
+      }
+      setProgressBar(null, choice.hashCode());
+
     }
   }
 
@@ -832,14 +1214,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          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");
+    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");
 
@@ -847,10 +1229,32 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice = chooser.getSelectedFile().getAbsolutePath();
+      final String choice = chooser.getSelectedFile().getAbsolutePath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
-      new Jalview2XML().LoadJalviewAlign(choice);
+      new Thread(new Runnable()
+      {
+        public void run()
+        {
+          setProgressBar("loading jalview project " + choice,
+                  choice.hashCode());
+          try
+          {
+            new Jalview2XML().LoadJalviewAlign(choice);
+          } catch (OutOfMemoryError oom)
+          {
+            new OOMWarning("Whilst loading project from " + choice, oom);
+          } catch (Exception ex)
+          {
+            Cache.log.error("Problems whilst loading project from "
+                    + choice, ex);
+            JOptionPane.showMessageDialog(Desktop.desktop,
+                    "Error whilst loading project from " + choice,
+                    "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+          }
+          setProgressBar(null, choice.hashCode());
+        }
+      }).start();
     }
   }
 
@@ -925,8 +1329,9 @@ 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 +1340,12 @@ 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 +1364,23 @@ 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 +1389,28 @@ 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());
             }
           }
@@ -1082,31 +1497,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client == null)
     {
       // Load and try to start a session.
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-              .getProperty("LAST_DIRECTORY"));
+      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.");
+      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)
+        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 +1525,105 @@ 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 +1642,6 @@ 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 +1660,7 @@ 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()
@@ -1246,9 +1753,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (v_client != null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-              .getProperty("LAST_DIRECTORY"), new String[]
-      { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+      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");
 
@@ -1260,6 +1767,8 @@ 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 +1790,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                   + choice, ex);
 
         }
+        removeProgressPanel(progpanel);
         if (warnmsg != null)
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -1297,7 +1807,7 @@ 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 +1894,6 @@ 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 +1908,8 @@ 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 +1919,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     public void paintComponent(Graphics g)
     {
-      if (showMemoryUsage)
+      if (showMemoryUsage && g != null && df != 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 +2058,7 @@ 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 +2067,43 @@ 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 +2116,152 @@ 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;
+
+  }
+
+  /**
+   * flag set if jalview GUI is being operated programmatically
+   */
+  private boolean inBatchMode = false;
+
+  /**
+   * check if jalview GUI is being operated programmatically
+   * 
+   * @return inBatchMode
+   */
+  public boolean isInBatchMode()
+  {
+    return inBatchMode;
+  }
+
+  /**
+   * set flag if jalview GUI is being operated programmatically
+   * 
+   * @param inBatchMode
+   */
+  public void setInBatchMode(boolean inBatchMode)
+  {
+    this.inBatchMode = inBatchMode;
+  }
+
+  public void startServiceDiscovery()
+  {
+    startServiceDiscovery(false);
+  }
+
+  public void startServiceDiscovery(boolean blocking)
+  {
+    boolean alive = true;
+    Thread t0 = null, t1 = null, t2 = null;
+
+    // todo: changesupport handlers need to be transferred
+    if (discoverer == null)
+    {
+      discoverer = new jalview.ws.jws1.Discoverer();
+      // register PCS handler for desktop.
+      discoverer.addPropertyChangeListener(changeSupport);
+    }
+    if (Cache.getDefault("SHOW_JWS1_SERVICES", true))
+    {
+      (t0 = new Thread(discoverer)).start();
+    }
+
+    try
+    {
+      if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+      {
+        // EnfinEnvision web service menu entries are rebuild every time the
+        // menu is shown, so no changeSupport events are needed.
+        jalview.ws.EnfinEnvision2OneWay.getInstance();
+        (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance()))
+                .start();
+      }
+    } catch (Exception e)
+    {
+      Cache.log
+              .info("Exception when trying to launch Envision2 workflow discovery.",
+                      e);
+      Cache.log.info(e.getStackTrace());
+    }
+    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    {
+      jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+              .addPropertyChangeListener(changeSupport);
+      (t2 = new Thread(jalview.ws.jws2.Jws2Discoverer.getDiscoverer()))
+              .start();
+    }
+    if (blocking)
+    {
+      while (alive)
+      {
+        try
+        {
+          Thread.sleep(15);
+        } catch (Exception e)
+        {
+        }
+        alive = (t1 != null && t1.isAlive())
+                || (t2 != null && t2.isAlive())
+                || (t0 != null && t0.isAlive());
+      }
+    }
+  }
+
+  /**
+   * start a thread to open a URL in the configured browser. Pops up a warning
+   * dialog to the user if there is an exception when calling out to the browser
+   * to open the URL.
+   * 
+   * @param url
+   */
+  public static void showUrl(final String url)
+  {
+    new Thread(new Runnable()
+    {
+      public void run()
+      {
+        try
+        {
+          jalview.util.BrowserLauncher.openURL(url);
+        } catch (Exception ex)
+        {
+          JOptionPane
+                  .showInternalMessageDialog(
+                          Desktop.desktop,
+                          "Unixers: Couldn't find default web browser."
+                                  + "\nAdd the full path to your browser in Preferences.",
+                          "Web browser not found",
+                          JOptionPane.WARNING_MESSAGE);
+
+          ex.printStackTrace();
+        }
+      }
+    }).start();
+  }
+
+  public static WsParamSetManager wsparamManager = null;
+
+  public static ParamManager getUserParameterStore()
+  {
+    if (wsparamManager == null)
+    {
+      wsparamManager = new WsParamSetManager();
+    }
+    return wsparamManager;
+  }
+
 }