X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=dbb6955bb565c6ed93e5941bcee3339be37ca0b6;hb=386cd5fbbcddbefe76728ed6d1c9e5f83d36b044;hp=bf0d052f8e7932dcc66e56af4afe25b0cce5c93f;hpb=439d5ad378494d0afa9668e2308ad605c51afcc0;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index bf0d052f8..dbb6955 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -19,6 +19,7 @@ package jalview.gui;
 
 import jalview.bin.Cache;
 import jalview.io.*;
+import jalview.ws.params.ParamManager;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
@@ -26,6 +27,7 @@ import java.awt.dnd.*;
 import java.awt.event.*;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
 import java.io.File;
@@ -52,78 +54,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         DropTargetListener, ClipboardOwner, IProgressIndicator
 {
 
-  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)
+   * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
    */
   public void addJalviewPropertyChangeListener(
           PropertyChangeListener listener)
@@ -134,7 +69,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * @param propertyName
    * @param listener
-   * @see jalview.gui.Desktop.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
+   * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
    *      java.beans.PropertyChangeListener)
    */
   public void addJalviewPropertyChangeListener(String propertyName,
@@ -146,7 +81,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * @param propertyName
    * @param listener
-   * @see jalview.gui.Desktop.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
+   * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
    *      java.beans.PropertyChangeListener)
    */
   public void removeJalviewPropertyChangeListener(String propertyName,
@@ -373,6 +308,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         Cache.log.debug("Filechooser init thread finished.");
       }
     }).start();
+    // Add the service change listener
+    changeSupport.addJalviewPropertyChangeListener("services",
+            new PropertyChangeListener()
+            {
+
+              @Override
+              public void propertyChange(PropertyChangeEvent evt)
+              {
+                Cache.log.debug("Firing service changed event for "
+                        + evt.getNewValue());
+                JalviewServicesChanged(evt);
+              }
+
+            });
   }
 
   /**
@@ -413,6 +362,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         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);
@@ -575,34 +536,33 @@ 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()
     {
@@ -618,6 +578,47 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
       }
     });
+    menuItem.addMouseListener(new MouseListener()
+    {
+      
+      @Override
+      public void mouseReleased(MouseEvent e)
+      {
+      }
+      
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+      }
+      
+      @Override
+      public void mouseExited(MouseEvent e)
+      {
+        try
+        {
+          frame.setSelected(false);
+        } catch (PropertyVetoException e1)
+        {
+        }
+      }
+      
+      @Override
+      public void mouseEntered(MouseEvent e)
+      {
+        try
+        {
+          frame.setSelected(true);
+        } catch (PropertyVetoException e1)
+        {
+        }
+      }
+      
+      @Override
+      public void mouseClicked(MouseEvent e)
+      {
+        
+      }
+    });
 
     windowMenu.add(menuItem);
 
@@ -754,8 +755,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   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"));
@@ -935,22 +936,20 @@ 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)"
-                    + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-                    + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
+    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,
 
     message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
@@ -1163,10 +1162,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   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");
@@ -1176,12 +1175,27 @@ 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());
+      setProgressBar("Saving jalview project " + choice.getName(),
+              choice.hashCode());
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
       // TODO catch and handle errors for savestate
-      new Jalview2XML().SaveState(choice);
-      removeProgressPanel(progpanel);
+      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());
 
     }
   }
@@ -1194,10 +1208,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   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");
 
@@ -1205,13 +1219,32 @@ 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());
+      final String choice = chooser.getSelectedFile().getAbsolutePath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
-      new Jalview2XML().LoadJalviewAlign(choice);
-      setProgressBar(null, choice.hashCode());
+      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();
     }
   }
 
@@ -1283,18 +1316,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     validate();
   }
 
-  public static int getViewCount(String viewId)
+  public static int getViewCount(String alignmentId)
   {
-    AlignViewport[] aps = getViewports(viewId);
+    AlignViewport[] aps = getViewports(alignmentId);
     return (aps == null) ? 0 : aps.length;
   }
 
   /**
    * 
-   * @param viewId
-   * @return all AlignmentPanels concerning the viewId sequence set
+   * @param alignmentId
+   * @return all AlignmentPanels concerning the alignmentId sequence set
    */
-  public static AlignmentPanel[] getAlignmentPanels(String viewId)
+  public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
   {
     int count = 0;
     if (Desktop.desktop == null)
@@ -1312,7 +1345,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         AlignFrame af = (AlignFrame) frames[t];
         for (int a = 0; a < af.alignPanels.size(); a++)
         {
-          if (viewId
+          if (alignmentId
                   .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
                           .getSequenceSetId()))
           {
@@ -1454,13 +1487,12 @@ 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);
 
@@ -1515,8 +1547,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
       bis.close();
       fos.close();
-      v_client = new jalview.gui.VamsasApplication(this, file, url
-              .toExternalForm());
+      v_client = new jalview.gui.VamsasApplication(this, file,
+              url.toExternalForm());
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error(
@@ -1545,8 +1577,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       return false;
     }
 
-    setProgressBar("Importing VAMSAS session from " + file.getName(), file
-            .hashCode());
+    setProgressBar("Importing VAMSAS session from " + file.getName(),
+            file.hashCode());
     try
     {
       v_client = new jalview.gui.VamsasApplication(this, file, null);
@@ -1560,8 +1592,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
     setupVamsasConnectedGui();
     v_client.initial_update(); // TODO: thread ?
-    setProgressBar("Importing VAMSAS session from " + file.getName(), file
-            .hashCode());
+    setProgressBar("Importing VAMSAS session from " + file.getName(),
+            file.hashCode());
     return v_client.inSession();
   }
 
@@ -1711,9 +1743,9 @@ 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");
 
@@ -1884,10 +1916,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         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());
+          g.drawString(
+                  "Total Free Memory: " + df.format(totalFreeMemory)
+                          + "MB; Max Memory: " + df.format(maxMemory)
+                          + "MB; " + df.format(percentUsage) + "%", 10,
+                  getHeight() - fm.getHeight());
         }
       }
     }
@@ -1953,6 +1986,42 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     avp.clear();
     return afs;
   }
+  public AppJmol[] getJmols()
+  {
+    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 AppJmol)
+        {
+          AppJmol af = (AppJmol) frames[i];
+          avp.addElement(af);
+        }
+      }
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+    if (avp.size() == 0)
+    {
+      return null;
+    }
+    AppJmol afs[] = new AppJmol[avp.size()];
+    for (int i = 0, j = avp.size(); i < j; i++)
+    {
+      afs[i] = (AppJmol) avp.elementAt(i);
+    }
+    avp.clear();
+    return afs;
+  }
 
   /**
    * Add Groovy Support to Jalview
@@ -2051,8 +2120,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         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);
@@ -2087,13 +2158,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     return v_client;
 
   }
+
   /**
    * flag set if jalview GUI is being operated programmatically
    */
-  private boolean inBatchMode=false;
+  private boolean inBatchMode = false;
 
   /**
    * check if jalview GUI is being operated programmatically
+   * 
    * @return inBatchMode
    */
   public boolean isInBatchMode()
@@ -2103,14 +2176,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   /**
    * set flag if jalview GUI is being operated programmatically
-   * @param inBatchMode 
+   * 
+   * @param inBatchMode
    */
   public void setInBatchMode(boolean inBatchMode)
   {
     this.inBatchMode = inBatchMode;
   }
 
-
   public void startServiceDiscovery()
   {
     startServiceDiscovery(false);
@@ -2146,17 +2219,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     } catch (Exception e)
     {
       Cache.log
-              .info(
-                      "Exception when trying to launch Envision2 workflow discovery.",
+              .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 (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
+      {
+        jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
+      }
+      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
+              changeSupport);
+      
+    }
+    Thread t3=null;
+    {
+      // TODO: do rest service discovery
     }
     if (blocking)
     {
@@ -2170,9 +2249,118 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
         alive = (t1 != null && t1.isAlive())
                 || (t2 != null && t2.isAlive())
+                || (t3 != null && t3.isAlive())
                 || (t0 != null && t0.isAlive());
       }
     }
   }
 
+  /**
+   * called to check if the service discovery process completed successfully.
+   * 
+   * @param evt
+   */
+  protected void JalviewServicesChanged(PropertyChangeEvent evt)
+  {
+    if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+    {
+      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+              .getErrorMessages();
+      if (ermsg != null)
+      {
+        if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
+        {
+        if (serviceChangedDialog == null)
+        {
+          // only run if we aren't already displaying one of these.
+          javax.swing.SwingUtilities
+                  .invokeLater(serviceChangedDialog = new Runnable()
+                  {
+                    public void run()
+                    {
+
+                      JOptionPane
+                              .showInternalMessageDialog(
+                                      Desktop.desktop,
+                                      ermsg
+                                                + "It may be that you have invalid JABA URLs\nin your web service preferences.\n\nGo to the Web services tab of the\nTools->Preferences dialog box to change them.\n",
+                                      "Preferences Problem",
+                                      JOptionPane.WARNING_MESSAGE);
+                      serviceChangedDialog = null;
+
+                    }
+                  });
+        }
+      }
+        else
+        {
+          Cache.log
+                  .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+                          + ermsg);
+        }
+      }
+    }
+  }
+
+  private Runnable serviceChangedDialog = null;
+
+  /**
+   * 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)
+  {
+    showUrl(url, Desktop.instance);
+  }
+  /**
+   * Like showUrl but allows progress handler to be specified
+   * @param url
+   * @param progress (null) or object implementing IProgressIndicator
+   */
+  public static void showUrl(final String url, final IProgressIndicator progress)
+  {
+    new Thread(new Runnable()
+    {
+      public void run()
+      {
+        try
+        {
+          if (progress!=null) {
+            progress.setProgressBar("Opening "+url, this.hashCode());
+          }
+          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();
+        }
+        if (progress!=null) {
+          progress.setProgressBar(null, this.hashCode());
+        }
+      }
+    }).start();
+  }
+
+  public static WsParamSetManager wsparamManager = null;
+
+  public static ParamManager getUserParameterStore()
+  {
+    if (wsparamManager == null)
+    {
+      wsparamManager = new WsParamSetManager();
+    }
+    return wsparamManager;
+  }
+
+
 }