JAL-1355 (basic i18n support)
[jalview.git] / src / jalview / gui / Desktop.java
index 294beac..7ca6338 100644 (file)
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ *  
  * 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 
@@ -23,6 +23,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
 import jalview.ws.params.ParamManager;
 
 import java.awt.BorderLayout;
@@ -59,7 +60,6 @@ import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -83,7 +83,6 @@ import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
-import javax.swing.JTextArea;
 import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.MenuEvent;
@@ -98,7 +97,8 @@ import javax.swing.event.HyperlinkEvent.EventType;
  * @version $Revision: 1.155 $
  */
 public class Desktop extends jalview.jbgui.GDesktop implements
-        DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider
+        DropTargetListener, ClipboardOwner, IProgressIndicator,
+        jalview.api.StructureSelectionManagerProvider
 {
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
@@ -106,7 +106,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * news reader - null if it was never started.
    */
-  private BlogReader jvnews=null;
+  private BlogReader jvnews = null;
 
   /**
    * @param listener
@@ -211,9 +211,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     public void dragFrame(JComponent f, int newX, int newY)
     {
-      if (newY<0)
+      if (newY < 0)
       {
-        newY=0;
+        newY = 0;
       }
       delegate.dragFrame(f, newX, newY);
     }
@@ -251,10 +251,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
             int newHeight)
     {
-      Rectangle b=desktop.getBounds();
-      if (newY<0)
+      Rectangle b = desktop.getBounds();
+      if (newY < 0)
       {
-        newY=0;
+        newY = 0;
       }
       delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
     }
@@ -294,18 +294,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     desktop.setBackground(Color.white);
     getContentPane().setLayout(new BorderLayout());
     // alternate config - have scrollbars - see notes in JAL-153
-    //JScrollPane sp = new JScrollPane();
-    //sp.getViewport().setView(desktop);
-    //getContentPane().add(sp, BorderLayout.CENTER);
+    // JScrollPane sp = new JScrollPane();
+    // sp.getViewport().setView(desktop);
+    // getContentPane().add(sp, BorderLayout.CENTER);
     getContentPane().add(desktop, BorderLayout.CENTER);
     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-    
-      
+
     // This line prevents Windows Look&Feel resizing all new windows to maximum
     // if previous window was maximised
     desktop.setDesktopManager(new MyDesktopManager(
             new DefaultDesktopManager()));
-    
+
     Rectangle dims = getLastKnownDimensions("");
     if (dims != null)
     {
@@ -331,7 +330,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     showConsole(showjconsole);
 
     showNews.setVisible(false);
-    
+
     this.addWindowListener(new WindowAdapter()
     {
       public void windowClosing(WindowEvent evt)
@@ -341,7 +340,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     });
 
     MouseAdapter ma;
-    this.addMouseListener(ma=new MouseAdapter()
+    this.addMouseListener(ma = new MouseAdapter()
     {
       public void mousePressed(MouseEvent evt)
       {
@@ -352,17 +351,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     });
     desktop.addMouseListener(ma);
-   
+
     this.addFocusListener(new FocusListener()
     {
-      
+
       @Override
       public void focusLost(FocusEvent e)
       {
         // TODO Auto-generated method stub
-        
+
       }
-      
+
       @Override
       public void focusGained(FocusEvent e)
       {
@@ -417,7 +416,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     final Desktop me = this;
     // Thread off the news reader, in case there are connection problems.
-    addDialogThread(new Runnable() {
+    addDialogThread(new Runnable()
+    {
       @Override
       public void run()
       {
@@ -429,22 +429,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     });
   }
+
   protected void showNews_actionPerformed(ActionEvent e)
   {
     showNews(showNews.isSelected());
   }
+
   void showNews(boolean visible)
   {
     {
-      Cache.log.debug((visible?"Showing":"Hiding")+" news.");
+      Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
       showNews.setSelected(visible);
       if (visible && !jvnews.isVisible())
       {
-        new Thread(new Runnable() {
+        new Thread(new Runnable()
+        {
           @Override
           public void run()
           {
-            long instance=System.currentTimeMillis();
+            long instance = System.currentTimeMillis();
             Desktop.instance.setProgressBar("Refreshing news", instance);
             jvnews.refreshNews();
             Desktop.instance.setProgressBar(null, instance);
@@ -555,7 +558,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   void showPasteMenu(int x, int y)
   {
     JPopupMenu popup = new JPopupMenu();
-    JMenuItem item = new JMenuItem("Paste To New Window");
+    JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
     item.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent evt)
@@ -645,8 +648,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (System.getProperty("java.awt.headless") != null
-            && System.getProperty("java.awt.headless").equals("true"))
+    if (instance == null || (System.getProperty("java.awt.headless") != null
+            && System.getProperty("java.awt.headless").equals("true")))
     {
       return;
     }
@@ -711,17 +714,17 @@ 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)
       {
@@ -732,7 +735,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
         }
       }
-      
+
       @Override
       public void mouseEntered(MouseEvent e)
       {
@@ -743,11 +746,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
         }
       }
-      
+
       @Override
       public void mouseClicked(MouseEvent e)
       {
-        
+
       }
     });
 
@@ -761,10 +764,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       frame.requestFocus();
     } catch (java.beans.PropertyVetoException ve)
     {
-    }
-    catch (java.lang.ClassCastException cex)
+    } catch (java.lang.ClassCastException cex)
     {
-      Cache.log.warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",cex);
+      Cache.log
+              .warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+                      cex);
     }
   }
 
@@ -897,8 +901,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Open local file");
-    chooser.setToolTipText("Open");
+    chooser.setDialogTitle(MessageManager.getString("label.open_local_file"));
+    chooser.setToolTipText(MessageManager.getString("action.open"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -940,7 +944,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     // This construct allows us to have a wider textfield
     // for viewing
-    JLabel label = new JLabel("Enter URL of Input File");
+    JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
     final JComboBox history = new JComboBox();
 
     JPanel panel = new JPanel(new GridLayout(2, 1));
@@ -965,7 +969,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
 
     int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
-            "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
+            MessageManager.getString("label.input_alignment_from_url"), JOptionPane.OK_CANCEL_OPTION);
 
     if (reply != JOptionPane.OK_OPTION)
     {
@@ -1041,16 +1045,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
       jconsole.stopConsole();
     }
-    if (jvnews!=null)
+    if (jvnews != null)
     {
       storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
-      
+
     }
-    if (dialogExecutor!=null)
+    if (dialogExecutor != null)
     {
       dialogExecutor.shutdownNow();
     }
-      
+
     System.exit(0);
   }
 
@@ -1074,11 +1078,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public void aboutMenuItem_actionPerformed(ActionEvent e)
   {
-//    StringBuffer message = getAboutMessage(false);
-//    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-//
-//    message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
-    new Thread(new Runnable() { public void run() {new SplashScreen(true);}}).start();
+    // StringBuffer message = getAboutMessage(false);
+    // JOptionPane.showInternalMessageDialog(Desktop.desktop,
+    //
+    // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+    new Thread(new Runnable()
+    {
+      public void run()
+      {
+        new SplashScreen(true);
+      }
+    }).start();
   }
 
   public StringBuffer getAboutMessage(boolean shortv)
@@ -1374,28 +1384,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         public void run()
         {
 
-      setProgressBar("Saving jalview project " + choice.getName(),
-              choice.hashCode());
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-      // TODO catch and handle errors for savestate
-      // TODO prevent user from messing with the Desktop whilst we're saving
-      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(me,
-                "Error whilst saving current state to " + choice.getName(),
-                "Couldn't save project", JOptionPane.WARNING_MESSAGE);
-      }
-      setProgressBar(null, choice.hashCode());
+          setProgressBar("Saving jalview project " + choice.getName(),
+                  choice.hashCode());
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                  choice.getParent());
+          // TODO catch and handle errors for savestate
+          // TODO prevent user from messing with the Desktop whilst we're saving
+          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(
+                    me,
+                    "Error whilst saving current state to "
+                            + choice.getName(), "Couldn't save project",
+                    JOptionPane.WARNING_MESSAGE);
+          }
+          setProgressBar(null, choice.hashCode());
         }
       }).start();
     }
@@ -1455,12 +1468,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   JPanel progressPanel;
-  ArrayList<JPanel> fileLoadingPanels=new ArrayList<JPanel>();
+
+  ArrayList<JPanel> fileLoadingPanels = new ArrayList<JPanel>();
+
   public void startLoading(final String fileName)
   {
     if (fileLoadingCount == 0)
     {
-      fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName + "   "));
+      fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName
+              + "   "));
     }
     fileLoadingCount++;
   }
@@ -1469,11 +1485,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (progressPanel == null)
     {
-      progressPanel = new JPanel(new GridLayout(1,1));
+      progressPanel = new JPanel(new GridLayout(1, 1));
       totalProgressCount = 0;
       instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
     }
-    JPanel thisprogress=new JPanel(new BorderLayout(10,5));
+    JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
     JProgressBar progressBar = new JProgressBar();
     progressBar.setIndeterminate(true);
 
@@ -1481,7 +1497,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     thisprogress.add(progressBar, BorderLayout.CENTER);
     progressPanel.add(thisprogress);
-    ((GridLayout)progressPanel.getLayout()).setRows(((GridLayout)progressPanel.getLayout()).getRows()+1);
+    ((GridLayout) progressPanel.getLayout())
+            .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
     ++totalProgressCount;
     instance.validate();
     return thisprogress;
@@ -1495,7 +1512,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       progressPanel.remove(progbar);
       GridLayout gl = (GridLayout) progressPanel.getLayout();
-      gl.setRows(gl.getRows()-1);
+      gl.setRows(gl.getRows() - 1);
       if (--totalProgressCount < 1)
       {
         this.getContentPane().remove(progressPanel);
@@ -1549,9 +1566,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         AlignFrame af = (AlignFrame) frames[t];
         for (int a = 0; a < af.alignPanels.size(); a++)
         {
-          if (alignmentId
-                  .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
-                          .getSequenceSetId()))
+          if (alignmentId.equals(((AlignmentPanel) af.alignPanels
+                  .elementAt(a)).av.getSequenceSetId()))
           {
             aps.add(af.alignPanels.elementAt(a));
           }
@@ -1696,7 +1712,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
       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(MessageManager.getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
 
       int value = chooser.showOpenDialog(this);
 
@@ -1706,8 +1722,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         if (!vamsasImport(chooser.getSelectedFile()))
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Couldn't import '" + fle + "' as a new vamsas session.",
-                  "Vamsas Document Import Failed",
+                  MessageManager.formatMessage("label.couldnt_import_as_vamsas_session", new String[]{fle}),
+                  MessageManager.getString("label.vamsas_document_import_failed"),
                   JOptionPane.ERROR_MESSAGE);
         }
       }
@@ -1850,7 +1866,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   protected void setupVamsasConnectedGui()
   {
-    vamsasStart.setText("Session Update");
+    vamsasStart.setText(MessageManager.getString("label.session_update"));
     vamsasSave.setVisible(true);
     vamsasStop.setVisible(true);
     vamsasImport.setVisible(false); // Document import to existing session is
@@ -1862,7 +1878,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     vamsasSave.setVisible(false);
     vamsasStop.setVisible(false);
     vamsasImport.setVisible(true);
-    vamsasStart.setText("New Vamsas Session");
+    vamsasStart.setText(MessageManager.getString("label.new_vamsas_session"));
   }
 
   public void vamsasStop_actionPerformed(ActionEvent e)
@@ -1898,7 +1914,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           JMenuItem sessit = new JMenuItem();
           sessit.setText(sess[i]);
-          sessit.setToolTipText("Connect to session " + sess[i]);
+          sessit.setToolTipText(MessageManager.formatMessage("label.connect_to_session", new String[]{sess[i]}));
           final Desktop dsktp = this;
           final String mysesid = sess[i];
           sessit.addActionListener(new ActionListener()
@@ -2121,9 +2137,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         if (fm != null)
         {
           g.drawString(
-                  "Total Free Memory: " + df.format(totalFreeMemory)
-                          + "MB; Max Memory: " + df.format(maxMemory)
-                          + "MB; " + df.format(percentUsage) + "%", 10,
+                         MessageManager.formatMessage("label.memory_stats", new String[]{df.format(totalFreeMemory),df.format(maxMemory),df.format(percentUsage)}), 10,
                   getHeight() - fm.getHeight());
         }
       }
@@ -2131,11 +2145,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * fixes stacking order after a modal dialog to ensure windows that should be on top actually are
+   * fixes stacking order after a modal dialog to ensure windows that should be
+   * on top actually are
    */
   public void relayerWindows()
   {
-    
+
   }
 
   protected JMenuItem groovyShell;
@@ -2145,7 +2160,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (jalview.bin.Cache.groovyJarsPresent())
     {
       groovyShell = new JMenuItem();
-      groovyShell.setText("Groovy Console...");
+      groovyShell.setText(MessageManager.getString("label.groovy_console"));
       groovyShell.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)
@@ -2197,6 +2212,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     avp.clear();
     return afs;
   }
+
   public AppJmol[] getJmols()
   {
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2274,8 +2290,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * Progress bars managed by the IProgressIndicator method.
    */
-  private Hashtable<Long,JPanel> progressBars;
-  private Hashtable<Long,IProgressIndicatorHandler> progressBarHandlers;
+  private Hashtable<Long, JPanel> progressBars;
+
+  private Hashtable<Long, IProgressIndicatorHandler> progressBarHandlers;
 
   /*
    * (non-Javadoc)
@@ -2286,14 +2303,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (progressBars == null)
     {
-      progressBars = new Hashtable<Long,JPanel>();
-      progressBarHandlers = new Hashtable<Long,IProgressIndicatorHandler>();
+      progressBars = new Hashtable<Long, JPanel>();
+      progressBarHandlers = new Hashtable<Long, IProgressIndicatorHandler>();
     }
 
     if (progressBars.get(new Long(id)) != null)
     {
-      JPanel progressPanel = progressBars
-              .remove(new Long(id));
+      JPanel progressPanel = progressBars.remove(new Long(id));
       if (progressBarHandlers.contains(new Long(id)))
       {
         progressBarHandlers.remove(new Long(id));
@@ -2324,7 +2340,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
     if (handler.canCancel())
     {
-      JButton cancel = new JButton("Cancel");
+      JButton cancel = new JButton(MessageManager.getString("action.cancel"));
       final IProgressIndicator us = this;
       cancel.addActionListener(new ActionListener()
       {
@@ -2419,7 +2435,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     boolean alive = true;
     Thread t0 = null, t1 = null, t2 = null;
-
+    // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
+    if (true)
+    {
     // todo: changesupport handlers need to be transferred
     if (discoverer == null)
     {
@@ -2427,29 +2445,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       // register PCS handler for desktop.
       discoverer.addPropertyChangeListener(changeSupport);
     }
-    // JAL-940 - disabled JWS1 service configuration - always start discoverer until we phase out completely
-    if (true)
-    {
+    // JAL-940 - disabled JWS1 service configuration - always start discoverer
+    // until we phase out completely
       (t0 = new Thread(discoverer)).start();
     }
 
-    try
+    // ENFIN services are EOLed as of Jalview 2.8.1 release
+    if (false)
     {
-      if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+      try
       {
-        // 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();
+        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());
       }
-    } 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))
     {
       if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
@@ -2458,9 +2480,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
               changeSupport);
-      
+
     }
-    Thread t3=null;
+    Thread t3 = null;
     {
       // TODO: do rest service discovery
     }
@@ -2506,43 +2528,43 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               {
 
                 /*
-                JalviewDialog jd =new JalviewDialog() {
-                  @Override
-                  protected void cancelPressed()
-                  {
-                    // TODO Auto-generated method stub
-                    
-                  }@Override
-                  protected void okPressed()
-                  {
-                    // TODO Auto-generated method stub
-                    
-                  }@Override
-                  protected void raiseClosed()
-                  {
-                    // TODO Auto-generated method stub
-                    
-                  }
-                };
-                jd.initDialogFrame(new JLabel("<html><table width=\"450\"><tr><td>"
-                                        + ermsg
-                                        + "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
-                                        + " or mis-configured HTTP proxy settings.<br/>"
-                                        + "Check the <em>Connections</em> and <em>Web services</em> tab of the"
-                                        + " Tools->Preferences dialog box to change them.</td></tr></table></html>"), true, true, "Web Service Configuration Problem", 450, 400);
-                
-                jd.waitForInput();
-                */
-                JOptionPane.showConfirmDialog(
-                        Desktop.desktop, 
-                        new JLabel("<html><table width=\"450\"><tr><td>"
-                                + ermsg+"</td></tr></table>"
-                                + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
-                                + " or mis-configured HTTP proxy settings.</p>"
-                                + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
-                                + " Tools->Preferences dialog box to change them.</p></html>"), "Web Service Configuration Problem",
+                 * JalviewDialog jd =new JalviewDialog() {
+                 * 
+                 * @Override protected void cancelPressed() { // TODO
+                 * Auto-generated method stub
+                 * 
+                 * }@Override protected void okPressed() { // TODO
+                 * Auto-generated method stub
+                 * 
+                 * }@Override protected void raiseClosed() { // TODO
+                 * Auto-generated method stub
+                 * 
+                 * } }; jd.initDialogFrame(new
+                 * JLabel("<html><table width=\"450\"><tr><td>" + ermsg +
+                 * "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
+                 * + " or mis-configured HTTP proxy settings.<br/>" +
+                 * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
+                 * +
+                 * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
+                 * ), true, true, "Web Service Configuration Problem", 450,
+                 * 400);
+                 * 
+                 * jd.waitForInput();
+                 */
+                JOptionPane
+                        .showConfirmDialog(
+                                Desktop.desktop,
+                                new JLabel(
+                                        "<html><table width=\"450\"><tr><td>"
+                                                + ermsg
+                                                + "</td></tr></table>"
+                                                + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+                                                + " or mis-configured HTTP proxy settings.</p>"
+                                                + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+                                                + " Tools->Preferences dialog box to change them.</p></html>"),
+                                "Web Service Configuration Problem",
                                 JOptionPane.DEFAULT_OPTION,
-                        JOptionPane.ERROR_MESSAGE);
+                                JOptionPane.ERROR_MESSAGE);
                 serviceChangedDialog = null;
 
               }
@@ -2572,12 +2594,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     showUrl(url, Desktop.instance);
   }
+
   /**
    * Like showUrl but allows progress handler to be specified
+   * 
    * @param url
-   * @param progress (null) or object implementing IProgressIndicator
+   * @param progress
+   *          (null) or object implementing IProgressIndicator
    */
-  public static void showUrl(final String url, final IProgressIndicator progress)
+  public static void showUrl(final String url,
+          final IProgressIndicator progress)
   {
     new Thread(new Runnable()
     {
@@ -2585,8 +2611,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         try
         {
-          if (progress!=null) {
-            progress.setProgressBar("Opening "+url, this.hashCode());
+          if (progress != null)
+          {
+            progress.setProgressBar("Opening " + url, this.hashCode());
           }
           jalview.util.BrowserLauncher.openURL(url);
         } catch (Exception ex)
@@ -2601,7 +2628,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
           ex.printStackTrace();
         }
-        if (progress!=null) {
+        if (progress != null)
+        {
           progress.setProgressBar(null, this.hashCode());
         }
       }
@@ -2620,47 +2648,57 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * static hyperlink handler proxy method for use by Jalview's internal windows 
+   * static hyperlink handler proxy method for use by Jalview's internal windows
+   * 
    * @param e
    */
   public static void hyperlinkUpdate(HyperlinkEvent e)
   {
     if (e.getEventType() == EventType.ACTIVATED)
     {
-      String url=null;
+      String url = null;
       try
       {
         url = e.getURL().toString();
         Desktop.showUrl(url);
       } catch (Exception x)
       {
-        if (url!=null) { 
-          if (Cache.log!=null) { 
-            Cache.log.error("Couldn't handle string "+url+" as a URL.");
-          } else {
-            System.err.println("Couldn't handle string "+url+" as a URL.");
+        if (url != null)
+        {
+          if (Cache.log != null)
+          {
+            Cache.log.error("Couldn't handle string " + url + " as a URL.");
+          }
+          else
+          {
+            System.err.println("Couldn't handle string " + url
+                    + " as a URL.");
           }
         }
         // ignore any exceptions due to dud links.
       }
 
-    }    
+    }
   }
+
   /**
    * single thread that handles display of dialogs to user.
    */
-  ExecutorService dialogExecutor=Executors.newSingleThreadExecutor();
+  ExecutorService dialogExecutor = Executors.newSingleThreadExecutor();
+
   /**
    * flag indicating if dialogExecutor should try to acquire a permit
    */
-  private volatile boolean dialogPause=true;
+  private volatile boolean dialogPause = true;
+
   /**
-   * pause the queue 
+   * pause the queue
    */
-  private java.util.concurrent.Semaphore block=new Semaphore(0);
-  
+  private java.util.concurrent.Semaphore block = new Semaphore(0);
+
   /**
    * add another dialog thread to the queue
+   * 
    * @param prompter
    */
   public void addDialogThread(final Runnable prompter)
@@ -2669,10 +2707,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       public void run()
       {
-        if (dialogPause) {
-          try { block.acquire(); } catch (InterruptedException x){};
+        if (dialogPause)
+        {
+          try
+          {
+            block.acquire();
+          } catch (InterruptedException x)
+          {
+          }
+          ;
         }
-        if (instance==null)
+        if (instance == null)
         {
           return;
         }
@@ -2689,8 +2734,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   public void startDialogQueue()
   {
-    // set the flag so we don't pause waiting for another permit and semaphore the current task to begin
-    dialogPause=false;
+    // set the flag so we don't pause waiting for another permit and semaphore
+    // the current task to begin
+    dialogPause = false;
     block.release();
   }
 }