JAL-1620 version bump and release notes
[jalview.git] / src / jalview / gui / Desktop.java
index f4d1885..7407cba 100644 (file)
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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.
+ * 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 
  * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -23,6 +26,8 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.ws.params.ParamManager;
 
@@ -85,9 +90,9 @@ import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
 import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
-import javax.swing.event.HyperlinkEvent.EventType;
 
 /**
  * Jalview Desktop
@@ -282,7 +287,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     instance = this;
     doVamsasClientCheck();
     doGroovyCheck();
-
+    doConfigureStructurePrefs();
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
     boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
@@ -313,13 +318,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     else
     {
       Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-      setBounds((int) (screenSize.width - 900) / 2,
-              (int) (screenSize.height - 650) / 2, 900, 650);
+      setBounds((screenSize.width - 900) / 2,
+              (screenSize.height - 650) / 2, 900, 650);
     }
     jconsole = new Console(this, showjconsole);
     // add essential build information
-    jconsole.setHeader("Jalview Desktop "
+    jconsole.setHeader("Jalview Version: "
             + jalview.bin.Cache.getProperty("VERSION") + "\n"
+            + "Jalview Installation: "
+            + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
+            + "\n"
             + "Build Date: "
             + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
             + "Java version: " + System.getProperty("java.version") + "\n"
@@ -412,6 +420,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             });
   }
 
+  public void doConfigureStructurePrefs()
+  {
+    // configure services
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(this);
+    if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+    {
+      ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
+              Preferences.ADD_TEMPFACT_ANN, true));
+    ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+    ssm.setSecStructServices(jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW,
+            true));
+    }
+    else
+    {
+      ssm.setAddTempFacAnnot(false);
+      ssm.setProcessSecondaryStructure(false);
+      ssm.setSecStructServices(false);
+    }
+  }
+
   public void checkForNews()
   {
     final Desktop me = this;
@@ -448,7 +477,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           public void run()
           {
             long instance = System.currentTimeMillis();
-            Desktop.instance.setProgressBar("Refreshing news", instance);
+            Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), instance);
             jvnews.refreshNews();
             Desktop.instance.setProgressBar(null, instance);
             jvnews.showNews();
@@ -558,7 +587,8 @@ 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)
@@ -601,38 +631,85 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * Adds and opens the given frame to the desktop
    * 
    * @param frame
-   *          DOCUMENT ME!
+   *          Frame to show
    * @param title
-   *          DOCUMENT ME!
+   *          Visible Title
    * @param w
-   *          DOCUMENT ME!
+   *          width
    * @param h
-   *          DOCUMENT ME!
+   *          height
    */
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, int w, int h)
   {
-    addInternalFrame(frame, title, w, h, true);
+    addInternalFrame(frame, title, true, w, h, true);
+  }
+
+
+  /**
+   * Add an internal frame to the Jalview desktop
+   * 
+   * @param frame
+   *          Frame to show
+   * @param title
+   *          Visible Title
+   * @param makeVisible
+   *          When true, display frame immediately, otherwise, caller must call
+   *          setVisible themselves.
+   * @param w
+   *          width
+   * @param h
+   *          height
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, boolean makeVisible,
+          int w, int h)
+  {
+    addInternalFrame(frame, title, makeVisible, w, h, true);
   }
 
   /**
-   * DOCUMENT ME!
+   * Add an internal frame to the Jalview desktop and make it visible
    * 
    * @param frame
-   *          DOCUMENT ME!
+   *          Frame to show
    * @param title
-   *          DOCUMENT ME!
+   *          Visible Title
    * @param w
-   *          DOCUMENT ME!
+   *          width
    * @param h
-   *          DOCUMENT ME!
+   *          height
    * @param resizable
-   *          DOCUMENT ME!
+   *          Allow resize
    */
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, int w, int h,
           boolean resizable)
   {
+    addInternalFrame(frame, title, true, w, h, resizable);
+  }
+
+  /**
+   * Add an internal frame to the Jalview desktop
+   * 
+   * @param frame
+   *          Frame to show
+   * @param title
+   *          Visible Title
+   * @param makeVisible
+   *          When true, display frame immediately, otherwise, caller must call
+   *          setVisible themselves.
+   * @param w
+   *          width
+   * @param h
+   *          height
+   * @param resizable
+   *          Allow resize
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, boolean makeVisible,
+          int w, int h, boolean resizable)
+  {
 
     // TODO: allow callers to determine X and Y position of frame (eg. via
     // bounds object).
@@ -648,15 +725,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (instance == null || (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;
     }
 
     openFrameCount++;
 
-    frame.setVisible(true);
+    frame.setVisible(makeVisible);
     frame.setClosable(true);
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
@@ -806,6 +884,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public void drop(DropTargetDropEvent evt)
   {
+    boolean success = true;
     Transferable t = evt.getTransferable();
     java.util.List files = null;
     java.util.List protocols = null;
@@ -854,6 +933,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     } catch (Exception e)
     {
+      success = false;
     }
 
     if (files != null)
@@ -882,8 +962,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
       } catch (Exception ex)
       {
+        success = false;
       }
     }
+    evt.dropComplete(success); // need this to ensure input focus is properly
+                               // transfered to any new windows created
   }
 
   /**
@@ -901,8 +984,9 @@ 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);
 
@@ -913,7 +997,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               .getSelectedFile().getParent());
 
       String format = null;
-      if (chooser.getSelectedFormat().equals("Jalview"))
+      if (chooser.getSelectedFormat() != null
+              && chooser.getSelectedFormat().equals("Jalview"))
       {
         format = "Jalview";
       }
@@ -944,7 +1029,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     // This construct allows us to have a wider textfield
     // for viewing
-    JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
+    JLabel label = new JLabel(
+            MessageManager.getString("label.input_file_url"));
     final JComboBox history = new JComboBox();
 
     JPanel panel = new JPanel(new GridLayout(2, 1));
@@ -969,7 +1055,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
 
     int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
-            MessageManager.getString("label.input_alignment_from_url"), JOptionPane.OK_CANCEL_OPTION);
+            MessageManager.getString("label.input_alignment_from_url"),
+            JOptionPane.OK_CANCEL_OPTION);
 
     if (reply != JOptionPane.OK_OPTION)
     {
@@ -997,7 +1084,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       if (format.equals("URL NOT FOUND"))
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "Couldn't locate " + url, "URL not found",
+                MessageManager.formatMessage("label.couldnt_locate", new String[]{url}), MessageManager.getString("label.url_not_found"),
                 JOptionPane.WARNING_MESSAGE);
 
         return;
@@ -1024,7 +1111,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(viewport);
-    Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+    Desktop.addInternalFrame(cap,
+            MessageManager.getString("label.cut_paste_alignmen_file"),
+            true, 600, 500);
   }
 
   /*
@@ -1099,7 +1188,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       message.append("<h1><strong>Version: "
               + jalview.bin.Cache.getProperty("VERSION")
-              + "</strong></h1><br>");
+              + "</strong></h1>");
       message.append("<strong>Last Updated: <em>"
               + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
               + "</em></strong>");
@@ -1146,11 +1235,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     message.append("<br>Authors:  "
             + jalview.bin.Cache
                     .getDefault(
-                            "AUTHORNAMES",
-                            "Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton")
-            + "<br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
-            + "<br>For help, see the FAQ at <a href=\"http://www.jalview.org\">www.jalview.org</a> and/or join the jalview-discuss@jalview.org mailing list"
-            + "<br>If  you use Jalview, please cite:"
+                            "AUTHORFNAMES",
+                            "The Jalview Authors (See AUTHORS file for current list)")
+            + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+            + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+            + "<br><br>If  you use Jalview, please cite:"
             + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
             + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
             + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
@@ -1168,13 +1257,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     try
     {
-      ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-      java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
-      javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
-      javax.help.HelpBroker hb = hs.createHelpBroker();
-      hb.setCurrentID("home");
-      hb.setDisplayed(true);
+      Help.showHelpWindow();
     } catch (Exception ex)
     {
     }
@@ -1367,11 +1450,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jar" }, new String[]
+            { "jvp" }, new String[]
             { "Jalview Project" }, "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save State");
+    chooser.setDialogTitle(MessageManager.getString("label.save_state"));
 
     int value = chooser.showSaveDialog(this);
 
@@ -1384,7 +1467,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         public void run()
         {
 
-          setProgressBar("Saving jalview project " + choice.getName(),
+          setProgressBar(MessageManager.formatMessage("label.saving_jalview_project", new String[]{choice.getName()}),
                   choice.hashCode());
           jalview.bin.Cache.setProperty("LAST_DIRECTORY",
                   choice.getParent());
@@ -1404,8 +1487,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                     ex);
             JOptionPane.showMessageDialog(
                     me,
-                    "Error whilst saving current state to "
-                            + choice.getName(), "Couldn't save project",
+                    MessageManager.formatMessage("label.error_whilst_saving_current_state_to", new String[]{ choice.getName()}),
+                    MessageManager.getString("label.couldnt_save_project"),
                     JOptionPane.WARNING_MESSAGE);
           }
           setProgressBar(null, choice.hashCode());
@@ -1424,10 +1507,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jar" }, new String[]
-            { "Jalview Project" }, "Jalview Project");
+            { "jvp", "jar" }, new String[]
+            { "Jalview Project", "Jalview Project (old)" },
+            "Jalview Project");
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Restore state");
+    chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -1440,7 +1524,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         public void run()
         {
-          setProgressBar("loading jalview project " + choice,
+          setProgressBar(MessageManager.formatMessage("label.loading_jalview_project", new String[]{choice}),
                   choice.hashCode());
           try
           {
@@ -1453,8 +1537,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             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);
+                       MessageManager.formatMessage("label.error_whilst_loading_project_from", new String[]{choice}),
+                    MessageManager.getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE);
           }
           setProgressBar(null, choice.hashCode());
         }
@@ -1475,8 +1559,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (fileLoadingCount == 0)
     {
-      fileLoadingPanels.add(addProgressPanel("Loading File: " + fileName
-              + "   "));
+      fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new String[]{fileName})));
     }
     fileLoadingCount++;
   }
@@ -1510,13 +1593,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (progressPanel != null)
     {
-      progressPanel.remove(progbar);
-      GridLayout gl = (GridLayout) progressPanel.getLayout();
-      gl.setRows(gl.getRows() - 1);
-      if (--totalProgressCount < 1)
+      synchronized (progressPanel)
       {
-        this.getContentPane().remove(progressPanel);
-        progressPanel = null;
+        progressPanel.remove(progbar);
+        GridLayout gl = (GridLayout) progressPanel.getLayout();
+        gl.setRows(gl.getRows() - 1);
+        if (--totalProgressCount < 1)
+        {
+          this.getContentPane().remove(progressPanel);
+          progressPanel = null;
+        }
       }
     }
     validate();
@@ -1527,9 +1613,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     fileLoadingCount--;
     if (fileLoadingCount < 1)
     {
-      for (JPanel flp : fileLoadingPanels)
+      while (fileLoadingPanels.size() > 0)
       {
-        removeProgressPanel(flp);
+        removeProgressPanel(fileLoadingPanels.remove(0));
       }
       fileLoadingPanels.clear();
       fileLoadingCount = 0;
@@ -1711,8 +1797,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               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.setDialogTitle(MessageManager.getString("label.open_saved_vamsas_session"));
+      chooser.setToolTipText(MessageManager
+              .getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
 
       int value = chooser.showOpenDialog(this);
 
@@ -1721,10 +1808,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         String fle = chooser.getSelectedFile().toString();
         if (!vamsasImport(chooser.getSelectedFile()))
         {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  MessageManager.formatMessage("label.couldnt_import_as_vamsas_session", new String[]{fle}),
-                  MessageManager.getString("label.vamsas_document_import_failed"),
-                  JOptionPane.ERROR_MESSAGE);
+          JOptionPane
+                  .showInternalMessageDialog(
+                          Desktop.desktop,
+                          MessageManager.formatMessage(
+                                  "label.couldnt_import_as_vamsas_session",
+                                  new String[]
+                                  { fle }),
+                          MessageManager
+                                  .getString("label.vamsas_document_import_failed"),
+                          JOptionPane.ERROR_MESSAGE);
         }
       }
     }
@@ -1797,22 +1890,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       return false;
     }
 
-    setProgressBar("Importing VAMSAS session from " + file.getName(),
+    setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{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());
+        setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{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(),
+    setProgressBar(MessageManager.formatMessage("status.importing_vamsas_session_from", new String[]{file.getName()}),
             file.hashCode());
     return v_client.inSession();
   }
@@ -1821,12 +1914,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (v_client != null)
     {
-      throw new Error(
-              "Trying to join a vamsas session when another is already connected.");
+      throw new Error(MessageManager.getString("error.try_join_vamsas_session_another"));
     }
     if (mysesid == null)
     {
-      throw new Error("Invalid vamsas session id.");
+      throw new Error(MessageManager.getString("error.invalid_vamsas_session_id"));
     }
     v_client = new VamsasApplication(this, mysesid);
     setupVamsasConnectedGui();
@@ -1878,7 +1970,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     vamsasSave.setVisible(false);
     vamsasStop.setVisible(false);
     vamsasImport.setVisible(true);
-    vamsasStart.setText(MessageManager.getString("label.new_vamsas_session"));
+    vamsasStart.setText(MessageManager
+            .getString("label.new_vamsas_session"));
   }
 
   public void vamsasStop_actionPerformed(ActionEvent e)
@@ -1914,7 +2007,9 @@ 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()
@@ -1970,15 +2065,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               { "Vamsas Document" }, "Vamsas Document");
 
       chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle("Save Vamsas Document Archive");
+      chooser.setDialogTitle(MessageManager.getString("label.save_vamsas_document_archive"));
 
       int value = chooser.showSaveDialog(this);
 
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         java.io.File choice = chooser.getSelectedFile();
-        JPanel progpanel = addProgressPanel("Saving VAMSAS Document to "
-                + choice.getName());
+        JPanel progpanel = addProgressPanel(MessageManager.formatMessage("label.saving_vamsas_doc", new String[]{choice.getName()}));
         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
         String warnmsg = null;
         String warnttl = null;
@@ -2030,7 +2124,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
     if (b)
     {
-      vamUpdate = this.addProgressPanel("Updating vamsas session");
+      vamUpdate = this.addProgressPanel(MessageManager.getString("label.updating_vamsas_session"));
     }
     vamsasStart.setVisible(!b);
     vamsasStop.setVisible(!b);
@@ -2132,12 +2226,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       if (showMemoryUsage && g != null && df != null)
       {
         if (percentUsage < 20)
+        {
           g.setColor(Color.red);
+        }
         FontMetrics fm = g.getFontMetrics();
         if (fm != null)
         {
-          g.drawString(
-                         MessageManager.formatMessage("label.memory_stats", new String[]{df.format(totalFreeMemory),df.format(maxMemory),df.format(percentUsage)}), 10,
+          g.drawString(MessageManager.formatMessage(
+                  "label.memory_stats",
+                  new String[]
+                  { df.format(totalFreeMemory), df.format(maxMemory),
+                      df.format(percentUsage) }), 10,
                   getHeight() - fm.getHeight());
         }
       }
@@ -2258,8 +2357,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // use reflection to avoid creating compilation dependency.
     if (!jalview.bin.Cache.groovyJarsPresent())
     {
-      throw new Error(
-              "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
+      throw new Error(MessageManager.getString("error.implementation_error_cannot_create_groovyshell"));
     }
     try
     {
@@ -2281,8 +2379,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               .showInternalMessageDialog(
                       Desktop.desktop,
 
-                      "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
-                      "Jalview Groovy Support Failed",
+                      MessageManager.getString("label.couldnt_create_groovy_shell"),
+                      MessageManager.getString("label.groovy_support_failed"),
                       JOptionPane.ERROR_MESSAGE);
     }
   }
@@ -2333,14 +2431,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
     {
-      throw new Error(
-              "call setProgressBar before registering the progress bar's handler.");
+      throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
     }
     progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+    final JPanel progressPanel = progressBars.get(new Long(id));
     if (handler.canCancel())
     {
-      JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+      JButton cancel = new JButton(
+              MessageManager.getString("action.cancel"));
       final IProgressIndicator us = this;
       cancel.addActionListener(new ActionListener()
       {
@@ -2348,10 +2446,7 @@ 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(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
         }
       });
       progressPanel.add(cancel, BorderLayout.EAST);
@@ -2438,15 +2533,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // 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)
-    {
-      discoverer = new jalview.ws.jws1.Discoverer();
-      // register PCS handler for desktop.
-      discoverer.addPropertyChangeListener(changeSupport);
-    }
-    // JAL-940 - disabled JWS1 service configuration - always start discoverer
-    // until we phase out completely
+      // todo: changesupport handlers need to be transferred
+      if (discoverer == null)
+      {
+        discoverer = new jalview.ws.jws1.Discoverer();
+        // register PCS handler for desktop.
+        discoverer.addPropertyChangeListener(changeSupport);
+      }
+      // JAL-940 - disabled JWS1 service configuration - always start discoverer
+      // until we phase out completely
       (t0 = new Thread(discoverer)).start();
     }
 
@@ -2559,7 +2654,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                                                 + 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>"
+                                                + "<br>or as a command-line argument, 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",
@@ -2613,7 +2708,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           if (progress != null)
           {
-            progress.setProgressBar("Opening " + url, this.hashCode());
+            progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new String[]{url}), this.hashCode());
           }
           jalview.util.BrowserLauncher.openURL(url);
         } catch (Exception ex)
@@ -2621,9 +2716,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           JOptionPane
                   .showInternalMessageDialog(
                           Desktop.desktop,
-                          "Unixers: Couldn't find default web browser."
-                                  + "\nAdd the full path to your browser in Preferences.",
-                          "Web browser not found",
+                          MessageManager.getString("label.web_browser_not_found_unix"),
+                          MessageManager.getString("label.web_browser_not_found"),
                           JOptionPane.WARNING_MESSAGE);
 
           ex.printStackTrace();
@@ -2739,4 +2833,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     dialogPause = false;
     block.release();
   }
+  @Override
+  protected void snapShotWindow_actionPerformed(ActionEvent e)
+  {
+    invalidate();
+    File of;
+    ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
+            "View of Desktop", getWidth(), getHeight(), of = new File(
+                    "Jalview_snapshot" + System.currentTimeMillis()
+                            + ".eps"), "View of desktop");
+    try {
+      paintAll(im.getGraphics());
+      im.writeImage();
+    } catch (Exception q)
+    {
+      Cache.log.error("Couldn't write snapshot to "+of.getAbsolutePath(),q);
+      return;
+    }
+    Cache.log.info("Successfully written snapshot to file "+of.getAbsolutePath());
+  }
 }