X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=62fd29dd674a958a61f5b43b3efc7101933a00c4;hb=dd3059c62cd80e712c0f6df866d6d69588e5f3eb;hp=8672dec0e38b7837f7f75d886a25175512f2ad05;hpb=73ec89ae5b826808f0e4aae382a10ea98dc33625;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
old mode 100755
new mode 100644
index 8672dec..62fd29d
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,18 +1,18 @@
 /*
- * 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
+ * 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
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
@@ -24,6 +24,7 @@ import jalview.analysis.CrossRef;
 import jalview.analysis.NJTree;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -75,8 +76,10 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -127,7 +130,7 @@ import javax.swing.SwingUtilities;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -144,6 +147,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public AlignmentPanel alignPanel;
 
   AlignViewport viewport;
+ 
+  public AlignViewControllerI avc;
+ 
 
   Vector alignPanels = new Vector();
 
@@ -159,7 +165,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Creates a new AlignFrame object with specific width and height.
-   *
+   * 
    * @param al
    * @param width
    * @param height
@@ -172,7 +178,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Creates a new AlignFrame object with specific width, height and
    * sequenceSetId
-   *
+   * 
    * @param al
    * @param width
    * @param height
@@ -187,7 +193,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Creates a new AlignFrame object with specific width, height and
    * sequenceSetId
-   *
+   * 
    * @param al
    * @param width
    * @param height
@@ -202,7 +208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * new alignment window with hidden columns
-   *
+   * 
    * @param al
    *          AlignmentI
    * @param hiddenColumns
@@ -221,7 +227,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
-   *
+   * 
    * @param al
    * @param hiddenColumns
    * @param width
@@ -238,7 +244,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
-   *
+   * 
    * @param al
    * @param hiddenColumns
    * @param width
@@ -267,7 +273,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Make a new AlignFrame from exisiting alignmentPanels
-   *
+   * 
    * @param ap
    *          AlignmentPanel
    * @param av
@@ -287,6 +293,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
     {
       BLOSUM62Colour.setEnabled(false);
@@ -329,13 +336,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     addKeyListener();
-
+    
   }
 
   /**
    * Change the filename and format for the alignment, and enable the 'reload'
    * button functionality.
-   *
+   * 
    * @param file
    *          valid filename
    * @param format
@@ -475,8 +482,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         case KeyEvent.VK_F2:
           viewport.cursorMode = !viewport.cursorMode;
-          statusBar.setText("Keyboard editing mode is "
-                  + (viewport.cursorMode ? "on" : "off"));
+          statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
           if (viewport.cursorMode)
           {
             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
@@ -557,6 +563,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
   {
     ap.alignFrame = this;
+    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
 
     alignPanels.addElement(ap);
 
@@ -691,7 +698,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Need to call this method when tabs are selected for multiple views, or when
    * loading from Jalview2XML.java
-   *
+   * 
    * @param av
    *          AlignViewport
    */
@@ -734,16 +741,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     rnahelicesColour
             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
     setShowProductsEnabled();
-
     updateEditMenuBar();
   }
+
   // methods for implementing IProgressIndicator
   // need to refactor to a reusable stub class
   Hashtable progressBars, progressBarHandlers;
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   @Override
@@ -807,7 +814,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     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()
       {
@@ -827,7 +834,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @return true if any progress bars are still active
    */
   @Override
@@ -880,6 +887,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
+                  && ((AlignFrame) frames[i]).fileName != null
                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
           {
             try
@@ -961,7 +969,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -986,8 +994,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (currentFileFormat == null)
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                "You must select a file format before saving!",
-                "File format not specified", JOptionPane.WARNING_MESSAGE);
+                MessageManager.getString("label.select_file_format_before_saving"),
+                MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
         value = chooser.showSaveDialog(this);
         return;
       }
@@ -1023,8 +1031,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
-      statusBar.setText("Successfully saved to file: " + fileName + " in "
-              + format + " format.");
+      statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+
 
     }
     else
@@ -1045,9 +1053,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         int reply = JOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
-                        "The Alignment contains hidden columns."
-                                + "\nDo you want to save only the visible alignment?",
-                        "Save / Omit Hidden Columns",
+                        MessageManager.getString("label.alignment_contains_hidden_columns"),
+                        MessageManager.getString("action.save_omit_hidden_columns"),
                         JOptionPane.YES_NO_OPTION,
                         JOptionPane.QUESTION_MESSAGE);
 
@@ -1057,8 +1064,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
       FormatAdapter f = new FormatAdapter();
-      String output = f.formatSequences(
-              format,
+      String output = f.formatSequences(format,
               viewport.getAlignment(), // class cast exceptions will
               // occur in the distant future
               omitHidden, f.getCacheSuffixDefault(format),
@@ -1078,8 +1084,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           out.print(output);
           out.close();
           this.setTitle(file);
-          statusBar.setText("Successfully saved to file: " + fileName
-                  + " in " + format + " format.");
+          statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
         } catch (Exception ex)
         {
           success = false;
@@ -1090,8 +1095,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!success)
     {
-      JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
-              + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
+              MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE);
     }
 
     return success;
@@ -1114,7 +1119,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1128,9 +1133,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       int reply = JOptionPane
               .showInternalConfirmDialog(
                       Desktop.desktop,
-                      "The Alignment contains hidden columns."
-                              + "\nDo you want to output only the visible alignment?",
-                      "Save / Omit Hidden Columns",
+                      MessageManager.getString("label.alignment_contains_hidden_columns"),
+                      MessageManager.getString("action.save_omit_hidden_columns"),
                       JOptionPane.YES_NO_OPTION,
                       JOptionPane.QUESTION_MESSAGE);
 
@@ -1160,7 +1164,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1179,7 +1183,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1191,7 +1195,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1210,7 +1214,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1262,7 +1266,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Close the current view or all views in the alignment frame. If the frame
    * only contains one view then the alignment will be removed from memory.
-   *
+   * 
    * @param closeAllTabs
    */
   @Override
@@ -1308,7 +1312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * close alignPanel2 and shuffle tabs appropriately.
-   *
+   * 
    * @param alignPanel2
    */
   public void closeView(AlignmentPanel alignPanel2)
@@ -1346,12 +1350,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       undoMenuItem.setEnabled(true);
       CommandI command = (CommandI) viewport.historyList.peek();
-      undoMenuItem.setText("Undo " + command.getDescription());
+      undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
     }
     else
     {
       undoMenuItem.setEnabled(false);
-      undoMenuItem.setText("Undo");
+      undoMenuItem.setText(MessageManager.getString("action.undo"));
     }
 
     if (viewport.redoList.size() > 0)
@@ -1359,12 +1363,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       redoMenuItem.setEnabled(true);
 
       CommandI command = (CommandI) viewport.redoList.peek();
-      redoMenuItem.setText("Redo " + command.getDescription());
+      redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
     }
     else
     {
       redoMenuItem.setEnabled(false);
-      redoMenuItem.setText("Redo");
+      redoMenuItem.setText(MessageManager.getString("action.redo"));
     }
   }
 
@@ -1384,7 +1388,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @return alignment objects for all views
    */
   AlignmentI[] getViewAlignments()
@@ -1409,7 +1413,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1445,7 +1449,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1527,7 +1531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param up
    *          DOCUMENT ME!
    */
@@ -1539,7 +1543,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
+    viewport.getAlignment().moveSelectedSequencesByOne(sg,
+            viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }
 
@@ -1627,7 +1632,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1691,12 +1696,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     Desktop.jalviewClipboard = new Object[]
     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
-    statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
+    statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1708,7 +1713,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -1720,7 +1725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Paste contents of Jalview clipboard
-   *
+   * 
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
    */
@@ -1781,6 +1786,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
+      ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+      int fgroup = -1;
 
       if (newAlignment)
       {
@@ -1848,6 +1855,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           newDs.clear(); // tidy up
         }
+        if (alignment.getAlignmentAnnotation() != null)
+        {
+          for (AlignmentAnnotation alan : alignment
+                  .getAlignmentAnnotation())
+          {
+            if (alan.graphGroup > fgroup)
+            {
+              fgroup = alan.graphGroup;
+            }
+          }
+        }
         if (pastedal.getAlignmentAnnotation() != null)
         {
           // Add any annotation attached to alignment.
@@ -1858,6 +1876,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
             {
               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+
               newann.padAnnotation(alwidth);
               alignment.addAnnotation(newann);
             }
@@ -1877,11 +1911,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (sequences[i].getAnnotation() != null)
         {
+          AlignmentAnnotation newann;
           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
           {
             annotationAdded = true;
-            sequences[i].getAnnotation()[a].adjustForAlignment();
-            sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+            newann = sequences[i].getAnnotation()[a];
+            newann.adjustForAlignment();
+            newann.padAnnotation(alwidth);
+            if (newann.graphGroup > -1)
+            {
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+            }
             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
             // was
             // duplicated
@@ -1921,6 +1975,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   newann.padAnnotation(avwidth);
                   alview[avnum].addAnnotation(newann); // annotation was
                   // duplicated earlier
+                  // TODO JAL-1145 graphGroups are not updated for sequence
+                  // annotation added to several views. This may cause
+                  // strangeness
                   alview[avnum].setAnnotationIndex(newann, a);
                 }
               }
@@ -1930,6 +1987,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         viewport.firePropertyChange("alignment", null,
                 alignment.getSequences());
+        if (alignPanels != null)
+        {
+          for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+          {
+            ap.validateAnnotationDimensions(false);
+          }
+        }
+        else
+        {
+          alignPanel.validateAnnotationDimensions(false);
+        }
 
       }
       else
@@ -1989,7 +2057,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2002,7 +2070,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2063,24 +2131,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
   @Override
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
-    viewport.getAlignment().deleteAllGroups();
-    viewport.sequenceColours = null;
-    viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
-    alignPanel.updateAnnotation();
-    alignPanel.paintAlignment(true);
+    if (avc.deleteGroups()) {
+      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+      alignPanel.updateAnnotation();
+      alignPanel.paintAlignment(true);
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2103,7 +2170,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2127,7 +2194,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2163,7 +2230,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2175,7 +2242,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2229,11 +2296,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 viewport.getSelectionGroup());
       }
 
-      statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
+      statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
 
       addHistoryItem(trimRegion);
 
-      for (SequenceGroup sg :viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
@@ -2249,7 +2316,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2277,8 +2344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText("Removed " + removeGapCols.getSize()
-            + " empty columns.");
+    statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
 
     // This is to maintain viewport position on first residue
     // of first sequence
@@ -2297,7 +2363,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2336,7 +2402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2360,7 +2426,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2377,7 +2443,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @param copyAnnotation
    *          if true then duplicate all annnotation, groups and settings
    * @return new alignment panel, already displayed.
@@ -2388,7 +2454,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @param viewTitle
    *          title of newly created view
    * @return new alignment panel, already displayed.
@@ -2399,7 +2465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   *
+   * 
    * @param viewTitle
    *          title of newly created view
    * @param copyAnnotation
@@ -2472,7 +2538,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     newap.av.viewName = newViewName;
 
     addAlignmentPanel(newap, true);
-
+    newap.alignmentChanged();
+    
     if (alignPanels.size() == 2)
     {
       viewport.gatherViewsHere = true;
@@ -2495,7 +2562,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2507,7 +2574,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2537,7 +2604,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
    */
   @Override
@@ -2552,7 +2619,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2565,7 +2632,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2601,7 +2668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * called by key handler and the hide all/show all menu items
-   *
+   * 
    * @param toggleSeqs
    * @param toggleCols
    */
@@ -2671,7 +2738,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
    * event.ActionEvent)
@@ -2684,7 +2751,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
    * .ActionEvent)
@@ -2701,7 +2768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
    * ActionEvent)
@@ -2730,7 +2797,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2743,7 +2810,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2756,7 +2823,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2769,7 +2836,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2782,7 +2849,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2795,7 +2862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2827,7 +2894,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Set or clear 'Show Sequence Features'
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -2844,7 +2911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Set or clear 'Show Sequence Features'
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -2868,7 +2935,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2886,7 +2953,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     editPane.setEditable(false);
     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
             .formatAsHtml();
-    editPane.setText("<html>" + contents.toString() + "</html>");
+    editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
     JInternalFrame frame = new JInternalFrame();
     frame.getContentPane().add(new JScrollPane(editPane));
 
@@ -2896,7 +2963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2936,7 +3003,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2948,19 +3015,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
   @Override
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
+    changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+            viewport.getHiddenRepSequences()));
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2972,7 +3040,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2984,7 +3052,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -2996,7 +3064,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3008,7 +3076,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3020,7 +3088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3032,7 +3100,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3044,7 +3112,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3080,7 +3148,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3092,7 +3160,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param cs
    *          DOCUMENT ME!
    */
@@ -3146,8 +3214,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.getColourAppliesToAllGroups())
     {
 
-
-      for (SequenceGroup sg:viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
         if (cs == null)
         {
@@ -3157,8 +3224,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg, viewport
-                  .getHiddenRepSequences());
+          sg.cs = new ClustalxColourScheme(sg,
+                  viewport.getHiddenRepSequences());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -3216,7 +3283,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3234,7 +3301,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3252,7 +3319,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3271,7 +3338,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3290,7 +3357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3346,8 +3413,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
               int option = JOptionPane.showInternalConfirmDialog(
                       jalview.gui.Desktop.desktop,
-                      "Remove from default list?",
-                      "Remove user defined colour",
+                      MessageManager.getString("label.remove_from_default_list"),
+                      MessageManager.getString("label.remove_user_defined_colour"),
                       JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
@@ -3386,7 +3453,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3398,7 +3465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3410,7 +3477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3427,7 +3494,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3443,7 +3510,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3459,7 +3526,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3476,7 +3543,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3488,7 +3555,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3499,7 +3566,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             || (viewport.getSelectionGroup().getSize() < 2))
     {
       JOptionPane.showInternalMessageDialog(this,
-              "You must select at least 2 sequences.", "Invalid Selection",
+              MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
               JOptionPane.WARNING_MESSAGE);
     }
     else
@@ -3512,7 +3579,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3525,9 +3592,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             || (viewport.getAlignment().getHeight() < 4))
     {
       JOptionPane.showInternalMessageDialog(this,
-              "Principal component analysis must take\n"
-                      + "at least 4 input sequences.",
-              "Sequence selection insufficient",
+              MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+              MessageManager.getString("label.sequence_selection_insufficient"),
               JOptionPane.WARNING_MESSAGE);
 
       return;
@@ -3561,7 +3627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3573,7 +3639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3585,7 +3651,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3597,7 +3663,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3609,7 +3675,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param type
    *          DOCUMENT ME!
    * @param pwType
@@ -3621,33 +3687,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     TreePanel tp;
 
-    if (viewport.getSelectionGroup() != null)
+    if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() > 0)
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
         JOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
-                        "You need to have more than two sequences selected to build a tree!",
-                        "Not enough sequences", JOptionPane.WARNING_MESSAGE);
+                        MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
+                        MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE);
         return;
       }
 
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      for (SequenceI _s:sg.getSequences())
+      for (SequenceI _s : sg.getSequences())
       {
-        if (_s.getLength() < sg
-                .getEndRes())
+        if (_s.getLength() < sg.getEndRes())
         {
           JOptionPane
                   .showMessageDialog(
                           Desktop.desktop,
-                          "The selected region to create a tree may\nonly contain residues or gaps.\n"
-                                  + "Try using the Pad function in the edit menu,\n"
-                                  + "or one of the multiple sequence alignment web services.",
-                          "Sequences in selection are not aligned",
+                          MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
+                          MessageManager.getString("label.sequences_selection_not_aligned"),
                           JOptionPane.WARNING_MESSAGE);
 
           return;
@@ -3665,10 +3729,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         JOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
-                        "The sequences must be aligned before creating a tree.\n"
-                                + "Try using the Pad function in the edit menu,\n"
-                                + "or one of the multiple sequence alignment web services.",
-                        "Sequences not aligned",
+                        MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
+                        MessageManager.getString("label.sequences_not_aligned"),
                         JOptionPane.WARNING_MESSAGE);
 
         return;
@@ -3696,7 +3758,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param title
    *          DOCUMENT ME!
    * @param order
@@ -3728,7 +3790,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Add a new sort by annotation score menu item
-   *
+   * 
    * @param sort
    *          the menu to add the option to
    * @param scoreLabel
@@ -3765,7 +3827,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * search the alignment and rebuild the sort by annotation score submenu the
    * last alignment annotation vector hash is stored to minimize cost of
    * rebuilding in subsequence calls.
-   *
+   * 
    */
   @Override
   public void buildSortByAnnotationScoresMenu()
@@ -3781,7 +3843,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // almost certainly a quicker way to do this - but we keep it simple
       Hashtable scoreSorts = new Hashtable();
       AlignmentAnnotation aann[];
-      for (SequenceI sqa:viewport.getAlignment().getSequences())
+      for (SequenceI sqa : viewport.getAlignment().getSequences())
       {
         aann = sqa.getAnnotation();
         for (int i = 0; aann != null && i < aann.length; i++)
@@ -3812,7 +3874,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * call. Listeners are added to remove the menu item when the treePanel is
    * closed, and adjust the tree leaf to sequence mapping when the alignment is
    * modified.
-   *
+   * 
    * @param treePanel
    *          Displayed tree window.
    * @param title
@@ -3881,7 +3943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Work out whether the whole set of sequences or just the selected set will
    * be submitted for multiple alignment.
-   *
+   * 
    */
   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
@@ -3896,7 +3958,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       /*
        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
        * SequenceI[sz = seqs.getSize(false)];
-       *
+       * 
        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
        * seqs.getSequenceAt(i); }
        */
@@ -3906,9 +3968,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       /*
        * Vector seqs = viewport.getAlignment().getSequences();
-       *
+       * 
        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       *
+       * 
        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
        * seqs.elementAt(i); } }
        */
@@ -3954,7 +4016,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -3982,13 +4044,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       } catch (Exception ex)
       {
         JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
-                "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
+                MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
       if (fin != null && fin.hasWarningMessage())
       {
         JOptionPane.showMessageDialog(Desktop.desktop,
-                fin.getWarningMessage(), "Possible problem with tree file",
+                fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
                 JOptionPane.WARNING_MESSAGE);
       }
     }
@@ -4020,7 +4082,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Add a treeviewer for the tree extracted from a newick file object to the
    * current alignment view
-   *
+   * 
    * @param nf
    *          the tree
    * @param title
@@ -4071,7 +4133,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Generates menu items and listener event actions for web service clients
-   *
+   * 
    */
   public void BuildWebServiceMenu()
   {
@@ -4093,6 +4155,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void run()
       {
+        final List<JMenuItem> legacyItems=new ArrayList<JMenuItem>();
         try
         {
           System.err.println("Building ws menu again "
@@ -4114,7 +4177,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   "Secondary Structure Prediction");
           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
           final JMenu analymenu = new JMenu("Analysis");
-          final JMenu dismenu = new JMenu("Disorder");
+          final JMenu dismenu = new JMenu("Protein Disorder");
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4124,28 +4187,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // TODO: refactor to allow list of AbstractName/Handler bindings to
             // be
             // stored or retrieved from elsewhere
-            Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+            // No MSAWS used any more:
+            // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
             Vector secstrpr = (Vector) Discoverer.services
                     .get("SecStrPred");
-            Vector seqsrch = null; // (Vector)
-                                   // Discoverer.services.get("SeqSearch");
-            // TODO: move GUI generation code onto service implementation - so a
-            // client instance attaches itself to the GUI with method call like
-            // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
-            // alignframe)
-            if (msaws != null)
-            {
-              // Add any Multiple Sequence Alignment Services
-              for (int i = 0, j = msaws.size(); i < j; i++)
-              {
-                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
-                        .get(i);
-                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
-                        .getServiceClient(sh);
-                impl.attachWSMenuEntry(msawsmenu, me);
-
-              }
-            }
             if (secstrpr != null)
             {
               // Add any secondary structure prediction services
@@ -4155,35 +4200,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .get(i);
                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
                         .getServiceClient(sh);
+                int p=secstrmenu.getItemCount();
                 impl.attachWSMenuEntry(secstrmenu, me);
-              }
-            }
-            if (seqsrch != null)
-            {
-              // Add any sequence search services
-              for (int i = 0, j = seqsrch.size(); i < j; i++)
-              {
-                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
-                        .elementAt(i);
-                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
-                        .getServiceClient(sh);
-                impl.attachWSMenuEntry(seqsrchmenu, me);
+                int q=secstrmenu.getItemCount();
+                for (int litm=p;litm<q; litm++)
+                {
+                  legacyItems.add(secstrmenu.getItem(litm));
+                }
               }
             }
           }
-
+          
           // Add all submenus in the order they should appear on the web
           // services menu
           wsmenu.add(msawsmenu);
           wsmenu.add(secstrmenu);
           wsmenu.add(dismenu);
           wsmenu.add(analymenu);
-          // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
-          // submens.add(msawsmenu);
-          // submens.add(secstrmenu);
-          // submens.add(dismenu);
-          // submens.add(analymenu);
-
           // No search services yet
           // wsmenu.add(seqsrchmenu);
 
@@ -4208,6 +4241,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   webService.add(me.webServiceNoServices);
                 }
                 // TODO: move into separate menu builder class.
+                boolean new_sspred=false;
                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
@@ -4216,6 +4250,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     if (jws2servs.hasServices())
                     {
                       jws2servs.attachWSMenuEntry(webService, me);
+                      for (Jws2Instance sv:jws2servs.getServices()) {
+                        if (sv.description.toLowerCase().contains("jpred"))
+                        {
+                          for (JMenuItem jmi:legacyItems)
+                          {
+                            jmi.setVisible(false);
+                          }
+                        }
+                      }
+                      
                     }
                     if (jws2servs.isRunning())
                     {
@@ -4226,7 +4270,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     }
                   }
                 }
-
                 build_urlServiceMenu(me.webService);
                 build_fetchdbmenu(webService);
                 for (JMenu item : wsmenu)
@@ -4242,6 +4285,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               } catch (Exception e)
               {
+                Cache.log
+                        .debug("Exception during web service menu building process.",
+                                e);
               }
               ;
             }
@@ -4259,7 +4305,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * construct any groupURL type service menu entries.
-   *
+   * 
    * @param webService
    */
   private void build_urlServiceMenu(JMenu webService)
@@ -4269,12 +4315,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
-     *
+     * 
      * @Override public void actionPerformed(ActionEvent e) {
      * jalview.datamodel.AlignmentView
      * .testSelectionViews(af.viewport.getAlignment(),
      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
-     *
+     * 
      * }); webService.add(testAlView);
      */
     // TODO: refactor to RestClient discoverer and merge menu entries for
@@ -4301,12 +4347,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
    * chooser = new JalviewFileChooser(jalview.bin.Cache.
    * getProperty("LAST_DIRECTORY"));
-   *
+   * 
    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
    * to Vamsas file"); chooser.setToolTipText("Export");
-   *
+   * 
    * int value = chooser.showSaveDialog(this);
-   *
+   * 
    * if (value == JalviewFileChooser.APPROVE_OPTION) {
    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
@@ -4314,7 +4360,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   /**
    * prototype of an automatically enabled/disabled analysis function
-   *
+   * 
    */
   protected void setShowProductsEnabled()
   {
@@ -4334,7 +4380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * search selection for sequence xRef products and build the show products
    * menu.
-   *
+   * 
    * @param selection
    * @param dataset
    * @return true if showProducts menu should be enabled.
@@ -4505,8 +4551,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       JOptionPane
               .showMessageDialog(
                       Desktop.desktop,
-                      "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
-                      "Translation Failed", JOptionPane.WARNING_MESSAGE);
+                      MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+                      MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -4535,15 +4581,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       al = null;
-      jalview.bin.Cache.log.debug("Exception during translation.", ex);
+      jalview.bin.Cache.log.error("Exception during translation. Please report this !", ex);
+      JOptionPane
+      .showMessageDialog(
+              Desktop.desktop,
+              MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"),
+              MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE);
+      return;
     }
     if (al == null)
     {
       JOptionPane
               .showMessageDialog(
                       Desktop.desktop,
-                      "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
-                      "Translation Failed", JOptionPane.WARNING_MESSAGE);
+                      MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
+                      MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -4555,7 +4607,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Try to load a features file onto the alignment.
-   *
+   * 
    * @param file
    *          contents or path to retrieve file
    * @param type
@@ -4742,10 +4794,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   || JOptionPane
                           .showConfirmDialog(
                                   this,
-                                  "Do you want to automatically associate the "
-                                          + filesmatched.size()
-                                          + " PDB files with sequences in the alignment that have the same name ?",
-                                  "Automatically Associate PDB files by name",
+                                  MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name",
+                                		  new String[]{Integer.valueOf(filesmatched.size()).toString()}),
+                                  MessageManager.getString("label.automatically_associate_pdb_files_by_name"),
                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
 
           {
@@ -4778,10 +4829,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
                           .showConfirmDialog(
                                   this,
-                                  "<html>Do you want to <em>ignore</em> the "
-                                          + filesnotmatched.size()
-                                          + " files whose names did not match any sequence IDs ?</html>",
-                                  "Ignore unmatched dropped files ?",
+                                  MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
+                                  MessageManager.getString("label.ignore_unmatched_dropped_files"),
                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
           {
             return;
@@ -4804,7 +4853,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * it's and Annotation file, then a JNet file, and finally a features file. If
    * all are false then the user may have dropped an alignment file onto this
    * AlignFrame.
-   *
+   * 
    * @param file
    *          either a filename or a URL string.
    */
@@ -4840,16 +4889,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               tcoffeeColour.setSelected(true);
               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
               isAnnotation = true;
-              statusBar
-                      .setText("Successfully pasted T-Coffee scores to alignment.");
+              statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
             }
             else
             {
-              // some problem - if no warning its probable that the ID matching process didn't work
-              JOptionPane.showMessageDialog(Desktop.desktop,
-                      tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
-                      "Problem reading T-COFFEE score file",
-                      JOptionPane.WARNING_MESSAGE);
+              // some problem - if no warning its probable that the ID matching
+              // process didn't work
+              JOptionPane
+                      .showMessageDialog(
+                              Desktop.desktop,
+                              tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
+                                      : tcf.getWarningMessage(),
+                              MessageManager.getString("label.problem_reading_tcoffee_score_file"),
+                              JOptionPane.WARNING_MESSAGE);
             }
           }
           else
@@ -4858,7 +4910,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         } catch (Exception x)
         {
-          Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+          Cache.log
+                  .debug("Exception when processing data source as T-COFFEE score file",
+                          x);
           tcf = null;
         }
         if (tcf == null)
@@ -4882,7 +4936,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             /*
              * if (format.equalsIgnoreCase("PDB")) {
-             *
+             * 
              * String pdbfn = ""; // try to match up filename with sequence id
              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
@@ -4927,6 +4981,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
+    } catch (OutOfMemoryError oom)
+    {
+      try
+      {
+        System.gc();
+      } catch (Exception x)
+      {
+      }
+      ;
+      new OOMWarning(
+              "loading data "
+                      + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+                              : "using " + protocol + " from " + file)
+                              : ".")
+                      + (format != null ? "(parsing as '" + format
+                              + "' file)" : ""), oom, Desktop.desktop);
     }
   }
 
@@ -4937,6 +5007,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
       viewport = alignPanel.av;
+      avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
     }
   }
@@ -4947,7 +5018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (SwingUtilities.isRightMouseButton(e))
     {
       String reply = JOptionPane.showInternalInputDialog(this,
-              "Enter View Name", "Edit View Name",
+              MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"),
               JOptionPane.QUESTION_MESSAGE);
 
       if (reply != null)
@@ -4984,7 +5055,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
    * )
@@ -4997,7 +5068,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
    * ActionEvent)
    */
@@ -5010,7 +5081,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * find the viewport amongst the tabs in this alignment frame and close that
    * tab
-   *
+   * 
    * @param av
    */
   public boolean closeView(AlignViewport av)
@@ -5227,7 +5298,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   ++i;
                   if (++icomp >= mcomp || i == (otherdb.size()))
                   {
-                    ifetch.setText(imname + " to '" + sname + "'");
+                    ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
                     dfetch.add(ifetch);
                     ifetch = new JMenu();
                     imname = null;
@@ -5239,7 +5310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               ++dbi;
               if (comp >= mcomp || dbi >= (dbclasses.length))
               {
-                dfetch.setText(mname + " to '" + dbclass + "'");
+                dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
                 rfetch.add(dfetch);
                 dfetch = new JMenu();
                 mname = null;
@@ -5283,7 +5354,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
    * awt.event.ActionEvent)
@@ -5297,7 +5368,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
    * .ActionEvent)
@@ -5312,7 +5383,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5326,7 +5397,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5340,7 +5411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5355,6 +5426,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
   {
+    showSequenceLogo.setState(true);
+    viewport.setShowSequenceLogo(true);
     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
@@ -5367,7 +5440,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
    * .event.ActionEvent)
@@ -5375,39 +5448,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
-    if (viewport.getSelectionGroup() != null)
-    {
-      SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
-              viewport.getSequenceSelection(),
-              viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()), viewport.getAlignment()
-                      .getGroups());
-      viewport.getAlignment().deleteAllGroups();
-      viewport.sequenceColours = null;
-      viewport.setSelectionGroup(null);
-      // set view properties for each group
-      for (int g = 0; g < gps.length; g++)
-      {
-        gps[g].setShowNonconserved(viewport.getShowUnconserved());
-        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
-        viewport.getAlignment().addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255),
-                (int) (Math.random() * 255), (int) (Math.random() * 255));
-        col = col.brighter();
-        for (SequenceI s:gps[g].getSequences())
-          viewport.setSequenceColour(
-                s, col)
-          ;
-      }
+    if (avc.makeGroupsFromSelection()) {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
       alignPanel.paintAlignment(true);
     }
   }
 
+  @Override
+  protected void createGroup_actionPerformed(ActionEvent e)
+  {
+    if (avc.createGroup())
+    {
+      alignPanel.alignmentChanged();
+    }
+  }
+
+  @Override
+  protected void unGroup_actionPerformed(ActionEvent e)
+  {
+    if (avc.unGroup())
+    {
+      alignPanel.alignmentChanged();
+    }
+  }
+
   /**
    * make the given alignmentPanel the currently selected tab
-   *
+   * 
    * @param alignmentPanel
    */
   public void setDisplayedView(AlignmentPanel alignmentPanel)