X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2a804ad6ea1abdb60f50a4ce0132ad1abbc17cce;hb=b58a17a47d215b541be4d8057eb88072c599087e;hp=d188d613bab846f4cbb8059489216a8bd24bf140;hpb=21c29b20790ac555b2e2a124a034f6c6b4486270;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d188d61..2a804ad 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,32 +1,40 @@
 /*
- * 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 2.8.2)
+ * 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;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.analysis.CrossRef;
 import jalview.analysis.NJTree;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.AlignViewControllerI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
 import jalview.commands.OrderCommand;
 import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
@@ -78,10 +86,10 @@ 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;
-import java.awt.Color;
 import java.awt.Component;
 import java.awt.GridLayout;
 import java.awt.Rectangle;
@@ -113,6 +121,7 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
@@ -133,7 +142,7 @@ import javax.swing.SwingUtilities;
  * @version $Revision$
  */
 public class AlignFrame extends GAlignFrame implements DropTargetListener,
-        IProgressIndicator
+        IProgressIndicator, AlignViewControllerGuiI
 {
 
   /** DOCUMENT ME!! */
@@ -146,6 +155,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
+  public AlignViewControllerI avc;
+
   Vector alignPanels = new Vector();
 
   /**
@@ -253,21 +264,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           int width, int height, String sequenceSetId, String viewId)
   {
     setSize(width, height);
-    viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
-
-    alignPanel = new AlignmentPanel(this, viewport);
 
     if (al.getDataset() == null)
     {
       al.setDataset(null);
     }
 
+    viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
+
+    alignPanel = new AlignmentPanel(this, viewport);
+
+
     addAlignmentPanel(alignPanel, true);
     init();
   }
 
   /**
-   * Make a new AlignFrame from exisiting alignmentPanels
+   * Make a new AlignFrame from existing alignmentPanels
    * 
    * @param ap
    *          AlignmentPanel
@@ -288,6 +301,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    avc = new jalview.controller.AlignViewController(this, viewport,
+            alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
     {
       BLOSUM62Colour.setEnabled(false);
@@ -319,6 +334,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
+    buildTreeMenu();
+    
     if (viewport.wrapAlignment)
     {
       wrapMenuItem_actionPerformed(null);
@@ -361,7 +378,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
                 && Character.isDigit(evt.getKeyChar()))
+        {
           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+        }
 
         switch (evt.getKeyCode())
         {
@@ -373,32 +392,48 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         case KeyEvent.VK_DOWN:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             moveSelectedSequences(false);
+          }
           if (viewport.cursorMode)
+          {
             alignPanel.seqPanel.moveCursor(0, 1);
+          }
           break;
 
         case KeyEvent.VK_UP:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             moveSelectedSequences(true);
+          }
           if (viewport.cursorMode)
+          {
             alignPanel.seqPanel.moveCursor(0, -1);
+          }
 
           break;
 
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+          }
           else
+          {
             alignPanel.seqPanel.moveCursor(-1, 0);
+          }
 
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+          }
           else
+          {
             alignPanel.seqPanel.moveCursor(1, 0);
+          }
           break;
 
         case KeyEvent.VK_SPACE:
@@ -476,7 +511,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         case KeyEvent.VK_F2:
           viewport.cursorMode = !viewport.cursorMode;
-          statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(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;
@@ -488,14 +525,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_F1:
           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)
           {
             ex.printStackTrace();
@@ -540,14 +570,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             viewport.firePropertyChange("alignment", null, viewport
                     .getAlignment().getSequences());
+          }
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             viewport.firePropertyChange("alignment", null, viewport
                     .getAlignment().getSequences());
+          }
           break;
         }
       }
@@ -557,6 +591,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
   {
     ap.alignFrame = this;
+    avc = new jalview.controller.AlignViewController(this, viewport,
+            alignPanel);
 
     alignPanels.addElement(ap);
 
@@ -710,6 +746,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleLeft.setVisible(av.wrapAlignment);
     scaleRight.setVisible(av.wrapAlignment);
     annotationPanelMenuItem.setState(av.showAnnotation);
+    /*
+     * Show/hide annotations only enabled if annotation panel is shown
+     */
+    showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -734,7 +777,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     rnahelicesColour
             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
     setShowProductsEnabled();
-
     updateEditMenuBar();
   }
 
@@ -801,14 +843,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     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));
     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()
       {
@@ -817,10 +859,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         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);
@@ -841,6 +880,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return false;
   }
 
+  @Override
+  public void setStatus(String text)
+  {
+    statusBar.setText(text);
+  };
+
   /*
    * Added so Castor Mapping file can obtain Jalview Version
    */
@@ -977,8 +1022,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             currentFileFormat, false);
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Alignment to file");
-    chooser.setToolTipText("Save");
+    chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+    chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
 
@@ -987,9 +1032,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       currentFileFormat = chooser.getSelectedFormat();
       if (currentFileFormat == null)
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                MessageManager.getString("label.select_file_format_before_saving"),
-                MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE);
+        JOptionPane
+                .showInternalMessageDialog(
+                        Desktop.desktop,
+                        MessageManager
+                                .getString("label.select_file_format_before_saving"),
+                        MessageManager
+                                .getString("label.file_format_not_specified"),
+                        JOptionPane.WARNING_MESSAGE);
         value = chooser.showSaveDialog(this);
         return;
       }
@@ -1025,8 +1075,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       success = new Jalview2XML().SaveAlignment(this, file, shortName);
 
-      statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
-
+      statusBar.setText(MessageManager.formatMessage(
+              "label.successfully_saved_to_file_in_format", new String[]
+              { fileName, format }));
 
     }
     else
@@ -1047,8 +1098,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         int reply = JOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
-                        MessageManager.getString("label.alignment_contains_hidden_columns"),
-                        MessageManager.getString("action.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);
 
@@ -1078,7 +1131,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           out.print(output);
           out.close();
           this.setTitle(file);
-          statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format}));
+          statusBar.setText(MessageManager.formatMessage(
+                  "label.successfully_saved_to_file_in_format",
+                  new String[]
+                  { fileName, format }));
         } catch (Exception ex)
         {
           success = false;
@@ -1089,8 +1145,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!success)
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}),
-              MessageManager.getString("label.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;
@@ -1127,8 +1186,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       int reply = JOptionPane
               .showInternalConfirmDialog(
                       Desktop.desktop,
-                      MessageManager.getString("label.alignment_contains_hidden_columns"),
-                      MessageManager.getString("action.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);
 
@@ -1146,8 +1207,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
               viewport.getAlignment(), omitHidden,
               viewport.getColumnSelection()));
-      Desktop.addInternalFrame(cap,
-              "Alignment output - " + e.getActionCommand(), 600, 500);
+      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+              "label.alignment_output_command", new String[]
+              { e.getActionCommand() }), 600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1199,6 +1261,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.makeEPS(f);
   }
 
+  public void createSVG(File f)
+  {
+    alignPanel.makeSVG(f);
+  }
   @Override
   public void pageSetup_actionPerformed(ActionEvent e)
   {
@@ -1243,8 +1309,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Load Jalview Annotations or Features File");
-    chooser.setToolTipText("Load Jalview Annotations / Features file");
+    chooser.setDialogTitle(MessageManager
+            .getString("label.load_jalview_annotations"));
+    chooser.setToolTipText(MessageManager
+            .getString("label.load_jalview_annotations"));
 
     int value = chooser.showOpenDialog(null);
 
@@ -1343,8 +1411,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = (CommandI) viewport.historyList.peek();
-      undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
+      CommandI command = viewport.historyList.peek();
+      undoMenuItem.setText(MessageManager.formatMessage(
+              "label.undo_command", new String[]
+              { command.getDescription() }));
     }
     else
     {
@@ -1356,8 +1426,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       redoMenuItem.setEnabled(true);
 
-      CommandI command = (CommandI) viewport.redoList.peek();
-      redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
+      CommandI command = viewport.redoList.peek();
+      redoMenuItem.setText(MessageManager.formatMessage(
+              "label.redo_command", new String[]
+              { command.getDescription() }));
     }
     else
     {
@@ -1415,8 +1487,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.historyList.empty())
+    {
       return;
-    CommandI command = (CommandI) viewport.historyList.pop();
+    }
+    CommandI command = viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand(getViewAlignments());
 
@@ -1455,7 +1529,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    CommandI command = (CommandI) viewport.redoList.pop();
+    CommandI command = viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand(getViewAlignments());
 
@@ -1568,37 +1642,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
     {
       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+      {
         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+      }
     }
 
     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
 
     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
     for (int i = 0; i < invertGroup.size(); i++)
+    {
       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+    }
 
     SlideSequencesCommand ssc;
     if (right)
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
               size, viewport.getGapCharacter());
+    }
     else
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
               size, viewport.getGapCharacter());
+    }
 
     int groupAdjustment = 0;
     if (ssc.getGapsInsertedBegin() && right)
     {
       if (viewport.cursorMode)
+      {
         alignPanel.seqPanel.moveCursor(size, 0);
+      }
       else
+      {
         groupAdjustment = size;
+      }
     }
     else if (!ssc.getGapsInsertedBegin() && !right)
     {
       if (viewport.cursorMode)
+      {
         alignPanel.seqPanel.moveCursor(-size, 0);
+      }
       else
+      {
         groupAdjustment = -size;
+      }
     }
 
     if (groupAdjustment != 0)
@@ -1619,7 +1709,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (!appendHistoryItem)
+    {
       addHistoryItem(ssc);
+    }
 
     repaint();
   }
@@ -1690,7 +1782,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     Desktop.jalviewClipboard = new Object[]
     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
-    statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()}));
+    statusBar.setText(MessageManager.formatMessage(
+            "label.copied_sequences_to_clipboard", new String[]
+            { Integer.valueOf(seqs.length).toString() }));
   }
 
   /**
@@ -1897,7 +1991,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // /////
         // ADD HISTORY ITEM
         //
-        addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+        addHistoryItem(new EditCommand(
+                MessageManager.getString("label.add_sequences"),
+                Action.PASTE,
                 sequences, 0, alignment.getWidth(), alignment));
       }
       // Add any annotations attached to sequences
@@ -1952,7 +2048,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
             if (sann == null)
+            {
               continue;
+            }
             for (int avnum = 0; avnum < alview.length; avnum++)
             {
               if (alview[avnum] != alignment)
@@ -2049,6 +2147,60 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
+  @Override
+  protected void expand_newalign(ActionEvent e)
+  {
+    try
+    {
+      AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
+              .getAlignment(), -1);
+      AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
+              DEFAULT_HEIGHT);
+      String newtitle = new String("Flanking alignment");
+
+      if (Desktop.jalviewClipboard != null
+              && Desktop.jalviewClipboard[2] != null)
+      {
+        Vector hc = (Vector) Desktop.jalviewClipboard[2];
+        for (int i = 0; i < hc.size(); i++)
+        {
+          int[] region = (int[]) hc.elementAt(i);
+          af.viewport.hideColumns(region[0], region[1]);
+        }
+      }
+
+      // >>>This is a fix for the moment, until a better solution is
+      // found!!<<<
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+              .transferSettings(
+                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+      // TODO: maintain provenance of an alignment, rather than just make the
+      // title a concatenation of operations.
+      {
+        if (title.startsWith("Copied sequences"))
+        {
+          newtitle = title;
+        }
+        else
+        {
+          newtitle = newtitle.concat("- from " + title);
+        }
+      }
+
+      Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Exception whilst pasting: " + ex);
+      // could be anything being pasted in here
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Viewing flanking region of alignment", oom);
+    }
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -2078,17 +2230,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Vector seqs = new Vector();
+    List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
     SequenceI seq;
     for (int i = 0; i < sg.getSize(); i++)
     {
       seq = sg.getSequenceAt(i);
-      seqs.addElement(seq);
+      seqs.add(seq);
     }
 
-    // If the cut affects all sequences, remove highlighted columns
+    // If the cut affects all sequences, warn, remove highlighted columns
     if (sg.getSize() == viewport.getAlignment().getHeight())
     {
+      int confirm = JOptionPane.showConfirmDialog(this,
+              MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+              MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+              JOptionPane.OK_CANCEL_OPTION);
+
+      if (confirm == JOptionPane.CANCEL_OPTION
+              || confirm == JOptionPane.CLOSED_OPTION)
+      {
+        return;
+      }
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
     }
@@ -2096,14 +2258,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     SequenceI[] cut = new SequenceI[seqs.size()];
     for (int i = 0; i < seqs.size(); i++)
     {
-      cut[i] = (SequenceI) seqs.elementAt(i);
+      cut[i] = seqs.get(i);
     }
 
     /*
      * //ADD HISTORY ITEM
      */
-    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
-            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+    addHistoryItem(new EditCommand(
+            MessageManager.getString("label.cut_sequences"), Action.CUT,
+            cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
             viewport.getAlignment()));
 
     viewport.setSelectionGroup(null);
@@ -2132,12 +2295,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @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);
+    }
   }
 
   /**
@@ -2291,7 +2454,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 viewport.getSelectionGroup());
       }
 
-      statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
+      statusBar.setText(MessageManager.formatMessage(
+              "label.removed_columns", new String[]
+              { Integer.valueOf(trimRegion.getSize()).toString() }));
 
       addHistoryItem(trimRegion);
 
@@ -2339,7 +2504,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
+    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
@@ -2502,7 +2669,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     boolean addFirstIndex = false;
     if (viewTitle == null || viewTitle.trim().length() == 0)
     {
-      viewTitle = "View";
+      viewTitle = MessageManager.getString("action.view");
       addFirstIndex = true;
     }
     else
@@ -2533,6 +2700,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     newap.av.viewName = newViewName;
 
     addAlignmentPanel(newap, true);
+    newap.alignmentChanged();
 
     if (alignPanels.size() == 2)
     {
@@ -2928,16 +3096,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on toggle of the 'Show annotations' menu item. This shows or hides
+   * the annotations panel as a whole.
+   * 
+   * The options to show/hide all annotations should be enabled when the panel
+   * is shown, and disabled when the panel is hidden.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
-    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+    final boolean setVisible = annotationPanelMenuItem.isSelected();
+    viewport.setShowAnnotation(setVisible);
+    alignPanel.setAnnotationVisible(setVisible);
+    this.showAllSeqAnnotations.setEnabled(setVisible);
+    this.hideAllSeqAnnotations.setEnabled(setVisible);
+    this.showAllAlAnnotations.setEnabled(setVisible);
+    this.hideAllAlAnnotations.setEnabled(setVisible);
   }
 
   @Override
@@ -2947,12 +3123,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     editPane.setEditable(false);
     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
             .formatAsHtml();
-    editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
+    editPane.setText(MessageManager.formatMessage("label.html_content",
+            new String[]
+            { contents.toString() }));
     JInternalFrame frame = new JInternalFrame();
     frame.getContentPane().add(new JScrollPane(editPane));
 
-    Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
-            + getTitle(), 500, 400);
+    Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
+            "label.alignment_properties", new String[]
+            { getTitle() }), 500, 400);
   }
 
   /**
@@ -2972,8 +3151,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
-            frame.getWidth(), frame.getHeight());
+    Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+            "label.overview_params", new String[]
+            { this.getTitle() }), frame.getWidth(), frame.getHeight());
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
@@ -3169,10 +3349,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-
         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
-        viewport.setGlobalColourScheme(cs);
       }
       else
       {
@@ -3358,7 +3535,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    if (e.getActionCommand().equals("User Defined..."))
+    if (e.getActionCommand().equals(
+            MessageManager.getString("action.user_defined")))
     {
       new UserDefinedColours(alignPanel, null);
     }
@@ -3407,8 +3585,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
               int option = JOptionPane.showInternalConfirmDialog(
                       jalview.gui.Desktop.desktop,
-                      MessageManager.getString("label.remove_from_default_list"),
-                      MessageManager.getString("label.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)
               {
@@ -3559,15 +3739,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if ((viewport.getSelectionGroup() == null)
             || (viewport.getSelectionGroup().getSize() < 2))
     {
-      JOptionPane.showInternalMessageDialog(this,
-              MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"),
+      JOptionPane.showInternalMessageDialog(this, MessageManager
+              .getString("label.you_must_select_least_two_sequences"),
+              MessageManager.getString("label.invalid_selection"),
               JOptionPane.WARNING_MESSAGE);
     }
     else
     {
       JInternalFrame frame = new JInternalFrame();
       frame.setContentPane(new PairwiseAlignPanel(viewport));
-      Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
+      Desktop.addInternalFrame(frame,
+              MessageManager.getString("action.pairwise_alignment"), 600,
+              500);
     }
   }
 
@@ -3585,10 +3768,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getSelectionGroup().getSize() > 0))
             || (viewport.getAlignment().getHeight() < 4))
     {
-      JOptionPane.showInternalMessageDialog(this,
-              MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
-              MessageManager.getString("label.sequence_selection_insufficient"),
-              JOptionPane.WARNING_MESSAGE);
+      JOptionPane
+              .showInternalMessageDialog(
+                      this,
+                      MessageManager
+                              .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
+                      MessageManager
+                              .getString("label.sequence_selection_insufficient"),
+                      JOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -3689,8 +3876,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         JOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
-                        MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"),
-                        MessageManager.getString("label.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;
       }
 
@@ -3704,8 +3894,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           JOptionPane
                   .showMessageDialog(
                           Desktop.desktop,
-                          MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
-                          MessageManager.getString("label.sequences_selection_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;
@@ -3723,8 +3915,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         JOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
-                        MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"),
-                        MessageManager.getString("label.sequences_not_aligned"),
+                        MessageManager
+                                .getString("label.sequences_must_be_aligned_before_creating_tree"),
+                        MessageManager
+                                .getString("label.sequences_not_aligned"),
                         JOptionPane.WARNING_MESSAGE);
 
         return;
@@ -3761,7 +3955,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addSortByOrderMenuItem(String title,
           final AlignmentOrder order)
   {
-    final JMenuItem item = new JMenuItem("by " + title);
+    final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
@@ -3877,6 +4071,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void buildTreeMenu()
   {
+    calculateTree.removeAll();
+    // build the calculate menu
+
+    for (final String type : new String[]
+    { "NJ", "AV" })
+    {
+      String treecalcnm = MessageManager.getString("label.tree_calc_"
+              + type.toLowerCase());
+      for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
+      {
+        JMenuItem tm = new JMenuItem();
+        ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
+        if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+        {
+          String smn = MessageManager.getStringOrReturn(
+                  "label.score_model_", sm.getName());
+          final String title = MessageManager.formatMessage(
+                  "label.treecalc_title", treecalcnm, smn);
+          tm.setText(title);//
+          tm.addActionListener(new java.awt.event.ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              NewTreePanel(type, (String) pwtype, title);
+            }
+          });
+          calculateTree.add(tm);
+        }
+
+      }
+    }
     sortByTreeMenu.removeAll();
 
     Vector comps = (Vector) PaintRefresher.components.get(viewport
@@ -3958,6 +4184,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        */
       msa = viewport.getAlignmentView(true);
     }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() == 1)
+    {
+      int option = JOptionPane
+              .showConfirmDialog(
+this,
+                      "More than one sequece group selection is required for this Job, click \n'Cancel' to edit your selection or 'Ok' to submit the entire sequence.",
+                      "Invalid selection",
+                      JOptionPane.OK_CANCEL_OPTION);
+      if (option == JOptionPane.OK_OPTION)
+      {
+        msa = viewport.getAlignmentView(false);
+      }
+
+    }
     else
     {
       /*
@@ -4021,8 +4262,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Select a newick-like tree file");
-    chooser.setToolTipText("Load a tree file");
+    chooser.setDialogTitle(MessageManager
+            .getString("label.select_newick_like_tree_file"));
+    chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
 
     int value = chooser.showOpenDialog(null);
 
@@ -4037,14 +4279,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       } catch (Exception ex)
       {
-        JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
-                MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE);
+        JOptionPane
+                .showMessageDialog(
+                        Desktop.desktop,
+                        ex.getMessage(),
+                        MessageManager
+                                .getString("label.problem_reading_tree_file"),
+                        JOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
       if (fin != null && fin.hasWarningMessage())
       {
-        JOptionPane.showMessageDialog(Desktop.desktop,
-                fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"),
+        JOptionPane.showMessageDialog(Desktop.desktop, fin
+                .getWarningMessage(), MessageManager
+                .getString("label.possible_problem_with_tree_file"),
                 JOptionPane.WARNING_MESSAGE);
       }
     }
@@ -4149,6 +4397,7 @@ 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 "
@@ -4171,6 +4420,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
           final JMenu analymenu = new JMenu("Analysis");
           final JMenu dismenu = new JMenu("Protein Disorder");
+          // final JMenu msawsmenu = new
+          // JMenu(MessageManager.getString("label.alignment"));
+          // final JMenu secstrmenu = new
+          // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
+          // final JMenu seqsrchmenu = new
+          // JMenu(MessageManager.getString("label.sequence_database_search"));
+          // final JMenu analymenu = new
+          // JMenu(MessageManager.getString("label.analysis"));
+          // final JMenu dismenu = new
+          // JMenu(MessageManager.getString("label.protein_disorder"));
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4180,28 +4439,11 @@ 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
@@ -4211,19 +4453,13 @@ 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));
+                }
               }
             }
           }
@@ -4234,12 +4470,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           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);
 
@@ -4264,6 +4494,7 @@ 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();
@@ -4272,6 +4503,17 @@ 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())
                     {
@@ -4282,7 +4524,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     }
                   }
                 }
-
                 build_urlServiceMenu(me.webService);
                 build_fetchdbmenu(webService);
                 for (JMenu item : wsmenu)
@@ -4348,12 +4589,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
               this);
     }
-
-    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
-    {
-      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
-              webService, this);
-    }
   }
 
   /*
@@ -4461,7 +4696,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void run()
       {
         final long sttime = System.currentTimeMillis();
-        ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+        ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
         try
         {
           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
@@ -4479,7 +4714,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               if (ds.getSequences() == null
                       || !ds.getSequences().contains(
                               sprods[s].getDatasetSequence()))
+              {
                 ds.addSequence(sprods[s].getDatasetSequence());
+              }
               sprods[s].updatePDBIds();
             }
             Alignment al = new Alignment(sprods);
@@ -4515,7 +4752,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           jalview.bin.Cache.log.error("Error when finding crossreferences",
                   e);
         }
-        ths.setProgressBar("Finished searching for sequences from " + fsrc,
+        ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
                 sttime);
       }
 
@@ -4564,14 +4801,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       JOptionPane
               .showMessageDialog(
                       Desktop.desktop,
-                      MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
-                      MessageManager.getString("label.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
     {
       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
-              DEFAULT_WIDTH, DEFAULT_HEIGHT);
+      Desktop.addInternalFrame(af, MessageManager.formatMessage(
+              "label.translation_of_params", new String[]
+              { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
     }
   }
 
@@ -4594,12 +4834,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       al = null;
-      jalview.bin.Cache.log.error("Exception during translation. Please report this !", 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);
+              .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)
@@ -4607,14 +4853,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       JOptionPane
               .showMessageDialog(
                       Desktop.desktop,
-                      MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
-                      MessageManager.getString("label.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
     {
       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
-              DEFAULT_WIDTH, DEFAULT_HEIGHT);
+      Desktop.addInternalFrame(af, MessageManager.formatMessage(
+              "label.translation_of_params", new String[]
+              { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
     }
   }
 
@@ -4807,9 +5056,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   || JOptionPane
                           .showConfirmDialog(
                                   this,
-                                  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"),
+                                  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)
 
           {
@@ -4822,7 +5078,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 PDBEntry pe = new AssociatePdbFileWithSeq()
                         .associatePdbWithSeq((String) fm[0],
-                                (String) fm[1], toassoc, false);
+                                (String) fm[1], toassoc, false,
+                                Desktop.instance);
                 if (pe != null)
                 {
                   System.err.println("Associated file : "
@@ -4842,8 +5099,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
                           .showConfirmDialog(
                                   this,
-                                  MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}),
-                                  MessageManager.getString("label.ignore_unmatched_dropped_files"),
+                                  "<html>"+MessageManager
+                                          .formatMessage(
+                                                  "label.ignore_unmatched_dropped_files_info",
+                                                  new String[]
+                                                  { Integer.valueOf(
+                                                          filesnotmatched
+                                                                  .size())
+                                                          .toString() })+"</html>",
+                                  MessageManager
+                                          .getString("label.ignore_unmatched_dropped_files"),
                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
           {
             return;
@@ -4902,7 +5167,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               tcoffeeColour.setSelected(true);
               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
               isAnnotation = true;
-              statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
+              statusBar
+                      .setText(MessageManager
+                              .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
             }
             else
             {
@@ -4911,9 +5178,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               JOptionPane
                       .showMessageDialog(
                               Desktop.desktop,
-                              tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment")
+                              tcf.getWarningMessage() == null ? MessageManager
+                                      .getString("label.check_file_matches_sequence_ids_alignment")
                                       : tcf.getWarningMessage(),
-                              MessageManager.getString("label.problem_reading_tcoffee_score_file"),
+                              MessageManager
+                                      .getString("label.problem_reading_tcoffee_score_file"),
                               JOptionPane.WARNING_MESSAGE);
             }
           }
@@ -5020,6 +5289,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
       viewport = alignPanel.av;
+      avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
     }
   }
@@ -5030,7 +5300,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (SwingUtilities.isRightMouseButton(e))
     {
       String reply = JOptionPane.showInternalInputDialog(this,
-              MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name,
+              MessageManager.getString("label.enter_view_name"),
+              MessageManager.getString("label.enter_view_name"),
               JOptionPane.QUESTION_MESSAGE);
 
       if (reply != null)
@@ -5125,12 +5396,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // TODO We probably want to store a sequence database checklist in
     // preferences and have checkboxes.. rather than individual sources selected
     // here
-    final JMenu rfetch = new JMenu("Fetch DB References");
-    rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+    final JMenu rfetch = new JMenu(
+            MessageManager.getString("action.fetch_db_references"));
+    rfetch.setToolTipText(MessageManager
+            .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
     webService.add(rfetch);
 
-    JMenuItem fetchr = new JMenuItem("Standard Databases");
-    fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+    final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
+            MessageManager.getString("option.trim_retrieved_seqs"));
+    trimrs.setToolTipText(MessageManager
+            .getString("label.trim_retrieved_sequences"));
+    trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+    trimrs.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        trimrs.setSelected(trimrs.isSelected());
+        Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+                Boolean.valueOf(trimrs.isSelected()).toString());
+      };
+    });
+    rfetch.add(trimrs);
+    JMenuItem fetchr = new JMenuItem(
+            MessageManager.getString("label.standard_databases"));
+    fetchr.setToolTipText(MessageManager
+            .getString("label.fetch_embl_uniprot"));
     fetchr.addActionListener(new ActionListener()
     {
 
@@ -5222,9 +5513,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
 
                 });
-                fetchr.setToolTipText("<html>"
-                        + JvSwingUtils.wrapTooltip("Retrieve from "
-                                + src.getDbName()) + "<html>");
+                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
                 dfetch.add(fetchr);
                 comp++;
               }
@@ -5234,8 +5523,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .toArray(new DbSourceProxy[0]);
                 // fetch all entry
                 DbSourceProxy src = otherdb.get(0);
-                fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
-                        + "'");
+                fetchr = new JMenuItem(MessageManager.formatMessage(
+                        "label.fetch_all_param", new String[]
+                        { src.getDbSource() }));
                 fetchr.addActionListener(new ActionListener()
                 {
                   @Override
@@ -5256,15 +5546,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                 });
 
-                fetchr.setToolTipText("<html>"
-                        + JvSwingUtils.wrapTooltip("Retrieve from all "
-                                + otherdb.size() + " sources in "
-                                + src.getDbSource() + "<br>First is :"
-                                + src.getDbName()) + "<html>");
+                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
                 dfetch.add(fetchr);
                 comp++;
                 // and then build the rest of the individual menus
-                ifetch = new JMenu("Sources from " + src.getDbSource());
+                ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
                 icomp = 0;
                 String imname = null;
                 int i = 0;
@@ -5277,7 +5563,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           0, 10) + "..." : dbname;
                   if (imname == null)
                   {
-                    imname = "from '" + sname + "'";
+                    imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
                   }
                   fetchr = new JMenuItem(msname);
                   final DbSourceProxy[] dassrc =
@@ -5304,13 +5590,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
                   });
                   fetchr.setToolTipText("<html>"
-                          + JvSwingUtils.wrapTooltip("Retrieve from "
-                                  + dbname) + "</html>");
+                          + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
                   ifetch.add(fetchr);
                   ++i;
                   if (++icomp >= mcomp || i == (otherdb.size()))
                   {
-                    ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname}));
+                    ifetch.setText(MessageManager.formatMessage(
+                            "label.source_to_target", imname, sname));
                     dfetch.add(ifetch);
                     ifetch = new JMenu();
                     imname = null;
@@ -5322,7 +5608,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               ++dbi;
               if (comp >= mcomp || dbi >= (dbclasses.length))
               {
-                dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass}));
+                dfetch.setText(MessageManager.formatMessage(
+                        "label.source_to_target", mname, dbclass));
                 rfetch.add(dfetch);
                 dfetch = new JMenu();
                 mname = null;
@@ -5460,34 +5747,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
-    if (viewport.getSelectionGroup() != null)
+    if (avc.makeGroupsFromSelection())
     {
-      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);
-      }
       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
    * 
@@ -5498,8 +5783,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!viewport.getSequenceSetId().equals(
             alignmentPanel.av.getSequenceSetId()))
     {
-      throw new Error(
-              "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+      throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
     }
     if (tabbedPane != null
             & alignPanels.indexOf(alignmentPanel) != tabbedPane
@@ -5508,6 +5792,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
     }
   }
+
+  /**
+   * Action on selection of menu options to Show or Hide annotations.
+   * 
+   * @param visible
+   * @param forSequences
+   *          update sequence-related annotations
+   * @param forAlignment
+   *          update non-sequence-related annotations
+   */
+  @Override
+  protected void setAnnotationsVisibility(boolean visible,
+          boolean forSequences, boolean forAlignment)
+  {
+    for (AlignmentAnnotation aa : alignPanel.getAlignment()
+            .getAlignmentAnnotation())
+    {
+      boolean apply = (aa.sequenceRef == null && forAlignment)
+              || (aa.sequenceRef != null && forSequences);
+      if (apply)
+      {
+        aa.visible = visible;
+      }
+    }
+    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.alignmentChanged();
+  }
+
+  /**
+   * Store selected annotation sort order for the view and repaint.
+   */
+  @Override
+  protected void sortAnnotations_actionPerformed()
+  {
+    this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+    this.alignPanel.av
+            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    alignPanel.paintAlignment(true);
+  }
 }
 
 class PrintThread extends Thread