X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=e546608959429e9c52203b7d2070b41c138b52b6;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=16e78f546ed8babed9b14fa2452476c9b44215c8;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 16e78f5..e546608 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,6 +20,10 @@
  */
 package jalview.jbgui;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 
@@ -63,6 +67,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu viewMenu = new JMenu();
 
+  protected JMenu annotationsMenu = new JMenu();
+
   protected JMenu colourMenu = new JMenu();
 
   protected JMenu calculateMenu = new JMenu();
@@ -142,7 +148,7 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-  
+
   protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 
   // protected JRadioButtonMenuItem covariationColour = new
@@ -187,8 +193,9 @@ public class GAlignFrame extends JInternalFrame
   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 
   JMenuItem deleteGroups = new JMenuItem();
-  
+
   JMenuItem createGroup = new JMenuItem();
+
   JMenuItem unGroup = new JMenuItem();
 
   JMenuItem delete = new JMenuItem();
@@ -207,6 +214,8 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem createPNG = new JMenuItem();
 
+  JMenuItem createSVG = new JMenuItem();
+
   protected JMenuItem font = new JMenuItem();
 
   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
@@ -246,7 +255,7 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem showTranslation = new JMenuItem();
 
   protected JMenuItem extractScores = new JMenuItem();
-  
+
   protected JMenuItem expandAlignment = new JMenuItem();
 
   protected JMenu showProducts = new JMenu();
@@ -301,6 +310,18 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem showAllhidden = new JMenuItem();
 
+  protected JMenuItem showAllSeqAnnotations = new JMenuItem();
+
+  protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
+
+  protected JMenuItem showAllAlAnnotations = new JMenuItem();
+
+  protected JMenuItem hideAllAlAnnotations = new JMenuItem();
+
+  protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
+
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 
   JMenuItem invertColSel = new JMenuItem();
@@ -353,8 +374,16 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
+  protected JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem();
+
   private JMenuItem grpsFromSelection = new JMenuItem();
 
+  private SequenceAnnotationOrder annotationSortOrder;
+
+  private boolean showAutoCalculatedAbove = false;
+
   public GAlignFrame()
   {
     try
@@ -370,6 +399,7 @@ public class GAlignFrame extends JInternalFrame
 
         item.addActionListener(new java.awt.event.ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             outputText_actionPerformed(e);
@@ -380,6 +410,7 @@ public class GAlignFrame extends JInternalFrame
       }
     } catch (Exception e)
     {
+      System.err.println(e.toString());
     }
 
     if (!new jalview.util.Platform().isAMac())
@@ -406,6 +437,7 @@ public class GAlignFrame extends JInternalFrame
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
+          @Override
           public void mousePressed(MouseEvent evt)
           {
             if (evt.isControlDown()
@@ -415,8 +447,10 @@ public class GAlignFrame extends JInternalFrame
 
               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)
               {
@@ -428,6 +462,7 @@ public class GAlignFrame extends JInternalFrame
               {
                 radioItem.addActionListener(new ActionListener()
                 {
+                  @Override
                   public void actionPerformed(ActionEvent evt)
                   {
                     userDefinedColour_actionPerformed(evt);
@@ -439,6 +474,7 @@ public class GAlignFrame extends JInternalFrame
         });
         radioItem.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent evt)
           {
             userDefinedColour_actionPerformed(evt);
@@ -542,11 +578,11 @@ public class GAlignFrame extends JInternalFrame
         purinePyrimidineColour.setSelected(true);
 
         break;
-        
+
       case ColourSchemeProperty.RNAINTERACTION:
-          RNAInteractionColour.setSelected(true);
+        RNAInteractionColour.setSelected(true);
 
-          break;
+        break;
       /*
        * case ColourSchemeProperty.COVARIATION:
        * covariationColour.setSelected(true);
@@ -577,6 +613,7 @@ public class GAlignFrame extends JInternalFrame
                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
     saveAs.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         saveAs_actionPerformed(e);
@@ -588,6 +625,7 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         closeMenuItem_actionPerformed(false);
@@ -595,98 +633,117 @@ public class GAlignFrame extends JInternalFrame
     });
     editMenu.setText(MessageManager.getString("action.edit"));
     viewMenu.setText(MessageManager.getString("action.view"));
+    annotationsMenu.setText(MessageManager.getString("action.annotations"));
     colourMenu.setText(MessageManager.getString("action.colour"));
     calculateMenu.setText(MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
-    selectAllSequenceMenuItem.setText(MessageManager.getString("action.select_all"));
+    selectAllSequenceMenuItem.setText(MessageManager
+            .getString("action.select_all"));
     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
     selectAllSequenceMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 selectAllSequenceMenuItem_actionPerformed(e);
               }
             });
-    deselectAllSequenceMenuItem.setText(MessageManager.getString("action.deselect_all"));
+    deselectAllSequenceMenuItem.setText(MessageManager
+            .getString("action.deselect_all"));
     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
     deselectAllSequenceMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 deselectAllSequenceMenuItem_actionPerformed(e);
               }
             });
-    invertSequenceMenuItem.setText(MessageManager.getString("action.invert_sequence_selection"));
+    invertSequenceMenuItem.setText(MessageManager
+            .getString("action.invert_sequence_selection"));
     invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
     invertSequenceMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 invertSequenceMenuItem_actionPerformed(e);
               }
             });
-    grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
+    grpsFromSelection.setText(MessageManager
+            .getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         makeGrpsFromSelection_actionPerformed(e);
       }
     });
-    expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
-    expandAlignment.setToolTipText(MessageManager.getString("label.view_flanking_regions"));
-    expandAlignment.addActionListener(new java.awt.event.ActionListener() {
+    expandAlignment.setText(MessageManager
+            .getString("action.view_flanking_regions"));
+    expandAlignment.setToolTipText(MessageManager
+            .getString("label.view_flanking_regions"));
+    expandAlignment.addActionListener(new java.awt.event.ActionListener()
+    {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         expand_newalign(e);
       }
     });
-    remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
+    remove2LeftMenuItem.setText(MessageManager
+            .getString("action.remove_left"));
     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask(), false));
     remove2LeftMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 remove2LeftMenuItem_actionPerformed(e);
               }
             });
-    remove2RightMenuItem.setText(MessageManager.getString("action.remove_right"));
+    remove2RightMenuItem.setText(MessageManager
+            .getString("action.remove_right"));
     remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask(), false));
     remove2RightMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 remove2RightMenuItem_actionPerformed(e);
               }
             });
-    removeGappedColumnMenuItem.setText(MessageManager.getString("action.remove_empty_columns"));
+    removeGappedColumnMenuItem.setText(MessageManager
+            .getString("action.remove_empty_columns"));
     removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeGappedColumnMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 removeGappedColumnMenuItem_actionPerformed(e);
               }
             });
-    removeAllGapsMenuItem.setText(MessageManager.getString("action.remove_all_gaps"));
+    removeAllGapsMenuItem.setText(MessageManager
+            .getString("action.remove_all_gaps"));
     removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask()
@@ -694,24 +751,29 @@ public class GAlignFrame extends JInternalFrame
     removeAllGapsMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 removeAllGapsMenuItem_actionPerformed(e);
               }
             });
-    justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
+    justifyLeftMenuItem.setText(MessageManager
+            .getString("action.left_justify_alignment"));
     justifyLeftMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 justifyLeftMenuItem_actionPerformed(e);
               }
             });
-    justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
+    justifyRightMenuItem.setText(MessageManager
+            .getString("action.right_justify_alignment"));
     justifyRightMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 justifyRightMenuItem_actionPerformed(e);
@@ -721,6 +783,7 @@ public class GAlignFrame extends JInternalFrame
     viewBoxesMenuItem.setState(true);
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         viewBoxesMenuItem_actionPerformed(e);
@@ -730,25 +793,30 @@ public class GAlignFrame extends JInternalFrame
     viewTextMenuItem.setState(true);
     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
+    showNonconservedMenuItem.setText(MessageManager
+            .getString("label.show_non_conversed"));
     showNonconservedMenuItem.setState(false);
     showNonconservedMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 showUnconservedMenuItem_actionPerformed(e);
               }
             });
-    sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
+    sortPairwiseMenuItem.setText(MessageManager
+            .getString("action.by_pairwise_id"));
     sortPairwiseMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 sortPairwiseMenuItem_actionPerformed(e);
@@ -757,15 +825,18 @@ public class GAlignFrame extends JInternalFrame
     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
+    sortLengthMenuItem
+            .setText(MessageManager.getString("action.by_length"));
     sortLengthMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 sortLengthMenuItem_actionPerformed(e);
@@ -774,54 +845,64 @@ public class GAlignFrame extends JInternalFrame
     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-    removeRedundancyMenuItem.setText(MessageManager.getString("action.remove_redundancy"));
+    removeRedundancyMenuItem.setText(MessageManager
+            .getString("action.remove_redundancy").concat("..."));
     removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
             .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
                     .getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeRedundancyMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 removeRedundancyMenuItem_actionPerformed(e);
               }
             });
-    pairwiseAlignmentMenuItem.setText(MessageManager.getString("action.pairwise_alignment"));
+    pairwiseAlignmentMenuItem.setText(MessageManager
+            .getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 pairwiseAlignmentMenuItem_actionPerformed(e);
               }
             });
-    PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
+    PCAMenuItem.setText(MessageManager
+            .getString("label.principal_component_analysis"));
     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem
-            .setText(MessageManager.getString("label.average_distance_identity"));
+    averageDistanceTreeMenuItem.setText(MessageManager
+            .getString("label.average_distance_identity"));
     averageDistanceTreeMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 averageDistanceTreeMenuItem_actionPerformed(e);
               }
             });
-    neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
+    neighbourTreeMenuItem.setText(MessageManager
+            .getString("label.neighbour_joining_identity"));
     neighbourTreeMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 neighbourTreeMenuItem_actionPerformed(e);
@@ -833,11 +914,13 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
-    outputTextboxMenu.setText(MessageManager.getString("label.out_to_textbox"));
+    outputTextboxMenu.setText(MessageManager
+            .getString("label.out_to_textbox"));
     clustalColour.setText(MessageManager.getString("label.clustalx"));
 
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         clustalColour_actionPerformed(e);
@@ -846,6 +929,7 @@ public class GAlignFrame extends JInternalFrame
     zappoColour.setText(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         zappoColour_actionPerformed(e);
@@ -854,15 +938,18 @@ public class GAlignFrame extends JInternalFrame
     taylorColour.setText(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         taylorColour_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+    hydrophobicityColour.setText(MessageManager
+            .getString("label.hydrophobicity"));
     hydrophobicityColour
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 hydrophobicityColour_actionPerformed(e);
@@ -871,14 +958,17 @@ public class GAlignFrame extends JInternalFrame
     helixColour.setText(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         helixColour_actionPerformed(e);
       }
     });
-    strandColour.setText(MessageManager.getString("label.strand_propensity"));
+    strandColour.setText(MessageManager
+            .getString("label.strand_propensity"));
     strandColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         strandColour_actionPerformed(e);
@@ -887,6 +977,7 @@ public class GAlignFrame extends JInternalFrame
     turnColour.setText(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         turnColour_actionPerformed(e);
@@ -895,30 +986,37 @@ public class GAlignFrame extends JInternalFrame
     buriedColour.setText(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         buriedColour_actionPerformed(e);
       }
     });
-    userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+    userDefinedColour.setText(MessageManager
+            .getString("action.user_defined"));
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         userDefinedColour_actionPerformed(e);
       }
     });
-    PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+    PIDColour
+            .setText(MessageManager.getString("label.percentage_identity"));
     PIDColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         PIDColour_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
+    BLOSUM62Colour
+            .setText(MessageManager.getString("label.blosum62_score"));
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         BLOSUM62Colour_actionPerformed(e);
@@ -927,28 +1025,33 @@ public class GAlignFrame extends JInternalFrame
     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         nucleotideColour_actionPerformed(e);
       }
     });
 
-    purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+    purinePyrimidineColour.setText(MessageManager
+            .getString("label.purine_pyrimidine"));
     purinePyrimidineColour
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 purinePyrimidineColour_actionPerformed(e);
               }
             });
-    
+
     RNAInteractionColour.setText("RNA Interaction type");
-    RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+    RNAInteractionColour
+            .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
-            	  RNAInteractionColour_actionPerformed(e);
+                RNAInteractionColour_actionPerformed(e);
               }
             });
     /*
@@ -958,40 +1061,128 @@ public class GAlignFrame extends JInternalFrame
      * covariationColour_actionPerformed(e); } });
      */
 
-    avDistanceTreeBlosumMenuItem.setText(MessageManager.getString("label.average_distance_bloslum62"));
+    avDistanceTreeBlosumMenuItem.setText(MessageManager
+            .getString("label.average_distance_bloslum62"));
     avDistanceTreeBlosumMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 avTreeBlosumMenuItem_actionPerformed(e);
               }
             });
-    njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
+    njTreeBlosumMenuItem.setText(MessageManager
+            .getString("label.neighbour_blosum62"));
     njTreeBlosumMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 njTreeBlosumMenuItem_actionPerformed(e);
               }
             });
     annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
-    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
-            "SHOW_ANNOTATIONS", true));
-    annotationPanelMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              public void actionPerformed(ActionEvent e)
-              {
-                annotationPanelMenuItem_actionPerformed(e);
-              }
-            });
-    colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
+    annotationPanelMenuItem.setText(MessageManager
+            .getString("label.show_annotations"));
+    annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
+            true));
+    annotationPanelMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationPanelMenuItem_actionPerformed(e);
+      }
+    });
+    showAllAlAnnotations.setText(MessageManager
+            .getString("label.show_all_al_annotations"));
+    final boolean isAnnotationPanelShown = annotationPanelMenuItem
+            .getState();
+    showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+    showAllAlAnnotations.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllAnnotations_actionPerformed(false, true);
+      }
+    });
+    hideAllAlAnnotations.setText(MessageManager
+            .getString("label.hide_all_al_annotations"));
+    hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+    hideAllAlAnnotations.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideAllAnnotations_actionPerformed(false, true);
+      }
+    });
+    showAllSeqAnnotations.setText(MessageManager
+            .getString("label.show_all_seq_annotations"));
+    showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+    showAllSeqAnnotations.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllAnnotations_actionPerformed(true, false);
+      }
+    });
+    hideAllSeqAnnotations.setText(MessageManager
+            .getString("label.hide_all_seq_annotations"));
+    hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+    hideAllSeqAnnotations.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideAllAnnotations_actionPerformed(true, false);
+      }
+    });
+    SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
+            .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+                    SequenceAnnotationOrder.NONE.name()));
+    sortAnnBySequence.setText(MessageManager
+            .getString("label.sort_annotations_by_sequence"));
+    sortAnnBySequence
+            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+    sortAnnBySequence.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        boolean newState = sortAnnBySequence.getState();
+        sortAnnByLabel.setSelected(false);
+        setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+                : SequenceAnnotationOrder.NONE);
+        sortAnnotations_actionPerformed();
+      }
+    });
+    sortAnnByLabel.setText(MessageManager
+            .getString("label.sort_annotations_by_label"));
+    sortAnnByLabel
+            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+    sortAnnByLabel.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        boolean newState = sortAnnByLabel.getState();
+        sortAnnBySequence.setSelected(false);
+        setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+                : SequenceAnnotationOrder.NONE);
+        sortAnnotations_actionPerformed();
+      }
+    });
+    colourTextMenuItem.setText(MessageManager
+            .getString("label.colour_text"));
     colourTextMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 colourTextMenuItem_actionPerformed(e);
@@ -1000,14 +1191,17 @@ public class GAlignFrame extends JInternalFrame
     htmlMenuItem.setText(MessageManager.getString("label.html"));
     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         htmlMenuItem_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
+    overviewMenuItem.setText(MessageManager
+            .getString("label.overview_window"));
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         overviewMenuItem_actionPerformed(e);
@@ -1020,6 +1214,7 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         undoMenuItem_actionPerformed(e);
@@ -1032,15 +1227,18 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         redoMenuItem_actionPerformed(e);
       }
     });
-    conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
+    conservationMenuItem.setText(MessageManager
+            .getString("action.by_conservation"));
     conservationMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 conservationMenuItem_actionPerformed(e);
@@ -1049,6 +1247,7 @@ public class GAlignFrame extends JInternalFrame
     noColourmenuItem.setText(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         noColourmenuItem_actionPerformed(e);
@@ -1057,6 +1256,7 @@ public class GAlignFrame extends JInternalFrame
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         wrapMenuItem_actionPerformed(e);
@@ -1068,16 +1268,19 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     printMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         printMenuItem_actionPerformed(e);
       }
     });
-    renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
+    renderGapsMenuItem
+            .setText(MessageManager.getString("action.show_gaps"));
     renderGapsMenuItem.setState(true);
     renderGapsMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 renderGapsMenuItem_actionPerformed(e);
@@ -1087,24 +1290,31 @@ public class GAlignFrame extends JInternalFrame
     findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask(), false));
+    findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.find_tip")));
     findMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         findMenuItem_actionPerformed(e);
       }
     });
-    abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
+    abovePIDThreshold.setText(MessageManager
+            .getString("label.above_identity_threshold"));
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
+    showSeqFeatures.setText(MessageManager
+            .getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         showSeqFeatures_actionPerformed(actionEvent);
@@ -1116,30 +1326,36 @@ public class GAlignFrame extends JInternalFrame
      * void actionPerformed(ActionEvent actionEvent) {
      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
      */
-    showDbRefsMenuitem.setText(MessageManager.getString("label.show_database_refs"));
+    showDbRefsMenuitem.setText(MessageManager
+            .getString("label.show_database_refs"));
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showDbRefs_actionPerformed(e);
       }
 
     });
-    showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.setText(MessageManager
+            .getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showNpFeats_actionPerformed(e);
       }
 
     });
-    showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
+    showGroupConservation.setText(MessageManager
+            .getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConservation_actionPerformed(e);
@@ -1147,62 +1363,99 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
+    showGroupConsensus.setText(MessageManager
+            .getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConsensus_actionPerformed(e);
       }
 
     });
-    showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
+    showConsensusHistogram.setText(MessageManager
+            .getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showConsensusHistogram_actionPerformed(e);
       }
 
     });
-    showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
+    showSequenceLogo.setText(MessageManager
+            .getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showSequenceLogo_actionPerformed(e);
       }
 
     });
-    normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo.setText(MessageManager
+            .getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         normaliseSequenceLogo_actionPerformed(e);
       }
 
     });
-    applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
+    applyAutoAnnotationSettings.setText(MessageManager
+            .getString("label.apply_all_groups"));
     applyAutoAnnotationSettings.setState(false);
     applyAutoAnnotationSettings.setVisible(true);
     applyAutoAnnotationSettings.addActionListener(new ActionListener()
     {
-
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         applyAutoAnnotationSettings_actionPerformed(e);
       }
+    });
 
+    ButtonGroup buttonGroup = new ButtonGroup();
+    buttonGroup.add(showAutoFirst);
+    buttonGroup.add(showAutoLast);
+    showAutoFirst.setText(MessageManager.getString("label.show_first"));
+    showAutoFirst.setSelected(Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE,
+            false));
+    showAutoFirst.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+        sortAnnotations_actionPerformed();
+      }
+    });
+    showAutoLast.setText(MessageManager.getString("label.show_last"));
+    showAutoLast.setSelected(!showAutoFirst.isSelected());
+    showAutoLast.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+        sortAnnotations_actionPerformed();
+      }
     });
 
     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         nucleotideColour_actionPerformed(e);
@@ -1221,12 +1474,14 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    deleteGroups.setText(MessageManager.getString("action.undefine_groups"));
+    deleteGroups
+            .setText(MessageManager.getString("action.undefine_groups"));
     deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask(), false));
     deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         deleteGroups_actionPerformed(e);
@@ -1238,6 +1493,7 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     createGroup.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         createGroup_actionPerformed(e);
@@ -1245,10 +1501,12 @@ public class GAlignFrame extends JInternalFrame
     });
     unGroup.setText(MessageManager.getString("action.remove_group"));
     unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
+            java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
     unGroup.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         unGroup_actionPerformed(e);
@@ -1261,6 +1519,7 @@ public class GAlignFrame extends JInternalFrame
 
     copy.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         copy_actionPerformed(e);
@@ -1272,16 +1531,16 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     cut.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cut_actionPerformed(e);
       }
     });
     delete.setText(MessageManager.getString("action.delete"));
-    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
     delete.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         delete_actionPerformed(e);
@@ -1295,6 +1554,7 @@ public class GAlignFrame extends JInternalFrame
                     | java.awt.event.KeyEvent.SHIFT_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pasteNew_actionPerformed(e);
@@ -1306,14 +1566,17 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pasteThis_actionPerformed(e);
       }
     });
-    applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
+    applyToAllGroups.setText(MessageManager
+            .getString("label.apply_colour_to_all_groups"));
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         applyToAllGroups_actionPerformed(e);
@@ -1321,26 +1584,32 @@ public class GAlignFrame extends JInternalFrame
     });
     createPNG.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         createPNG(null);
       }
     });
-    createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
+    createPNG.setActionCommand(MessageManager
+            .getString("label.save_png_image"));
     createPNG.setText("PNG");
+
     font.setText(MessageManager.getString("action.font"));
     font.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         font_actionPerformed(e);
       }
     });
 
-    seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
+    seqLimits.setText(MessageManager
+            .getString("label.show_sequence_limits"));
     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         seqLimit_actionPerformed(e);
@@ -1349,15 +1618,30 @@ public class GAlignFrame extends JInternalFrame
     epsFile.setText("EPS");
     epsFile.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         createEPS(null);
       }
     });
-    LoadtreeMenuItem.setActionCommand(MessageManager.getString("label.load_tree_for_sequence_set"));
-    LoadtreeMenuItem.setText(MessageManager.getString("label.load_associated_tree"));
+
+    createSVG.setText("SVG");
+    createSVG.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        createSVG(null);
+      }
+    });
+
+    LoadtreeMenuItem.setActionCommand(MessageManager
+            .getString("label.load_tree_for_sequence_set"));
+    LoadtreeMenuItem.setText(MessageManager
+            .getString("label.load_associated_tree"));
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         LoadtreeMenuItem_actionPerformed(e);
@@ -1368,6 +1652,7 @@ public class GAlignFrame extends JInternalFrame
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
     scaleAbove.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         scaleAbove_actionPerformed(e);
@@ -1378,6 +1663,7 @@ public class GAlignFrame extends JInternalFrame
     scaleLeft.setText(MessageManager.getString("action.scale_left"));
     scaleLeft.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         scaleLeft_actionPerformed(e);
@@ -1388,6 +1674,7 @@ public class GAlignFrame extends JInternalFrame
     scaleRight.setText(MessageManager.getString("action.scale_right"));
     scaleRight.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         scaleRight_actionPerformed(e);
@@ -1395,10 +1682,12 @@ public class GAlignFrame extends JInternalFrame
     });
     centreColumnLabelsMenuItem.setVisible(true);
     centreColumnLabelsMenuItem.setState(false);
-    centreColumnLabelsMenuItem.setText(MessageManager.getString("label.centre_column_labels"));
+    centreColumnLabelsMenuItem.setText(MessageManager
+            .getString("label.centre_column_labels"));
     centreColumnLabelsMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 centreColumnLabels_actionPerformed(e);
@@ -1406,10 +1695,12 @@ public class GAlignFrame extends JInternalFrame
             });
     followHighlightMenuItem.setVisible(true);
     followHighlightMenuItem.setState(true);
-    followHighlightMenuItem.setText(MessageManager.getString("label.automatic_scrolling"));
+    followHighlightMenuItem.setText(MessageManager
+            .getString("label.automatic_scrolling"));
     followHighlightMenuItem.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         followHighlight_actionPerformed();
@@ -1417,53 +1708,65 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
+    modifyPID.setText(MessageManager
+            .getString("label.modify_identity_thereshold"));
     modifyPID.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         modifyPID_actionPerformed(e);
       }
     });
-    modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
+    modifyConservation.setText(MessageManager
+            .getString("label.modify_conservation_thereshold"));
     modifyConservation
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 modifyConservation_actionPerformed(e);
               }
             });
-    sortByTreeMenu.setText(MessageManager.getString("action.by_tree_order"));
+    sortByTreeMenu
+            .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
     sort.addMenuListener(new MenuListener()
     {
+      @Override
       public void menuSelected(MenuEvent e)
       {
         buildTreeMenu();
       }
 
+      @Override
       public void menuDeselected(MenuEvent e)
       {
       }
 
+      @Override
       public void menuCanceled(MenuEvent e)
       {
       }
     });
-    sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
+    sortByAnnotScore.setText(MessageManager
+            .getString("label.sort_by_score"));
     sort.add(sortByAnnotScore);
-    sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+    sort.addMenuListener(new javax.swing.event.MenuListener()
     {
 
+      @Override
       public void menuCanceled(MenuEvent e)
       {
       }
 
+      @Override
       public void menuDeselected(MenuEvent e)
       {
       }
 
+      @Override
       public void menuSelected(MenuEvent e)
       {
         buildSortByAnnotationScoresMenu();
@@ -1471,7 +1774,8 @@ public class GAlignFrame extends JInternalFrame
     });
     sortByAnnotScore.setVisible(false);
 
-    calculateTree.setText(MessageManager.getString("action.calculate_tree"));
+    calculateTree
+            .setText(MessageManager.getString("action.calculate_tree"));
 
     jMenu2.setText(MessageManager.getString("label.export_image"));
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
@@ -1479,6 +1783,7 @@ public class GAlignFrame extends JInternalFrame
             .getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         padGapsMenuitem_actionPerformed(e);
@@ -1488,22 +1793,27 @@ public class GAlignFrame extends JInternalFrame
     vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
     vamsasStore.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
+    showTranslation.setText(MessageManager
+            .getString("label.translate_cDNA"));
     showTranslation.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showTranslation_actionPerformed(e);
       }
     });
-    extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
+    extractScores.setText(MessageManager.getString("label.extract_scores")
+            + "...");
     extractScores.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         extractScores_actionPerformed(e);
@@ -1518,88 +1828,110 @@ public class GAlignFrame extends JInternalFrame
      * public void actionPerformed(ActionEvent e) {
      * showProducts_actionPerformed(e); } });
      */
-    openFeatureSettings.setText(MessageManager.getString("label.feature_settings"));
+    openFeatureSettings.setText(MessageManager
+            .getString("label.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         featureSettings_actionPerformed(e);
       }
     });
-    fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
+    fetchSequence
+            .setText(MessageManager.getString("label.fetch_sequences"));
     fetchSequence.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         fetchSequence_actionPerformed(e);
       }
     });
 
-    annotationColour.setText(MessageManager.getString("action.by_annotation"));
+    annotationColour.setText(MessageManager
+            .getString("action.by_annotation"));
     annotationColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         annotationColour_actionPerformed(e);
       }
     });
 
-    rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
+    rnahelicesColour.setText(MessageManager
+            .getString("action.by_rna_helixes"));
     rnahelicesColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         rnahelicesColour_actionPerformed(e);
       }
     });
 
-    associatedData.setText(MessageManager.getString("label.load_features_annotations"));
+    associatedData.setText(MessageManager
+            .getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         associatedData_actionPerformed(e);
       }
     });
-    autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
+    autoCalculate.setText(MessageManager
+            .getString("label.autocalculate_consensus"));
     autoCalculate.setState(jalview.bin.Cache.getDefault(
             "AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         autoCalculate_actionPerformed(e);
       }
     });
-    sortByTree.setText(MessageManager.getString("label.sort_alignment_new_tree"));
+    sortByTree.setText(MessageManager
+            .getString("label.sort_alignment_new_tree"));
     sortByTree
-            .setToolTipText("<html>" + MessageManager.getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+            .setToolTipText("<html>"
+                    + MessageManager
+                            .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
     sortByTree
             .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         sortByTreeOption_actionPerformed(e);
       }
     });
 
-    listenToViewSelections.setText(MessageManager.getString("label.listen_for_selections"));
+    listenToViewSelections.setText(MessageManager
+            .getString("label.listen_for_selections"));
     listenToViewSelections
-            .setToolTipText("<html>" + MessageManager.getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+            .setToolTipText("<html>"
+                    + MessageManager
+                            .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
     listenToViewSelections.setState(false);
     listenToViewSelections.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         listenToViewSelections_actionPerformed(e);
       }
     });
 
-    addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
+    addSequenceMenu
+            .setText(MessageManager.getString("label.add_sequences"));
     addFromFile.setText(MessageManager.getString("label.from_file"));
     addFromFile.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         addFromFile_actionPerformed(e);
@@ -1608,6 +1940,7 @@ public class GAlignFrame extends JInternalFrame
     addFromText.setText(MessageManager.getString("label.from_textbox"));
     addFromText.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         addFromText_actionPerformed(e);
@@ -1616,22 +1949,27 @@ public class GAlignFrame extends JInternalFrame
     addFromURL.setText(MessageManager.getString("label.from_url"));
     addFromURL.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         addFromURL_actionPerformed(e);
       }
     });
-    exportFeatures.setText(MessageManager.getString("label.export_features"));
+    exportFeatures.setText(MessageManager
+            .getString("label.export_features"));
     exportFeatures.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         exportFeatures_actionPerformed(e);
       }
     });
-    exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
+    exportAnnotations.setText(MessageManager
+            .getString("label.export_annotations"));
     exportAnnotations.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         exportAnnotations_actionPerformed(e);
@@ -1640,85 +1978,104 @@ public class GAlignFrame extends JInternalFrame
     statusPanel.setLayout(gridLayout1);
     jMenu3.setText(MessageManager.getString("action.show"));
     showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
-    showAllSeqs.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+    showAllSeqs.setToolTipText(MessageManager
+            .getString("label.toggle_sequence_visibility"));
     showAllSeqs.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showAllSeqs_actionPerformed(e);
       }
     });
     showAllColumns.setText(MessageManager.getString("label.all_columns"));
-    showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+    showAllColumns.setToolTipText(MessageManager
+            .getString("label.toggle_columns_visibility"));
     showAllColumns.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showAllColumns_actionPerformed(e);
       }
     });
     hideMenu.setText(MessageManager.getString("action.hide"));
-    hideSelSequences.setText(MessageManager.getString("label.selected_sequences"));
-    hideSelSequences.setToolTipText(MessageManager.getString("label.toggle_sequence_visibility"));
+    hideSelSequences.setText(MessageManager
+            .getString("label.selected_sequences"));
+    hideSelSequences.setToolTipText(MessageManager
+            .getString("label.toggle_sequence_visibility"));
     hideSelSequences.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hideSelSequences_actionPerformed(e);
       }
     });
-    hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
-    hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+    hideSelColumns.setText(MessageManager
+            .getString("label.selected_columns"));
+    hideSelColumns.setToolTipText(MessageManager
+            .getString("label.toggle_columns_visibility"));
     hideSelColumns.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hideSelColumns_actionPerformed(e);
       }
     });
-    hideAllSelection.setText(MessageManager.getString("label.selected_region"));
+    hideAllSelection.setText(MessageManager
+            .getString("label.selected_region"));
     hideAllSelection.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hideAllSelection_actionPerformed(e);
       }
     });
     // TODO: should be hidden if no selection exists.
-    hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
+    hideAllButSelection.setText(MessageManager
+            .getString("label.all_but_selected_region"));
     hideAllButSelection.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hideAllButSelection_actionPerformed(e);
       }
     });
-    showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
-    showAllhidden
-            .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
+    showAllhidden.setText(MessageManager
+            .getString("label.all_sequences_columns"));
+    showAllhidden.setToolTipText(MessageManager
+            .getString("label.toggles_visibility_hidden_selected_regions"));
     showAllhidden.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showAllhidden_actionPerformed(e);
       }
     });
-
-    hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
+    hiddenMarkers.setText(MessageManager
+            .getString("action.show_hidden_markers"));
     hiddenMarkers.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hiddenMarkers_actionPerformed(e);
       }
     });
-    invertColSel.setText(MessageManager.getString("action.invert_column_selection"));
+    invertColSel.setText(MessageManager
+            .getString("action.invert_column_selection"));
     invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
                     .getMenuShortcutKeyMask()
                     | java.awt.event.KeyEvent.ALT_MASK, false));
     invertColSel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         invertColSel_actionPerformed(e);
@@ -1726,6 +2083,7 @@ public class GAlignFrame extends JInternalFrame
     });
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         JTabbedPane pane = (JTabbedPane) evt.getSource();
@@ -1735,6 +2093,7 @@ public class GAlignFrame extends JInternalFrame
     });
     tabbedPane.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         tabbedPane_mousePressed(e);
@@ -1742,6 +2101,7 @@ public class GAlignFrame extends JInternalFrame
     });
     tabbedPane.addFocusListener(new FocusAdapter()
     {
+      @Override
       public void focusGained(FocusEvent e)
       {
         tabbedPane_focusGained(e);
@@ -1753,6 +2113,7 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     save.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         save_actionPerformed(e);
@@ -1762,6 +2123,7 @@ public class GAlignFrame extends JInternalFrame
     reload.setText(MessageManager.getString("action.reload"));
     reload.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         reload_actionPerformed(e);
@@ -1773,15 +2135,20 @@ public class GAlignFrame extends JInternalFrame
                     .getMenuShortcutKeyMask(), false));
     newView.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         newView_actionPerformed(e);
       }
     });
-    tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
-    textColour.setText(MessageManager.getString("label.colour_text") + "...");
+    tabbedPane.setToolTipText("<html><i>"
+            + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+            + "</i></html>");
+    textColour.setText(MessageManager.getString("label.colour_text")
+            + "...");
     textColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         textColour_actionPerformed(e);
@@ -1789,9 +2156,11 @@ public class GAlignFrame extends JInternalFrame
     });
     formatMenu.setText(MessageManager.getString("action.format"));
     selectMenu.setText(MessageManager.getString("action.select"));
-    idRightAlign.setText(MessageManager.getString("label.right_align_sequence_id"));
+    idRightAlign.setText(MessageManager
+            .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         idRightAlign_actionPerformed(e);
@@ -1803,6 +2172,7 @@ public class GAlignFrame extends JInternalFrame
             java.awt.event.KeyEvent.VK_G, 0, false));
     gatherViews.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         gatherViews_actionPerformed(e);
@@ -1814,33 +2184,41 @@ public class GAlignFrame extends JInternalFrame
             java.awt.event.KeyEvent.VK_X, 0, false));
     expandViews.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         expandViews_actionPerformed(e);
       }
     });
-    pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
+    pageSetup
+            .setText(MessageManager.getString("action.page_setup") + "...");
     pageSetup.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pageSetup_actionPerformed(e);
       }
     });
-    alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
+    alignmentProperties.setText(MessageManager
+            .getString("label.alignment_props") + "...");
     alignmentProperties.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         alignmentProperties();
       }
     });
-    tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
-    autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
+    tooltipSettingsMenu.setText(MessageManager
+            .getString("label.sequence_id_tooltip"));
+    autoAnnMenu.setText(MessageManager
+            .getString("label.autocalculated_annotation"));
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
     alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(annotationsMenu);
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
@@ -1890,7 +2268,19 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(hideMenu);
     viewMenu.addSeparator();
     viewMenu.add(followHighlightMenuItem);
-    viewMenu.add(annotationPanelMenuItem);
+    annotationsMenu.add(annotationPanelMenuItem);
+    annotationsMenu.addSeparator();
+    annotationsMenu.add(showAllAlAnnotations);
+    annotationsMenu.add(hideAllAlAnnotations);
+    annotationsMenu.addSeparator();
+    annotationsMenu.add(showAllSeqAnnotations);
+    annotationsMenu.add(hideAllSeqAnnotations);
+    annotationsMenu.add(sortAnnBySequence);
+    annotationsMenu.add(sortAnnByLabel);
+    annotationsMenu.addSeparator();
+    autoAnnMenu.add(showAutoFirst);
+    autoAnnMenu.add(showAutoLast);
+    autoAnnMenu.addSeparator();
     autoAnnMenu.add(applyAutoAnnotationSettings);
     autoAnnMenu.add(showConsensusHistogram);
     autoAnnMenu.add(showSequenceLogo);
@@ -1898,7 +2288,7 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.addSeparator();
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
-    viewMenu.add(autoAnnMenu);
+    annotationsMenu.add(autoAnnMenu);
     viewMenu.addSeparator();
     viewMenu.add(showSeqFeatures);
     // viewMenu.add(showSeqFeaturesHeight);
@@ -1937,7 +2327,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
-    colourMenu.add(rnahelicesColour);  
+    colourMenu.add(rnahelicesColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
@@ -1950,7 +2340,8 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(sortByTree);
     calculateMenu.addSeparator();
     calculateMenu.add(extractScores);
-    webServiceNoServices = new JMenuItem(MessageManager.getString("label.no_services"));
+    webServiceNoServices = new JMenuItem(
+            MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
@@ -1962,6 +2353,7 @@ public class GAlignFrame extends JInternalFrame
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
+    jMenu2.add(createSVG);
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
@@ -2008,6 +2400,59 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  /**
+   * Action on clicking sort annotations by type.
+   * 
+   * @param sortOrder
+   */
+  protected void sortAnnotations_actionPerformed()
+  {
+  }
+
+  /**
+   * Action on clicking Show all annotations.
+   * 
+   * @param forSequences
+   *          update sequence-related annotations
+   * @param forAlignment
+   *          update non-sequence-related annotations
+   */
+  protected void showAllAnnotations_actionPerformed(boolean forSequences,
+          boolean forAlignment)
+  {
+    setAnnotationsVisibility(true, forSequences, forAlignment);
+  }
+
+  /**
+   * Action on clicking Hide all annotations.
+   * 
+   * @param forSequences
+   *          update sequence-related annotations
+   * @param forAlignment
+   *          update non-sequence-related annotations
+   */
+  protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+          boolean forAlignment)
+  {
+    setAnnotationsVisibility(false, forSequences, forAlignment);
+  }
+
+  /**
+   * Set the visibility of annotations to true or false. Can act on
+   * sequence-related annotations, or alignment-related, or both.
+   * 
+   * @param visible
+   * @param forSequences
+   *          update sequence-related annotations
+   * @param forAlignment
+   *          update non-sequence-related annotations
+   */
+  protected void setAnnotationsVisibility(boolean visible,
+          boolean forSequences, boolean forAlignment)
+  {
+
+  }
+
   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
@@ -2321,11 +2766,10 @@ public class GAlignFrame extends JInternalFrame
   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
   {
   }
-  
+
   protected void RNAInteractionColour_actionPerformed(ActionEvent e)
   {
   }
-  
 
   /*
    * protected void covariationColour_actionPerformed(ActionEvent e) { }
@@ -2366,11 +2810,11 @@ public class GAlignFrame extends JInternalFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
   }
-  
+
   protected void createGroup_actionPerformed(ActionEvent e)
   {
   }
-  
+
   protected void unGroup_actionPerformed(ActionEvent e)
   {
   }
@@ -2420,6 +2864,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  public void createSVG(java.io.File f)
+  {
+
+  }
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -2651,6 +3099,26 @@ public class GAlignFrame extends JInternalFrame
   protected void expand_newalign(ActionEvent e)
   {
     // TODO Auto-generated method stub
-    
+
+  }
+
+  protected boolean isShowAutoCalculatedAbove()
+  {
+    return showAutoCalculatedAbove;
+  }
+
+  protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
+  {
+    this.showAutoCalculatedAbove = showAutoCalculatedAbove;
+  }
+
+  protected SequenceAnnotationOrder getAnnotationSortOrder()
+  {
+    return annotationSortOrder;
+  }
+
+  protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+  {
+    this.annotationSortOrder = annotationSortOrder;
   }
 }