git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
Merge remote-tracking branch 'origin/merge/JAL-845_JAL-1640' into
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1bee953..4b36729 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -35,8 +35,11 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
 import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
 
 import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
@@ -50,6 +53,7 @@ import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JRadioButtonMenuItem;
 import javax.swing.JTabbedPane;
+import javax.swing.KeyStroke;
 import javax.swing.SwingUtilities;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
@@ -216,6 +220,8 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem createBioJS = new JMenuItem();
 
+  JMenuItem createSVG = new JMenuItem();
+
   protected JMenuItem font = new JMenuItem();
 
   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
@@ -254,6 +260,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem showTranslation = new JMenuItem();
 
+  protected JMenu cdna = new JMenu();
+
   protected JMenuItem extractScores = new JMenuItem();
 
   protected JMenuItem expandAlignment = new JMenuItem();
@@ -266,6 +274,8 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem annotationColour = new JMenuItem();
 
+  JMenuItem annotationColumn = new JMenuItem();
+
   protected JMenuItem rnahelicesColour = new JMenuItem();
 
   JMenuItem associatedData = new JMenuItem();
@@ -336,7 +346,7 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem textColour = new JMenuItem();
 
-  JMenu formatMenu = new JMenu();
+  protected JMenu formatMenu = new JMenu();
 
   JMenu selectMenu = new JMenu();
 
@@ -384,6 +394,8 @@ public class GAlignFrame extends JInternalFrame
 
   private boolean showAutoCalculatedAbove = false;
 
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+
   public GAlignFrame()
   {
     try
@@ -397,7 +409,7 @@ public class GAlignFrame extends JInternalFrame
         JMenuItem item = new JMenuItem(
                 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 
-        item.addActionListener(new java.awt.event.ActionListener()
+        item.addActionListener(new ActionListener()
         {
           @Override
           public void actionPerformed(ActionEvent e)
@@ -606,81 +618,85 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     fileMenu.setText(MessageManager.getString("action.file"));
+
     saveAs.setText(MessageManager.getString("action.save_as") + "...");
-    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask()
-                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
-    saveAs.addActionListener(new ActionListener()
+    ActionListener al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         saveAs_actionPerformed(e);
       }
-    });
+    };
+    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
+            | KeyEvent.SHIFT_MASK, false);
+    addMenuActionAndAccelerator(keyStroke, saveAs, al);
+
     closeMenuItem.setText(MessageManager.getString("action.close"));
-    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         closeMenuItem_actionPerformed(false);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
+
     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.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);
-              }
-            });
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        selectAllSequenceMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
+
     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);
-              }
-            });
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        deselectAllSequenceMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
+
     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);
-              }
-            });
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        invertSequenceMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
     grpsFromSelection.setText(MessageManager
             .getString("action.make_groups_selection"));
-    grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+    grpsFromSelection.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -692,7 +708,7 @@ public class GAlignFrame extends JInternalFrame
             .getString("action.view_flanking_regions"));
     expandAlignment.setToolTipText(MessageManager
             .getString("label.view_flanking_regions"));
-    expandAlignment.addActionListener(new java.awt.event.ActionListener()
+    expandAlignment.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -702,86 +718,84 @@ public class GAlignFrame extends JInternalFrame
     });
     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);
-              }
-            });
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        remove2LeftMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
+
     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);
-              }
-            });
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        remove2RightMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
+
     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);
-              }
-            });
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        removeGappedColumnMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
+
     removeAllGapsMenuItem.setText(MessageManager
             .getString("action.remove_all_gaps"));
-    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
-            .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
-                    .getDefaultToolkit().getMenuShortcutKeyMask()
-                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
-    removeAllGapsMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                removeAllGapsMenuItem_actionPerformed(e);
-              }
-            });
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
+            | KeyEvent.SHIFT_MASK, false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        removeAllGapsMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
     justifyLeftMenuItem.setText(MessageManager
             .getString("action.left_justify_alignment"));
-    justifyLeftMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                justifyLeftMenuItem_actionPerformed(e);
-              }
-            });
+    justifyLeftMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        justifyLeftMenuItem_actionPerformed(e);
+      }
+    });
     justifyRightMenuItem.setText(MessageManager
             .getString("action.right_justify_alignment"));
-    justifyRightMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                justifyRightMenuItem_actionPerformed(e);
-              }
-            });
+    justifyRightMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        justifyRightMenuItem_actionPerformed(e);
+      }
+    });
     viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
     viewBoxesMenuItem.setState(true);
-    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+    viewBoxesMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -791,7 +805,7 @@ public class GAlignFrame extends JInternalFrame
     });
     viewTextMenuItem.setText(MessageManager.getString("action.text"));
     viewTextMenuItem.setState(true);
-    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    viewTextMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -802,28 +816,26 @@ public class GAlignFrame extends JInternalFrame
     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);
-              }
-            });
+    showNonconservedMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showUnconservedMenuItem_actionPerformed(e);
+      }
+    });
     sortPairwiseMenuItem.setText(MessageManager
             .getString("action.by_pairwise_id"));
-    sortPairwiseMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                sortPairwiseMenuItem_actionPerformed(e);
-              }
-            });
+    sortPairwiseMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortPairwiseMenuItem_actionPerformed(e);
+      }
+    });
     sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
-    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+    sortIDMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -833,17 +845,16 @@ public class GAlignFrame extends JInternalFrame
     });
     sortLengthMenuItem
             .setText(MessageManager.getString("action.by_length"));
-    sortLengthMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                sortLengthMenuItem_actionPerformed(e);
-              }
-            });
+    sortLengthMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortLengthMenuItem_actionPerformed(e);
+      }
+    });
     sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
-    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    sortGroupMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -851,34 +862,34 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-    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);
-              }
-            });
+
+    removeRedundancyMenuItem.setText(MessageManager.getString(
+            "action.remove_redundancy").concat("..."));
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        removeRedundancyMenuItem_actionPerformed(e);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
     pairwiseAlignmentMenuItem.setText(MessageManager
             .getString("action.pairwise_alignment"));
-    pairwiseAlignmentMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                pairwiseAlignmentMenuItem_actionPerformed(e);
-              }
-            });
+    pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        pairwiseAlignmentMenuItem_actionPerformed(e);
+      }
+    });
     PCAMenuItem.setText(MessageManager
             .getString("label.principal_component_analysis"));
-    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+    PCAMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -888,26 +899,24 @@ public class GAlignFrame extends JInternalFrame
     });
     averageDistanceTreeMenuItem.setText(MessageManager
             .getString("label.average_distance_identity"));
-    averageDistanceTreeMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                averageDistanceTreeMenuItem_actionPerformed(e);
-              }
-            });
+    averageDistanceTreeMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        averageDistanceTreeMenuItem_actionPerformed(e);
+      }
+    });
     neighbourTreeMenuItem.setText(MessageManager
             .getString("label.neighbour_joining_identity"));
-    neighbourTreeMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                neighbourTreeMenuItem_actionPerformed(e);
-              }
-            });
+    neighbourTreeMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        neighbourTreeMenuItem_actionPerformed(e);
+      }
+    });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
@@ -918,7 +927,7 @@ public class GAlignFrame extends JInternalFrame
             .getString("label.out_to_textbox"));
     clustalColour.setText(MessageManager.getString("label.clustalx"));
 
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    clustalColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -927,7 +936,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     zappoColour.setText(MessageManager.getString("label.zappo"));
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    zappoColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -936,7 +945,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     taylorColour.setText(MessageManager.getString("label.taylor"));
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    taylorColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -946,17 +955,16 @@ public class GAlignFrame extends JInternalFrame
     });
     hydrophobicityColour.setText(MessageManager
             .getString("label.hydrophobicity"));
-    hydrophobicityColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                hydrophobicityColour_actionPerformed(e);
-              }
-            });
+    hydrophobicityColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hydrophobicityColour_actionPerformed(e);
+      }
+    });
     helixColour.setText(MessageManager.getString("label.helix_propensity"));
-    helixColour.addActionListener(new java.awt.event.ActionListener()
+    helixColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -966,7 +974,7 @@ public class GAlignFrame extends JInternalFrame
     });
     strandColour.setText(MessageManager
             .getString("label.strand_propensity"));
-    strandColour.addActionListener(new java.awt.event.ActionListener()
+    strandColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -975,7 +983,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     turnColour.setText(MessageManager.getString("label.turn_propensity"));
-    turnColour.addActionListener(new java.awt.event.ActionListener()
+    turnColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -984,7 +992,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     buriedColour.setText(MessageManager.getString("label.buried_index"));
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    buriedColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -994,7 +1002,7 @@ public class GAlignFrame extends JInternalFrame
     });
     userDefinedColour.setText(MessageManager
             .getString("action.user_defined"));
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    userDefinedColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1004,7 +1012,7 @@ public class GAlignFrame extends JInternalFrame
     });
     PIDColour
             .setText(MessageManager.getString("label.percentage_identity"));
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    PIDColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1014,7 +1022,7 @@ public class GAlignFrame extends JInternalFrame
     });
     BLOSUM62Colour
             .setText(MessageManager.getString("label.blosum62_score"));
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    BLOSUM62Colour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1023,7 +1031,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
-    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    nucleotideColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1034,55 +1042,51 @@ public class GAlignFrame extends JInternalFrame
 
     purinePyrimidineColour.setText(MessageManager
             .getString("label.purine_pyrimidine"));
-    purinePyrimidineColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                purinePyrimidineColour_actionPerformed(e);
-              }
-            });
+    purinePyrimidineColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        purinePyrimidineColour_actionPerformed(e);
+      }
+    });
 
     RNAInteractionColour.setText("RNA Interaction type");
-    RNAInteractionColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                RNAInteractionColour_actionPerformed(e);
-              }
-            });
+    RNAInteractionColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        RNAInteractionColour_actionPerformed(e);
+      }
+    });
     /*
      * covariationColour.setText("Covariation");
-     * covariationColour.addActionListener(new java.awt.event.ActionListener() {
-     * public void actionPerformed(ActionEvent e) {
-     * covariationColour_actionPerformed(e); } });
+     * covariationColour.addActionListener(new ActionListener() { public void
+     * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
+     * });
      */
 
     avDistanceTreeBlosumMenuItem.setText(MessageManager
             .getString("label.average_distance_bloslum62"));
-    avDistanceTreeBlosumMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                avTreeBlosumMenuItem_actionPerformed(e);
-              }
-            });
+    avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        avTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
     njTreeBlosumMenuItem.setText(MessageManager
             .getString("label.neighbour_blosum62"));
-    njTreeBlosumMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                njTreeBlosumMenuItem_actionPerformed(e);
-              }
-            });
+    njTreeBlosumMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        njTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText(MessageManager
             .getString("label.show_annotations"));
@@ -1179,17 +1183,16 @@ public class GAlignFrame extends JInternalFrame
     });
     colourTextMenuItem.setText(MessageManager
             .getString("label.colour_text"));
-    colourTextMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                colourTextMenuItem_actionPerformed(e);
-              }
-            });
+    colourTextMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        colourTextMenuItem_actionPerformed(e);
+      }
+    });
     htmlMenuItem.setText(MessageManager.getString("label.html"));
-    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    htmlMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1212,7 +1215,7 @@ public class GAlignFrame extends JInternalFrame
 
     overviewMenuItem.setText(MessageManager
             .getString("label.overview_window"));
-    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    overviewMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1220,45 +1223,47 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);
       }
     });
+
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
-    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         undoMenuItem_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
+
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
-    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         redoMenuItem_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
     conservationMenuItem.setText(MessageManager
             .getString("action.by_conservation"));
-    conservationMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                conservationMenuItem_actionPerformed(e);
-              }
-            });
+    conservationMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(e);
+      }
+    });
     noColourmenuItem.setText(MessageManager.getString("label.none"));
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    noColourmenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1267,7 +1272,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
-    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    wrapMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1275,47 +1280,50 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
+
     printMenuItem.setText(MessageManager.getString("action.print") + "...");
-    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         printMenuItem_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
+
     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);
-              }
-            });
+    renderGapsMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        renderGapsMenuItem_actionPerformed(e);
+      }
+    });
+
     findMenuItem.setText(MessageManager.getString("action.find"));
-    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
-    findMenuItem.addActionListener(new java.awt.event.ActionListener()
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         findMenuItem_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+
     abovePIDThreshold.setText(MessageManager
             .getString("label.above_identity_threshold"));
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    abovePIDThreshold.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1442,8 +1450,7 @@ public class GAlignFrame extends JInternalFrame
     buttonGroup.add(showAutoLast);
     showAutoFirst.setText(MessageManager.getString("label.show_first"));
     showAutoFirst.setSelected(Cache.getDefault(
-            Preferences.SHOW_AUTOCALC_ABOVE,
-            false));
+            Preferences.SHOW_AUTOCALC_ABOVE, false));
     showAutoFirst.addActionListener(new ActionListener()
     {
       @Override
@@ -1466,7 +1473,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
-    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    nucleotideColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1489,69 +1496,74 @@ public class GAlignFrame extends JInternalFrame
 
     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()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         deleteGroups_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
     createGroup.setText(MessageManager.getString("action.create_groups"));
-    createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    createGroup.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         createGroup_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
     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));
-    unGroup.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
+            | KeyEvent.SHIFT_MASK, false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         unGroup_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
     copy.setText(MessageManager.getString("action.copy"));
-    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
 
-    copy.addActionListener(new java.awt.event.ActionListener()
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         copy_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, copy, al);
+
     cut.setText(MessageManager.getString("action.cut"));
-    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    cut.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         cut_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, cut, al);
+
     delete.setText(MessageManager.getString("action.delete"));
-    delete.addActionListener(new java.awt.event.ActionListener()
+    delete.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1559,35 +1571,38 @@ public class GAlignFrame extends JInternalFrame
         delete_actionPerformed(e);
       }
     });
+
     pasteMenu.setText(MessageManager.getString("action.paste"));
     pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
-    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask()
-                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
-    pasteNew.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
+            | KeyEvent.SHIFT_MASK, false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         pasteNew_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, pasteNew, al);
+
     pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
-    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    pasteThis.addActionListener(new java.awt.event.ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         pasteThis_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
     applyToAllGroups.setText(MessageManager
             .getString("label.apply_colour_to_all_groups"));
-    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+    applyToAllGroups.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1595,7 +1610,7 @@ public class GAlignFrame extends JInternalFrame
         applyToAllGroups_actionPerformed(e);
       }
     });
-    createPNG.addActionListener(new java.awt.event.ActionListener()
+    createPNG.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1606,8 +1621,9 @@ public class GAlignFrame extends JInternalFrame
     createPNG.setActionCommand(MessageManager
             .getString("label.save_png_image"));
     createPNG.setText("PNG");
+
     font.setText(MessageManager.getString("action.font"));
-    font.addActionListener(new java.awt.event.ActionListener()
+    font.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1618,7 +1634,7 @@ public class GAlignFrame extends JInternalFrame
     seqLimits.setText(MessageManager
             .getString("label.show_sequence_limits"));
     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
-    seqLimits.addActionListener(new java.awt.event.ActionListener()
+    seqLimits.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1627,7 +1643,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     epsFile.setText("EPS");
-    epsFile.addActionListener(new java.awt.event.ActionListener()
+    epsFile.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1635,11 +1651,22 @@ public class GAlignFrame extends JInternalFrame
         createEPS(null);
       }
     });
+
+    createSVG.setText("SVG");
+    createSVG.addActionListener(new 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()
+    LoadtreeMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1650,7 +1677,7 @@ public class GAlignFrame extends JInternalFrame
 
     scaleAbove.setVisible(false);
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
-    scaleAbove.addActionListener(new java.awt.event.ActionListener()
+    scaleAbove.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1661,7 +1688,7 @@ public class GAlignFrame extends JInternalFrame
     scaleLeft.setVisible(false);
     scaleLeft.setSelected(true);
     scaleLeft.setText(MessageManager.getString("action.scale_left"));
-    scaleLeft.addActionListener(new java.awt.event.ActionListener()
+    scaleLeft.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1672,7 +1699,7 @@ public class GAlignFrame extends JInternalFrame
     scaleRight.setVisible(false);
     scaleRight.setSelected(true);
     scaleRight.setText(MessageManager.getString("action.scale_right"));
-    scaleRight.addActionListener(new java.awt.event.ActionListener()
+    scaleRight.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1684,15 +1711,14 @@ public class GAlignFrame extends JInternalFrame
     centreColumnLabelsMenuItem.setState(false);
     centreColumnLabelsMenuItem.setText(MessageManager
             .getString("label.centre_column_labels"));
-    centreColumnLabelsMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                centreColumnLabels_actionPerformed(e);
-              }
-            });
+    centreColumnLabelsMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        centreColumnLabels_actionPerformed(e);
+      }
+    });
     followHighlightMenuItem.setVisible(true);
     followHighlightMenuItem.setState(true);
     followHighlightMenuItem.setText(MessageManager
@@ -1710,7 +1736,7 @@ public class GAlignFrame extends JInternalFrame
 
     modifyPID.setText(MessageManager
             .getString("label.modify_identity_thereshold"));
-    modifyPID.addActionListener(new java.awt.event.ActionListener()
+    modifyPID.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1720,15 +1746,14 @@ public class GAlignFrame extends JInternalFrame
     });
     modifyConservation.setText(MessageManager
             .getString("label.modify_conservation_thereshold"));
-    modifyConservation
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                modifyConservation_actionPerformed(e);
-              }
-            });
+    modifyConservation.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed(e);
+      }
+    });
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1753,7 +1778,7 @@ public class GAlignFrame extends JInternalFrame
     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
@@ -1809,6 +1834,55 @@ public class GAlignFrame extends JInternalFrame
         showTranslation_actionPerformed(e);
       }
     });
+
+    /*
+     * cDNA menu options
+     */
+    cdna.setText(MessageManager.getString("label.cdna"));
+    // link to available cDNA
+    JMenuItem linkCdna = new JMenuItem(
+            MessageManager.getString("label.link_cdna"));
+    linkCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.link_cdna_tip")));
+    linkCdna.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        linkCdna_actionPerformed();
+      }
+    });
+    cdna.add(linkCdna);
+    // align linked cDNA
+    JMenuItem alignCdna = new JMenuItem(
+            MessageManager.getString("label.align_cdna"));
+    alignCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.align_cdna_tip")));
+    alignCdna.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        alignCdna_actionPerformed();
+      }
+    });
+    cdna.add(alignCdna);
+
+    // view alignment as cDNA (when known)
+    JMenuItem viewAsCdna = new JMenuItem(
+            MessageManager.getString("label.view_as_cdna"));
+    viewAsCdna.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.view_as_cdna_tip")));
+    viewAsCdna.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        viewAsCdna_actionPerformed();
+      }
+    });
+    cdna.add(viewAsCdna);
+
     extractScores.setText(MessageManager.getString("label.extract_scores")
             + "...");
     extractScores.addActionListener(new ActionListener()
@@ -1819,15 +1893,11 @@ public class GAlignFrame extends JInternalFrame
         extractScores_actionPerformed(e);
       }
     });
-    extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
-    // score extraction
+    extractScores.setVisible(true);
+    // JBPNote: TODO: make gui for regex based score extraction
+
+    // for show products actions see AlignFrame.canShowProducts
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-    /*
-     * showProducts.addActionListener(new ActionListener() {
-     * 
-     * public void actionPerformed(ActionEvent e) {
-     * showProducts_actionPerformed(e); } });
-     */
     openFeatureSettings.setText(MessageManager
             .getString("label.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
@@ -1860,6 +1930,17 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
+    annotationColumn.setText(MessageManager
+            .getString("action.select_by_annotation"));
+    annotationColumn.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColumn_actionPerformed(e);
+      }
+    });
+
     rnahelicesColour.setText(MessageManager
             .getString("action.by_rna_helixes"));
     rnahelicesColour.addActionListener(new ActionListener()
@@ -2067,20 +2148,22 @@ public class GAlignFrame extends JInternalFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
+
     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()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+            | KeyEvent.ALT_MASK, false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         invertColSel_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
       @Override
@@ -2107,18 +2190,20 @@ public class GAlignFrame extends JInternalFrame
         tabbedPane_focusGained(e);
       }
     });
+
     save.setText(MessageManager.getString("action.save"));
-    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    save.addActionListener(new ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         save_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, save, al);
+
     reload.setEnabled(false);
     reload.setText(MessageManager.getString("action.reload"));
     reload.addActionListener(new ActionListener()
@@ -2129,18 +2214,20 @@ public class GAlignFrame extends JInternalFrame
         reload_actionPerformed(e);
       }
     });
+
     newView.setText(MessageManager.getString("action.new_view"));
-    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
-                    .getMenuShortcutKeyMask(), false));
-    newView.addActionListener(new ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         newView_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, newView, al);
+
     tabbedPane.setToolTipText("<html><i>"
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
@@ -2166,30 +2253,33 @@ public class GAlignFrame extends JInternalFrame
         idRightAlign_actionPerformed(e);
       }
     });
+
     gatherViews.setEnabled(false);
     gatherViews.setText(MessageManager.getString("action.gather_views"));
-    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_G, 0, false));
-    gatherViews.addActionListener(new ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         gatherViews_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, gatherViews, al);
+
     expandViews.setEnabled(false);
     expandViews.setText(MessageManager.getString("action.expand_views"));
-    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-            java.awt.event.KeyEvent.VK_X, 0, false));
-    expandViews.addActionListener(new ActionListener()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+    al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         expandViews_actionPerformed(e);
       }
-    });
+    };
+    addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
     pageSetup
             .setText(MessageManager.getString("action.page_setup") + "...");
     pageSetup.addActionListener(new ActionListener()
@@ -2335,6 +2425,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
+    calculateMenu.add(cdna);
     calculateMenu.add(showProducts);
     calculateMenu.add(autoCalculate);
     calculateMenu.add(sortByTree);
@@ -2354,6 +2445,7 @@ public class GAlignFrame extends JInternalFrame
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
     jMenu2.add(createBioJS);
+    jMenu2.add(createSVG);
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
@@ -2393,6 +2485,7 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(unGroup);
     selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
+    selectMenu.add(annotationColumn);
     calculateMenu.add(expandAlignment);
     // TODO - determine if the listenToViewSelections button is needed : see bug
     // JAL-574
@@ -2401,6 +2494,34 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
+   * Adds the given action listener and key accelerator to the given menu item.
+   * Also saves in a lookup table to support lookup of action by key stroke.
+   * 
+   * @param keyStroke
+   * @param menuItem
+   * @param actionListener
+   */
+  protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
+          JMenuItem menuItem, ActionListener actionListener)
+  {
+    menuItem.setAccelerator(keyStroke);
+    accelerators.put(keyStroke, menuItem);
+    menuItem.addActionListener(actionListener);
+  }
+
+  protected void viewAsCdna_actionPerformed()
+  {
+  }
+
+  protected void alignCdna_actionPerformed()
+  {
+  }
+
+  protected void linkCdna_actionPerformed()
+  {
+  }
+
+  /**
    * Action on clicking sort annotations by type.
    * 
    * @param sortOrder
@@ -2566,10 +2687,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void showProducts_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void buildSortByAnnotationScoresMenu()
   {
   }
@@ -2869,6 +2986,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  public void createSVG(java.io.File f)
+  {
+
+  }
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -2967,6 +3088,11 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  public void annotationColumn_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   public void rnahelicesColour_actionPerformed(ActionEvent e)
   {
 
@@ -3122,4 +3248,25 @@ public class GAlignFrame extends JInternalFrame
   {
     this.annotationSortOrder = annotationSortOrder;
   }
+
+  public Map<KeyStroke, JMenuItem> getAccelerators()
+  {
+    return this.accelerators;
+  }
+
+  /**
+   * Returns the selected index of the tabbed pane, or -1 if none selected
+   * (including the case where the tabbed pane has not been made visible).
+   * 
+   * @return
+   */
+  public int getTabIndex()
+  {
+    return tabbedPane.getSelectedIndex();
+  }
+
+  public JPanel getStatusPanel()
+  {
+    return statusPanel;
+  }
 }