JAL-1264 adding show/hide annotation options to applet

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 75d09d3..befa3b1 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,14 +20,6 @@
  */
 package jalview.jbgui;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
@@ -60,72 +52,34 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
 public class GAlignFrame extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
 
-  protected JMenu fileMenu = new JMenu();
-
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu editMenu = new JMenu();
-
-  protected JMenu viewMenu = new JMenu();
-
-  protected JMenu annotationsMenu = new JMenu();
-
   protected JMenu colourMenu = new JMenu();
 
-  protected JMenu calculateMenu = new JMenu();
-
   protected JMenu webService = new JMenu();
 
   protected JMenuItem webServiceNoServices;
 
-  protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
-
-  protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
-
-  protected JMenuItem invertSequenceMenuItem = new JMenuItem();
-
-  protected JMenuItem remove2LeftMenuItem = new JMenuItem();
-
-  protected JMenuItem remove2RightMenuItem = new JMenuItem();
-
-  protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
-
-  protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-
   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
 
-  protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
-
-  protected JMenuItem sortIDMenuItem = new JMenuItem();
-
-  protected JMenuItem sortLengthMenuItem = new JMenuItem();
-
-  protected JMenuItem sortGroupMenuItem = new JMenuItem();
-
   protected JMenu sortByAnnotScore = new JMenu();
 
-  protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
-
-  protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
-
-  protected JMenuItem PCAMenuItem = new JMenuItem();
-
-  protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
-
-  protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
   public JLabel statusBar = new JLabel();
 
-  protected JMenuItem saveAs = new JMenuItem();
-
   protected JMenu outputTextboxMenu = new JMenu();
 
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
@@ -161,20 +115,12 @@ public class GAlignFrame extends JInternalFrame
 
   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
 
-  JMenuItem njTreeBlosumMenuItem = new JMenuItem();
-
-  JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-
   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 
-  JMenuItem htmlMenuItem = new JMenuItem();
-
-  JMenuItem overviewMenuItem = new JMenuItem();
-
   protected JMenuItem undoMenuItem = new JMenuItem();
 
   protected JMenuItem redoMenuItem = new JMenuItem();
@@ -185,60 +131,30 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 
-  JMenuItem printMenuItem = new JMenuItem();
-
   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 
-  JMenuItem findMenuItem = new JMenuItem();
-
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 
-  JMenuItem deleteGroups = new JMenuItem();
-
-  JMenuItem createGroup = new JMenuItem();
-
-  JMenuItem unGroup = new JMenuItem();
-
-  JMenuItem delete = new JMenuItem();
-
   JMenuItem copy = new JMenuItem();
 
   JMenuItem cut = new JMenuItem();
 
   JMenu pasteMenu = new JMenu();
 
-  JMenuItem pasteNew = new JMenuItem();
-
-  JMenuItem pasteThis = new JMenuItem();
-
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
 
-  JMenuItem createPNG = new JMenuItem();
-
-  JMenuItem createBioJS = new JMenuItem();
-
-  JMenuItem createSVG = new JMenuItem();
-
-  protected JMenuItem font = new JMenuItem();
-
   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 
-  JMenuItem epsFile = new JMenuItem();
-
-  JMenuItem LoadtreeMenuItem = new JMenuItem();
-
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 
-  protected JMenuItem modifyPID = new JMenuItem();
-
   protected JMenuItem modifyConservation = new JMenuItem();
 
   protected JMenu sortByTreeMenu = new JMenu();
@@ -247,8 +163,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu calculateTree = new JMenu();
 
-  JMenu jMenu2 = new JMenu();
-
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
@@ -257,68 +171,20 @@ public class GAlignFrame extends JInternalFrame
 
   protected ButtonGroup colours = new ButtonGroup();
 
-  JMenuItem vamsasStore = new JMenuItem();
-
   protected JMenuItem showTranslation = new JMenuItem();
 
-  protected JMenuItem extractScores = new JMenuItem();
-
-  protected JMenuItem expandAlignment = new JMenuItem();
-
   protected JMenu showProducts = new JMenu();
 
-  public JMenuItem openFeatureSettings = new JMenuItem();
-
-  JMenuItem fetchSequence = new JMenuItem();
-
-  JMenuItem annotationColour = new JMenuItem();
-
-  JMenuItem annotationColumn = new JMenuItem();
-
   protected JMenuItem rnahelicesColour = new JMenuItem();
 
-  JMenuItem associatedData = new JMenuItem();
-
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
 
-  JMenu addSequenceMenu = new JMenu();
-
-  JMenuItem addFromFile = new JMenuItem();
-
-  JMenuItem addFromText = new JMenuItem();
-
-  JMenuItem addFromURL = new JMenuItem();
-
-  JMenuItem exportAnnotations = new JMenuItem();
-
-  JMenuItem exportFeatures = new JMenuItem();
-
   protected JPanel statusPanel = new JPanel();
 
-  GridLayout gridLayout1 = new GridLayout();
-
-  JMenu showMenu = new JMenu();
-
-  JMenuItem showAllSeqs = new JMenuItem();
-
-  JMenuItem showAllColumns = new JMenuItem();
-
-  JMenu hideMenu = new JMenu();
-
-  JMenuItem hideSelSequences = new JMenuItem();
-
-  JMenuItem hideSelColumns = new JMenuItem();
-
-  JMenuItem hideAllButSelection = new JMenuItem();
-
-  JMenuItem hideAllSelection = new JMenuItem();
-
-  JMenuItem showAllhidden = new JMenuItem();
-
   protected JMenuItem showAllSeqAnnotations = new JMenuItem();
 
   protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
@@ -329,28 +195,14 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
 
-  protected JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem();
-
-  protected JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem();
-
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 
-  JMenuItem invertColSel = new JMenuItem();
-
   protected JTabbedPane tabbedPane = new JTabbedPane();
 
-  JMenuItem save = new JMenuItem();
-
   protected JMenuItem reload = new JMenuItem();
 
-  JMenuItem newView = new JMenuItem();
-
-  JMenuItem textColour = new JMenuItem();
-
   protected JMenu formatMenu = new JMenu();
 
-  JMenu selectMenu = new JMenu();
-
   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
@@ -361,18 +213,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem expandViews = new JMenuItem();
 
-  JMenuItem pageSetup = new JMenuItem();
-
-  JMenuItem alignmentProperties = new JMenuItem();
-
-  JMenu tooltipSettingsMenu = new JMenu();
-
-  private JMenuItem justifyLeftMenuItem = new JMenuItem();
-
-  private JMenuItem justifyRightMenuItem = new JMenuItem();
-
-  JMenu autoAnnMenu = new JMenu();
-
   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
@@ -385,12 +225,6 @@ 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;
@@ -619,9 +453,8 @@ public class GAlignFrame extends JInternalFrame
 
   private void jbInit() throws Exception
   {
-    fileMenu.setText(MessageManager.getString("action.file"));
-
-    saveAs.setText(MessageManager.getString("action.save_as") + "...");
+    JMenuItem saveAs = new JMenuItem(
+            MessageManager.getString("action.save_as") + "...");
     ActionListener al = new ActionListener()
     {
       @Override
@@ -648,14 +481,17 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 
-    editMenu.setText(MessageManager.getString("action.edit"));
-    viewMenu.setText(MessageManager.getString("action.view"));
-    annotationsMenu.setText(MessageManager.getString("action.annotations"));
+    JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
+    JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
+    JMenu annotationsMenu = new JMenu(
+            MessageManager.getString("action.annotations"));
+    JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
     colourMenu.setText(MessageManager.getString("action.colour"));
-    calculateMenu.setText(MessageManager.getString("action.calculate"));
+    JMenu calculateMenu = new JMenu(
+            MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
-
-    selectAllSequenceMenuItem.setText(MessageManager
+    JMenuItem selectAllSequenceMenuItem = new JMenuItem(
+            MessageManager
             .getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
@@ -669,8 +505,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
 
-    deselectAllSequenceMenuItem.setText(MessageManager
-            .getString("action.deselect_all"));
+    JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
+            MessageManager.getString("action.deselect_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
     al = new ActionListener()
     {
@@ -682,8 +518,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
 
-    invertSequenceMenuItem.setText(MessageManager
-            .getString("action.invert_sequence_selection"));
+    JMenuItem invertSequenceMenuItem = new JMenuItem(
+            MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -696,8 +532,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
 
-    grpsFromSelection.setText(MessageManager
-            .getString("action.make_groups_selection"));
+    JMenuItem grpsFromSelection = new JMenuItem(
+            MessageManager.getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(new ActionListener()
     {
       @Override
@@ -706,8 +542,8 @@ public class GAlignFrame extends JInternalFrame
         makeGrpsFromSelection_actionPerformed(e);
       }
     });
-    expandAlignment.setText(MessageManager
-            .getString("action.view_flanking_regions"));
+    JMenuItem expandAlignment = new JMenuItem(
+            MessageManager.getString("action.view_flanking_regions"));
     expandAlignment.setToolTipText(MessageManager
             .getString("label.view_flanking_regions"));
     expandAlignment.addActionListener(new ActionListener()
@@ -718,8 +554,8 @@ public class GAlignFrame extends JInternalFrame
         expand_newalign(e);
       }
     });
-    remove2LeftMenuItem.setText(MessageManager
-            .getString("action.remove_left"));
+    JMenuItem remove2LeftMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -732,8 +568,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
 
-    remove2RightMenuItem.setText(MessageManager
-            .getString("action.remove_right"));
+    JMenuItem remove2RightMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -746,8 +582,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
 
-    removeGappedColumnMenuItem.setText(MessageManager
-            .getString("action.remove_empty_columns"));
+    JMenuItem removeGappedColumnMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -760,8 +596,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
 
-    removeAllGapsMenuItem.setText(MessageManager
-            .getString("action.remove_all_gaps"));
+    JMenuItem removeAllGapsMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.SHIFT_MASK, false);
@@ -775,8 +611,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 
-    justifyLeftMenuItem.setText(MessageManager
-            .getString("action.left_justify_alignment"));
+    JMenuItem justifyLeftMenuItem = new JMenuItem(
+            MessageManager.getString("action.left_justify_alignment"));
     justifyLeftMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -785,8 +621,8 @@ public class GAlignFrame extends JInternalFrame
         justifyLeftMenuItem_actionPerformed(e);
       }
     });
-    justifyRightMenuItem.setText(MessageManager
-            .getString("action.right_justify_alignment"));
+    JMenuItem justifyRightMenuItem = new JMenuItem(
+            MessageManager.getString("action.right_justify_alignment"));
     justifyRightMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -826,8 +662,8 @@ public class GAlignFrame extends JInternalFrame
         showUnconservedMenuItem_actionPerformed(e);
       }
     });
-    sortPairwiseMenuItem.setText(MessageManager
-            .getString("action.by_pairwise_id"));
+    JMenuItem sortPairwiseMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_pairwise_id"));
     sortPairwiseMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -836,7 +672,8 @@ public class GAlignFrame extends JInternalFrame
         sortPairwiseMenuItem_actionPerformed(e);
       }
     });
-    sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
+    JMenuItem sortIDMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_id"));
     sortIDMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -845,8 +682,8 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortLengthMenuItem
-            .setText(MessageManager.getString("action.by_length"));
+    JMenuItem sortLengthMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_length"));
     sortLengthMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -855,7 +692,8 @@ public class GAlignFrame extends JInternalFrame
         sortLengthMenuItem_actionPerformed(e);
       }
     });
-    sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
+    JMenuItem sortGroupMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_group"));
     sortGroupMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -865,8 +703,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    removeRedundancyMenuItem.setText(MessageManager.getString(
-            "action.remove_redundancy").concat("..."));
+    JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
+            .getString("action.remove_redundancy").concat("..."));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -879,8 +717,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
 
-    pairwiseAlignmentMenuItem.setText(MessageManager
-            .getString("action.pairwise_alignment"));
+    JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
+            MessageManager.getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -889,8 +727,8 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    PCAMenuItem.setText(MessageManager
-            .getString("label.principal_component_analysis"));
+    JMenuItem PCAMenuItem = new JMenuItem(
+            MessageManager.getString("label.principal_component_analysis"));
     PCAMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -899,8 +737,8 @@ public class GAlignFrame extends JInternalFrame
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText(MessageManager
-            .getString("label.average_distance_identity"));
+    JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
+            MessageManager.getString("label.average_distance_identity"));
     averageDistanceTreeMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -909,8 +747,8 @@ public class GAlignFrame extends JInternalFrame
         averageDistanceTreeMenuItem_actionPerformed(e);
       }
     });
-    neighbourTreeMenuItem.setText(MessageManager
-            .getString("label.neighbour_joining_identity"));
+    JMenuItem neighbourTreeMenuItem = new JMenuItem(
+            MessageManager.getString("label.neighbour_joining_identity"));
     neighbourTreeMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -919,7 +757,8 @@ public class GAlignFrame extends JInternalFrame
         neighbourTreeMenuItem_actionPerformed(e);
       }
     });
-    this.getContentPane().setLayout(borderLayout1);
+
+    this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -928,7 +767,6 @@ public class GAlignFrame extends JInternalFrame
     outputTextboxMenu.setText(MessageManager
             .getString("label.out_to_textbox"));
     clustalColour.setText(MessageManager.getString("label.clustalx"));
-
     clustalColour.addActionListener(new ActionListener()
     {
       @Override
@@ -1069,8 +907,8 @@ public class GAlignFrame extends JInternalFrame
      * });
      */
 
-    avDistanceTreeBlosumMenuItem.setText(MessageManager
-            .getString("label.average_distance_bloslum62"));
+    JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
+            MessageManager.getString("label.average_distance_bloslum62"));
     avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1079,8 +917,8 @@ public class GAlignFrame extends JInternalFrame
         avTreeBlosumMenuItem_actionPerformed(e);
       }
     });
-    njTreeBlosumMenuItem.setText(MessageManager
-            .getString("label.neighbour_blosum62"));
+    JMenuItem njTreeBlosumMenuItem = new JMenuItem(
+            MessageManager.getString("label.neighbour_blosum62"));
     njTreeBlosumMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1151,8 +989,11 @@ public class GAlignFrame extends JInternalFrame
     SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
                     SequenceAnnotationOrder.NONE.name()));
-    sortAnnBySequence.setText(MessageManager
-            .getString("label.sort_annotations_by_sequence"));
+    final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
+            MessageManager.getString("label.sort_annotations_by_sequence"));
+    final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
+            MessageManager.getString("label.sort_annotations_by_label"));
+
     sortAnnBySequence
             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     sortAnnBySequence.addActionListener(new ActionListener()
@@ -1167,8 +1008,6 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
-    sortAnnByLabel.setText(MessageManager
-            .getString("label.sort_annotations_by_label"));
     sortAnnByLabel
             .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
     sortAnnByLabel.addActionListener(new ActionListener()
@@ -1193,7 +1032,9 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
-    htmlMenuItem.setText(MessageManager.getString("label.html"));
+
+    JMenuItem htmlMenuItem = new JMenuItem(
+            MessageManager.getString("label.html"));
     htmlMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1203,9 +1044,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    // TODO uncomment when supported by MassageManager
-    // createBioJS.setText(MessageManager.getString("label.biojs_html_export"));
-    createBioJS.setText("BioJS");
+    JMenuItem createBioJS = new JMenuItem(
+            MessageManager.getString("label.biojs_html_export"));
     createBioJS.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
@@ -1215,8 +1055,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    overviewMenuItem.setText(MessageManager
-            .getString("label.overview_window"));
+    JMenuItem overviewMenuItem = new JMenuItem(
+            MessageManager.getString("label.overview_window"));
     overviewMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1283,7 +1123,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    printMenuItem.setText(MessageManager.getString("action.print") + "...");
+    JMenuItem printMenuItem = new JMenuItem(
+            MessageManager.getString("action.print") + "...");
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1308,7 +1149,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    findMenuItem.setText(MessageManager.getString("action.find"));
+    JMenuItem findMenuItem = new JMenuItem(
+            MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
@@ -1448,9 +1290,12 @@ public class GAlignFrame extends JInternalFrame
     });
 
     ButtonGroup buttonGroup = new ButtonGroup();
+    final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
+            MessageManager.getString("label.show_first"));
+    final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
+            MessageManager.getString("label.show_last"));
     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()
@@ -1462,7 +1307,6 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
-    showAutoLast.setText(MessageManager.getString("label.show_last"));
     showAutoLast.setSelected(!showAutoFirst.isSelected());
     showAutoLast.addActionListener(new ActionListener()
     {
@@ -1496,8 +1340,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    deleteGroups
-            .setText(MessageManager.getString("action.undefine_groups"));
+    JMenuItem deleteGroups = new JMenuItem(
+            MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1510,7 +1354,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 
-    createGroup.setText(MessageManager.getString("action.create_groups"));
+    JMenuItem createGroup = new JMenuItem(
+            MessageManager.getString("action.create_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1523,7 +1368,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, createGroup, al);
 
-    unGroup.setText(MessageManager.getString("action.remove_group"));
+    JMenuItem unGroup = new JMenuItem(
+            MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.SHIFT_MASK, false);
@@ -1564,7 +1410,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
 
-    delete.setText(MessageManager.getString("action.delete"));
+    JMenuItem delete = new JMenuItem(
+            MessageManager.getString("action.delete"));
     delete.addActionListener(new ActionListener()
     {
       @Override
@@ -1575,7 +1422,8 @@ public class GAlignFrame extends JInternalFrame
     });
 
     pasteMenu.setText(MessageManager.getString("action.paste"));
-    pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
+    JMenuItem pasteNew = new JMenuItem(
+            MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.SHIFT_MASK, false);
@@ -1589,7 +1437,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
 
-    pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
+    JMenuItem pasteThis = new JMenuItem(
+            MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1612,6 +1461,7 @@ public class GAlignFrame extends JInternalFrame
         applyToAllGroups_actionPerformed(e);
       }
     });
+    JMenuItem createPNG = new JMenuItem("PNG");
     createPNG.addActionListener(new ActionListener()
     {
       @Override
@@ -1622,9 +1472,8 @@ public class GAlignFrame extends JInternalFrame
     });
     createPNG.setActionCommand(MessageManager
             .getString("label.save_png_image"));
-    createPNG.setText("PNG");
 
-    font.setText(MessageManager.getString("action.font"));
+    JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
     font.addActionListener(new ActionListener()
     {
       @Override
@@ -1644,7 +1493,7 @@ public class GAlignFrame extends JInternalFrame
         seqLimit_actionPerformed(e);
       }
     });
-    epsFile.setText("EPS");
+    JMenuItem epsFile = new JMenuItem("EPS");
     epsFile.addActionListener(new ActionListener()
     {
       @Override
@@ -1654,7 +1503,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    createSVG.setText("SVG");
+    JMenuItem createSVG = new JMenuItem("SVG");
     createSVG.addActionListener(new ActionListener()
     {
       @Override
@@ -1664,16 +1513,16 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    LoadtreeMenuItem.setActionCommand(MessageManager
+    JMenuItem loadTreeMenuItem = new JMenuItem(
+            MessageManager.getString("label.load_associated_tree"));
+    loadTreeMenuItem.setActionCommand(MessageManager
             .getString("label.load_tree_for_sequence_set"));
-    LoadtreeMenuItem.setText(MessageManager
-            .getString("label.load_associated_tree"));
-    LoadtreeMenuItem.addActionListener(new ActionListener()
+    loadTreeMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        LoadtreeMenuItem_actionPerformed(e);
+        loadTreeMenuItem_actionPerformed(e);
       }
     });
 
@@ -1736,8 +1585,8 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    modifyPID.setText(MessageManager
-            .getString("label.modify_identity_thereshold"));
+    JMenuItem modifyPID = new JMenuItem(
+            MessageManager.getString("label.modify_identity_thereshold"));
     modifyPID.addActionListener(new ActionListener()
     {
       @Override
@@ -1804,7 +1653,6 @@ public class GAlignFrame extends JInternalFrame
     calculateTree
             .setText(MessageManager.getString("action.calculate_tree"));
 
-    jMenu2.setText(MessageManager.getString("label.export_image"));
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem.setState(jalview.bin.Cache
             .getDefault("PAD_GAPS", false));
@@ -1816,8 +1664,9 @@ public class GAlignFrame extends JInternalFrame
         padGapsMenuitem_actionPerformed(e);
       }
     });
+    JMenuItem vamsasStore = new JMenuItem(
+            MessageManager.getString("label.vamsas_store"));
     vamsasStore.setVisible(false);
-    vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
     vamsasStore.addActionListener(new ActionListener()
     {
       @Override
@@ -1837,8 +1686,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    extractScores.setText(MessageManager.getString("label.extract_scores")
-            + "...");
+    JMenuItem extractScores = new JMenuItem(
+            MessageManager.getString("label.extract_scores") + "...");
     extractScores.addActionListener(new ActionListener()
     {
       @Override
@@ -1852,8 +1701,9 @@ public class GAlignFrame extends JInternalFrame
 
     // for show products actions see AlignFrame.canShowProducts
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-    openFeatureSettings.setText(MessageManager
-            .getString("label.feature_settings"));
+
+    JMenuItem openFeatureSettings = new JMenuItem(
+            MessageManager.getString("label.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
       @Override
@@ -1862,8 +1712,8 @@ public class GAlignFrame extends JInternalFrame
         featureSettings_actionPerformed(e);
       }
     });
-    fetchSequence
-            .setText(MessageManager.getString("label.fetch_sequences"));
+    JMenuItem fetchSequence = new JMenuItem(
+            MessageManager.getString("label.fetch_sequences"));
     fetchSequence.addActionListener(new ActionListener()
     {
       @Override
@@ -1873,8 +1723,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColour.setText(MessageManager
-            .getString("action.by_annotation"));
+    JMenuItem annotationColour = new JMenuItem(
+            MessageManager.getString("action.by_annotation"));
     annotationColour.addActionListener(new ActionListener()
     {
       @Override
@@ -1884,8 +1734,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColumn.setText(MessageManager
-            .getString("action.select_by_annotation"));
+    JMenuItem annotationColumn = new JMenuItem(
+            MessageManager.getString("action.select_by_annotation"));
     annotationColumn.addActionListener(new ActionListener()
     {
       @Override
@@ -1906,8 +1756,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    associatedData.setText(MessageManager
-            .getString("label.load_features_annotations"));
+    JMenuItem associatedData = new JMenuItem(
+            MessageManager.getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
     {
       @Override
@@ -1961,9 +1811,10 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    addSequenceMenu
-            .setText(MessageManager.getString("label.add_sequences"));
-    addFromFile.setText(MessageManager.getString("label.from_file"));
+    JMenu addSequenceMenu = new JMenu(
+            MessageManager.getString("label.add_sequences"));
+    JMenuItem addFromFile = new JMenuItem(
+            MessageManager.getString("label.from_file"));
     addFromFile.addActionListener(new ActionListener()
     {
       @Override
@@ -1972,7 +1823,8 @@ public class GAlignFrame extends JInternalFrame
         addFromFile_actionPerformed(e);
       }
     });
-    addFromText.setText(MessageManager.getString("label.from_textbox"));
+    JMenuItem addFromText = new JMenuItem(
+            MessageManager.getString("label.from_textbox"));
     addFromText.addActionListener(new ActionListener()
     {
       @Override
@@ -1981,7 +1833,8 @@ public class GAlignFrame extends JInternalFrame
         addFromText_actionPerformed(e);
       }
     });
-    addFromURL.setText(MessageManager.getString("label.from_url"));
+    JMenuItem addFromURL = new JMenuItem(
+            MessageManager.getString("label.from_url"));
     addFromURL.addActionListener(new ActionListener()
     {
       @Override
@@ -1990,8 +1843,8 @@ public class GAlignFrame extends JInternalFrame
         addFromURL_actionPerformed(e);
       }
     });
-    exportFeatures.setText(MessageManager
-            .getString("label.export_features"));
+    JMenuItem exportFeatures = new JMenuItem(
+            MessageManager.getString("label.export_features"));
     exportFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -2000,8 +1853,8 @@ public class GAlignFrame extends JInternalFrame
         exportFeatures_actionPerformed(e);
       }
     });
-    exportAnnotations.setText(MessageManager
-            .getString("label.export_annotations"));
+    JMenuItem exportAnnotations = new JMenuItem(
+            MessageManager.getString("label.export_annotations"));
     exportAnnotations.addActionListener(new ActionListener()
     {
       @Override
@@ -2010,9 +1863,9 @@ public class GAlignFrame extends JInternalFrame
         exportAnnotations_actionPerformed(e);
       }
     });
-    statusPanel.setLayout(gridLayout1);
-    showMenu.setText(MessageManager.getString("action.show"));
-    showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
+    statusPanel.setLayout(new GridLayout());
+    JMenuItem showAllSeqs = new JMenuItem(
+            MessageManager.getString("label.all_sequences"));
     showAllSeqs.setToolTipText(MessageManager
             .getString("label.toggle_sequence_visibility"));
     showAllSeqs.addActionListener(new ActionListener()
@@ -2023,7 +1876,8 @@ public class GAlignFrame extends JInternalFrame
         showAllSeqs_actionPerformed(e);
       }
     });
-    showAllColumns.setText(MessageManager.getString("label.all_columns"));
+    JMenuItem showAllColumns = new JMenuItem(
+            MessageManager.getString("label.all_columns"));
     showAllColumns.setToolTipText(MessageManager
             .getString("label.toggle_columns_visibility"));
     showAllColumns.addActionListener(new ActionListener()
@@ -2034,9 +1888,9 @@ public class GAlignFrame extends JInternalFrame
         showAllColumns_actionPerformed(e);
       }
     });
-    hideMenu.setText(MessageManager.getString("action.hide"));
-    hideSelSequences.setText(MessageManager
-            .getString("label.selected_sequences"));
+    JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
+    JMenuItem hideSelSequences = new JMenuItem(
+            MessageManager.getString("label.selected_sequences"));
     hideSelSequences.setToolTipText(MessageManager
             .getString("label.toggle_sequence_visibility"));
     hideSelSequences.addActionListener(new ActionListener()
@@ -2047,8 +1901,8 @@ public class GAlignFrame extends JInternalFrame
         hideSelSequences_actionPerformed(e);
       }
     });
-    hideSelColumns.setText(MessageManager
-            .getString("label.selected_columns"));
+    JMenuItem hideSelColumns = new JMenuItem(
+            MessageManager.getString("label.selected_columns"));
     hideSelColumns.setToolTipText(MessageManager
             .getString("label.toggle_columns_visibility"));
     hideSelColumns.addActionListener(new ActionListener()
@@ -2059,8 +1913,8 @@ public class GAlignFrame extends JInternalFrame
         hideSelColumns_actionPerformed(e);
       }
     });
-    hideAllSelection.setText(MessageManager
-            .getString("label.selected_region"));
+    JMenuItem hideAllSelection = new JMenuItem(
+            MessageManager.getString("label.selected_region"));
     hideAllSelection.addActionListener(new ActionListener()
     {
       @Override
@@ -2070,8 +1924,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     // TODO: should be hidden if no selection exists.
-    hideAllButSelection.setText(MessageManager
-            .getString("label.all_but_selected_region"));
+    JMenuItem hideAllButSelection = new JMenuItem(
+            MessageManager.getString("label.all_but_selected_region"));
     hideAllButSelection.addActionListener(new ActionListener()
     {
       @Override
@@ -2080,8 +1934,8 @@ public class GAlignFrame extends JInternalFrame
         hideAllButSelection_actionPerformed(e);
       }
     });
-    showAllhidden.setText(MessageManager
-            .getString("label.all_sequences_columns"));
+    JMenuItem showAllhidden = new JMenuItem(
+            MessageManager.getString("label.all_sequences_columns"));
     showAllhidden.setToolTipText(MessageManager
             .getString("label.toggles_visibility_hidden_selected_regions"));
     showAllhidden.addActionListener(new ActionListener()
@@ -2103,8 +1957,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    invertColSel.setText(MessageManager
-            .getString("action.invert_column_selection"));
+    JMenuItem invertColSel = new JMenuItem(
+            MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.ALT_MASK, false);
@@ -2155,7 +2009,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    save.setText(MessageManager.getString("action.save"));
+    JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -2179,7 +2033,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    newView.setText(MessageManager.getString("action.new_view"));
+    JMenuItem newView = new JMenuItem(
+            MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -2195,8 +2050,8 @@ public class GAlignFrame extends JInternalFrame
     tabbedPane.setToolTipText("<html><i>"
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
-    textColour.setText(MessageManager.getString("label.colour_text")
-            + "...");
+    JMenuItem textColour = new JMenuItem(
+            MessageManager.getString("label.colour_text") + "...");
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2206,7 +2061,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     formatMenu.setText(MessageManager.getString("action.format"));
-    selectMenu.setText(MessageManager.getString("action.select"));
+    JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
     idRightAlign.setText(MessageManager
             .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
@@ -2244,8 +2099,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
 
-    pageSetup
-            .setText(MessageManager.getString("action.page_setup") + "...");
+    JMenuItem pageSetup = new JMenuItem(
+            MessageManager.getString("action.page_setup") + "...");
     pageSetup.addActionListener(new ActionListener()
     {
       @Override
@@ -2254,8 +2109,8 @@ public class GAlignFrame extends JInternalFrame
         pageSetup_actionPerformed(e);
       }
     });
-    alignmentProperties.setText(MessageManager
-            .getString("label.alignment_props") + "...");
+    JMenuItem alignmentProperties = new JMenuItem(
+            MessageManager.getString("label.alignment_props") + "...");
     alignmentProperties.addActionListener(new ActionListener()
     {
       @Override
@@ -2264,10 +2119,14 @@ public class GAlignFrame extends JInternalFrame
         alignmentProperties();
       }
     });
-    tooltipSettingsMenu.setText(MessageManager
-            .getString("label.sequence_id_tooltip"));
-    autoAnnMenu.setText(MessageManager
-            .getString("label.autocalculated_annotation"));
+    JMenu tooltipSettingsMenu = new JMenu(
+            MessageManager.getString("label.sequence_id_tooltip"));
+    JMenu autoAnnMenu = new JMenu(
+            MessageManager.getString("label.autocalculated_annotation"));
+
+    JMenu exportImageMenu = new JMenu(
+            MessageManager.getString("label.export_image"));
+    JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
@@ -2288,10 +2147,10 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(pageSetup);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
-    fileMenu.add(jMenu2);
+    fileMenu.add(exportImageMenu);
     fileMenu.add(exportFeatures);
     fileMenu.add(exportAnnotations);
-    fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
@@ -2314,6 +2173,7 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.add(justifyRightMenuItem);
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
+
     viewMenu.add(newView);
     viewMenu.add(expandViews);
     viewMenu.add(gatherViews);
@@ -2323,6 +2183,18 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(showComplementMenuItem);
     viewMenu.addSeparator();
     viewMenu.add(followHighlightMenuItem);
+    viewMenu.addSeparator();
+    viewMenu.add(showSeqFeatures);
+    // viewMenu.add(showSeqFeaturesHeight);
+    viewMenu.add(openFeatureSettings);
+    tooltipSettingsMenu.add(showDbRefsMenuitem);
+    tooltipSettingsMenu.add(showNpFeatsMenuitem);
+    viewMenu.add(tooltipSettingsMenu);
+    viewMenu.addSeparator();
+    viewMenu.add(alignmentProperties);
+    viewMenu.addSeparator();
+    viewMenu.add(overviewMenuItem);
+
     annotationsMenu.add(annotationPanelMenuItem);
     annotationsMenu.addSeparator();
     annotationsMenu.add(showAllAlAnnotations);
@@ -2344,18 +2216,7 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
-    viewMenu.addSeparator();
-    viewMenu.add(showSeqFeatures);
-    // viewMenu.add(showSeqFeaturesHeight);
 
-    viewMenu.add(openFeatureSettings);
-    tooltipSettingsMenu.add(showDbRefsMenuitem);
-    tooltipSettingsMenu.add(showNpFeatsMenuitem);
-    viewMenu.add(tooltipSettingsMenu);
-    viewMenu.addSeparator();
-    viewMenu.add(alignmentProperties);
-    viewMenu.addSeparator();
-    viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
     colourMenu.add(textColour);
     colourMenu.addSeparator();
@@ -2405,11 +2266,11 @@ public class GAlignFrame extends JInternalFrame
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
     sort.add(sortByTreeMenu);
-    jMenu2.add(htmlMenuItem);
-    jMenu2.add(epsFile);
-    jMenu2.add(createPNG);
-    jMenu2.add(createBioJS);
-    jMenu2.add(createSVG);
+    exportImageMenu.add(htmlMenuItem);
+    exportImageMenu.add(epsFile);
+    exportImageMenu.add(createPNG);
+    exportImageMenu.add(createBioJS);
+    exportImageMenu.add(createSVG);
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
@@ -2942,7 +2803,7 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
 
   }