JAL-819 menu options to reinstate missing auto-calculated annotation

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 075b490..63bc050 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -207,6 +207,12 @@ public class GAlignFrame extends JInternalFrame
 
   private SplitContainerI splitFrame;
 
+  protected JMenu autoAnnMenu;
+
+  protected JRadioButtonMenuItem showAutoFirst;
+
+  protected JRadioButtonMenuItem showAutoLast;
+
   public GAlignFrame()
   {
     try
@@ -875,9 +881,9 @@ public class GAlignFrame extends JInternalFrame
     });
 
     ButtonGroup buttonGroup = new ButtonGroup();
-    final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
+    showAutoFirst = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_first"));
-    final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
+    showAutoLast = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_last"));
     buttonGroup.add(showAutoFirst);
     buttonGroup.add(showAutoLast);
@@ -1709,7 +1715,7 @@ public class GAlignFrame extends JInternalFrame
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
-    JMenu autoAnnMenu = new JMenu(
+    autoAnnMenu = new JMenu(
             MessageManager.getString("label.autocalculated_annotation"));
 
     JMenu exportImageMenu = new JMenu(
@@ -1805,17 +1811,7 @@ public class GAlignFrame extends JInternalFrame
     annotationsMenu.add(sortAnnBySequence);
     annotationsMenu.add(sortAnnByLabel);
     annotationsMenu.addSeparator();
-    autoAnnMenu.add(showAutoFirst);
-    autoAnnMenu.add(showAutoLast);
-    autoAnnMenu.addSeparator();
-    autoAnnMenu.add(applyAutoAnnotationSettings);
-    autoAnnMenu.add(showConsensusHistogram);
-    autoAnnMenu.add(showSequenceLogo);
-    autoAnnMenu.add(normaliseSequenceLogo);
-    autoAnnMenu.addSeparator();
-    autoAnnMenu.add(showGroupConservation);
-    autoAnnMenu.add(showGroupConsensus);
-    annotationsMenu.add(autoAnnMenu);
+    annotationsMenu.add(autoAnnMenu); // autoAnnMenu is populated later
 
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);