X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=9491d33c30b90cc03001a61884db502290a1e899;hb=202e77bdd4533a7cfa409eb91de58d31e3d1135f;hp=3aebcda54ec76d0bceb6e9ee25f18e6c9a7fc490;hpb=549275b6bba6105f8c3b1fff191c01643111e622;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 3aebcda..9491d33 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -601,12 +601,9 @@ public class GAlignFrame extends JInternalFrame
         hideAllAnnotations_actionPerformed(true, false);
       }
     });
-    SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
-            .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
-                    SequenceAnnotationOrder.NONE.name()));
-    sortAnnBySequence = new JCheckBoxMenuItem(
+    sortAnnBySequence = new JMenuItem(
             MessageManager.getString("label.sort_annotations_by_sequence"));
-    sortAnnByLabel = new JCheckBoxMenuItem(
+    sortAnnByLabel = new JMenuItem(
             MessageManager.getString("label.sort_annotations_by_label"));
 
     sortAnnBySequence.addActionListener(new ActionListener()
@@ -615,7 +612,7 @@ public class GAlignFrame extends JInternalFrame
       public void actionPerformed(ActionEvent e)
       {
         setAnnotationSortOrder(SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
-        sortAnnotations();
+        sortAnnotations(false);
       }
     });
     sortAnnByLabel.addActionListener(new ActionListener()
@@ -624,7 +621,7 @@ public class GAlignFrame extends JInternalFrame
       public void actionPerformed(ActionEvent e)
       {
         setAnnotationSortOrder(SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
-        sortAnnotations();
+        sortAnnotations(false);
       }
     });
     colourTextMenuItem = new JCheckBoxMenuItem(
@@ -882,7 +879,7 @@ public class GAlignFrame extends JInternalFrame
       {
         if (setShowAutoCalculatedAbove(showAutoFirst.isSelected()))
         {
-          sortAnnotations();
+          sortAnnotations(true);
         }
       }
     });
@@ -894,7 +891,7 @@ public class GAlignFrame extends JInternalFrame
       {
         if (setShowAutoCalculatedAbove(!showAutoLast.isSelected()))
         {
-          sortAnnotations();
+          sortAnnotations(true);
         }
       }
     });
@@ -2012,11 +2009,12 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
-   * Action on clicking sort annotations by type.
+   * Action on clicking sort annotations by type, or change position of
+   * autocalculated annotation
    * 
-   * @param sortOrder
+   * @param autoCalcOnly
    */
-  protected void sortAnnotations()
+  protected void sortAnnotations(boolean autoCalcOnly)
   {
   }