JAL-3081 autocalculated annotation first/last leaves others unchanged

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 3aebcda..7caf7ea 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -601,9 +601,6 @@ public class GAlignFrame extends JInternalFrame
         hideAllAnnotations_actionPerformed(true, false);
       }
     });
-    SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
-            .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
-                    SequenceAnnotationOrder.NONE.name()));
     sortAnnBySequence = new JCheckBoxMenuItem(
             MessageManager.getString("label.sort_annotations_by_sequence"));
     sortAnnByLabel = new JCheckBoxMenuItem(
@@ -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)
   {
   }