JAL-3081 autocalculated annotation first/last leaves others unchanged

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index aba1e3d..b27d66d 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -826,13 +826,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * if currently set to 'Custom' (manual) ordering.
    */
   @Override
-  public void sortAnnotations()
+  public void sortAnnotations(boolean autoCalcOnly)
   {
     SequenceAnnotationOrder sortBy = av.getSortAnnotationsBy();
     if (sortBy != SequenceAnnotationOrder.CUSTOM)
     {
       final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
-              av.isShowAutocalculatedAbove());
+              av.isShowAutocalculatedAbove(), autoCalcOnly);
       sorter.sort(getAlignment().getAlignmentAnnotation(), sortBy);
     }
   }