JAL-1152 menu tweaks plus new option to put Autocalc at top or below.

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index dd21819..d610931 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -741,7 +741,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void paintAlignment(boolean updateOverview)
   {
-    new AnnotationSorter(getAlignment()).sort(getAlignment()
+    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+            av.isShowAutocalculatedAbove());
+    sorter.sort(getAlignment()
             .getAlignmentAnnotation(),
             av.getSortAnnotationsBy());
     repaint();