*/
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();