* 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);
}
}