public void sort(AlignmentAnnotation[] alignmentAnnotations,
SequenceAnnotationOrder order)
{
public void sort(AlignmentAnnotation[] alignmentAnnotations,
SequenceAnnotationOrder order)
{
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);
// cache 'alignment sequence position' for the annotations
saveSequenceIndices(alignmentAnnotations);