{
// TODO consider using AlignmentView to prune to visible region
// TODO prune sequence annotation and groups to visible region
+ // TODO: JAL-1486 - set start and end for output correctly. basically, AlignmentView.getVisibleContigs does this.
Alignment alv = new Alignment(replaceStrings(
alignment.getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();