}
/**
- * create sequences with each seuqence string replaced with the one given in
+ * create sequences with each sequence string replaced with the one given in
* omitHiddenCOlumns
*
* @param seqs
{
if (omitHidden != null)
{
- //
+ // TODO consider using AlignmentView to prune to visible region
+ // TODO prune sequence annotation and groups to visible region
Alignment alv = new Alignment(replaceStrings(
alignment.getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();