+ AlignmentI newAl = new Alignment(seqs);
+ if (stoLocation != null)
+ {
+ for (AlignmentAnnotation annot : al.getAlignmentAnnotation())
+ {
+ if (annot.label.contains("Reference") || "RF".equals(annot.label))
+ {
+ newAl.addAnnotation(annot);
+ }
+ }
+ }
+ StockholmFile file = new StockholmFile(newAl);