- // Replace all internal gaps with . and external spaces with ~
- s[i] = new Sequence(sqs[i].getName(), sqs[i].getSequenceAsString()
- .replace('-', '.'), sqs[i].getStart(), sqs[i].getEnd());
+ /*
+ * modify to MSF format: uses '.' for internal gaps,
+ * and '~' for leading or trailing gaps
+ */
+ String seqString = sqs[i].getSequenceAsString().replace('-', '.');