// use the following regex to decide an annotations (whole) line is NOT an RNA
// SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
private static final Regex NOT_RNASS = new Regex(
- "^[^<>[\\](){}A-DF-Za-df-z]*$");
+ "^[^<>[\\](){}ADFJ-RUVWYZadfj-ruvwyz]*$");
StringBuffer out; // output buffer
if (!r.search(nextLine()))
{
throw new IOException(MessageManager
- .getString("exception.stockholm_invalid_format"));
+ .getString("exception.stockholm_invalid_format") +" ("+r+")");
}
else
{