// 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
{
}
}
- // output annotations
+ // output description and annotations
+
while (i < slen && (seq = s[i]) != null)
{
+ if (seq.getDescription()!=null)
+ {
+ // out.append("#=GR ");
+ out.append(new Format("%-" + maxid + "s").form(
+ "#=GS " + printId(seq, jvSuffix) + " DE " + seq.getDescription()));
+ out.append(newline);
+ }
+
AlignmentAnnotation[] alAnot = seq.getAnnotation();
if (alAnot != null)
{