r = new Regex("# STOCKHOLM ([\\d\\.]+)");
if (!r.search(nextLine()))
{
- throw new IOException(MessageManager
- .getString("exception.stockholm_invalid_format"));
+ throw new IOException(
+ MessageManager.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)
{