Have you tried parsing the XML output. While the text parser does 'fake' XML by emitting SAX events I think that the XML parser may be a lot more stable (the XML output of blast is more stable, at least recently anyway).
I know this isn't the best solution to your problem but the default text output of BLAST is not the most parseable. In fact it is probably the least machine readable of all the blast outputs and definitely the least stable. - Mark On Sun, Jan 25, 2009 at 7:54 PM, Charles Imbusch <[email protected]> wrote: > > Hello Mark, > > same here. I'm parsing plain text output. > > Cheers, > Charles > > Mark Schreiber schrieb: >> >> Is this XML parsing or blast text output? >> >> - Mark _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
