[Biojava-l] SAX2 support for Fasta

[Simon Brocklehurst]

Keith James wrote:

> Inspired by the bootcamp, I've added a SAX2 event emitter for Fasta
> searches. This may be used in the same way as the others. It's backed
> by the same Fasta parser as the
> org.biojava.bio.program.search.FastaSearchBuilder, i.e. uses 'm 10'
> output.

Excellent!

> Thanks to the CAT team for making implementing this a relatively
> painless task for an XML novice.
>
> There's a Fasta2XML demo in demos/eventbasedparsing which I used to
> generate an XML file. I verified this against the DTD using Xerces and
> it's fine, apart from the biojava:HitId elements having whitespace in
> them:
>
> [Error] foo.xml:835:26: The content of element type "biojava:HitId"
> must match "EMPTY"
>
> It think this is just the SimpleXMLEmitter not calling the
> writeEmptyElement() methods. The Blast XML output has the same symptom.

I'll try to take a look at this, but if you're in the mood for fixing it
don't let me stop you ;-)

S.
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com