[Biojava-l] Parsing ClustalW output

[Simon Brocklehurst]

Johan Hattne wrote:

> Hi, all.
>
> Has anybody had any luck in parsing output from ClustalW using biojava's
> ClustalWAlignmentSAXParser? I can get it to return the sequences' names,
> but I'm hoping to get at the sequence's symbols. I've looped through the
> attribute lists sent to my handler's startElement() method, but there only
> seems to be one attribute: the name.

Hi Johan,

*Hopefully*, this is an easy one to solve.  The sequence symbols themselves are
returned as PCDATA - i.e. they aren't returned as attributes.  You can get at the
PCData in the characters method (as opposed to the startElement method) in your
ContentHandler.

Let me know if it works.

Simon
--
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