[Biojava-l] Adventures in BlastLikeSax parsing

[Simon Brocklehurst]

Hi Mark,

"Schreiber, Mark" wrote:

> Hi,
>
> Am I correct in thinking that to parse a blast output all I need to do is
> make a content handler by extending default handler and defining
> characters(), startElement() and endElement?

Absolutely.

> Also can any of the Qnames in BlastSAXParser be used for an
> Attribute.getValue(String s) method?

I'm not sure I understand your question.  You can certainly use
Attribute.getValue(String s) to get values of attributes with given names.

> Is there a complete list of Qnames that
> can be used?

There is a DTD which descibies all the Elements and Attributes reported by the
parser:

http://cvs.biojava.org/cgi-bin/viewcvs/viewcvs.cgi/biojava-live/dtd/BlastLikeDataSetCollection.dtd?rev=1.2&content-type=text/vnd.viewcvs-markup&cvsroot=biojava

Another good way to get a handle on the output is to run the BlastLike2XML
application in the demos section - this will convert your Blast output file to
XML.

Let me know how you get on.

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