[Biojava-l] Adventures in BlastLikeSax parsing

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Tue, 20 Mar 2001 09:42:56 +0000

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?


> 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


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

Let me know how you get on.

Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK