[Biojava-l] Adventures in BlastLikeSax parsing

[Schreiber, Mark]

Hi,

How much varience is there between blast versions and how well does the
SaxLikeBlastParser cope? Is there a way to produce a "standard" blast
output?

Mark

> -----Original Message-----
> From: Simon Brocklehurst
> [mailto:simon.brocklehurst@CambridgeAntibody.com]
> Sent: Tuesday, March 20, 2001 9:43 PM
> To: Schreiber, Mark
> Cc: 'Biojava-L (E-mail)
> Subject: Re: [Biojava-l] Adventures in BlastLikeSax parsing
> 
> 
> 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-liv
e/dtd/BlastLikeDataSetCollection.dtd?rev=1.2&content-type=text/vnd.viewcvs-m
arkup&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