[Biojava-l] Blast xml parser question -- new to Biojava

[Richard HOLLAND]

See http://biojava.org/docs/bj_in_anger/BlastParser.htm

Currently only a partial mapping is returned by the default parser. To
get full results you have to write your own SearchContentHandler to give
to the blast parser, an outline of which is given at
http://biojava.org/docs/bj_in_anger/blastecho.htm

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Renee Halbrook
> Sent: Friday, August 19, 2005 5:51 AM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Blast xml parser question -- new to Biojava
> 
> 
> Hi,
> I am pretty new to Biojava. I am trying to use the
> blast xml parser. (Specifically, I am using
> org.biojava.bio.program.sax.blastxml.BlastParserFacade
> in biojava v1.4 )
> Is it possible to get the accession number from blast
> output? (equivalent to <Hit_accession> in results.xml
> from blast results)  
> Is there another class that I should be using,
> instead, that provides a more complete mapping of the
> xml file?
> Is there a resource on advice on how to extend this
> class,  to give more specific results?
> 
> Thanks in advance for any help on this.
> 
> Regards,
> Renee Halbrook
> 
> 
> 
> 		
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