[Biojava-dev] NCBI-Blast 2.2.6

[Schreiber, Mark]

Yah for NCBI breaking their output again!!!

As a temporary measure you might want to take a look at the BlastXML
parser in biojava-live. There have been a few posts on the list about it
recently but I think it is up and running? Any comments on this David?

- Mark


> -----Original Message-----
> From: Osborne, John [mailto:jko1 at cdc.gov] 
> Sent: Thursday, 3 July 2003 8:15 a.m.
> To: 'biojava-dev at biojava.org'
> Subject: [Biojava-dev] NCBI-Blast 2.2.6
> 
> 
> Hi,
> 
> Is anyone (Greg Cox?) working on a 2.2.6 NCBI Blast 
> compatible BlastLikeSaxParser?  
> 
> I thought I could take a nice biojava shortcut this afternoon 
> to help with a blast parsing problem and ran into the 
> versioning issue.  Tried with lazy mode, but no luck.  It 
> died with a null pointer exception in 
> HitSectionSAXParser.firstHSPEvent (298) which is strange 
> since I think it should have found the "Database:" tag which 
> is in the 2.2.6 version.  I'm not sure at this point whether 
> it is worth getting in the biojava source code or modifying 
> an old blast parser of my own.  Any suggestions appreciated.
> 
>  -John
> 
> 
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> 
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