[Biojava-l] BLAST Parser in Anger!

[Schreiber, Mark]

Hi -

There are some deficiencies in the blast parsing API. I know that there
is some reluctance to add new methods to the interface as things will
break, however blast parsing is a core task and it would be v good if we
could make this more functional. One way to get around the interface
thing is to simlply extend it and then make all the classes we have now
implement the extended interface.

Another way is to simply break the interface before bj1.3 is released
and make it stable from there on.

Can we please, please sort this out before bj1.3 is released? Perhaps
the development team could get together over a beer at the hackathon and
nut this one out. It really can't be that hard can it?

Hear endeth the sermon.

- Mark

> -----Original Message-----
> From: staatsb [mailto:staatsb at mail.nih.gov] 
> Sent: Tuesday, 28 January 2003 6:19 a.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] BLAST Parser in Anger!
> 
> 
> I was successful in getting the BLAST parser to work outlined by the 
> "BioJava in Anger" doc by changing the version number too 
> 2.0.11 (thank 
> you Mark Schreiber X2).  However, a few of the APIs dont seem to 
> function i.e.  getSequenceID() is not recognized, but I dont think 
> thats due to the version change.  Also, I have noticed many API calls 
> to certain BLAST file features missing i.e. getQueryID, getGaps, 
> getQuerySequence, getSubjectSequence, and more.  Are these really 
> missing or does the programmer (me) need to define them from the APIs 
> existing  structure?  Has anyone else been able to obtain these 
> features with the missing APIs?  Can anyone offer any advise, 
> suggestions, explanations, etc, to these issues?
> 
> Thanks
> 
> Brian Staats
> Bioinformatics Programmer Analyst
> NIH/NCI/Core Genotyping Facility
> staatsb at mail.nih.gov
> 
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