[Biojava-l] BLAST Parser in Anger!

[Matthew Pocock]

Please, let's get it right b4 1.3 goes live - I know we're meant to be 
only making small changes now, but blast parsing is so important that 
it's worth doing properly.

Mark, do you have a list of methods you want added/removed/renamed, or 
are the problems more deep-seated than that?

Matthew

Schreiber, Mark wrote:
> 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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>>Biojava-l mailing list  -  Biojava-l at biojava.org 
>>http://biojava.org/mailman/listinfo/biojava-l
>>
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