[Biojava-dev] RE: [Biojava-l] BLAST Parser in Anger!

[Schreiber, Mark]

Hi -

I don't think the problems are deepseated. Actually the BlastParsing API
is really good. Basically if we can add appropriate accessor methods for
all the info available in the BlastLikeDataCollection.dtd then the API
will pretty much do everything you could want.

The other option would be to write a SAX parser for the new NCBI blast
dtd. This might be a bit of a major overhaul but it could be a nice
standardization.

I think it would be worth delaying 1.3 till we get this fully
functional.

- Mark


> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk] 
> Sent: Tuesday, 28 January 2003 11:00 p.m.
> To: Schreiber, Mark
> Cc: staatsb; biojava-l at biojava.org; biojava-dev at biojava.org
> Subject: Re: [Biojava-l] BLAST Parser in Anger!
> 
> 
> 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
> >>
> >>_______________________________________________
> >>Biojava-l mailing list  -  Biojava-l at biojava.org
> >>http://biojava.org/mailman/listinfo/biojava-l
> >>
> > 
> > 
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