[Biojava-dev] blast parsing continued

[Schreiber, Mark]

Hi -

Is it possible to have it as an alternative model? EG for biojava 1.3 we
could have 2 blast parsing alternatives and possibly one could
gracefully give way when and if we release biojava2.

I don't see anything wrong with having 2 approaches, look at SAX and DOM
from the XML world. Put them both in and let them duke it out :)
Ultimately the users will use which ever one is more appropriate. If
everyone stops using one and starts using the new on then we can drop
it.

- Mark

> -----Original Message-----
> From: Doug Rusch [mailto:drusch@tcag.org] 
> Sent: Tuesday, 19 November 2002 11:23 a.m.
> To: Simon Brocklehurst; smh1008@cus.cam.ac.uk
> Cc: biojava-dev@biojava.org
> Subject: RE: [Biojava-dev] blast parsing continued
> 
> 
> I agree that checking in the code I have now is a problem. 
> Breaking the HMMer, FASTA, and possibly wu-blast parser would 
> be very bad, not to mention that it requires java 1.4. Short 
> of overhauling all the existing tool parsers, there are only 
> a few options that I can see
> 
> 1) branching
> 2) creating new packages parallel to the existing parsing code
>    (search/ssbind/sax)
> 3) starting a code base for BioJava 2
> 
> I would like to make my code available for the community to 
> look at, test, and comment on but not at the inconvience of a 
> large number of biojava's users. Is there a prefered solution?
> 
> Doug Rusch, PhD
> TCAG.org
> 
> -----Original Message-----
> From:	Simon Brocklehurst 
> [mailto:simon.brocklehurst@CambridgeAntibody.com]
> Sent:	Mon 11/18/02 6:37 AM
> To:	smh1008@cus.cam.ac.uk
> Cc:	Doug Rusch; biojava-dev@biojava.org
> Subject:	Re: [Biojava-dev] blast parsing continued
> David Huen wrote:
> > 
> > On Friday 15 Nov 2002 7:28 pm, Doug Rusch wrote:
> > It would seem to me that the safer though perhaps less 
> elegant option 
> > would be to develop it such that the existing DTD is a 
> subset of a new 
> > interim DTD proposal in which you introduce new elements 
> that pass the 
> > additional information you propose.  I believe CAT uses the 
> existing 
> > parsers inhouse as may perhaps others and it does seem an 
> > inappropriate time for drastic action on the parsing package.
> 
> Please don't worry about CAT - we maintain separate code 
> bases for our in-house projects versus code we contribute to 
> Open Source projects. Thus we are entirely safe in the 
> knowledge that people cannot break our systems as a result of 
> the design choices they make.
> 
> Introducing changes to a software framework that are 
> incompatible with previous versions is not usually a design 
> choice that should be be taken lightly.  If you break 
> peoples' code, they are unlikely to thank you for it.  It 
> takes time to build credibility in this area.
> 
> > On another note, is there a statement in the current DTD 
> licensing us 
> > to use it?
> 
> If there isn't, this is an omission in error - it should have 
> the standard LGPL header.  We made the DTD avaiable to the 
> biojava community so that it was in full control of any and 
> all changes.
> 
> Simon
> --
> Dr Simon M. Brocklehurst, Ph.D.
> Director of Informatics & Robotics
> 
> Cambridge Antibody Technology
> The Science Park
> Melbourn
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> 
> Telephone: + 44 (0) 1763 263233
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> Email: mailto:simon.brocklehurst@cambridgeantibody.com
> http://www.cambridgeantibody.com
> 
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