[Biojava-dev] blast parsing continued

[Doug Rusch]

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
Cambridgeshire
SG8 6JJ, UK

Telephone: + 44 (0) 1763 263233
Facsimile + 44 (0) 1763 263413
Email: mailto:simon.brocklehurst@cambridgeantibody.com
http://www.cambridgeantibody.com

Cambridge Antibody Technology Limited *
Registered Office: The Science Park, Melbourn, Cambridgeshire,
SG8 6JJ, UK. Registered in England and Wales number 2451177
(* Cambridge Antibody Technology Limited is a member of the
Cambridge Antibody Technology Group of Companies)

Confidentiality Note: This information and any attachments is
confidential and only for use by the individual or entity to
whom it has been sent. Any unauthorised dissemination,
distribution or copying of this message is strictly prohibited.
If you are not the intended recipient please inform the sender
immediately by reply e-mail and delete this message from your system.
Thank you for your co-operation.