[Biojava-dev] blast parsing continued

[David Huen]

Could I have a copy of whatever DTD you might settle upon please?

I have a NCBI Blast XML parser that I use that I'd like to check in and an 
adaptor to implement to make the events match those expected by downstream 
builders.

Regards,
David Huen

On Friday 15 Nov 2002 3:01 pm, Doug Rusch wrote:
> Well a rollback would make me happier :) Branching would also be
> an option. If branching is too messy, it might be worth while
> to circulate my current DTD through the biojava-dev mailing list
> for comments. What do you think?
>
> Doug
>
> -----Original Message-----
> From: Keith James [mailto:kdj@sanger.ac.uk]
> Sent: Friday, November 15, 2002 4:20 AM
> To: Doug Rusch
> Cc: biojava-dev@biojava.org
> Subject: Re: [Biojava-dev] blast parsing continued
>
> >>>>> "Doug" == Doug Rusch <drusch@tcag.org> writes:
>
>     Doug> I have no problem adding my solution to the repository
>     Doug> however I dont have the permissions to do that. Also, I
>     Doug> should point out that the changes have rather large
>     Doug> consequences.  I like the design for the StAX based parsing
>     Doug> but to maintain that design requires adding the defline and
>     Doug> length of the query and subject sequence requires changing
>     Doug> the DTD. Such changes ripple outwards till most of the
>     Doug> parsing code has to be modified. I am still not satisfied
>     Doug> with the DTD and need to add components that would be
>     Doug> optional (such as the stats collected at the end of the
>     Doug> blast report).
>
> [...]
>
> Hi Doug,
>
> I can see the issues involved. Perhaps the best thing I can do right
> now is to roll back the interface (& related) changes I made, if we
> are agreed that the SequenceDB route is the best way. This would be
> necessary whatever happens. I'm more convinced about that approach
> now. The design was right, it was just my implementation which sucked
>
> :)
>
> Keith

-- 

David Huen, Ph.D.              Email: smh1008@cus.cam.ac.uk
Dept. of Genetics              Fax  : +44 1223 333992
University of Cambridge        Phone: +44 1223 333982/766478
Cambridge, CB2 3UH
U.K.