[Biojava-dev] blast parsing continued

[Doug Rusch]

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

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -