[Biojava-l] ACeDB?

[Thomas Down]

On Wed, Jan 26, 2000 at 06:31:12PM +0000, Ewan Birney wrote:
> On Wed, 26 Jan 2000, Matthew Pocock wrote:
> 
> > Mike,
> > Hope that helps. Does anybody else have a view on this?
> 
> That it shouldn't be in the "core" biojava stuff perhaps ;)

No, sure, it's not core code in the same way as the sequence
interfaces.  But I would like to see BioJava interfaces for
interacting with as many different tools as possible -- some
classes for invoking/parsing Blast and friends would be nice,
too.

That said, once the codebase is settling down a bit, it might
be worth looking into setting up some CVS modules, so you
can do something like
  
  cvs co BiojavaCore

if you ONLY want things like Sequence interaces.


Incidentally, for anyone who's interested in the ACeDB stuff,
I'm afraid the backend driver (in org.biojava.bio.acedb.socket)
isn't working right now.  Once the TCP/IP socket transport in
the ACeDB server has settled down (hopefully in a week or two)
I'll update the driver, and it should all start working.
In the meantime, I'd be interested to know what other ACeDB
users (especially people who've heavily used AcePerl) think
of the interfaces in org.biojava.bio.acedb.*

Thomas.
-- 
``Science is magic that works''  -- Kurt Vonnegut.