On Mon, 30 Jul 2001, David Huen wrote: > On Mon, 30 Jul 2001, Thomas Down wrote: > > > On Mon, Jul 30, 2001 at 01:48:57PM +0100, Ewan Birney wrote: > > > > > > > David, have you looked at the BPDB schema? How welll do you > > think it meets your needs? > > > I haven't looked at the BPDB schema yet, I'll try to do that this evening. > To save me navigating thru a framework for a package in a language I don't > understand, do you have a URL to the relevant SQL schema please? check out bioperl-db from anonymous cvs and then the sql/basic-mysqldb.sql I'll send it to you. > > Will Ewan and you be down at the Brocklehurst beer bash on Wed? Perhaps > it might be easier to trash out with a pad of paper how far we can achieve > commonality without extreme complexity. > Apologies no. I am in california :( > What design I've got so far is a pretty direct mapping of Biojava > sequence/feature objects onto a database and relies on using sequence and > feature ids to get a hierarchy (features have parent fields so select on > that field gets me the next level) and as you mentioned, a BLOB to chuck > the bundle into (I was tempted to use a BLOB for an entire sequence but > that's taking the piss and not very editable). I'm trying to make it such > that I can either choose some form of lazy instantiation for Biojava > objects (and save memory at the expense of more database transactions) or > have the whole sequence object instantiated at a go. I'm trying to keep > it simple as I'm sure I'll find design errors necessitating a rewrite and > I'd rather that happened earlier rather than later when a lot has been > invested into a design. The primary objective for me is that other than > the original call to get such an object, all subsequent manipulations > should as if you were working on a standard Biojava object. Take a look at bioperl-db. It aint so bad ;) _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
