[DAS2] RE: Modifying com.affymetrix.igb.das2 classes

[Helt,Gregg]

Okay, I just split the code that was in Das2VersionedSource.  Now
regions and types (w/o ontology) are handled in Das2VersionedSource, and
ontology, materials, results, and assays are handled by a subclass,
Das2VersionedSourcePlus.  I might do some further refactoring at a later
date, but for right now this works (and compiles/runs).

I also went ahead and committed almost all my DAS/2 code changes to the
genoviz repository.

	Gregg

> -----Original Message-----
> From: das2-bounces at portal.open-bio.org
[mailto:das2-bounces at portal.open-
> bio.org] On Behalf Of Helt,Gregg
> Sent: Monday, February 06, 2006 7:35 PM
> To: Brian O'Connor
> Cc: DAS/2; Marc Carlson
> Subject: [DAS2] RE: Modifying com.affymetrix.igb.das2 classes
> 
> 
> You're right, it looks like some of this code was already getting
moved
> over to the das2.assay and das2.ontology packages as subclasses of
> Das2VersionedSource.
> 
> However it's not clear to me if the equivalent of source and versioned
> source for assay, ontology, and other domains are going to be similar
> enough to the DAS/2 sequence domain to justify sharing a base
> class/interface.  What do/will they share?
> 
> I'll go ahead with changes to the das2 package, and look into moving
> much of this code into a das2.sequence package.
> 
> 	Thanks,
> 	Gregg
> 
> > -----Original Message-----
> > From: Brian O'Connor [mailto:boconnor at ucla.edu]
> > Sent: Monday, February 06, 2006 7:09 PM
> > To: Helt,Gregg
> > Cc: Marc Carlson; Allen Day; DAS/2
> > Subject: Re: Modifying com.affymetrix.igb.das2 classes
> >
> > Hi Gregg,
> >
> > Go for it!! Marc and I can take a look at it again when you're happy
> > with the changes. The versioned source object really needed an
> overhaul
> > anyway to deal with the multiple domains of the DAS/2 server. I
think
> > there should be a VersionedSource parent and then children for each
> > domain (i.e. VersionedSourceAssay). I think Marc started to do this
> but
> > he was afraid to alter the VersionedSource object too much for fear
of
> > breaking the IGB client.
> >
> > --Brian
> >
> > Helt,Gregg wrote:
> >
> > > Brian and Marc,
> > >
> > > I'm about to start seriously modifying the IGB DAS/2 classes in
the
> > > com.affymetrix.igb.das2 package. There's code in there you wrote
to
> > > work with materials, assays, results, and ontology. I think we
> > > discussed at some point splitting this stuff out into a separate
> > > package(s). Which sounds good, especially since (as I understand
> it),
> > > these domains are separate from the DAS/2 "sequence" domain. The
> only
> > > place there's a lot of mixture of code for these domains with the
> > > sequence parts is in Das2VersionedSource. Is it okay if I move
this
> > > out (or comment it out) of Das2VersionedSource while I renovate
> other
> > > parts of the class?
> > >
> > > thanks,
> > >
> > > Gregg
> > >
> 
> 
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