[Biojava-l] RE: Biojava-l digest, Vol 1 #23 - 4 msgs

[Dickson, Mike]

> Date: Sat, 12 Feb 2000 03:39:08 +0000 (GMT)
> From: Ewan Birney <birney@ebi.ac.uk>
> To: admin@embnet.uio.no
> cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] IDL
> 
> On Fri, 11 Feb 2000, David Martin wrote:
> 
> > 
> > I have a few pennys worth to throw in here..
> > 
> > Firstly I think that IDL is definitely the way to go to get a good
design
> > and interoperatability between the various bio* development efforts.

<snip>

> > Maybe you already have very good reasons for not taking this approach,
but
> > it is occasionally neccessary to do something a bit different to extend
> > our capabilities rather than biojava being a clone of bioperl (worthy a
> > goal though that is)

I'll be honest,  I was fairly disappointed with the emergence of a new IDL
to express
sequences.  Ewan made a comment on this list suggesting that an effort to
provide a 
mapping between the LSR model and the new one might be a nice thing to do.
I guess I
have an alternate view on this.  If the community at large would like to
encourage 
vendors to participate in OpenSource/Community Source or general *open*
efforts, it
might be better to encourage the the use of the standards work that has been
done
instead of continuing to invent alternatives.  Of course most any position
can be 
rationalized and there might be very good reasons for doing sonmething
different.  
NetGenics' SYNERGY is different that the LSR model.  I *am* commited to
migrate to
it and for those things I don't like I'll continue to try to work
constructively
for changes.  I'd like to believe that others would make a similar
commitment.

The problem with bridges and adaptors is that as we try to solve higher
order 
problems that require extensions the adaptor approach becomes combanitoric.
Having a solid base to build on that is consistent is pretty much a
requirement if
your goal is interoperability.  Hence my commitment to the LSR.

The implementation classes used in Synergy will probably mostly stay the
same as we move to the LSR model.  That is, we hava strong seperation of
interface and implementation.  Having *implementation* centric IDL just
seems silly to me.   If you want implementation centric interfaces with Java
as the target language then use Java interfaces for that purpose.  

Sorry for being so direct.  That's my style.  I've been following biojava
for a little while now and there is some very excellent work being done.
I'd love to see it interoperate and leverage the very excellent work we did
in the LSR.  I just have a different idea of how that should happen.

Mike Dickson
mdickson@netgenics.com