[BioPython] IDL's

Ewan Birney birney@sanger.ac.uk
Fri, 17 Sep 1999 19:37:23 +0100 (BST)

On Fri, 17 Sep 1999, Bradley Marshall wrote:

> OK,  
> One thing that I'm still fuzzy on is how much to coform to idl's. 
> Originally I tried to conform to the LSR IDL and use only the given
> interfaces.  Andrew said he wanted lighter weight objects (which I
> agree with fully) and that with these we could still conform to the LSR
> spec.  I really like Ewan's bioperl IDL, but that's even less like the
> LSR proposal.  

The thing about interfaces is that you can have any object behind an
interface, from complex to simple, and one object can quite sensibly
support more than one interface (often does).

> 	I guess how question is: in designing classes, how close/far to IDL's
> do you have to be to retain object sharing through Corba/other
> interface languages?  Additionally, how do you make two objects talk
> that have different IDL's?  One of my problem's may be that I don't
> fully understand Corba yet.

You need to have the information. for example, the LSR BioSequence object
has features, so if you are expecting people to get information about
features via a LSR wrapper to your object, your object needs features.

I really sense that you haven't played with corba enough to get it - it
took me a while so that is no slight on your programming
ability/style/etc. If I could suggest that you use the bioperl idl as more
of a guide than LSR. I have been involved in both, so this is not a
standards war - just LSR is made for a different auidence than you. (of
course, make your own decisions about what is in or out...). The LSR
definition is for enterprise-wide, client friendly stuff - there are alot
of issues there you just don't want to get into.

One thing to think about is the BioPython sequence object both *wrapping*
a IDL BioSource::Seq object and serving/supplying a BioSource::Seq object
(ie, being both client and server). 

I need to knock up a little example object (probably in C) which you can
then play with via Fnorb. Sounds good?

> 	Thanks guys.
> Brad
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Ewan Birney. Work: +44 (0)1223 494992. Mobile: +44 (0)7970 151230