[Biocorba-l] BSANE and bioCORBA

[Juha Muilu]

Ewan,
Thanks for the response!

Ewan Birney wrote:
> 
> I think the sensible proposal is that BioCorba 0.3 is equivalent to the
> Sequence core of BSANE  - does this sound ok to people? I guess I think
> 
> Jason
> Alan
> Brad
> (ideally Matt)
> 
> should say yes first to this before we go for it. We also need a proposal
> from Juha for BioCorba 0.3 that we can kick around...

How does the models I have on my web-pages look like? 

Perhaps we should first start discussion what is missing or is too much
in the current models. Step by step. Our wish list is to have at least:
     - Proper identifiers. we have found model used in the CosNaming
services good
     - Other kind of annotations besides  the seq features (also the
value should
       be any)
     - Have a high level entity (currently named as Identifiable),
       which can be used with the annotations. 
     - Composite sequence locations

> 
> I don't want to force BioCorba development into the OMG development model
> of voting etc because I think it sucks, but I am more than happy to bend
> BioCorba to play well with BSANE in the Sequence area.

What is the alternative? I do not see voting as bad idea.

> 
> Personally from my perspective, I would be happy to kill off AnonymousSeq
> - this was something really driven by Matt Pocock - Matt - are you tuned
> in?

I have used AnonymousSequence as a superclass of SymbolArray (=
BioJava's SymbolList). It made possible (it seems) to have orthogonal
sequence extension, which has the Alphabet, without forcing people to
use it they do not want. 

> 
> A possible use of AnonymousSeq is in the SeqFeature->get_PrimarySeq which
> is still unclear actually whether this returns just this SeqFeature's
> subseq (in which case it should be an AnonymousSeq as it doesn't really
> have an id) or the entire_seq (in which case it should be a PrimarySeq)
> 
> In any case, we should sort out the semantics.
> 
> The other thing I would *really* like is to remove the
> 
> get_PrimarySeqVector
> 
> from PrimarySeqDB and replace it with
> 
> get_PrimarySeqIterator

Perhaps we should use the iterator/list pattern used in the BSA. It is
actually quite good!

> 
> The vector call is almost unimplementable for most DB implementations I
> have got, where as the Iterator is trivially implementable. Alan - this is
> your baby here - can we change this?
> 
> Juha -
> 
> Can I suggest that you send a proposal for BioCorba 0.3 just as plain,
> commented IDL (no DOC files; no long OMG submission things... ) which
> 
> (a) is just the part of BSANE that is the BioCorba 0.3 part
> 
> (b) does not add in massive new things without having a serious "I want to
> add CORBA::Collection to this to do..." type post here.


Fine. I have some IDLs here:
http://corba.ebi.ac.uk/~muilu/uml/bsane_v3/idl
Perhaps those contain too much changes?  

Alan has also made lot of work with the new bioCORBA version trying to
approach consensus from the bioCORBA side.

> 
> Would this suit everyone?
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------
> 
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 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
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