[Biocorba-l] BSANE and bioCORBA

[Ewan Birney]

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...




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.


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?


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


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.



Would this suit everyone?







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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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