[Biocorba-l] BSANE and bioCORBA

[Ewan Birney]

On Sat, 2 Jun 2001, Juha Muilu wrote:

> Alan Robinson wrote:
> > 
> > On Thu, 31 May 2001, Ewan Birney wrote:
> > 
> > > 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.
> > 
> > I interpreted and implemented this as returning the complete sequence of
> > the parent object.
> > 
> > However, being able to get the sequence of the feature itself would be
> > useful. But, this would be a convenience method, since the sequence is
> > also available via the Seq's subseq method using location parameters
> > (though it may be a pain for the client if it's a composite location). And
> > then there the issue of how it relates to location fuzziness.
> 
> Is it necessary to have this (get_primarySeq) method at all because it may be
> misused? 
> 
> What kind of use cases there are for having the method and also the
> seq_primary_id? I have assumed only navigation  from Sequence to feature 
> is necessary.

Going from feature back to the sequence is very common and in general the
function which is doing this only has the feature and does not have the
original sequence.

definite mistake to leave it out  :)


I am cool with alan's interpretation of primary_seq. I'd like the
convience function as well but this does lead to the bugbear of how the
convience function deals with composites and fuzzies ... probably best to
have a rigorous definition (composites spliced and fuzziesgiven back as
maximal hard numbers?

<aside>I HATE fuzzies . useless things. useless... useless</aside>


> 
> > 
> > In retrospect, I probably made a bad call in my implementation, since
> > there is already a method in SeqFeature called 'seq_primary_id'.
> > 
> > How have the other bio* servers implemented this? I'm happy to go with the
> > consensus!
> > 
> > Alan.
> > 
> > --
> > ============================================================
> > Alan J. Robinson, D.Phil.             Tel:+44-(0)1223 494444
> > European Bioinformatics Institute     Fax:+44-(0)1223 494468
> > EMBL Outstation - Hinxton             Email:  alan@ebi.ac.uk
> > Wellcome Trust Genome Campus
> > Hinxton, Cambridge
> > CB10 1SD, UK                http://industry.ebi.ac.uk/~alan/
> > ============================================================
> > 
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> 
> -- 
>  +--------------------------------------------------------------------+
>  |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
>  |European Bioinformatics Institute | Phone:  +44 (0)1223 494 624     |
>  |Wellcome Trust Genome Campus      | Fax:    +44 (0)1223 494 468     |
>  |Hinxton, Cambridge CB10 1SD, UK   | http://industry.ebi.ac.uk/~muilu|
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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