[Biocorba-l] BSANE and bioCORBA

[Juha Muilu]

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.

> 
> 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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