[Biocorba-l] BSANE and bioCORBA

[Alan Robinson]

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.

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.


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Alan J. Robinson, D.Phil.             Tel:+44-(0)1223 494444
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