[Biocorba-l] BSANE and bioCORBA

[Alan Robinson]

Btw, since I (and others) are on the Biocorba list, there's really no need
to include specific email addresses when replying.

My thoughts on Seq's and Features:

 1) We need a method to navigate from feature to sequence. But what should
    this return? [And should we allow for mutable sequences?]

	a) The ID of the parent (but which ID?: display, primary, or
	   accession)
	b) An object reference to the parent Seq object

	I prefer 1a using primary id (since normally primary_id ==
	accession_number, and it maybe allows for some degree of sequence
	mutability).


 2) A convenience method in a feature to return the sequence would be
    'convenient'. But what should this return?

	a) The sequence as a string.
	b) An 'AnonymousSeq' or even 'PrimarySeq' object.

	I initially prefer 2a with semantics as outlined by Ewan and also 
	used by the start() and end() functions in SeqFeature; but I could
	be swung to 2b - it might be more work for the server writer, but
	would it be more useful for the client? (Then again, perhaps it's
	better to keep SeqFeature simple and have a factory method defined 
	elsewhere that may be handed a Seq and Location objects and
	returns a new PrimarySeq?)


Alan.


On Sun, 3 Jun 2001, Ewan Birney wrote:

> Juha Muilu wrote:
> 
> > 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>

--
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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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