[Biocorba-l] BSANE and bioCORBA

[Juha Muilu]

Ewan Birney wrote:
> 
> On Sun, 3 Jun 2001, Alan Robinson wrote:
> 
> >
> > 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).
> 
> I am firmly in the (b) camp. Often the subroutine which gets a sequence
> feature has no way of getting a database object in which to use (a). I
> vote with all my fingers and all my toes for objects coming back.
> 

I also like the b solution. The argument is valid.


> >
> >
> >  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?)
> >
> 
> Ambivelent about this. Marginal leanings towards (a) as I find (b) - which
> is what we have in Bioperl - just gets in my way ;)

I am in favor of 2b. 

If the return type is AnonymousSequence then we have also possibility to
return plain SymbolArray, which inherits from the AnonymousSequence
(btw, not sure how people feel about this inheritance). Also the
sequence can span just that location and we do not have invent new id
for it (is this original purpose of the AnonymousSequence?)

I am still bit confused. Why application has to return SeqFeature as a
result? Why cannot it return just a sequence, which has that feature? It
seems that in both cases we have to create SeqFeature and Sequence
anyway..


> 
> >
> > 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>
> >
> > --
> > ============================================================
> > 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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> >
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------
> 
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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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