[Biocorba-l] 'start' and 'end' on SeqFeature

[Alan Robinson]

I have a feeling this reply to Ewan never got through to the BioCORBA
mailing list because of it being down over the last 48 hours...

--
============================================================
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/
============================================================

On Mon, 12 Feb 2001, Ewan Birney wrote:

> Alan -
> 
> nice to see this post. 
> 
> One thing that came back from bioperl (from my perspective) is that the
> SeqFeature interface with
> 
>    $feature->start 
>    $feature->end
> 
> should still be (a) maintained and (b) not throw exceptions.
> 
> Does this sync with your thoughts? Would you prefer to see something
> different?

Yep - SeqFeature retains methods to return 'start' and end' without
throwing exceptions (just as in BioCorba-0.2 and like bioperl):

  interface SeqFeature : Annotation
  {
    long start();
    long end();
    short strand();

    // ... other gubbins...

  };


Caveats:

 - It's up to the user to decide how much they trust these naive values
   (99% of the time, I'm sure they'll be fine).

 - It's up to the implementor to provide a sensible answer (normally I'd
   say the extreme 3' and 5' ends of any feature).

     i.e. for (20.25)..(100.110) => start=20 / end = 110


--
============================================================
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/
============================================================

On Mon, 12 Feb 2001, Ewan Birney wrote:

> 
> 
> Alan -
> 
> nice to see this post. 
> 
> 
> One thing that came back from bioperl (from my perspective) is that the
> SeqFeature interface with
> 
>    $feature->start 
>    $feature->end
> 
> should still be (a) maintained and (b) not throw exceptions.