[Bioperl-l] Gene Interface discussion

Ewan Birney birney@ebi.ac.uk
Mon, 5 Feb 2001 10:55:54 +0000 (GMT)


On Sun, 4 Feb 2001, Hilmar Lapp wrote:

> Ewan Birney wrote:
> > 
> > The definition of SeqFeatureI is extended somewhat. SeqFeatureI
> > objects are now allowed to have component SeqFeatures (sub_SeqFeature
> > call) which are on different sequences to the parent SeqFeature.
> > 
> > There is a new method to SeqFeatureI - is_single_sequence which
> > returns TRUE if all component SeqFeatures are on the same sequence as
> > this SeqFeature, and returns FALSE if not. This will allow clients to
> > easily find (and possibly skip) these "expanded" seq features.
> > 
> > The ->start and ->end calls on a non single sequence composite
> > seqfeature should return the start and end point of the component
> > sequence features which lie on the "focus" sequence of this
> > seqfeature (ie, whatever ->entire_seq and ->seqname implies).
> > 
> > Clients should be aware that when is_single_sequence == 0, concepts
> > like "overlap" and "length" are not necessarily easy to define or
> > interpret. This is for the client code to deal with. 
> 
> This is from a mail from Dec 13th and still not dealt with. Do we
> still want to add is_single_sequence()? There are now two
> conditions for is_single_sequence() to return 0:
> 
>         1) traversing the complete sub_SeqFeature() tree reveals
>         features with $subfeat->seqname() != $feat->seqname()
>         2) if
> $feat->location()->isa('Bio::Location::SplitLocationI')
> 	and traversing the sub_Location() tree reveals sublocations
>         with $subloc->seq_id() != $loc->seq_id().
> 
> An option would be to add is_single_sequence() (or give it another
> name) to SplitLocationI.

I would claim that is_single_sequence should be a SplitLocationI only
method interestingly. 

Getting into the sub_SeqFeature stuff is encouraging abuse (not that we
don't have ample ability to completely abuse this model... I sound like a
broken record don't I...) 

anyway - just SplitLocationI in my view...


> 
> What do people think? Ewan, Jason? Comments not only appreciated
> but solicited.
> 
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> -----------------------------------------------------------------
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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