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
<birney@ebi.ac.uk>.
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