[Bioperl-l] Bio::Range and Bio::Range

[Heikki Lehvaslaiho]

Hilmar Lapp wrote:
> 
> Heikki Lehvaslaiho wrote:
> >
> > I'd like to update Bio::RangeI and Bio::Range before  branching to
> > 0.7.
> > OK Hilmar?
> >
> 
> It is, but see below.

Done and committed.

> > 4. Rename union and intersection to _union and _intersection in
> > Bio::RangeI. They return an array of three values. Instantiable
> > classes like Bio::Range should recreate union and intersection and
> > return a new object created from the array values. (->overlap_extent
> > is kept as it is.)
> >
> > Shout if you object or these plans threaten to break something.
> >
> 
> Indeed. You're suggesting to change an interface in a not
> backward-compatible way. In BioPerl the likelihood that this is a
> problem for any code outside of BioPerl is not high since most
> people don't implement interfaces themselves.
> 
> Apart from that, the question is whether we want to require
> implementing classes to provide these methods. If yes, they should
> definitely be present in the interface. Methods with an underscore
> (i.e., methods that are not part of the public API) do not make
> much sense in an interface IMHO. If you think they're not defined
> properly, you can change the definition.


You are right. The reason I was fumbling with undescores was I did not
realize it is possible to use $self->new to create an instance of a
_calling_ object. Using that syntax, the changes to into union and
intersection are now in Bio::RangeI.

	-Heikki

 
>         Hilmar
> 
> --
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> -----------------------------------------------------------------

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