[Bioperl-l] Bio::RangeI intersection proposal

Chris Fields cjfields at uiuc.edu
Wed Jun 21 11:16:17 EDT 2006


I personally have no objections as long as it doesn't break API.  Don't know
how the senior guys feel (Jason, Brian, Heikki, Hilmar...); I'm not a user
of Bio::Map modules myself.

Actually, sounds weird to have me say "senior guys"; I'm 35 years old!

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Wednesday, June 21, 2006 3:21 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Bio::RangeI intersection proposal
> 
> Bio::Map::PositionI (in bioperl-live) needs intersections of a list of
> ranges. It inherits from Bio::RangeI but unlike RangeI's union,
> intersection does not take a list. PositionI currently calls
> intersection repeatedly to handle a list.
> 
> If there is no particular reason for this limitation, I propose making
> RangeI intersection handle lists natively. This won't do any harm to
> existing code at the time of the change, but its possible that someone
> has written a module that implements RangeI but overrides intersection
> (without making it accept a list), so that future code written that
> expects a RangeI to handle lists will break when getting a RangeI from
> that module.
> 
> So the question is, has anyone overridden intersection in RangeI? Is the
> small risk of possible breakage compensated by the benefit of
> intersections of a list of ranges (which is surely useful in lots of
> situations, not just for PositionI)?
> 
> I'm tempted to go ahead with this unless there are objections.
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