[Bioperl-l] Bio::RangeI intersection proposal

Sendu Bala bix at sendu.me.uk
Wed Jun 21 04:20:37 EDT 2006


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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