[Bioperl-l] Bio::Map changes

Sendu Bala bix at sendu.me.uk
Tue Jun 20 16:22:45 EDT 2006


Some initial changes have been made to some modules in Bio::Map to allow 
Positions to have a range (Bio::Map::PositionI implements Bio::RangeI).
(see http://bugzilla.open-bio.org/show_bug.cgi?id=1998)

Further changes are needed in some remaining Bio::Map modules for this 
addition to be complete (a number of Bio::Map related tests in the test 
suite currently fail), notably Bio::Map::Cyto* since they had 
implemented their own Range-related features.

I propose bringing all Bio::Map into line so it behaves with and makes 
good use of the RangeI nature of Position. Beyond this initial change I 
want to add relative positioning and more, but I'll describe that in a 
future post to this thread.

Can anyone see any issues with ranged positions (it's done in a backward 
compatible way)? Do any developers want to maintain control of a 
Bio::Map module or shall I just dive in?



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