[Bioperl-l] Bio::Map changes

Sendu Bala bix at sendu.me.uk
Thu Jun 22 09:28:25 EDT 2006


Sendu Bala wrote:
> 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

Range is now done.

The next step is to tidy up all of Bio::Map*, which involves a major 
reimplementation of the whole system (but with no significant API 
change). Basically, the current system is a awkward mix of older 'marker 
has a single position on a map' and new 'markers have multiple positions 
on multiple maps'. This gives us strange things like SimpleMap's 
add_element method which adds a reference to the element to the map 
without the element itself knowing it is now on the map (because it is 
Position that defines what maps an element is on).

The reimplementation will make Position central to the model, allowing 
for lots of other things to work properly without anything becoming 
inconsistent (as is currently the case).

The general tidy up will involve redoing and perhaps even removing 
things. For instance, OrderedPositionWithDistance has never worked so 
will be deleted (with OrderedPosition gaining the distance functionality 
its docs says it already has).

But now is the time to speak up and change my mind if necessary!


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