[Bioperl-l] Markers and Maps

[Heikki Lehvaslaiho]

I've committed a set of reworked Bio::Map classes. The underlying logic
behind existing classes was rewritten. All old tests pass and more.
I also put in new classes for managing and comparing cytogenetic locations
of type '2p13.1-q12' or 'Xq' or simply 'Y'.


This description is in Bio::Map::Marker.pm:
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A Marker is a central object in Bio::Map name space. A Map is a holder
class for objects. A Marker has a Position in a Map.  A Marker can be
compared to an other Markers using boolean methods. Positions can have
non-numeric values or other methods to store the locations, so they
have a method numeric() which does the conversion. 

A Marker has a convinience method position() which is able to create
Positions of required class from scalars by calling method
get_position_object().

For more complex situations, a Marker can have multiple positions in
multiple Maps. It is therefore possible to extract Positions (all or
belonging to certain Map) and compare Markers to them. It is up to the
programmer to make sure position values and Maps they belong to can be
sensibly compared.
----------------------------------------------------------------------

A dia UML model of the current setup is in models/bio_map.dia.

Enjoy,
	-Heikki


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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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