[Bioperl-l] Markers and Maps

[Heikki Lehvaslaiho]

Zhiliang Hu wrote:
> 
> Dear Heikki,
> 
> I am very interested in your Bio::Map.  However I cannot find it on
> CPAN nor www.bioperl.org sites.  How may I obtain a copy?

Zhiliang,

And others I confused by not being explicit,

When we on the bioperl list use the term "commit" we mean that we have added
files into the bioperl CVS (Concurrent Versioning System) repository.
Occasionally, a snapshot of the repository is taken and placed into CPAN. We
are in the process of making a release 1.0 of bioperl, but right now the
only way to access these modules are using CVS. You can use it anonymously
(download only), too. See

http://cvs.bioperl.org/

> By the way, is your moduel capable of making comparative maps?

The schema, as it is now, consists of classes capable of holding map and
marker infomation, only. The idea is that there markers can belong to
several maps. There is no logic in there compute anything out of them. Nor
is there any drawing code. All that can be added in due time if there is
enough interest in willing hands to type in the code. 

Yours,
	-Heikki

> Best regards,
> 
> Zhiliang
> 
> On Mon, 11 Feb 2002, Heikki Lehvaslaiho wrote:
> 
> >
> > 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:
> > ----------------------------------------------------------------------
> > 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

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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