[Bioperl-l] Using Graph?

Heikki Lehvaslaiho heikki@ebi.ac.uk
07 Nov 2002 09:45:30 +0000


Background: 

I needed to find the shortest path of location mapping between
coordinate systems and not finding anything useful from CPAN, wrote
Bio::Coordinate::Graph that allowed me to do exactly what I wanted. 
Nat pointed out the 'Graph' to me:

On Wed, 2002-11-06 at 00:03, Nathan (Nat) Goodman wrote:
> 3)  Did you consider using an existing general purpose graph package?  I’ve
> used the one in CPAN which works reasonably well.  I realize it’s overkill
> here, but graphs are such a basic modeling tool that there may be some value
> in adopting a standard graph package for BioPerl.  Then, modules dealing
> with taxonomies and phylogenies, etc., etc. could use the standard graph
> package instead of everyone coding their own special case.

I had a look at it and seems pretty good. (Written by a Finn, so it has
to be good. ;-)  ) Most importantly, it is really general purpose.

http://search.cpan.org/author/JHI/Graph-0.20101/
it has a dependecy for
http://search.cpan.org/author/JMM/Heap-0.50/


Question:

Is anyone in a position to start using Graph now or in near future?
I'd be much more confortable to add one more dependency into bioperl if
I knew that other modules will be using it, too.

Any opinions welcome,

			-Heikki
 
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________