[Bioperl-l] Using Graph?

[Heikki Lehvaslaiho]

Ok. Ill start using it once I have time to convert my code. 

On Thu, 2002-11-07 at 18:05, Hilmar Lapp wrote:
> It is already a dependency, just a silent one :) The OntologyEngineI 
implementation by Chris Zmasek depends on it, I just haven't gotten 
around to document this. Yes, it is an excellent module and installs 
smoothly out of the box.
> 
> 	-hilmar

A very silent one. There can not be any tests needing it since I have
not seen errors from it...
Hold on. It is not part of Bioperl, yet, or is it in some cvs module I
do not use? Where is it?

	-Heikki

> > -----Original Message-----
> > From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk]
> > Sent: Thursday, November 07, 2002 1:46 AM
> > To: Bioperl
> > Subject: [Bioperl-l] Using Graph?
> > 
> > 
> > 
> > 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
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> > 
-- 
______ _/      _/_____________________________________________________
      _/      _/                      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
___ _/_/_/_/_/________________________________________________________