[Bioperl-l] Using Graph?

[Heikki Lehvaslaiho]

On Fri, 2002-11-08 at 10:22, Heikki Lehvaslaiho wrote:
> Ok. Ill start using it once I have time to convert my code. 

Hmm. I tried using Graph. It has three methods for finding the shortest
path: SSSP_DAG, SSSP_Dijkstra and SSSP_Bellman_Ford. Using perl 5.8.0,
DAG and Bellan-Ford hang and I am not sure if their result is correct
even when I've patched the faulty code. Let's see what the author of the
package has to say. 

In the previous version SSSP_Dijkstra used to hang according to a bug
report on the CPAN. 

	-Heikki

 
> 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
> ___ _/_/_/_/_/________________________________________________________
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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
___ _/_/_/_/_/________________________________________________________