[Bioperl-l] OT: Breadth-First Search Algorithm - BFS

[Hilmar Lapp]

Well, that depends on what you want to do with the ontology (or its 
engine, respectively). If all that you want is the methods defined in 
Bio::Ontology::OntologyI, then there is no effect. If you want to 
obtain $ontology->engine->graph() and then run those algorithms that 
are buggy, well then the bugs will have an effect obviously ...

Does this answer your question?

	-hilmar

On Friday, February 27, 2004, at 01:59  PM, Roels, Steven wrote:

>
> Nat,
>
> Thanks for the heads-up.
>
> Anyone know off-hand how, if at all, these bugs impact
> Bio::Ontology::SimpleGOEngine?
>
> Thanks,
>
> -Steve
>
> *****************************************************************
> Steve Roels, Ph.D.
> Senior Scientist I - Computational Biology     Phone: (617) 761-6820
> Millennium Pharmaceuticals, Inc.         FAX:   (617) 577-3555
> 640 Memorial Drive                       Email: roels at mpi.com
> Cambridge, MA 02139-4853
> *****************************************************************
>
>> -----Original Message-----
>> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf
>> Of Nathan (Nat) Goodman
>> Sent: Friday, February 27, 2004 4:31 PM
>> To: bioperl-l at portal.open-bio.org
>> Cc: 'Jeremy Semeiks'
>> Subject: RE: [Bioperl-l] OT: Breadth-First Search Algorithm - BFS
>>
>> Graph::Base is seriously broken.  I urge anyone who's using it to 
>> check
>> the bug list at
>> http://rt.cpan.org/NoAuth/Bugs.html?Dist=Graph.
>>
>> The developer, Jarkko Hietaniemi, is well aware of the problems and is
>> working on a rewrite.  In the meantime, I have a very simple graph
>> package that I'm happy to share.  It handles undirected, unlabelled
>> graphs only.  It provides depth and breadth first search, all pairs
>> shortest path, enumeration of all paths in a graph, as well as the
>> basics.
>>
>> Best,
>> Nat
>> ----------
>>
>> Jose M? Glez Izarzugaza wrote:
>>>> I'm working with a graph and I need to calculate the values of C and
>> L, to do so, I need an algorithm to calculate the distance to the 
>> other
>> elements....
>>>> A good one is BFS algorithm.
>>
>> Jeremy replied:
>>> One solution is to use the Graph::Base module on CPAN:
>>>
>>> http://search.cpan.org/~jhi/Graph-0.20101/lib/Graph/Base.pm
>>
>>
>>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------