Bio::Ontology::SimpleGOEngine::GraphAdaptor.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for Bio::Ontology::SimpleGOEngine

SYNOPSIS

   use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
 
   my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;
 
 

DESCRIPTION

This is a think adaptor to simplify use of the old and new versions of the standard CPAN Graph module (old is versions 0.2x; new is 0.5x and beyond) within Bio::Ontology::SimpleGOEngine.

This module implements only those Graph methods used by SimpleGOEngine. It is far from a complete compatibility layer! It also implements workarounds for cerain performance problems in the current versions of Graph v0.5x.

This class provides a 'new' method that determines which version of Graph is available. The object returned by 'new' is blessed into this class if the new version of Graph is available, else into the subclass

   Bio::Ontology::SimpleGOEngine::GraphAdaptor02
 
 

This class provides implementations for the required graph methods using the new version of Graph. In most cases, these are simple pass-throughs. Methods that differ in v0.2x are implemented in the subclass.

The methods implemented here or in the subclasses are listed below. In all cases, we implemented the Graph v0.5x interface. Consult the Graph v0.5x man page for details.

   add_vertex
   has_vertex
   add_edge
   has_edge
   vertices
   edges
   edges_at
   predecessors
   successors
   set_vertex_attribute
   get_vertex_attribute
   set_edge_attribute
   get_edge_attribute
   source_vertices
   sink_vertices
 
 

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Nat Goodman

Email: natg at shore.net

Address:

   Institute for Systems Biology
   1441 N 34th St
   Seattle, WA 98103-8904
 
 

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Usage   : $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor->new()
  Function: Creates a new graph
  Returns : Bio::Ontology::SimpleGOEngine::GraphAdaptor02 or 
            Bio::Ontology::SimpleGOEngine::GraphAdaptor05 object, 
            depending on which Graph version is available
  Args    : none
 
 

_graph

  Title   : _graph
  Usage   : $self->_graph();
  Function: Internal method to access 'real' graph
  Returns : Graph::Directed object 
  Args    : none
 
 

_vertex_attributes

  Title   : _vertex_attributes
  Usage   : $self->vertex_attributes();
  Function: Internal method to access HASH used to store vertex attributes
  Returns : Graph::Directed object 
  Args    : none
 
 

_edge_attributes

  Title   : _edge_attributes
  Usage   : $self->edge_attributes();
  Function: Internal method to access HASH used to store edge attributes
  Returns : Graph::Directed object 
  Args    : none
 
 

_vertex2attributes

  Title   : _vertex2attributes
  Usage   : $value=$graph->_vertex2attributes($v_->{ATTRIBUTE};
            $graph->_vertex2attributes($v)->{ATTRIBUTE}=$value;
  Function: Internal method to access attributes for a specific vertex
  Returns : HASH
  Args    : none
 
 

_edge2attributes

  Title   : _edge2attributes
  Usage   : $value=$graph->_edge2attributes($u,$v)->{ATTRIBUTE};
            $graph->_edge2attributes($u,$v)->{ATTRIBUTE}=$value;
  Function: Internal method to access HASH used to store edge attributes
  Returns : HASH
  Args    : none