Bio::Ontology::SimpleGOEngine::GraphAdaptor(3)

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