Reference

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

Graph adaptor for Bio::Ontology::SimpleGOEngine

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 an adaptor to simplify use of versions of the standard CPAN Graph module (old is versions 0.2x; new is 0.5x and beyond) within Bio::Ontology::SimpleGOEngine. Prior versions of this module supported Graph version older than 0.5, however we are removing support for these older version post BioPerl 1.6.901. If you absolutely require an old version of Graph, please use an older version of BioPerl.

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

This class provides implementations for the required graph methods using the new version of Graph. In most cases, these are simple pass-throughs

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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:

  https://github.com/bioperl/bioperl-live/issues

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

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