/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Ontology::SimpleGOEngine::GraphAdaptor

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.

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:

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