Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for
Bio::Ontology::SimpleGOEngine
use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;
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
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
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.
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
Nat Goodman
Email: natg at shore.net
Address:
Institute for Systems Biology
1441 N 34th St
Seattle, WA 98103-8904
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
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
Title : _graph
Usage : $self->_graph();
Function: Internal method to access 'real' graph
Returns : Graph::Directed object
Args : none
Title : _vertex_attributes
Usage : $self->vertex_attributes();
Function: Internal method to access HASH used to store vertex attributes
Returns : Graph::Directed object
Args : none
Title : _edge_attributes
Usage : $self->edge_attributes();
Function: Internal method to access HASH used to store edge attributes
Returns : Graph::Directed object
Args : none
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
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