Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for Bio::Ontology::SimpleGOEngine
use Bio::Ontology::SimpleGOEngine::GraphAdaptor; my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;
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
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
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.
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/
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
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.