| Bio::Ontology::SimpleGOEngine::GraphAdaptor(3pm) | User Contributed Perl Documentation | Bio::Ontology::SimpleGOEngine::GraphAdaptor(3pm) |
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.
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:
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
| 2020-10-28 | perl v5.30.3 |