noble (3) Bio::Ontology::SimpleGOEngine::GraphAdaptor.3pm.gz

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