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Bio::Ontology::SimpleGUseriContributednPerlgDo:SimpleGOEngine::GraphAdaptor(3)

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

perl v5.32.1			Bio::Ontology::SimpleGOEngine::GraphAdaptor(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX

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