# $Id: GraphAdaptor.pm 10525 2006-09-26 22:03:22Z sendu $
#
# BioPerl Graph adaptor for Bio::Ontology::SimpleGOEngine
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Nat Goodman <natg at shore.net>
#
# (c) Nathan Goodman natg@shore.net 2005
# (c) ISB, Institute for Systems Biology 2005
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for
Bio::Ontology::SimpleGOEngine
=head1 SYNOPSIS
use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;
=head1 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
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Nat Goodman
Email: natg at shore.net
Address:
Institute for Systems Biology
1441 N 34th St
Seattle, WA 98103-8904
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Ontology::SimpleGOEngine::GraphAdaptor;
use Graph::Directed;
use strict;
use base qw(Bio::Root::Root);
=head2 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
=cut
sub new {
my( $class ) = @_;
$class = ref $class || $class;
my $self= bless( {}, $class );
$self->{_graph}=Graph::Directed->new();
$self->{_vertex_attributes}={};
$self->{_edge_attributes}={};
return $self;
}
# Here are the main methods
sub add_vertex {
my $self=shift;
$self->_graph->add_vertex(@_);
}
sub has_vertex {
my $self=shift;
$self->_graph->has_vertex(@_);
}
sub add_edge {
my $self=shift;
$self->_graph->add_edge(@_);
}
sub has_edge {
my $self=shift;
$self->_graph->has_edge(@_);
}
sub vertices {
my $self=shift;
$self->_graph->vertices(@_);
}
sub edges {
my $self=shift;
$self->_graph->edges(@_);
}
sub edges_at {
my $self=shift;
$self->_graph->edges_at(@_);
}
sub predecessors {
my $self=shift;
$self->_graph->predecessors(@_);
}
sub successors {
my $self=shift;
$self->_graph->successors(@_);
}
sub source_vertices {
my $self=shift;
$self->_graph->source_vertices();
}
sub sink_vertices {
my $self=shift;
$self->_graph->sink_vertices();
}
# The following methods workaround a performance problem in Graph v0.5x
# when attributes are attached to the graph
sub set_vertex_attribute {
my($self,$v,$attribute,$value)=@_;
$self->_vertex2attributes($v)->{$attribute}=$value;
}
sub get_vertex_attribute {
my($self,$v,$attribute)=@_;
$self->_vertex2attributes($v)->{$attribute};
}
sub set_edge_attribute {
my($self,$u,$v,$attribute,$value)=@_;
$self->_edge2attributes($u,$v)->{$attribute}=$value;
}
sub get_edge_attribute {
my($self,$u,$v,$attribute)=@_;
$self->_edge2attributes($u,$v)->{$attribute};
}
=head2 _graph
Title : _graph
Usage : $self->_graph();
Function: Internal method to access 'real' graph
Returns : Graph::Directed object
Args : none
=cut
sub _graph {$_[0]->{_graph}; }
=head2 _vertex_attributes
Title : _vertex_attributes
Usage : $self->vertex_attributes();
Function: Internal method to access HASH used to store vertex attributes
Returns : Graph::Directed object
Args : none
=cut
sub _vertex_attributes {$_[0]->{_vertex_attributes}; }
=head2 _edge_attributes
Title : _edge_attributes
Usage : $self->edge_attributes();
Function: Internal method to access HASH used to store edge attributes
Returns : Graph::Directed object
Args : none
=cut
sub _edge_attributes {$_[0]->{_edge_attributes}; }
=head2 _vertex2attributes
Title : _vertex2attributes
Usage : $value=$graph->_vertex2attributes($v_->{ATTRIBUTE};
$graph->_vertex2attributes($v)->{ATTRIBUTE}=$value;
Function: Internal method to access attributes for a specific vertex
Returns : HASH
Args : none
=cut
sub _vertex2attributes {
my($self,$vertex)=@_;
$self->_vertex_attributes->{$vertex} or $self->_vertex_attributes->{$vertex}={};
}
=head2 _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
=cut
sub _edge2attributes {
my($self,$u,$v)=@_;
$self->_edge_attributes->{$u,$v} or $self->_edge_attributes->{$u,$v}={};
}
1;