# $Id: GraphAdaptor02.pm 10525 2006-09-26 22:03:22Z sendu $
#
# BioPerl adaptor for old Graph verions (0.2x) for use in
# FAST::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
# 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
FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor02 - Graph adaptor (v02.x) for
FAST::Bio::Ontology::SimpleGOEngine
=head1 DESCRIPTION
Internal subclass of FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor for
Graph v0.2x.
Call this via FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor
=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:
=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...
use strict;
# edges
# v0.2x returns (u0,v0, u1,v1, ...)
# v0.5x returns ([u0,v0], [u1,v1], ...)
sub edges {
my $self=shift;
my @edges02=$self->_graph->edges(@_);
my @edges;
while (@edges02) {
my($u,$v)=(shift @edges02,shift @edges02);
push(@edges,[$u,$v]);
}
@edges;
}
# edges_at
# v0.2x uses edges() method and returns (u0,v0, u1,v1, ...)
# v0.5x returns ([u0,v0], [u1,v1], ...)
sub edges_at {
my $self=shift;
$self->edges(@_);
}
# set_vertex_attribute
# v0.2x uses set_attribute($attribute,$v,$value)
sub set_vertex_attribute {
my($self,$v,$attribute,$value)=@_;
$self->_graph->set_attribute($attribute,$v,$value);
}
# get_vertex_attribute
# v0.2x uses get_attribute($attribute,$v)
sub get_vertex_attribute {
my($self,$v,$attribute)=@_;
$self->_graph->get_attribute($attribute,$v);
}
# set_edge_attribute
# v0.2x uses set_attribute($attribute,$u,$v,$value)
sub set_edge_attribute {
my($self,$u,$v,$attribute,$value)=@_;
$self->_graph->set_attribute($attribute,$u,$v,$value);
}
# get_edge_attribute
# v0.2x uses get_attribute($attribute,$u,$v)
sub get_edge_attribute {
my($self,$u,$v,$attribute)=@_;
$self->_graph->get_attribute($attribute,$u,$v);
}
1;