branch-1-6/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm

   1 # $Id: GraphAdaptor02.pm 10525 2006-09-26 22:03:22Z sendu $
   2 #
   3 # BioPerl adaptor for old Graph verions (0.2x) for use in
   4 # Bio::Ontology::SimpleGOEngine
   5 #
   6 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   7 #
   8 # Cared for by Nat Goodman <natg at shore.net>
   9 #
  10 # (c) Nathan Goodman natg@shore.net 2005
  11 # (c) ISB, Institute for Systems Biology 2005
  12 #
  13 # You may distribute this module under the same terms as perl itself.
  14 # Refer to the Perl Artistic License (see the license accompanying this
  15 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  16 # for the terms under which you may use, modify, and redistribute this module.
  17 #
  18 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  19 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  20 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  21 #
  22 # You may distribute this module under the same terms as perl itself
  23
  24 # POD documentation - main docs before the code
  25
  26 =head1 NAME
  27
  28 Bio::Ontology::SimpleGOEngine::GraphAdaptor02 - Graph adaptor (v02.x) for
  29 Bio::Ontology::SimpleGOEngine
  30
  31 =head1 DESCRIPTION
  32
  33 Internal subclass of Bio::Ontology::SimpleGOEngine::GraphAdaptor for
  34 Graph v0.2x.
  35
  36 Call this via Bio::Ontology::SimpleGOEngine::GraphAdaptor
  37
  38 =head1 FEEDBACK
  39
  40 =head2 Mailing Lists
  41
  42 User feedback is an integral part of the evolution of this and other
  43 Bioperl modules. Send your comments and suggestions preferably to the
  44 Bioperl mailing lists  Your participation is much appreciated.
  45
  46   bioperl-l@bioperl.org                  - General discussion
  47   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  48
  49 =head2 Support
  50
  51 Please direct usage questions or support issues to the mailing list:
  52
  53 I<bioperl-l@bioperl.org>
  54
  55 rather than to the module maintainer directly. Many experienced and
  56 reponsive experts will be able look at the problem and quickly
  57 address it. Please include a thorough description of the problem
  58 with code and data examples if at all possible.
  59
  60 =head2 Reporting Bugs
  61
  62 report bugs to the Bioperl bug tracking system to help us keep track
  63 the bugs and their resolution.  Bug reports can be submitted via the
  64 web:
  65
  66   http://bugzilla.open-bio.org/
  67
  68 =head1 AUTHOR
  69
  70 Nat Goodman
  71
  72 Email: natg at shore.net
  73
  74 Address:
  75
  76   Institute for Systems Biology
  77   1441 N 34th St
  78   Seattle, WA 98103-8904
  79
  80 =head1 APPENDIX
  81
  82 The rest of the documentation details each of the object
  83 methods. Internal methods are usually preceded with a _
  84
  85 =cut
  86
  87 # Let the code begin...
  88
  89 package Bio::Ontology::SimpleGOEngine::GraphAdaptor02;
  90
  91
  92 use strict;
  93
  94 use base qw(Bio::Ontology::SimpleGOEngine::GraphAdaptor);
  95
  96 # edges
  97 #   v0.2x returns (u0,v0, u1,v1, ...)
  98 #   v0.5x returns ([u0,v0], [u1,v1], ...)
  99 sub edges {
 100   my $self=shift;
 101   my @edges02=$self->_graph->edges(@_);
 102   my @edges;
 103   while (@edges02) {
 104     my($u,$v)=(shift @edges02,shift @edges02);
 105     push(@edges,[$u,$v]);
 106   }
 107   @edges;
 108 }
 109
 110 # edges_at
 111 #   v0.2x uses edges() method and returns (u0,v0, u1,v1, ...)
 112 #   v0.5x returns ([u0,v0], [u1,v1], ...)
 113 sub edges_at {
 114   my $self=shift;
 115   $self->edges(@_);
 116 }
 117
 118 # set_vertex_attribute
 119 #   v0.2x uses set_attribute($attribute,$v,$value)
 120 sub set_vertex_attribute {
 121   my($self,$v,$attribute,$value)=@_;
 122   $self->_graph->set_attribute($attribute,$v,$value);
 123 }
 124
 125 # get_vertex_attribute
 126 #   v0.2x uses get_attribute($attribute,$v)
 127 sub get_vertex_attribute {
 128   my($self,$v,$attribute)=@_;
 129   $self->_graph->get_attribute($attribute,$v);
 130 }
 131
 132 # set_edge_attribute
 133 #   v0.2x uses set_attribute($attribute,$u,$v,$value)
 134 sub set_edge_attribute {
 135   my($self,$u,$v,$attribute,$value)=@_;
 136   $self->_graph->set_attribute($attribute,$u,$v,$value);
 137 }
 138
 139 # get_edge_attribute
 140 #   v0.2x uses get_attribute($attribute,$u,$v)
 141 sub get_edge_attribute {
 142   my($self,$u,$v,$attribute)=@_;
 143   $self->_graph->get_attribute($attribute,$u,$v);
 144 }
 145
 146 1;