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