lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm

   1 # $Id: GraphAdaptor.pm 10525 2006-09-26 22:03:22Z sendu $
   2 #
   3 # BioPerl Graph adaptor for Bio::Ontology::SimpleGOEngine
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Nat Goodman <natg at shore.net>
   8 #
   9 # (c) Nathan Goodman natg@shore.net 2005
  10 # (c) ISB, Institute for Systems Biology 2005
  11 #
  12 # You may distribute this module under the same terms as perl itself.
  13 # Refer to the Perl Artistic License (see the license accompanying this
  14 # software package, or see http://www.perl.com/language/misc/Artistic.html)
  15 # for the terms under which you may use, modify, and redistribute this module.
  16 #
  17 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
  18 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
  19 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
  20 #
  21 # You may distribute this module under the same terms as perl itself
  22
  23 # POD documentation - main docs before the code
  24
  25 =head1 NAME
  26
  27 Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for
  28 Bio::Ontology::SimpleGOEngine
  29
  30 =head1 SYNOPSIS
  31
  32   use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
  33
  34   my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;
  35
  36 =head1 DESCRIPTION
  37
  38 This is an adaptor to simplify use of versions of the standard CPAN Graph module
  39 (old is versions 0.2x; new is 0.5x and beyond) within
  40 Bio::Ontology::SimpleGOEngine. Prior versions of this module supported Graph
  41 version older than 0.5, however we are removing support for these older version
  42 post BioPerl 1.6.901. If you absolutely require an old version of Graph, please
  43 use an older version of BioPerl.
  44
  45 This module implements only those Graph methods used by SimpleGOEngine. It is
  46 far from a complete compatibility layer! It also implements workarounds for
  47 certain performance problems in the current versions of Graph v0.5x.
  48
  49 This class provides implementations for the required graph methods using the new
  50 version of Graph. In most cases, these are simple pass-throughs
  51
  52 The methods implemented here or in the subclasses are listed below.
  53 In all cases, we implemented the Graph v0.5x interface.  Consult the
  54 Graph v0.5x man page for details.
  55
  56   add_vertex
  57   has_vertex
  58   add_edge
  59   has_edge
  60   vertices
  61   edges
  62   edges_at
  63   predecessors
  64   successors
  65   set_vertex_attribute
  66   get_vertex_attribute
  67   set_edge_attribute
  68   get_edge_attribute
  69   source_vertices
  70   sink_vertices
  71
  72 =head1 FEEDBACK
  73
  74 =head2 Mailing Lists
  75
  76 User feedback is an integral part of the evolution of this and other
  77 Bioperl modules. Send your comments and suggestions preferably to the
  78 Bioperl mailing lists  Your participation is much appreciated.
  79
  80   bioperl-l@bioperl.org                  - General discussion
  81   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  82
  83 =head2 Support
  84
  85 Please direct usage questions or support issues to the mailing list:
  86
  87 I<bioperl-l@bioperl.org>
  88
  89 rather than to the module maintainer directly. Many experienced and
  90 reponsive experts will be able look at the problem and quickly
  91 address it. Please include a thorough description of the problem
  92 with code and data examples if at all possible.
  93
  94 =head2 Reporting Bugs
  95
  96 report bugs to the Bioperl bug tracking system to help us keep track
  97 the bugs and their resolution.  Bug reports can be submitted via the
  98 web:
  99
 100   https://github.com/bioperl/bioperl-live/issues
 101
 102 =head1 AUTHOR
 103
 104 Nat Goodman
 105
 106 Email: natg at shore.net
 107
 108 Address:
 109
 110   Institute for Systems Biology
 111   1441 N 34th St
 112   Seattle, WA 98103-8904
 113
 114 =head1 APPENDIX
 115
 116 The rest of the documentation details each of the object
 117 methods. Internal methods are usually preceded with a _
 118
 119 =cut
 120
 121 # Let the code begin...
 122
 123 package Bio::Ontology::SimpleGOEngine::GraphAdaptor;
 124
 125 use Graph::Directed;
 126
 127 use strict;
 128
 129 use base qw(Bio::Root::Root);
 130
 131 =head2 new
 132
 133  Title   : new
 134  Usage   : $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor->new()
 135  Function: Creates a new graph
 136  Returns : Bio::Ontology::SimpleGOEngine::GraphAdaptor02 or
 137            Bio::Ontology::SimpleGOEngine::GraphAdaptor05 object,
 138            depending on which Graph version is available
 139  Args    : none
 140
 141 =cut
 142
 143 sub new {
 144   my( $class ) = @_;
 145   $class = ref $class || $class;
 146
 147   my $self= bless( {}, $class );
 148   $self->{_graph}=Graph::Directed->new();
 149   $self->{_vertex_attributes}={};
 150   $self->{_edge_attributes}={};
 151   return $self;
 152 }
 153
 154 # Here are the main methods
 155
 156 sub add_vertex {
 157   my $self=shift;
 158   $self->_graph->add_vertex(@_);
 159 }
 160 sub has_vertex {
 161   my $self=shift;
 162   $self->_graph->has_vertex(@_);
 163 }
 164 sub add_edge {
 165   my $self=shift;
 166   $self->_graph->add_edge(@_);
 167 }
 168 sub has_edge {
 169   my $self=shift;
 170   $self->_graph->has_edge(@_);
 171 }
 172 sub vertices {
 173   my $self=shift;
 174   $self->_graph->vertices(@_);
 175 }
 176 sub edges {
 177   my $self=shift;
 178   $self->_graph->edges(@_);
 179 }
 180 sub edges_at {
 181   my $self=shift;
 182   $self->_graph->edges_at(@_);
 183 }
 184 sub predecessors {
 185   my $self=shift;
 186   $self->_graph->predecessors(@_);
 187 }
 188 sub successors {
 189   my $self=shift;
 190   $self->_graph->successors(@_);
 191 }
 192 sub source_vertices {
 193   my $self=shift;
 194   $self->_graph->source_vertices();
 195 }
 196 sub sink_vertices {
 197   my $self=shift;
 198   $self->_graph->sink_vertices();
 199 }
 200 # The following methods workaround a performance problem in Graph v0.5x
 201 # when attributes are attached to the graph
 202 sub set_vertex_attribute {
 203   my($self,$v,$attribute,$value)=@_;
 204   $self->_vertex2attributes($v)->{$attribute}=$value;
 205 }
 206 sub get_vertex_attribute {
 207   my($self,$v,$attribute)=@_;
 208   $self->_vertex2attributes($v)->{$attribute};
 209 }
 210 sub set_edge_attribute {
 211   my($self,$u,$v,$attribute,$value)=@_;
 212   $self->_edge2attributes($u,$v)->{$attribute}=$value;
 213 }
 214 sub get_edge_attribute {
 215   my($self,$u,$v,$attribute)=@_;
 216   $self->_edge2attributes($u,$v)->{$attribute};
 217 }
 218
 219 =head2 _graph
 220
 221  Title   : _graph
 222  Usage   : $self->_graph();
 223  Function: Internal method to access 'real' graph
 224  Returns : Graph::Directed object
 225  Args    : none
 226
 227 =cut
 228
 229 sub _graph {$_[0]->{_graph}; }
 230
 231 =head2 _vertex_attributes
 232
 233  Title   : _vertex_attributes
 234  Usage   : $self->vertex_attributes();
 235  Function: Internal method to access HASH used to store vertex attributes
 236  Returns : Graph::Directed object
 237  Args    : none
 238
 239 =cut
 240
 241 sub _vertex_attributes {$_[0]->{_vertex_attributes}; }
 242
 243 =head2 _edge_attributes
 244
 245  Title   : _edge_attributes
 246  Usage   : $self->edge_attributes();
 247  Function: Internal method to access HASH used to store edge attributes
 248  Returns : Graph::Directed object
 249  Args    : none
 250
 251 =cut
 252
 253 sub _edge_attributes {$_[0]->{_edge_attributes}; }
 254
 255 =head2 _vertex2attributes
 256
 257  Title   : _vertex2attributes
 258  Usage   : $value=$graph->_vertex2attributes($v_->{ATTRIBUTE};
 259            $graph->_vertex2attributes($v)->{ATTRIBUTE}=$value;
 260  Function: Internal method to access attributes for a specific vertex
 261  Returns : HASH
 262  Args    : none
 263
 264 =cut
 265
 266 sub _vertex2attributes {
 267   my($self,$vertex)=@_;
 268   $self->_vertex_attributes->{$vertex} or $self->_vertex_attributes->{$vertex}={};
 269 }
 270
 271 =head2 _edge2attributes
 272
 273  Title   : _edge2attributes
 274  Usage   : $value=$graph->_edge2attributes($u,$v)->{ATTRIBUTE};
 275            $graph->_edge2attributes($u,$v)->{ATTRIBUTE}=$value;
 276  Function: Internal method to access HASH used to store edge attributes
 277  Returns : HASH
 278  Args    : none
 279
 280 =cut
 281
 282 sub _edge2attributes {
 283   my($self,$u,$v)=@_;
 284   $self->_edge_attributes->{$u,$v} or $self->_edge_attributes->{$u,$v}={};
 285 }
 286
 287 1;