Bio/Graph/Edge.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Graph::Edge
   4 #
   5 # You may distribute this module under the same terms as perl itself
   6 # POD documentation - main docs before the code
   7
   8 =head1 NAME
   9
  10 Bio::Graph::Edge - encapsulation of an interaction between 2 Bio::Seq objects
  11
  12 =head1 SYNOPSIS
  13
  14   ## get an interaction between two nodes ##
  15
  16   my $edge  = $gr->edge( $gr->nodes_by_id('P12345'),
  17                          $gr->nodes_by_id('P23456'));
  18   my $id    = $edge->object_id();
  19   my $wt    = $edge->weight();
  20   my @nodes = $edge->nodes();
  21
  22 =head1 DESCRIPTION
  23
  24 This class contains information about a bimolecular interaction.
  25 At present it just contains data about its component node, a weight
  26 (if set) and an identifier. Subclasses could hold more specific
  27 information.
  28
  29 =head1 FEEDBACK
  30
  31 =head2 Mailing Lists
  32
  33 User feedback is an integral part of the evolution of this and other
  34 Bioperl modules. Send your comments and suggestions preferably to one
  35 of the Bioperl mailing lists. Your participation is much appreciated.
  36
  37   bioperl-l@bioperl.org                  - General discussion
  38   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  39
  40 =head2 Reporting Bugs
  41
  42 Report bugs to the Bioperl bug tracking system to help us keep track
  43 the bugs and their resolution.  Bug reports can be submitted via the
  44 web:
  45
  46   http://bugzilla.open-bio.org/
  47
  48 =head1 AUTHOR - Richard Adams
  49
  50 Email richard.adams@ed.ac.uk
  51
  52 =cut
  53
  54 use strict;
  55 package Bio::Graph::Edge;
  56 use base qw(Bio::Root::Root Bio::IdentifiableI);
  57
  58
  59 =head2 new
  60
  61  Name       : new
  62  Purpose    : constructor for an edge object
  63  Usage      : my $edge = Bio::Graph::Edge->new(nodes => [$node1,$node2]
  64                                                id => $id);
  65               $graph->add_edge($edge);
  66  Returns    : a new Bio::Graph::Edge object
  67  Arguments  : hash nodes            => array reference of 2 nodes
  68                    id               => edge id
  69                    weight(optional) => weight score.
  70
  71 =cut
  72
  73 sub new {
  74       ##array based, not hash based ##..., therefore does not use
  75       #Bio::Root::Root->new().
  76
  77         my ($caller, @args) = @_;
  78         my $class  = ref ($caller) || $caller;
  79         my $self    = [];
  80         bless ($self, $class);
  81
  82         my ($weight, $id, $nodes) = $self->_rearrange([qw( WEIGHT ID NODES)], @args);
  83         $self->[0] = $nodes->[0];
  84         $self->[1] = $nodes->[1];
  85         $self->[2] = defined($weight)?$weight:undef;
  86         $self->[3] = defined($id)?$id:undef;
  87         return $self;
  88
  89 }
  90
  91 =head2 weight
  92
  93  Name      : weight
  94  Purpose   : get/setter for weight score
  95  Usage     : my $weight = $edge->weight();
  96  Returns   : anumber
  97  Arguments : void/ a number
  98
  99 =cut
 100
 101 sub weight {
 102         my $self = shift;
 103         if (@_) {$self->[2] = shift;}
 104         return defined($self->[2])?$self->[2]:undef;
 105 }
 106
 107 =head2 object_id
 108
 109  Name      : object_id
 110  Purpose   : get/setter for object_id
 111  Usage     : my $id = $edge->object_id();
 112  Returns   : a string identifier
 113  Arguments : void/ an identifier
 114
 115 =cut
 116
 117 sub object_id {
 118         my $self            = shift;
 119         if (@_) {
 120                 my $v  = shift;
 121                 if (ref ($v)) {
 122                         $self->throw ("Edge ID must be a text value, not a [".
 123                                                         ref($v). "].");
 124                         }
 125                 $self->[3] = shift;
 126         }
 127         return defined($self->[3])?$self->[3]:undef;
 128 }
 129
 130 =head2  nodes
 131
 132  Name      : nodes
 133  Purpose   : get/setter for nodes
 134  Usage     : my @nodes = $edge->nodes();
 135  Returns   : a 2 element list of nodes /void
 136  Arguments : void/ a 2 element list of nodes.
 137
 138 =cut
 139
 140 sub nodes {
 141         my ($self, @args) = @_;
 142         if (@args >= 2 ) {
 143                 $self->[0] =  $args[0];
 144                 $self->[1] =  $args[1];
 145                 }
 146         return ($self->[0], $self->[1]);
 147 }
 148
 149 1;