lib/Bio/Network/Interaction.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Network::Interaction
   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::Network::Interaction - describes a protein-protein interaction
  11
  12 =head1 SYNOPSIS
  13
  14   # Add an interaction with some attributes
  15   use Bio::Network::Interaction;
  16
  17   my $interx = Bio::Network::Interaction->new(-weight => $score,
  18                                             -id => $id);
  19   $gr->add_interaction(-nodes => [($node1,$node2)],
  20                        -interaction => $interx);
  21
  22   # Retrieve an interaction using an identifier
  23   my $interaction = $gr->get_interaction_by_id($id);
  24
  25   my $id = $interaction->primary_id;
  26   my $wt = $interaction->weight;
  27   my @nodes = $interaction->nodes;
  28
  29 =head1 DESCRIPTION
  30
  31 This class contains information about a bi-molecular interaction.
  32 At present it just contains data about a weight (optional) and an
  33 identifier. Subclasses could hold more specific information. A pair
  34 of nodes can have more than one Interaction object associated with it.
  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 one
  42 of the 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 Support
  48
  49 Please direct usage questions or support issues to the mailing list:
  50
  51 I<bioperl-l@bioperl.org>
  52
  53 rather than to the module maintainer directly. Many experienced and
  54 reponsive experts will be able look at the problem and quickly
  55 address it. Please include a thorough description of the problem
  56 with code and data examples if at all possible.
  57
  58 =head2 Reporting Bugs
  59
  60 Report bugs to the Bioperl bug tracking system to help us keep track
  61 the bugs and their resolution.  Bug reports can be submitted via the
  62 web:
  63
  64   http://bugzilla.open-bio.org/
  65
  66 =head1 AUTHORS
  67
  68 Brian Osborne bosborne at alum.mit.edu
  69 Richard Adams richard.adams@ed.ac.uk
  70
  71 Maintained by Brian Osborne
  72
  73 =cut
  74
  75 use strict;
  76 package Bio::Network::Interaction;
  77 use base qw(Bio::Root::Root Bio::AnnotatableI Bio::Annotation::Collection);
  78
  79
  80 =head2 new
  81
  82  Name       : new
  83  Purpose    : Constructor for an Interaction object
  84  Usage      : my $interx = Bio::Network::Interaction->new(-id => $id);
  85  Returns    : A new Bio::Network::Interaction object
  86  Arguments  : -id                => interaction id
  87               -weight (optional) => weight score
  88
  89 =cut
  90
  91 sub new {
  92         my ($caller,@args) = @_;
  93         my $class = ref ($caller) || $caller;
  94         my $self = {};
  95         bless ($self, $class);
  96
  97         my ($weight,$id) = $self->_rearrange([qw( WEIGHT ID )], @args);
  98         $self->{_weight} = defined($weight) ? $weight : undef;
  99         $self->{_id} = defined($id) ? $id : undef;
 100         return $self;
 101 }
 102
 103 =head2 weight
 104
 105  Name      : weight
 106  Purpose   : Get or set a weight or score
 107  Usage     : my $weight = $interx->weight()
 108                      or
 109              $interx->weight(3)
 110  Returns   : a number
 111  Arguments : Nothing or a number
 112
 113 =cut
 114
 115 sub weight {
 116         my $self = shift;
 117         $self->{_weight} = shift if @_;
 118         return defined($self->{_weight}) ? $self->{_weight} : undef;
 119 }
 120
 121 =head2 primary_id
 122
 123  Name      : primary_id
 124  Purpose   : Get or set the primary_id
 125  Usage     : my $id = $interx->primary_id()
 126                        or
 127              $interx->primary_id("SIB4")
 128  Returns   : A string identifier
 129  Arguments : Nothing or an identifier
 130
 131 =cut
 132
 133 sub primary_id {
 134         my $self = shift;
 135         if (@_) {
 136                 my $v  = shift;
 137                 $self->throw ("Primary interaction ID must be a text value, not a [" .
 138                                                   ref($v). "].") if (ref ($v));
 139                 $self->{_id} = $v;
 140         }
 141         return defined($self->{_id}) ? $self->{_id} : undef;
 142 }
 143
 144 =head2 nodes
 145
 146  Name       : nodes
 147  Purpose    : Get the pair of nodes for an Interaction
 148  Usage      : my $count = $interx->nodes
 149                        or
 150               my @nodes = $interx->nodes
 151  Returns    : Gets an array of 2 Nodes or a count of the number of
 152               Nodes
 153  Arguments  :
 154  Notes      : Getting a count of the number of Nodes in an Interaction
 155               will almost always return 2, but there is a formal possibility
 156               that a Node could interact with itself, returning 1
 157
 158 =cut
 159
 160 sub nodes {
 161         my $self = shift;
 162         my @nodes = @{$self->{_nodes}};
 163         wantarray ? return @nodes : return scalar @nodes;
 164 }
 165
 166 =head2 annotation
 167
 168  Title   : annotation
 169  Usage   : my $annotation = $ix->annotation
 170                    or
 171            $ix->annotation($annotation)
 172  Function: Gets or sets the annotation
 173  Returns : Bio::AnnotationCollectionI object
 174  Args    : None or Bio::AnnotationCollectionI object
 175
 176 See L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection>
 177 for more information
 178
 179 =cut
 180
 181 sub annotation {
 182         my ($obj,$value) = @_;
 183         if ( defined $value ) {
 184                 $obj->throw("Object of class " . ref($value) . " does not implement ".
 185                                                 "Bio::AnnotationCollectionI.")
 186                   unless $value->isa("Bio::AnnotationCollectionI");
 187                 $obj->{'_annotation'} = $value;
 188         } elsif( ! defined $obj->{'_annotation'}) {
 189                 $obj->{'_annotation'} = Bio::Annotation::Collection->new();
 190         }
 191         return $obj->{'_annotation'};
 192 }
 193
 194 =head2 object_id
 195
 196  Name      : object_id
 197  Purpose   : Alias to primary_id
 198  Usage     : my $id = $edge->object_id()
 199  Notes     : Deprecated
 200
 201 =cut
 202
 203 sub object_id {
 204         my ($self,$id) = @_;
 205         $id ? $self->primary_id($id) : return $self->primary_id;
 206 }
 207
 208 1;
 209
 210 __END__