branch-1-6/Bio/Tools/Primer/Pair.pm

   1 # $Id$
   2 # BioPerl module for Bio::Tools::Primer::Pair
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Tools::Primer::Pair - two primers on left and right side
  17
  18 =head1 SYNOPSIS
  19
  20     use Bio::Tools::Primer::Pair;
  21
  22     my $pair = Bio::Tools::Primer::Pair->new( -left => $leftp , -right => $rightp);
  23
  24     # helper functions
  25
  26     print "GC percentage different",$pf->gc_difference(),"\n";
  27     print "product length is ",$pf->product_length,"\n";
  28
  29
  30
  31 =head1 DESCRIPTION
  32
  33 Primer Pairs represents one primer in a primer pair. This object is mainly for
  34 designing primers, and probably principly used in the primer design system
  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
  42 the Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
  62 web:
  63
  64   http://bugzilla.open-bio.org/
  65
  66 =head1 AUTHOR - Ewan Birney
  67
  68 Email birney-at-ebi.ac.uk
  69
  70 =head1 APPENDIX
  71
  72 The rest of the documentation details each of the object methods.
  73 Internal methods are usually preceded with a _
  74
  75 =cut
  76
  77
  78 # Let the code begin...
  79
  80
  81
  82 package Bio::Tools::Primer::Pair;
  83
  84 use base qw(Bio::Root::Root);
  85
  86 sub new {
  87     my ( $caller, @args) = @_;
  88     my ($self) = $caller->SUPER::new(@args);
  89
  90     my ($left,$right) = $self->_rearrange([qw(LEFT RIGHT)],@args);
  91
  92     if( !defined $left || !defined $right ) {
  93         $self->throw("Pair must be initialised with left and right primers");
  94     }
  95
  96     $self->left($left);
  97     $self->right($right);
  98
  99     # done - we hope
 100     return $self;
 101 }
 102
 103 sub left {
 104     my $self = shift;
 105     my $left = shift;
 106
 107     if( defined $left ) {
 108         if( !ref $left || !$left->isa("Bio::Tools::Primer::Feature") ) {
 109             $self->throw("left primer must be a Bio::Tools::Primer::Feature, not $left");
 110         }
 111         $self->{'left'} = $left;
 112     }
 113
 114     return $self->{'left'};
 115 }
 116
 117
 118 sub right {
 119     my $self = shift;
 120     my $right = shift;
 121
 122     if( defined $right ) {
 123         if( !ref $right || !$right->isa("Bio::Tools::Primer::Feature") ) {
 124             $self->throw("right primer must be a Bio::Tools::Primer::Feature, not $right");
 125         }
 126         $self->{'right'} = $right;
 127     }
 128
 129     return $self->{'right'};
 130 }
 131
 132 sub gc_difference {
 133     my $self = shift;
 134
 135     return abs ( $self->left->gc_percent - $self->right->gc_percent );
 136 }
 137
 138 sub product_length {
 139     my $self = shift;
 140
 141     return $self->right->end - $self->left->start +1;
 142 }
 143
 144
 145 1;