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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Mapper::Pair
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24
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25 =head1 SYNOPSIS
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26
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27 =head1 DESCRIPTION
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28
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29 Two regions mapped between different coordinate systems are each
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30 represented by a Bio::EnsEMBL::Mapper::Unit and joined together as a
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31 Bio::EnsEMBL::Mapper::Pair.
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32
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33 =head1 METHODS
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34
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35 =cut
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36
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37 package Bio::EnsEMBL::Mapper::Pair;
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38
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39 use strict;
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40
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41 sub new {
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42 my ( $proto, $from, $to, $ori ) = @_;
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43
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44 my $class = ref($proto) || $proto;
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45
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46 return
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47 bless( { 'from' => $from, 'to' => $to, 'ori' => $ori }, $class );
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48 }
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49
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50 =head2 to
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51
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52 Arg 1 Bio::EnsEMBL::Mapper::Unit $seqobj
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53 from and to represent the two regions
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54 which are mapped to each other
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55 Function accessor method
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56 Returntype Bio::EnsEMBL::Mapper::Unit
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57 Exceptions none
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58 Caller Bio::EnsEMBL::Mapper::Pair
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59 Status : Stable
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60
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61 =cut
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62
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63 sub to {
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64 my ( $self, $value ) = @_;
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65
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66 if ( defined($value) ) {
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67 $self->{'to'} = $value;
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68 }
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69
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70 return $self->{'to'};
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71 }
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72
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73 =head2 from
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74
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75 Arg 1 Bio::EnsEMBL::Mapper::Unit $seqobj
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76 from and to represent the two regions
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77 which are mapped to each other
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78 Function accessor method
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79 Returntype Bio::EnsEMBL::Mapper::Unit
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80 Exceptions none
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81 Caller Bio::EnsEMBL::Mapper::Pair
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82 Status : Stable
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83
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84 =cut
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85 sub from {
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86 my ( $self, $value ) = @_;
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87
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88 if ( defined($value) ) {
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89 $self->{'from'} = $value;
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90 }
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91
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92 return $self->{'from'};
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93 }
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94
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95 =head2 ori
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96
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97 Arg 1 Bio::EnsEMBL::Mapper::Unit $ori
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98 Function accessor method
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99 relative orientation of the the
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100 two mapped regions
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101 Returntype Bio::EnsEMBL::Mapper::Unit
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102 Exceptions none
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103 Caller Bio::EnsEMBL::Mapper::Pair
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104 Status : Stable
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105
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106 =cut
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107
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108 sub ori {
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109 my ( $self, $value ) = @_;
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110
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111 if ( defined($value) ) {
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112 $self->{'ori'} = $value;
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113 }
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114
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115 return $self->{'ori'};
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116 }
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117
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118 1;
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