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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::Unit - One side of a map 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
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38 package Bio::EnsEMBL::Mapper::Unit;
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39
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40 use strict;
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41
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42 sub new {
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43 my ( $proto, $id, $start, $end ) = @_;
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44
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45 my $class = ref($proto) || $proto;
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46
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47 return
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48 bless( { 'id' => $id, 'start' => $start, 'end' => $end }, $class );
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49 }
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50
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51 =head2 id
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52
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53 Arg 1 int|char $id
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54 the id of the object (e.g. seq_region_name) which is mapped
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55 Function accessor method
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56 Returntype int|char
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57 Exceptions none
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58 Caller Bio::EnsEMBL::Mapper::Unit
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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 id {
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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->{'id'} = $value;
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68 }
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69
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70 return $self->{'id'};
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71 }
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72
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73 =head2 start
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74
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75 Arg 1 int $start
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76 the start coordinate of the mapped
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77 region which this object represents
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78 Function accessor method
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79 Returntype int
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80 Exceptions none
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81 Caller Bio::EnsEMBL::Mapper::Unit
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82 Status Stable
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83
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84 =cut
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85
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86 sub start {
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87 my ( $self, $value ) = @_;
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88
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89 if ( defined($value) ) {
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90 $self->{'start'} = $value;
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91 }
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92
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93 return $self->{'start'};
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94 }
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95
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96 =head2 end
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97
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98 Arg 1 int $end
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99 the end coordinate of the mapped
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100 region which this object represents
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101 Function accessor method
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102 Returntype int
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103 Exceptions none
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104 Caller Bio::EnsEMBL::Mapper::Unit
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105 Status Stable
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106
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107 =cut
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108
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109 sub end {
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110 my ( $self, $value ) = @_;
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111
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112 if ( defined($value) ) {
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113 $self->{'end'} = $value;
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114 }
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115
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116 return $self->{'end'};
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117 }
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118
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119 1;
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