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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::Gap
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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 Representation of a gap in a sequence; returned from Mapper.pm when the
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30 target region is in a gap.
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31
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32 =head1 METHODS
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33
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34 =cut
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35
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36 package Bio::EnsEMBL::Mapper::Gap;
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37
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38 use strict;
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39
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40 =head2 new
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41
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42 Arg [1] : int $start
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43 Arg [2] : int $end
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44 Example : $gap = Bio::EnsEMBL::Mapper::Gap($start, $end);
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45 Description: Creates a new Gap object.
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46 Returntype : Bio::EnsEMBL::Mapper::Gap
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47 Exceptions : none
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48 Caller : Bio::EnsEMBL::Mapper
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49 Status : Stable
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50
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51 =cut
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52
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53 sub new {
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54 my ( $proto, $start, $end, $rank ) = @_;
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55
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56 my $class = ref($proto) || $proto;
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57
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58 return bless( { 'start' => $start, 'end' => $end, 'rank' => $rank || 0 }, $class );
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59 }
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60
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61 =head2 start
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62
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63 Arg [1] : (optional) int $start
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64 start coordinate of gap region
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65 Example : $start = $gap->start();
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66 Description: Getter/Setter for the start attribute
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67 Returntype : int
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68 Exceptions : none
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69 Caller : general
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70 Status : Stable
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71
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72 =cut
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73
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74 sub start {
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75 my ( $self, $value ) = @_;
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76
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77 if ( defined($value) ) {
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78 $self->{'start'} = $value;
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79 }
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80
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81 return $self->{'start'};
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82 }
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83
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84 =head2 end
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85
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86 Arg [1] : (optional) int $newval
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87 The new value to set the end coordinate to
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88 Example : $end = $gap->end()
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89 Description: Getter/Setter for the end coordinate of the gap region
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90 Returntype : string
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91 Exceptions : none
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92 Caller : general
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93 Status : Stable
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94
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95 =cut
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96
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97 sub end {
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98 my ( $self, $value ) = @_;
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99
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100 if ( defined($value) ) {
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101 $self->{'end'} = $value;
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102 }
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103
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104 return $self->{'end'};
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105 }
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106
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107 =head2 length
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108
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109 Arg [1] : none
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110 Example : $len = $gap->length();
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111 Description: Getter for the length of this gap region
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112 Returntype : int
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113 Exceptions : none
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114 Caller : general
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115 Status : Stable
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116
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117 =cut
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118
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119 sub length {
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120 my ($self) = @_;
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121
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122 return $self->{'end'} - $self->{'start'} + 1;
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123 }
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124
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125 sub rank {
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126 my ( $self, $value ) = @_;
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127
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128 if ( defined($value) ) {
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129 $self->{'rank'} = $value;
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130 }
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131
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132 return $self->{'rank'};
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133 }
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134
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135 1;
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