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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::Map::QtlFeature
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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 Represents a QtlFeature in the EnsEMBL database. QtlFeatures are
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30 generally very long and its not clear wether a representation in Contig
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31 coordinates actually makes sense. In the database they will have
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32 chromosomal coordinates.
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33
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34 =head1 METHODS
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35
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36 =cut
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37
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38 package Bio::EnsEMBL::Map::QtlFeature;
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39
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40 use strict;
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41 use vars qw(@ISA);
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42
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43 use Bio::EnsEMBL::Feature;
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44
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45 @ISA = qw(Bio::EnsEMBL::Feature);
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46
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47
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48 =head2 new
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49
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50 Arg [1] : Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor $adaptor
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51 Example : none
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52 Description: Create a QtlFeature
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53 Returntype : Bio::EnsEMBL::Map::QtlFeature
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54 Exceptions : none
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55 Caller : general, DBSQL::QtlFeatureAdaptor
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56 Status : Stable
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57
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58 =cut
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59
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60 sub new {
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61 my ( $class, $adaptor, $slice, $start, $end, $qtl, $analysis ) = @_;
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62
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63 $class = ref( $class ) ||$class;
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64 my $self = bless( {
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65 'slice' => $slice,
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66 'start' => $start,
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67 'end' => $end,
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68 'qtl' => $qtl,
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69 'analysis' => $analysis,
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70 'strand' => 0
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71 }, $class );
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72
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73 $self->adaptor($adaptor);
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74 return $self;
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75 }
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76
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77
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78 =head2 qtl
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79
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80 Arg [1] : Bio::EnsEMBL::Map::Qtl $qtl
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81 the qtl object for this feature
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82 Example : none
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83 Description: return the Qtl object associated with this location
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84 Returntype : Bio::EnsEMBL::Map::Qtl
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85 Exceptions : none
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86 Caller : general
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87 Status : Stable
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88
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89 =cut
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90
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91 sub qtl {
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92 my $self = shift;
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93
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94 if(@_) {
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95 $self->{'qtl'} = shift;
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96 }
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97
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98 return $self->{'qtl'};
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99 }
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100
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101
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102
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103 =head2 strand
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104
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105 Arg [1] : none
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106 Example : $strand = $qtl_feat->strand();
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107 Description: Overrides the Feature strand method to always return a
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108 value of 0 for qtl features (they are unstranded features)
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109 Returntype : int (always 0)
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110 Exceptions : none
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111 Caller : general
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112 Status : Stable
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113
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114 =cut
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115
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116 sub strand {
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117 my $self = shift;
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118 return 0;
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119 }
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120
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121
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122
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123 =head2 move
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124
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125 Arg [1] : $start - The new end of this qtl feature
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126 Arg [2] : $end - The new start of this qtl feature
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127 Arg [3] : $strand - ignored always set to 0
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128 Example : $qtl_feat->move(1, 10_000);
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129 Description: Overrides superclass move() method to ensure strand is always 0.
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130 See Bio::EnsEMBL::Feature::move
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131 Returntype : none
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132 Exceptions : none
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133 Caller : general
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134 Status : Stable
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135
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136 =cut
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137
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138 sub move {
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139 my ($self, $start, $end, $strand) = @_;
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140
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141 #maintain a strandedness of 0
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142 return $self->SUPER::move($start,$end,0);
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143 }
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144
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145
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146
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147 1;
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148
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149
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