annotate variant_effect_predictor/Bio/EnsEMBL/RepeatFeature.pm @ 1:d6778b5d8382 draft default tip

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author willmclaren
date Fri, 03 Aug 2012 10:05:43 -0400
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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::RepeatFeature - A feature representing a repeat on a piece of
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24 sequence.
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25
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26 =head1 SYNOPSIS
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27
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28 my $rf = new Bio::EnsEMBL::Feature(
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29 -start => 100,
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30 -end => 220,
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31 -strand => -1,
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32 -slice => $slice,
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33 -analysis => $analysis,
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34 -repeat_consensus => $rc,
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35 -hstart => 10,
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36 -hend => 100,
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37 -hstrand => 1,
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38 -score => 83.2
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39 );
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40
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41 my $hstart = $feat->hstart;
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42 my $hend = $feat->hend;
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43
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44 # move the feature to the chromosomal coordinate system
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45 $feature = $feature->transform('chromosome');
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46
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47 # move the feature to a different slice
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48 # (possibly on another coord system)
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49 $feature = $feature->transfer($new_slice);
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50
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51 # project the feature onto another coordinate system possibly across
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52 # boundaries:
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53 @projection = @{ $feature->project('contig') };
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54
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55 # change the start, end, and strand of the feature in place
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56 $feature->move( $new_start, $new_end, $new_strand );
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57
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58 =head1 DESCRIPTION
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59
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60 This a feature representing a repeat region on a sequence
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61
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62 =head1 METHODS
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63
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64 =cut
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65
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66 package Bio::EnsEMBL::RepeatFeature;
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67
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68 use strict;
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69
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70 use Bio::EnsEMBL::Utils::Exception qw(throw);
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71 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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72
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73 use base qw/Bio::EnsEMBL::Feature/;
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74
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75 =head2 new
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76
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77 Arg [REPEAT_CONSENSUS] : Bio::EnsEMBL::RepeatConsensus (optional)
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78 The repeat consensus for this repeat feature
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79 Arg [HSTART] : int (optional)
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80 The hit start on the consensus sequence
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81 Arg [HEND] : int (optional)
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82 The hit end on the consensus sequence
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83 Arg [SCORE] : float (optional)
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84 The score
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85 Arg [...] : Named arguments to superclass constructor
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86 (see Bio::EnsEMBL::Feaure)
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87 Example : $rf = Bio::EnsEMBL::RepeatFeature->new(-REPEAT_CONSENSUS => $rc,
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88 -HSTART => 10,
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89 -HEND => 100,
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90 -SCORE => 58.0,
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91 -START => 1_000_100,
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92 -END => 1_000_190,
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93 -STRAND => 1,
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94 -ANALYSIS => $an,
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95 -SLICE => $chr_slice);
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96 Description: Creates a new Bio::EnsEMBL::RepeatFeature object
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97 Returntype : Bio::EnsEMBL::RepeatFeature
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98 Exceptions : none
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99 Caller : RepeatFeatureAdaptors
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100 Status : Stable
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101
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102 =cut
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103
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104 sub new {
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105 my $caller = shift;
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106
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107 my $class = ref($caller) || $caller;
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108
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109 my $self = $class->SUPER::new(@_);
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110
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111 my ($repeat_consensus, $hstart, $hend, $score) =
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112 rearrange(['REPEAT_CONSENSUS','HSTART','HEND','SCORE'], @_);
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113
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114 $self->repeat_consensus($repeat_consensus);
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115 $self->{'hstart'} = $hstart;
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116 $self->{'hend'} = $hend;
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117 $self->{'score'} = $score;
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118
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119 return $self;
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120 }
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121
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122
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123 =head2 repeat_consensus
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124
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125 Arg [1] : (optional) Bio::EnsEMBL::RepeatConsensus
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126 Example : $repeat_consensus = $repeat->repeat_consensus;
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127 Description: Getter/Setter for the repeat consensus of this repeat
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128 Returntype : Bio::EnsEMBL::RepeatConsensus
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129 Exceptions : none
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130 Caller : general
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131 Status : Stable
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132
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133 =cut
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134
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135 sub repeat_consensus {
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136 my $self = shift;
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137
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138 if(@_) {
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139 my $rc = shift;
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140 if(defined($rc)) {
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141 if(!ref($rc) || !$rc->isa('Bio::EnsEMBL::RepeatConsensus')) {
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142 throw('RepeatConsensus arg must be a Bio::EnsEMBL::RepeatConsensus');
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143 }
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144 }
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145 $self->{'repeat_consensus'} = $rc;
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146 }
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147
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148 return $self->{'repeat_consensus'};
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149 }
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150
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151
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152
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153 =head2 hstart
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154
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155 Arg [1] : (optional) int $hstart
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156 Example : $hit_start = $repeat->hstart;
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157 Description: Getter/Setter for the start bp of this repeat match on the
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158 consensus sequence.
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159 Returntype : int
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160 Exceptions : none
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161 Caller : general
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162 Status : Stable
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163
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164 =cut
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165
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166 sub hstart {
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167 my $self = shift;
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168 $self->{'hstart'} = shift if(@_);
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169 return $self->{'hstart'};
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170 }
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171
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172
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173 =head2 score
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174
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175 Arg [1] : (optional) float $score
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176 Example : $score = $repeat->score();
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177 Description: Getter/Setter for the score of this repeat feature
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178 Returntype : int
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179 Exceptions : none
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180 Caller : general
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181 Status : Stable
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182
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183 =cut
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184
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185 sub score {
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186 my $self = shift;
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187 $self->{'score'} = shift if(@_);
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188 return $self->{'score'};
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189 }
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190
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191
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192
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193 =head2 hend
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194
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195 Arg [1] : (optional) int $hend
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196 Example : $hit_end = $repeat->hend;
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197 Description: Getter/Setter for the end bp of this repeat match on the
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198 consensus sequence.
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199 Returntype : int
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200 Exceptions : none
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201 Caller : general
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202 Status : Stable
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203
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204 =cut
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205
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206 sub hend {
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207 my $self = shift;
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208 $self->{'hend'} = shift if(@_);
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209 return $self->{'hend'};
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210 }
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211
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212
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213
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214 =head2 hstrand
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215
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216 Arg [1] : none
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217 Example : none
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218 Description: always returns 1. method exists for consistancy with other
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219 features.
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220 Returntype : int
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221 Exceptions : none
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222 Caller : general
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223 Status : Stable
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224
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225 =cut
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willmclaren
parents:
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226
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willmclaren
parents:
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227 sub hstrand {
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willmclaren
parents:
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228 return 1;
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willmclaren
parents:
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229 }
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parents:
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230
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parents:
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231
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parents:
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232 =head2 display_id
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parents:
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233
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parents:
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234 Arg [1] : none
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parents:
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235 Example : print $rf->display_id();
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parents:
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236 Description: This method returns a string that is considered to be
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willmclaren
parents:
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237 the 'display' identifier. For repeat_features this is the
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willmclaren
parents:
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238 name of the repeat consensus if it is available otherwise it is
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willmclaren
parents:
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239 an empty string.
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willmclaren
parents:
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240 Returntype : string
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willmclaren
parents:
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241 Exceptions : none
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willmclaren
parents:
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242 Caller : web drawing code
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willmclaren
parents:
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243 Status : Stable
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willmclaren
parents:
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244
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willmclaren
parents:
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245 =cut
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parents:
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246
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willmclaren
parents:
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247 sub display_id {
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willmclaren
parents:
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248 my $self = shift;
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parents:
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249
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parents:
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250 my $id = '';
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parents:
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251
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parents:
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252 my $rc = $self->{'repeat_consensus'};
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parents:
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253 if($rc) {
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willmclaren
parents:
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254 $id = $rc->name();
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parents:
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255 }
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parents:
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256
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willmclaren
parents:
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257 return $id;
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willmclaren
parents:
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258 }
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parents:
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259
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parents:
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260
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parents:
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261 1;
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willmclaren
parents:
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262
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willmclaren
parents:
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263 __END__
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parents:
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264
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willmclaren
parents:
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265 =head1 NAME - Bio::EnsEMBL::RepeatFeature
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willmclaren
parents:
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266
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willmclaren
parents:
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267 =head1 AUTHOR
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parents:
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268
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willmclaren
parents:
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269 James Gilbert B<email> jgrg@sanger.ac.uk
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willmclaren
parents:
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270