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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::SimpleFeature - A simple feature with a location and label
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24
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25 =head1 SYNOPSIS
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26
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27 use Bio::EnsEMBL::SimpleFeature;
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28
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29 $feature = Bio::EnsEMBL::SimpleFeature->new(
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30 -start => 100,
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31 -end => 220,
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32 -strand => -1,
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33 -slice => $slice,
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34 -analysis => $analysis,
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35 -score => 58,
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36 -display_label => 'EponineTSS',
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37 -dbID => 1230,
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38 -adaptor => $adaptor
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39 );
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40
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41 =head1 DESCRIPTION
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42
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43 This is a simple feature which extends the Feature class to add
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44 display_label and score attributes.
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45
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46 =head1 METHODS
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47
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48 =cut
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49
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50 use strict;
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51
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52 package Bio::EnsEMBL::SimpleFeature;
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53
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54 use vars qw(@ISA);
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55
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56 use Bio::EnsEMBL::Feature;
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57 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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58 use Scalar::Util qw(weaken isweak);
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59
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60 @ISA = qw(Bio::EnsEMBL::Feature);
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61
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62
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63 =head2 new
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64
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65 Arg [DISPLAY_LABEL]: The label assigned to this simple feature
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66 Arg [...] : Named arguments passed to superclass
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67 Example : $feature = Bio::EnsEMBL::SimpleFeature->new
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68 (-start => 1,
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69 -end => 100,
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70 -strand => 1,
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71 -slice => $slice,
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72 -analysis => $analysis,
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73 -adaptor => $adaptor,
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74 -dbID => 10,
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75 -display_label => 'EponineTSS',
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76 -score => 100);
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77 Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses
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78 of this method are instantiated, rather than this class itself.
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79 Returntype : Bio::EnsEMBL::Feature
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80 Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND arguments
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81 Caller : general, subclass constructors
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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 new {
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87 my $caller = shift;
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88
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89 #allow this to be called as class or object method
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90 my $class = ref($caller) || $caller;
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91 my $self = $class->SUPER::new(@_);
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92
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93 my ($display_label, $score) = rearrange(['DISPLAY_LABEL','SCORE'],@_);
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94
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95 $self->{'display_label'} = $display_label;
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96 $self->{'score'} = $score;
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97
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98 return $self;
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99 }
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100
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101
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102 =head2 new_fast
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103
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104 Arg [1] : hashref to be blessed
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105 Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
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106 Exceptions : none
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107 Returntype : Bio::EnsEMBL::Feature
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108 Caller : general, subclass constructors
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109 Status : Stable
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110
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111 =cut
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112
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113
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114 sub new_fast {
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115 my $class = shift;
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116 my $hashref = shift;
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117 my $self = bless $hashref, $class;
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118 weaken($self->{adaptor}) if ( ! isweak($self->{adaptor}) );
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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 display_label
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124
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125 Arg [1] : (optional) string $value
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126 Example : $label = $simple_feature->display_label();
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127 Description: Getter/Setter for the display label associated with this
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128 feature.
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129 Returntype : string
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130 Exceptions : none
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131 Caller : general
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132 Status : Stable
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133
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134 =cut
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135
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136 sub display_label{
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137 my $self = shift;
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138
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139 $self->{'display_label'} = shift if(@_);
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140
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141 return $self->{'display_label'};
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142 }
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143
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144
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145 =head2 display_id
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146
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147 Arg [1] : none
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148 Example : print $rf->display_id();
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149 Description: This method returns a string that is considered to be
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150 the 'display' identifier. For simple features this is the
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151 display_label if it is available otherwise it is an empty
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152 string.
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153 Returntype : string
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154 Exceptions : none
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155 Caller : web drawing code
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156 Status : Stable
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157
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158 =cut
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159
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160 sub display_id {
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161 my $self = shift;
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162 return $self->{'display_label'} || '';
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163 }
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164
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165
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166
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167 =head2 score
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168
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169 Arg [1] : (optional) string $value
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170 Example : $score = $simple_feature->score();
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171 Description: Getter/Setter for the score associated with this
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172 feature.
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173 Returntype : string
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174 Exceptions : none
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175 Caller : general
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176 Status : Stable
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177
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178 =cut
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179
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180 sub score {
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181 my $self = shift;
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182 $self->{'score'} = shift if(@_);
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183 return $self->{'score'};
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184 }
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185
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186
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187 1;
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