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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::SeqFeatureI
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24
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25 =head1 DESCRIPTION
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26
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27 Do not use this class. It is deprecated and has been replaced by
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28 Bio::EnsEMBL::Feature.
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29
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30 =head1 METHODS
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31
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32 =cut
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33
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34
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35 # Let the code begin...
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36
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37
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38 package Bio::EnsEMBL::SeqFeatureI;
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39
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40 use vars qw(@ISA);
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41 use strict;
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42 use Carp;
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43
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44 # Object preamble - inherits from Bio::Root::Object
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45
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46 use Bio::SeqFeatureI;
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47 use Bio::EnsEMBL::Root;
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48
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49 @ISA = qw(Bio::EnsEMBL::Root Bio::SeqFeatureI);
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50
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51
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52 =head1 Abstract methods
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53
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54 These methods must be implemented in all subclasses.
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55
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56
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57 =head2 analysis
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58
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59 Title : analysis
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60 Usage : $sf->analysis();
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61 Function: Store details of the program/database
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62 and versions used to create this feature.
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63
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64 Example :
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65 Returns :
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66 Args :
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67
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68
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69 =cut
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70
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71 sub analysis {
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72 my ($self,$value) = @_;
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73
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74 $self->throw("Have not implemeneted analysis");
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75
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76 }
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77
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78 =head2 validate
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79
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80 Title : validate
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81 Usage : $sf->validate;
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82 Function: Checks whether all the data is present in the
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83 object.
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84 Example :
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85 Returns :
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86 Args :
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87
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88
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89 =cut
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90
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91 sub validate {
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92 my ($self,$value) = @_;
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93
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94 $self->throw("Have not implemeneted validate");
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95
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96
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97 }
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98
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99
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100 sub id {
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101 my ($self,$value) = @_;
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102
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103 $self->throw("Have not implemented id");
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104 }
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105
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106 =head2 percent_id
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107
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108 Title : percent_id
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109 Usage : $pid = $feat->percent_id()
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110 $feat->percent_id($pid)
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111 Function: get/set on percentage identity information
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112 Returns : float
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113 Args : none if get, the new value if set
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114
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115 =cut
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116
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117 sub percent_id {
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118 my ($self) = @_;
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119 $self->throw("percent_id() not yet implemented");
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120 }
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121
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122 =head2 e_value
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123
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124 Title : p_value
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125 Usage : $p_val = $feat->p_value()
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126 $feat->p_value($p_val)
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127 Function: get/set on p value information
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128 Returns : float
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129 Args : none if get, the new value if set
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130
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131 =cut
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132
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133 sub e_value {
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134 my ($self) = @_;
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135 $self->throw("e value() not yet implemented");
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136 }
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137
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138 =head2 phase
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139
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140 Title : phase
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141 Usage : $phase = $feat->phase()
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142 $feat->phase($phase)
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143 Function: get/set on start phase of predicted exon feature
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144 Returns : [0,1,2]
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145 Args : none if get, 0,1 or 2 if set.
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146
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147 =cut
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148
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149 sub phase {
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150 my ($self) = @_;
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151 $self->throw("phase() not yet implemented");
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152 }
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153
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154 =head2 end_phase
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155
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156 Title : end_phase
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157 Usage : $end_phase = $feat->end_phase()
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158 $feat->end_phase($end_phase)
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159 Function: get/set on end phase of predicted exon feature
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160 Returns : [0,1,2]
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161 Args : none if get, 0,1 or 2 if set.
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162
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163 =cut
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164
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165 sub end_phase {
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166 my ($self) = @_;
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167 $self->throw("end_phase() not yet implemented");
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168 }
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169
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170
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171 # this is a bit too sneaky.
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172 sub location {
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173 my ($self)= @_;
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174 return $self;
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175 }
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176
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177
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178 1;
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