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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::IdMapping::TinyTranslation - lightweight translation object
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24
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25 =head1 SYNOPSIS
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26
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27 if ( my $tl = $tr->translation ) {
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28 my $lightweight_tl =
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29 Bio::EnsEMBL::IdMapping::TinyTranslation->new_fast( [
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30 $tl->dbID, $tl->stable_id,
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31 $tl->version, $tl->created_date,
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32 $tl->modified_date, $tr->dbID,
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33 $tr->translate->seq, ( $tr->is_known ? 1 : 0 ),
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34 ] );
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35 }
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36
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37 =head1 DESCRIPTION
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38
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39 This is a lightweight translation object for the stable Id mapping. See
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40 the documentation in TinyFeature for general considerations about its
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41 design.
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42
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43 =head1 METHODS
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44
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45 transcript_id
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46 seq
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47 is_known
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48
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49 =cut
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50
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51 package Bio::EnsEMBL::IdMapping::TinyTranslation;
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52
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53 # internal data structure (array indices):
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54 #
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55 # 0-4 see TinyFeature
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56 # 5 transcript_id
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57 # 6 seq
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58 # 7 is_known
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59
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60
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61 use strict;
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62 use warnings;
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63 no warnings 'uninitialized';
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64
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65 use Bio::EnsEMBL::IdMapping::TinyFeature;
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66 our @ISA = qw(Bio::EnsEMBL::IdMapping::TinyFeature);
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67
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68 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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69
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70
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71 =head2 transcript_id
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72
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73 Arg[1] : (optional) Int - the transcript internal Id ("dbID")
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74 Description : Getter/setter for the transcript internal Id this translation is
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75 attached to.
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76 Return type : Int
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77 Exceptions : none
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78 Caller : general
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79 Status : At Risk
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80 : under development
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81
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82 =cut
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83
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84 sub transcript_id {
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85 my $self = shift;
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86 $self->[5] = shift if (@_);
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87 return $self->[5];
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88 }
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89
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90
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91 =head2 seq
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92
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93 Arg[1] : (optional) String - the translation's sequence
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94 Description : Getter/setter for the translation's sequence.
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95 Return type : String
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96 Exceptions : none
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97 Caller : general
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98 Status : At Risk
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99 : under development
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100
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101 =cut
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102
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103 sub seq {
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104 my $self = shift;
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105 $self->[6] = shift if (@_);
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106 return $self->[6];
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107 }
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108
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109
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110 =head2 is_known
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111
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112 Arg[1] : (optional) Boolean - the translation's "known" status
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113 Description : Getter/setter for the translation's "known" status.
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114 Return type : Boolean
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115 Exceptions : none
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116 Caller : general
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117 Status : At Risk
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118 : under development
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119
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120 =cut
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121
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122 sub is_known {
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123 my $self = shift;
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124 $self->[7] = shift if (@_);
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125 return $self->[7];
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126 }
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127
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128
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129 1;
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130
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