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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::Variation::BaseTranscriptVariationAllele
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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::Variation::BaseTranscriptVariationAllele;
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28
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29 =head1 DESCRIPTION
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30
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31 An helper class for representing an overlap of a Transcript and a
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32 Variation allele (either sequence or structural). Should not be invoked
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33 directly.
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34
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35 =cut
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36
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37 package Bio::EnsEMBL::Variation::BaseTranscriptVariationAllele;
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38
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39 use strict;
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40 use warnings;
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41
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42 use base qw(Bio::EnsEMBL::Variation::VariationFeatureOverlapAllele);
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43
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44 =head2 base_transcript_variation
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45
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46 Description: Get/set the associated BaseTranscriptVariation
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47 Returntype : Bio::EnsEMBL::Variation::BaseTranscriptVariation
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48 Exceptions : throws if the argument is the wrong type
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49 Status : At Risk
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50
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51 =cut
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52
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53 sub base_transcript_variation {
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54 my ($self, $btv) = @_;
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55 assert_ref($btv, 'Bio::EnsEMBL::Variation::BaseTranscriptVariation') if $btv;
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56 return $self->variation_feature_overlap($btv);
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57 }
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58
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59 =head2 transcript
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60
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61 Description: Get the associated Transcript
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62 Returntype : Bio::EnsEMBL::Transcript
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63 Exceptions : none
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64 Status : At Risk
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65
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66 =cut
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67
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68 sub transcript {
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69 my $self = shift;
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70 return $self->base_transcript_variation->transcript;
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71 }
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72
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73 =head2 base_variation_feature
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74
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75 Description: Get the associated BaseVariationFeature
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76 Returntype : Bio::EnsEMBL::Variation::BaseVariationFeature
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77 Exceptions : none
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78 Status : At Risk
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79
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80 =cut
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81
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82 sub base_variation_feature {
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83 my $self = shift;
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84 return $self->base_transcript_variation->base_variation_feature;
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85 }
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86
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87 1; |
