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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::TranscriptStructuralVariationAllele
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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::TranscriptStructuralVariationAllele;
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28
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29 =head1 DESCRIPTION
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30
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31 A TranscriptStructuralVariationAllele object represents a single allele of a
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32 TranscriptStructuralVariation.
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33
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34 =cut
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35
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36 package Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele;
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37
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38 use strict;
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39 use warnings;
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40
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41 use base qw(Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele Bio::EnsEMBL::Variation::BaseTranscriptVariationAllele);
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42
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43 sub new_fast {
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44 my ($class, $hashref) = @_;
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45
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46 # swap a transcript_structural_variation argument for a structural_variation_overlap one
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47
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48 if ($hashref->{transcript_structural_variation}) {
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49 $hashref->{structural_variation_overlap} = delete $hashref->{transcript_structural_variation};
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50 }
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51
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52 # and call the superclass
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53
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54 return $class->SUPER::new_fast($hashref);
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55 }
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56
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57 =head2 transcript_structural_variation
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58
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59 Description: Get the associated TranscriptStructuralVariation
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60 Returntype : Bio::EnsEMBL::Variation::TranscriptStructuralVariation
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61 Exceptions : none
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62 Status : At Risk
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63
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64 =cut
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65
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66 sub transcript_structural_variation {
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67 my ($self, $svo) = @_;
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68 if ($svo) {
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69 assert_ref($svo, 'Bio::EnsEMBL::Variation::TranscriptStructuralVariation');
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70 }
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71 return $self->base_variation_feature_overlap($svo);
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72 }
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73
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74
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75 1;
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76
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