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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 package Bio::EnsEMBL::Variation::IntergenicVariation;
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22
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23 use strict;
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24 use warnings;
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25
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26 use Bio::EnsEMBL::Variation::IntergenicVariationAllele;
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27
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28 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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29
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30 use base qw(Bio::EnsEMBL::Variation::VariationFeatureOverlap);
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31
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32 sub new {
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33 my $class = shift;
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34
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35 my %args = @_;
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36
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37 for my $arg (keys %args) {
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38 if (lc($arg) eq '-feature') {
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39 throw("Intergenic variations do not have an associated feature!");
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40 }
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41 }
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42
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43 # call the superclass constructor
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44 my $self = $class->SUPER::new(%args) || return undef;
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45
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46 # rebless the alleles from vfoas to ivas
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47 map { bless $_, 'Bio::EnsEMBL::Variation::IntergenicVariationAllele' }
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48 @{ $self->get_all_IntergenicVariationAlleles };
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49
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50 return $self;
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51 }
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52
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53 sub feature {
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54 my $self = shift;
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55 warning("Intergenic variants do not have an associated feature!") if @_;
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56 return undef;
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57 }
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58
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59 sub add_IntergenicVariationAllele {
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60 my $self = shift;
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61 return $self->SUPER::add_VariationFeatureOverlapAllele(@_);
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62 }
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63
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64 sub get_reference_IntergenicVariationAllele {
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65 my $self = shift;
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66 return $self->SUPER::get_reference_VariationFeatureOverlapAllele(@_);
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67 }
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68
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69 sub get_all_alternate_IntergenicVariationAlleles {
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70 my $self = shift;
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71 return $self->SUPER::get_all_alternate_VariationFeatureOverlapAlleles(@_);
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72 }
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73
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74 sub get_all_IntergenicVariationAlleles {
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75 my $self = shift;
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76 return $self->SUPER::get_all_VariationFeatureOverlapAlleles(@_);
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77 }
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78
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79 1;
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