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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 # Ensembl module for Bio::EnsEMBL::Variation::SupportingStructuralVariation
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22 #
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23 # Copyright (c) 2011 Ensembl
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24 #
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25
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26
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27 =head1 NAME
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28
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29 Bio::EnsEMBL::Variation::SupportingStructuralVariation - A supporting evidence for a structural variation.
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30
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31 =head1 SYNOPSIS
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32
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33 # Supporting evidence of a structural variation
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34 $ssv = Bio::EnsEMBL::Variation::SupportingStructuralVariation->new
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35 (-supporting_structural_evidence => 'ssv001'
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36 -structural_variation => $structural_variation);
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37
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38 ...
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39
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40
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41 =head1 DESCRIPTION
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42
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43 This is a class representing the supporting evidence of a structural variation
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44 from the ensembl-variation database.
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45
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46 =head1 METHODS
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47
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48 =cut
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49
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50 use strict;
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51 use warnings;
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52
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53 package Bio::EnsEMBL::Variation::SupportingStructuralVariation;
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54
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55 use Bio::EnsEMBL::Variation::BaseStructuralVariation;
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56 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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57
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58 our @ISA = ('Bio::EnsEMBL::Variation::BaseStructuralVariation');
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59
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60
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61 sub new {
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62 my $caller = shift;
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63 my $class = ref($caller) || $caller;
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64
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65 my $self = Bio::EnsEMBL::Variation::BaseStructuralVariation->new(@_);
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66 return(bless($self, $class));
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67 }
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68
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69
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70 =head2 get_all_StructuralVariations
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71 Example : $ssv = $obj->get_all_StructuralVariations()
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72 Description: Getter of the structural variations supported by the supporting evidence.
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73 Returntype : reference to list of Bio::EnsEMBL::Variation::StructuralVariation objects
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74 Exceptions : none
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75 Caller : general
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76 Status : At Risk
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77
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78 =cut
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79
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80 sub get_all_StructuralVariations {
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81 my $self = shift;
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82
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83 if(defined $self->{'adaptor'}) {
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84 my $sva = $self->{'adaptor'}->db()->get_StructuralVariationAdaptor();
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85 return $sva->fetch_all_by_supporting_evidence($self);
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86 }
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87 else {
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88 warn("No variation database attached");
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89 return [];
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90 }
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91 }
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92
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93 1;
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94
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