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1 package Bio::EnsEMBL::Variation::StructuralVariationOverlap;
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2
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3 use strict;
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4 use warnings;
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5
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6 use Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele;
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7
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8 use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
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9 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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10 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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11
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12 use base qw(Bio::EnsEMBL::Variation::BaseVariationFeatureOverlap);
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13
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14 sub new {
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15
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16 my $class = shift;
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17
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18 my %args = @_;
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19
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20 # swap a '-structural_variation_feature' argument for a '-base_variation_feature' one for the superclass
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21
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22 for my $arg (keys %args) {
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23 if (lc($arg) eq '-structural_variation_feature') {
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24 $args{'-base_variation_feature'} = delete $args{$arg};
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25 }
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26 }
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27
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28 # call the superclass constructor
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29 my $self = $class->SUPER::new(%args);
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30
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31 # construct a fake 'allele'
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32
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33 $self->add_StructuralVariationOverlapAllele(
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34 Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
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35 structural_variation_overlap => $self,
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36 })
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37 );
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38
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39 return $self;
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40 }
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41
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42 sub new_fast {
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43 my ($class, $hashref) = @_;
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44
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45 # swap a 'structural_variation_feature' argument for a 'base_variation_feature' one for the superclass
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46
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47 if ($hashref->{structural_variation_feature}) {
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48 $hashref->{base_variation_feature} = delete $hashref->{structural_variation_feature};
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49 }
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50
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51 # and call the superclass
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52
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53 my $self = $class->SUPER::new_fast($hashref);
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54
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55 # for my $ssv (@{ $self->structural_variation_feature->structural_variation->get_all_SupportingStructuralVariants }) {
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56 # for my $ssvf (@{ $ssv->get_all_StructuralVariationFeatures }) {
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57 # $self->add_StructuralVariationOverlapAllele(
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58 # Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
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59 # structural_variation_overlap => $self,
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60 # })
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61 # );
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62 # }
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63 # }
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64
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65 unless (@{ $self->get_all_alternate_StructuralVariationOverlapAlleles }) {
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66
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67 # construct a fake 'allele'
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68
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69 $self->add_StructuralVariationOverlapAllele(
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70 Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
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71 structural_variation_overlap => $self,
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72 })
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73 );
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74 }
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75
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76 return $self;
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77 }
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78
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79 sub structural_variation_feature {
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80 my $self = shift;
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81 return $self->base_variation_feature(@_);
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82 }
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83
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84 =head2 add_StructuralVariationOverlapAllele
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85
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86 Arg [1] : A Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele instance
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87 Description: Add an allele to this StructuralVariationOverlap
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88 Returntype : none
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89 Exceptions : throws if the argument is not the expected type
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90 Status : At Risk
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91
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92 =cut
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93
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94 sub add_StructuralVariationOverlapAllele {
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95 my ($self, $svoa) = @_;
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96 assert_ref($svoa, 'Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele');
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97 return $self->SUPER::add_BaseVariationFeatureOverlapAllele($svoa);
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98 }
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99
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100 =head2 get_reference_StructuralVariationOverlapAllele
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101
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102 Description: Get the object representing the reference allele of this StructuralVariationOverlap
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103 Returntype : Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele instance
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104 Exceptions : none
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105 Status : At Risk
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106
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107 =cut
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108
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109 sub get_reference_StructuralVariationOverlapAllele {
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110 my $self = shift;
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111 return $self->SUPER::get_reference_BaseVariationFeatureOverlapAllele(@_);
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112 }
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113
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114 =head2 get_all_alternate_StructuralVariationOverlapAlleles
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115
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116 Description: Get a list of the alternate alleles of this StructuralVariationOverlap
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117 Returntype : listref of Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele objects
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118 Exceptions : none
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119 Status : At Risk
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120
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121 =cut
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122
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123 sub get_all_alternate_StructuralVariationOverlapAlleles {
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124 my $self = shift;
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125 return $self->SUPER::get_all_alternate_BaseVariationFeatureOverlapAlleles(@_);
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126 }
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127
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128 =head2 get_all_StructuralVariationOverlapAlleles
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129
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130 Description: Get a list of the all the alleles, both reference and alternate, of
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131 this StructuralVariationOverlap
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132 Returntype : listref of Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele objects
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133 Exceptions : none
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134 Status : At Risk
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135
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136 =cut
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137
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138 sub get_all_StructuralVariationOverlapAlleles {
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139 my $self = shift;
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140 return $self->SUPER::get_all_BaseVariationFeatureOverlapAlleles(@_);
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141 }
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142
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143 1;
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144
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