|
0
|
1 package Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele;
|
|
|
2
|
|
|
3 use strict;
|
|
|
4 use warnings;
|
|
|
5
|
|
|
6 use base qw(Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele);
|
|
|
7
|
|
|
8 sub new_fast {
|
|
|
9 my ($class, $hashref) = @_;
|
|
|
10
|
|
|
11 # swap a transcript_variation argument for a variation_feature_overlap one
|
|
|
12
|
|
|
13 if ($hashref->{structural_variation_overlap}) {
|
|
|
14 $hashref->{base_variation_feature_overlap} =
|
|
|
15 delete $hashref->{structural_variation_overlap};
|
|
|
16 }
|
|
|
17
|
|
|
18 # and call the superclass
|
|
|
19
|
|
|
20 return $class->SUPER::new_fast($hashref);
|
|
|
21 }
|
|
|
22
|
|
|
23 =head2 structural_variation_overlap
|
|
|
24
|
|
|
25 Description: Get the associated StructuralVariationOverlap
|
|
|
26 Returntype : Bio::EnsEMBL::Variation::StructuralVariationOverlap
|
|
|
27 Exceptions : none
|
|
|
28 Status : At Risk
|
|
|
29
|
|
|
30 =cut
|
|
|
31
|
|
|
32 sub structural_variation_overlap {
|
|
|
33 my ($self, $svo) = @_;
|
|
|
34 if ($svo) {
|
|
|
35 assert_ref($svo, 'Bio::EnsEMBL::Variation::StructuralVariationOverlap');
|
|
|
36 }
|
|
|
37 return $self->base_variation_feature_overlap($svo);
|
|
|
38 }
|
|
|
39
|
|
|
40
|
|
|
41 =head2 structural_variation_feature
|
|
|
42
|
|
|
43 Description: Get the associated StructuralVariationFeature
|
|
|
44 Returntype : Bio::EnsEMBL::Variation::StructuralVariationFeature
|
|
|
45 Exceptions : none
|
|
|
46 Status : At Risk
|
|
|
47
|
|
|
48 =cut
|
|
|
49
|
|
|
50 sub structural_variation_feature {
|
|
|
51 my $self = shift;
|
|
|
52 return $self->structural_variation_overlap->structural_variation_feature;
|
|
|
53 }
|
|
|
54
|
|
|
55 1;
|
|
|
56
|
