view variant_effect_predictor/Bio/EnsEMBL/Variation/StructuralVariationOverlapAllele.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

package Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele);

sub new_fast {
    my ($class, $hashref) = @_;

    # swap a transcript_variation argument for a variation_feature_overlap one

    if ($hashref->{structural_variation_overlap}) {
        $hashref->{base_variation_feature_overlap} = 
            delete $hashref->{structural_variation_overlap};
    }
    
    # and call the superclass

    return $class->SUPER::new_fast($hashref);
}

=head2 structural_variation_overlap

  Description: Get the associated StructuralVariationOverlap
  Returntype : Bio::EnsEMBL::Variation::StructuralVariationOverlap
  Exceptions : none
  Status     : At Risk

=cut

sub structural_variation_overlap {
    my ($self, $svo) = @_;
    if ($svo) {
        assert_ref($svo, 'Bio::EnsEMBL::Variation::StructuralVariationOverlap');
    }
    return $self->base_variation_feature_overlap($svo);
}


=head2 structural_variation_feature

  Description: Get the associated StructuralVariationFeature
  Returntype : Bio::EnsEMBL::Variation::StructuralVariationFeature
  Exceptions : none
  Status     : At Risk

=cut

sub structural_variation_feature {
    my $self = shift;
    return $self->structural_variation_overlap->structural_variation_feature;
}

1;