view variant_effect_predictor/Bio/EnsEMBL/Variation/StructuralVariationOverlap.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::StructuralVariationOverlap;

use strict;
use warnings;

use Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele;

use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);

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

sub new {

    my $class = shift;
    
    my %args = @_;

    # swap a '-structural_variation_feature' argument for a '-base_variation_feature' one for the superclass

    for my $arg (keys %args) {
        if (lc($arg) eq '-structural_variation_feature') {
            $args{'-base_variation_feature'} = delete $args{$arg};
        }
    }

    # call the superclass constructor
    my $self = $class->SUPER::new(%args);
    
    # construct a fake 'allele'
    
    $self->add_StructuralVariationOverlapAllele(
        Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
            structural_variation_overlap    => $self,
        })
    );

    return $self;
}

sub new_fast {
    my ($class, $hashref) = @_;
    
    # swap a 'structural_variation_feature' argument for a 'base_variation_feature' one for the superclass
    
    if ($hashref->{structural_variation_feature}) {
        $hashref->{base_variation_feature} = delete $hashref->{structural_variation_feature};
    }
    
    # and call the superclass

    my $self = $class->SUPER::new_fast($hashref);

#    for my $ssv (@{ $self->structural_variation_feature->structural_variation->get_all_SupportingStructuralVariants }) {
#        for my $ssvf (@{ $ssv->get_all_StructuralVariationFeatures }) {
#            $self->add_StructuralVariationOverlapAllele(
#                Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
#                    structural_variation_overlap    => $self,
#                })
#            );
#        }
#    }

    unless (@{ $self->get_all_alternate_StructuralVariationOverlapAlleles }) {

        # construct a fake 'allele'
        
        $self->add_StructuralVariationOverlapAllele(
            Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
                structural_variation_overlap    => $self,
            })
        );
    }

    return $self;
}

sub structural_variation_feature {
    my $self = shift;
    return $self->base_variation_feature(@_);
}

=head2 add_StructuralVariationOverlapAllele

  Arg [1]    : A Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele instance
  Description: Add an allele to this StructuralVariationOverlap
  Returntype : none
  Exceptions : throws if the argument is not the expected type
  Status     : At Risk

=cut

sub add_StructuralVariationOverlapAllele {
    my ($self, $svoa) = @_;
    assert_ref($svoa, 'Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele');
    return $self->SUPER::add_BaseVariationFeatureOverlapAllele($svoa);
}

=head2 get_reference_StructuralVariationOverlapAllele

  Description: Get the object representing the reference allele of this StructuralVariationOverlap
  Returntype : Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele instance
  Exceptions : none
  Status     : At Risk

=cut

sub get_reference_StructuralVariationOverlapAllele {
    my $self = shift;
    return $self->SUPER::get_reference_BaseVariationFeatureOverlapAllele(@_);
}

=head2 get_all_alternate_StructuralVariationOverlapAlleles

  Description: Get a list of the alternate alleles of this StructuralVariationOverlap
  Returntype : listref of Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele objects
  Exceptions : none
  Status     : At Risk

=cut

sub get_all_alternate_StructuralVariationOverlapAlleles {
    my $self = shift;
    return $self->SUPER::get_all_alternate_BaseVariationFeatureOverlapAlleles(@_);
}

=head2 get_all_StructuralVariationOverlapAlleles

  Description: Get a list of the all the alleles, both reference and alternate, of 
               this StructuralVariationOverlap
  Returntype : listref of Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele objects
  Exceptions : none
  Status     : At Risk

=cut

sub get_all_StructuralVariationOverlapAlleles {
    my $self = shift;
    return $self->SUPER::get_all_BaseVariationFeatureOverlapAlleles(@_);
}

1;