Mercurial > repos > mahtabm > ensembl
view variant_effect_predictor/Bio/EnsEMBL/Variation/IntergenicStructuralVariation.pm @ 3:d30fa12e4cc5 default tip
Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.
author | devteam <devteam@galaxyproject.org> |
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date | Mon, 13 Jan 2014 10:38:30 -0500 |
parents | 1f6dce3d34e0 |
children |
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=head1 LICENSE Copyright (c) 1999-2012 The European Bioinformatics Institute and Genome Research Limited. All rights reserved. This software is distributed under a modified Apache license. For license details, please see http://www.ensembl.org/info/about/code_licence.html =head1 CONTACT Please email comments or questions to the public Ensembl developers list at <dev@ensembl.org>. Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>. =cut package Bio::EnsEMBL::Variation::IntergenicStructuralVariation; use strict; use warnings; use Bio::EnsEMBL::Variation::IntergenicStructuralVariationAllele; use Bio::EnsEMBL::Utils::Exception qw(throw warning); use base qw(Bio::EnsEMBL::Variation::StructuralVariationOverlap); sub new { my $class = shift; my %args = @_; for my $arg (keys %args) { if (lc($arg) eq '-feature') { throw("Intergenic variations do not have an associated feature!"); } } # call the superclass constructor my $self = $class->SUPER::new(%args) || return undef; # rebless the alleles from vfoas to ivas map { bless $_, 'Bio::EnsEMBL::Variation::IntergenicStructuralVariationAllele' } @{ $self->get_all_IntergenicStructuralVariationAlleles }; return $self; } sub feature { my $self = shift; warning("Intergenic variants do not have an associated feature!") if @_; return undef; } sub add_IntergenicStructuralVariationAllele { my $self = shift; return $self->SUPER::add_StructuralVariationOverlapAllele(@_); } sub get_reference_IntergenicStructuralVariationAllele { my $self = shift; return $self->SUPER::get_reference_StructuralVariationOverlapAllele(@_); } sub get_all_alternate_IntergenicStructuralVariationAlleles { my $self = shift; return $self->SUPER::get_all_alternate_StructuralVariationOverlapAlleles(@_); } sub get_all_IntergenicStructuralVariationAlleles { my $self = shift; return $self->SUPER::get_all_StructuralVariationOverlapAlleles(@_); } 1;