Mercurial > repos > mahtabm > ensembl
view variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptStructuralVariationAllele.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 =head1 NAME Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele =head1 SYNOPSIS use Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele; =head1 DESCRIPTION A TranscriptStructuralVariationAllele object represents a single allele of a TranscriptStructuralVariation. =cut package Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele; use strict; use warnings; use base qw(Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele Bio::EnsEMBL::Variation::BaseTranscriptVariationAllele); sub new_fast { my ($class, $hashref) = @_; # swap a transcript_structural_variation argument for a structural_variation_overlap one if ($hashref->{transcript_structural_variation}) { $hashref->{structural_variation_overlap} = delete $hashref->{transcript_structural_variation}; } # and call the superclass return $class->SUPER::new_fast($hashref); } =head2 transcript_structural_variation Description: Get the associated TranscriptStructuralVariation Returntype : Bio::EnsEMBL::Variation::TranscriptStructuralVariation Exceptions : none Status : At Risk =cut sub transcript_structural_variation { my ($self, $svo) = @_; if ($svo) { assert_ref($svo, 'Bio::EnsEMBL::Variation::TranscriptStructuralVariation'); } return $self->base_variation_feature_overlap($svo); } 1;