Mercurial > repos > mahtabm > ensembl
view variant_effect_predictor/Bio/EnsEMBL/Variation/SupportingStructuralVariation.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 # Ensembl module for Bio::EnsEMBL::Variation::SupportingStructuralVariation # # Copyright (c) 2011 Ensembl # =head1 NAME Bio::EnsEMBL::Variation::SupportingStructuralVariation - A supporting evidence for a structural variation. =head1 SYNOPSIS # Supporting evidence of a structural variation $ssv = Bio::EnsEMBL::Variation::SupportingStructuralVariation->new (-supporting_structural_evidence => 'ssv001' -structural_variation => $structural_variation); ... =head1 DESCRIPTION This is a class representing the supporting evidence of a structural variation from the ensembl-variation database. =head1 METHODS =cut use strict; use warnings; package Bio::EnsEMBL::Variation::SupportingStructuralVariation; use Bio::EnsEMBL::Variation::BaseStructuralVariation; use Bio::EnsEMBL::Utils::Exception qw(throw warning); our @ISA = ('Bio::EnsEMBL::Variation::BaseStructuralVariation'); sub new { my $caller = shift; my $class = ref($caller) || $caller; my $self = Bio::EnsEMBL::Variation::BaseStructuralVariation->new(@_); return(bless($self, $class)); } =head2 get_all_StructuralVariations Example : $ssv = $obj->get_all_StructuralVariations() Description: Getter of the structural variations supported by the supporting evidence. Returntype : reference to list of Bio::EnsEMBL::Variation::StructuralVariation objects Exceptions : none Caller : general Status : At Risk =cut sub get_all_StructuralVariations { my $self = shift; if(defined $self->{'adaptor'}) { my $sva = $self->{'adaptor'}->db()->get_StructuralVariationAdaptor(); return $sva->fetch_all_by_supporting_evidence($self); } else { warn("No variation database attached"); return []; } } 1;