diff variant_effect_predictor/Bio/EnsEMBL/Variation/RegulatoryFeatureVariation.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/RegulatoryFeatureVariation.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,84 @@
+=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 <[e-mail]>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <[e-mail]>.
+
+=cut
+
+package Bio::EnsEMBL::Variation::RegulatoryFeatureVariation;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::RegulatoryFeatureVariationAllele;
+use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(overlap);
+
+use base qw(Bio::EnsEMBL::Variation::RegulationVariation);
+
+sub new {
+    my $class = shift;
+
+    my %args = @_;
+
+    # swap a '-regulatory_feature' argument for a '-feature' one for the superclass
+
+    for my $arg (keys %args) {
+        if (lc($arg) eq '-regulatory_feature') {
+            $args{'-feature'} = delete $args{$arg};
+        }
+    }
+   
+    # call the superclass constructor
+    my $self = $class->SUPER::new(%args) || return undef;
+    
+    # rebless the alleles from vfoas to rfvas
+    map { bless $_, 'Bio::EnsEMBL::Variation::RegulatoryFeatureVariationAllele' } 
+        @{ $self->get_all_RegulatoryFeatureVariationAlleles };
+    
+    return $self;
+}
+
+sub regulatory_feature_stable_id {
+    my $self = shift;
+    return $self->SUPER::feature_stable_id(@_);
+}
+
+sub regulatory_feature {
+    my ($self, $rf) = @_;
+    return $self->SUPER::feature($rf, 'RegulatoryFeature');
+}
+
+sub add_RegulatoryFeatureVariationAllele {
+    my $self = shift;
+    return $self->SUPER::add_VariationFeatureOverlapAllele(@_);
+}
+
+sub get_reference_RegulatoryFeatureVariationAllele {
+    my $self = shift;
+    return $self->SUPER::get_reference_VariationFeatureOverlapAllele(@_);
+}
+
+sub get_all_alternate_RegulatoryFeatureVariationAlleles {
+    my $self = shift;
+    return $self->SUPER::get_all_alternate_VariationFeatureOverlapAlleles(@_);
+}
+
+sub get_all_RegulatoryFeatureVariationAlleles {
+    my $self = shift;
+    return $self->SUPER::get_all_VariationFeatureOverlapAlleles(@_);
+}
+
+1;