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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/BaseTranscriptVariationAllele.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,87 @@
+=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
+
+=head1 NAME
+
+Bio::EnsEMBL::Variation::BaseTranscriptVariationAllele
+
+=head1 SYNOPSIS
+
+    use Bio::EnsEMBL::Variation::BaseTranscriptVariationAllele;
+
+=head1 DESCRIPTION
+
+An helper class for representing an overlap of a Transcript and a
+Variation allele (either sequence or structural). Should not be invoked
+directly.
+
+=cut
+
+package Bio::EnsEMBL::Variation::BaseTranscriptVariationAllele;
+
+use strict;
+use warnings;
+
+use base qw(Bio::EnsEMBL::Variation::VariationFeatureOverlapAllele);
+
+=head2 base_transcript_variation
+
+  Description: Get/set the associated BaseTranscriptVariation
+  Returntype : Bio::EnsEMBL::Variation::BaseTranscriptVariation
+  Exceptions : throws if the argument is the wrong type
+  Status     : At Risk
+
+=cut
+
+sub base_transcript_variation {
+    my ($self, $btv) = @_;
+    assert_ref($btv, 'Bio::EnsEMBL::Variation::BaseTranscriptVariation') if $btv;
+    return $self->variation_feature_overlap($btv);
+}
+
+=head2 transcript
+
+  Description: Get the associated Transcript
+  Returntype : Bio::EnsEMBL::Transcript
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub transcript {
+    my $self = shift;
+    return $self->base_transcript_variation->transcript;
+}
+
+=head2 base_variation_feature
+
+  Description: Get the associated BaseVariationFeature
+  Returntype : Bio::EnsEMBL::Variation::BaseVariationFeature
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub base_variation_feature {
+    my $self = shift;
+    return $self->base_transcript_variation->base_variation_feature;
+}
+
+1;
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