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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptStructuralVariationAllele.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,76 @@
+=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::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;
+