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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/StructuralVariationOverlapAllele.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,56 @@
+package Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele;
+
+use strict;
+use warnings;
+
+use base qw(Bio::EnsEMBL::Variation::BaseVariationFeatureOverlapAllele);
+
+sub new_fast {
+    my ($class, $hashref) = @_;
+
+    # swap a transcript_variation argument for a variation_feature_overlap one
+
+    if ($hashref->{structural_variation_overlap}) {
+        $hashref->{base_variation_feature_overlap} = 
+            delete $hashref->{structural_variation_overlap};
+    }
+    
+    # and call the superclass
+
+    return $class->SUPER::new_fast($hashref);
+}
+
+=head2 structural_variation_overlap
+
+  Description: Get the associated StructuralVariationOverlap
+  Returntype : Bio::EnsEMBL::Variation::StructuralVariationOverlap
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub structural_variation_overlap {
+    my ($self, $svo) = @_;
+    if ($svo) {
+        assert_ref($svo, 'Bio::EnsEMBL::Variation::StructuralVariationOverlap');
+    }
+    return $self->base_variation_feature_overlap($svo);
+}
+
+
+=head2 structural_variation_feature
+
+  Description: Get the associated StructuralVariationFeature
+  Returntype : Bio::EnsEMBL::Variation::StructuralVariationFeature
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub structural_variation_feature {
+    my $self = shift;
+    return $self->structural_variation_overlap->structural_variation_feature;
+}
+
+1;
+