diff variant_effect_predictor/Bio/EnsEMBL/Variation/StructuralVariationOverlap.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/StructuralVariationOverlap.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,144 @@
+package Bio::EnsEMBL::Variation::StructuralVariationOverlap;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele;
+
+use Bio::EnsEMBL::Utils::Scalar qw(assert_ref);
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+
+use base qw(Bio::EnsEMBL::Variation::BaseVariationFeatureOverlap);
+
+sub new {
+
+    my $class = shift;
+    
+    my %args = @_;
+
+    # swap a '-structural_variation_feature' argument for a '-base_variation_feature' one for the superclass
+
+    for my $arg (keys %args) {
+        if (lc($arg) eq '-structural_variation_feature') {
+            $args{'-base_variation_feature'} = delete $args{$arg};
+        }
+    }
+
+    # call the superclass constructor
+    my $self = $class->SUPER::new(%args);
+    
+    # construct a fake 'allele'
+    
+    $self->add_StructuralVariationOverlapAllele(
+        Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
+            structural_variation_overlap    => $self,
+        })
+    );
+
+    return $self;
+}
+
+sub new_fast {
+    my ($class, $hashref) = @_;
+    
+    # swap a 'structural_variation_feature' argument for a 'base_variation_feature' one for the superclass
+    
+    if ($hashref->{structural_variation_feature}) {
+        $hashref->{base_variation_feature} = delete $hashref->{structural_variation_feature};
+    }
+    
+    # and call the superclass
+
+    my $self = $class->SUPER::new_fast($hashref);
+
+#    for my $ssv (@{ $self->structural_variation_feature->structural_variation->get_all_SupportingStructuralVariants }) {
+#        for my $ssvf (@{ $ssv->get_all_StructuralVariationFeatures }) {
+#            $self->add_StructuralVariationOverlapAllele(
+#                Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
+#                    structural_variation_overlap    => $self,
+#                })
+#            );
+#        }
+#    }
+
+    unless (@{ $self->get_all_alternate_StructuralVariationOverlapAlleles }) {
+
+        # construct a fake 'allele'
+        
+        $self->add_StructuralVariationOverlapAllele(
+            Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele->new_fast({
+                structural_variation_overlap    => $self,
+            })
+        );
+    }
+
+    return $self;
+}
+
+sub structural_variation_feature {
+    my $self = shift;
+    return $self->base_variation_feature(@_);
+}
+
+=head2 add_StructuralVariationOverlapAllele
+
+  Arg [1]    : A Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele instance
+  Description: Add an allele to this StructuralVariationOverlap
+  Returntype : none
+  Exceptions : throws if the argument is not the expected type
+  Status     : At Risk
+
+=cut
+
+sub add_StructuralVariationOverlapAllele {
+    my ($self, $svoa) = @_;
+    assert_ref($svoa, 'Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele');
+    return $self->SUPER::add_BaseVariationFeatureOverlapAllele($svoa);
+}
+
+=head2 get_reference_StructuralVariationOverlapAllele
+
+  Description: Get the object representing the reference allele of this StructuralVariationOverlap
+  Returntype : Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele instance
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub get_reference_StructuralVariationOverlapAllele {
+    my $self = shift;
+    return $self->SUPER::get_reference_BaseVariationFeatureOverlapAllele(@_);
+}
+
+=head2 get_all_alternate_StructuralVariationOverlapAlleles
+
+  Description: Get a list of the alternate alleles of this StructuralVariationOverlap
+  Returntype : listref of Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele objects
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub get_all_alternate_StructuralVariationOverlapAlleles {
+    my $self = shift;
+    return $self->SUPER::get_all_alternate_BaseVariationFeatureOverlapAlleles(@_);
+}
+
+=head2 get_all_StructuralVariationOverlapAlleles
+
+  Description: Get a list of the all the alleles, both reference and alternate, of 
+               this StructuralVariationOverlap
+  Returntype : listref of Bio::EnsEMBL::Variation::StructuralVariationOverlapAllele objects
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub get_all_StructuralVariationOverlapAlleles {
+    my $self = shift;
+    return $self->SUPER::get_all_BaseVariationFeatureOverlapAlleles(@_);
+}
+
+1;
+