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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptStructuralVariation.pm	Fri Aug 03 10:04:48 2012 -0400
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+=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::TranscriptStructuralVariation
+
+=head1 SYNOPSIS
+
+    use Bio::EnsEMBL::Variation::TranscriptStructuralVariation;
+
+    my $tv = Bio::EnsEMBL::Variation::TranscriptVariation->new(
+        -transcript                   => $transcript,
+        -structural_variation_feature => $svf
+    );
+
+=head1 DESCRIPTION
+
+A TranscriptStructuralVariation object represents a structural variation feature
+which is in close proximity to an Ensembl transcript. A
+TranscriptStructuralVariation object has several attributes which define the
+relationship of the variation to the transcript.
+
+=cut
+
+package Bio::EnsEMBL::Variation::TranscriptStructuralVariation;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele;
+
+use base qw(Bio::EnsEMBL::Variation::StructuralVariationOverlap Bio::EnsEMBL::Variation::BaseTranscriptVariation);
+
+sub new {
+
+    my $class = shift;
+    
+    my %args = @_;
+
+    # swap a '-transcript' argument for a '-feature' one for the superclass
+
+    for my $arg (keys %args) {
+        if (lc($arg) eq '-transcript') {
+            $args{'-feature'} = delete $args{$arg};
+        }
+    }
+
+    # call the superclass constructor
+    my $self = $class->SUPER::new(%args) || return undef;
+
+    # rebless the alleles from vfoas to tvas
+    map { bless $_, 'Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele' } 
+        @{ $self->get_all_TranscriptStructuralVariationAlleles };
+    
+    return $self;
+}
+
+=head2 add_TranscriptStructuralVariationAllele
+
+  Arg [1]    : A Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele instance
+  Description: Add an allele to this TranscriptStructuralVariation
+  Returntype : none
+  Exceptions : throws if the argument is not the expected type
+  Status     : At Risk
+
+=cut
+
+sub add_TranscriptStructuralVariationAllele {
+    my ($self, $svoa) = @_;
+    assert_ref($svoa, 'Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele');
+    return $self->SUPER::add_BaseVariationFeatureOverlapAllele($svoa);
+}
+
+=head2 get_reference_TranscriptStructuralVariationAllele
+
+  Description: Get the object representing the reference allele of this TranscriptStructuralVariation
+  Returntype : Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele instance
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub get_reference_TranscriptStructuralVariationAllele {
+    my $self = shift;
+    return $self->SUPER::get_reference_BaseVariationFeatureOverlapAllele(@_);
+}
+
+=head2 get_all_alternate_TranscriptStructuralVariationAlleles
+
+  Description: Get a list of the alternate alleles of this TranscriptStructuralVariation
+  Returntype : listref of Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele objects
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub get_all_alternate_TranscriptStructuralVariationAlleles {
+    my $self = shift;
+    return $self->SUPER::get_all_alternate_BaseVariationFeatureOverlapAlleles(@_);
+}
+
+=head2 get_all_TranscriptStructuralVariationAlleles
+
+  Description: Get a list of the all the alleles, both reference and alternate, of 
+               this TranscriptStructuralVariation
+  Returntype : listref of Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele objects
+  Exceptions : none
+  Status     : At Risk
+
+=cut
+
+sub get_all_TranscriptStructuralVariationAlleles {
+    my $self = shift;
+    return $self->SUPER::get_all_BaseVariationFeatureOverlapAlleles(@_);
+}
+
+1;
+