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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/PepDnaAlignFeature.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,96 @@
+=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::PepDnaAlignFeature - Ensembl specific pep-dna pairwise
+alignment feature
+
+=head1 SYNOPSIS
+
+  See BaseAlignFeature
+
+=head1 METHODS
+
+=cut 
+
+package Bio::EnsEMBL::PepDnaAlignFeature;
+
+use Bio::EnsEMBL::BaseAlignFeature;
+
+use vars qw(@ISA);
+use strict;
+
+@ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
+
+=head2 transform 
+
+  Arg [1]    : none
+  Example    : none
+  Description: Overwrites Bio:EnsEMBL:Feature->transform as
+               to give error message
+  Status     : Stable
+
+=cut
+
+sub transform {
+  my $self = shift;
+
+  $self->throw( "PepDnaAlignFeatures cant be transformed as".
+		" they are not on EnsEMBL coord system" );
+}
+
+=head2 _hit_unit
+
+  Arg [1]    : none
+  Example    : none
+  Description: PRIVATE implementation of abstract superclass method.  Returns
+               3 as the 'unit' used for the hit sequence.
+  Returntype : int
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::BaseAlignFeature
+  Status     : Stable
+
+
+=cut
+
+sub _hit_unit {
+  return 3;
+}
+
+=head2 _query_unit
+
+  Arg [1]    : none
+  Example    : none
+  Description: PRIVATE implementation of abstract superclass method.  Returns
+               1 as the 'unit' used for the query sequence.
+  Returntype : int
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::BaseAlignFeature
+  Status     : Stable
+
+
+=cut
+
+sub _query_unit {
+  return 1;
+}
+
+1;