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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Mapper/IndelPair.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,55 @@
+=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::Mapper::IndelPair
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+Two regions mapped between different coordinate systems are each
+represented by a Bio::EnsEMBL::Mapper::Unit and joined together as a
+Bio::EnsEMBL::Mapper::Pair, when one of the regions is an indel.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::Mapper::IndelPair;
+
+use vars qw(@ISA);
+use strict;
+
+@ISA = qw(Bio::EnsEMBL::Mapper::Pair);
+
+sub new {
+  my ($proto, @args) = @_;
+
+  my $class = ref($proto) || $proto;
+
+  my $self = $class->SUPER::new(@args);    # create the Pair object
+  $self->{'indel'} = 1;                    # and add the Indel flag
+
+  return $self;
+}
+
+1;