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IndelPair.pm
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00001 =head1 LICENSE
00002 
00003   Copyright (c) 1999-2012 The European Bioinformatics Institute and
00004   Genome Research Limited.  All rights reserved.
00005 
00006   This software is distributed under a modified Apache license.
00007   For license details, please see
00008 
00009     http://www.ensembl.org/info/about/code_licence.html
00010 
00011 =head1 CONTACT
00012 
00013   Please email comments or questions to the public Ensembl
00014   developers list at <dev@ensembl.org>.
00015 
00016   Questions may also be sent to the Ensembl help desk at
00017   <helpdesk@ensembl.org>.
00018 
00019 =cut
00020 
00021 =head1 NAME
00022 
00023 Bio::EnsEMBL::Mapper::IndelPair
00024 
00025 =head1 SYNOPSIS
00026 
00027 =head1 DESCRIPTION
00028 
00029 Two regions mapped between different coordinate systems are each
00030 represented by a Bio::EnsEMBL::Mapper::Unit and joined together as a
00031 Bio::EnsEMBL::Mapper::Pair, when one of the regions is an indel.
00032 
00033 =head1 METHODS
00034 
00035 =cut
00036 
00037 package Bio::EnsEMBL::Mapper::IndelPair;
00038 
00039 use vars qw(@ISA);
00040 use strict;
00041 
00042 @ISA = qw(Bio::EnsEMBL::Mapper::Pair);
00043 
00044 sub new {
00045   my ($proto, @args) = @_;
00046 
00047   my $class = ref($proto) || $proto;
00048 
00049   my $self = $class->SUPER::new(@args);    # create the Pair object
00050   $self->{'indel'} = 1;                    # and add the Indel flag
00051 
00052   return $self;
00053 }
00054 
00055 1;