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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Mapper::IndelPair
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24
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25 =head1 SYNOPSIS
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26
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27 =head1 DESCRIPTION
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28
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29 Two regions mapped between different coordinate systems are each
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30 represented by a Bio::EnsEMBL::Mapper::Unit and joined together as a
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31 Bio::EnsEMBL::Mapper::Pair, when one of the regions is an indel.
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32
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33 =head1 METHODS
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34
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35 =cut
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36
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37 package Bio::EnsEMBL::Mapper::IndelPair;
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38
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39 use vars qw(@ISA);
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40 use strict;
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41
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42 @ISA = qw(Bio::EnsEMBL::Mapper::Pair);
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43
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44 sub new {
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45 my ($proto, @args) = @_;
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46
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47 my $class = ref($proto) || $proto;
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48
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49 my $self = $class->SUPER::new(@args); # create the Pair object
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50 $self->{'indel'} = 1; # and add the Indel flag
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51
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52 return $self;
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53 }
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54
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55 1;
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