Raw content of Bio::EnsEMBL::Mapper::IndelCoordinate
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Mapper::IndelCoordinate
=head1 SYNOPSIS
=head1 DESCRIPTION
Representation of a indel in a sequence; returned from Mapper.pm when
the target region is in a deletion.
=head1 METHODS
=cut
package Bio::EnsEMBL::Mapper::IndelCoordinate;
use Bio::EnsEMBL::Mapper::Gap;
use Bio::EnsEMBL::Mapper::Coordinate;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::EnsEMBL::Mapper::Coordinate Bio::EnsEMBL::Mapper::Gap);
=head2 new
Arg [1] : Bio::EnsEMBL::Mapper::Gap $gap
Arg [2] : Bio::EnsEMBL::Mapper::Coordinate $coordinate
Example : $indelCoord = Bio::EnsEMBL::Mapper::IndelCoordinate($gap, $coordinate);
Description: Creates a new IndelCoordinate object.
Returntype : Bio::EnsEMBL::Mapper::IndelCoordinate
Exceptions : none
Caller : Bio::EnsEMBL::Mapper
=cut
sub new {
my ( $proto, $gap, $coordinate ) = @_;
my $class = ref($proto) || $proto;
return
bless( { 'start' => $coordinate->start(),
'end' => $coordinate->end(),
'strand' => $coordinate->strand(),
'id' => $coordinate->id(),
'coord_system' => $coordinate->coord_system(),
'gap_start' => $gap->start(),
'gap_end' => $gap->end()
},
$class );
}
=head2 gap_start
Arg[1] : (optional) int $gap_start
Example : $gap_start = $ic->gap_start()
Description : Getter/Setter for the start of the Gap region
ReturnType : int
Exceptions : none
Caller : general
=cut
sub gap_start {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'gap_start'} = $value;
}
return $self->{'gap_start'};
}
=head2 gap_end
Arg[1] : (optional) int $gap_end
Example : $gap_end = $ic->gap_end()
Description : Getter/Setter for the end of the Gap region
ReturnType : int
Exceptions : none
Caller : general
=cut
sub gap_end {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'gap_end'} = $value;
}
return $self->{'gap_end'};
}
=head2 gap_length
Args : None
Example : $gap_length = $ic->gap_length()
Description : Getter for the length of the Gap region
ReturnType : int
Exceptions : none
Caller : general
=cut
sub gap_length {
my ($self) = @_;
return $self->{'gap_end'} - $self->{'gap_start'} + 1;
}
1;
]]>