Raw content of Bio::EnsEMBL::Mapper::Gap
<![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::Gap
=head1 SYNOPSIS
=head1 DESCRIPTION
Representation of a gap in a sequence; returned from Mapper.pm when the
target region is in a gap.
=head1 METHODS
=cut
package Bio::EnsEMBL::Mapper::Gap;
use strict;
=head2 new
Arg [1] : int $start
Arg [2] : int $end
Example : $gap = Bio::EnsEMBL::Mapper::Gap($start, $end);
Description: Creates a new Gap object.
Returntype : Bio::EnsEMBL::Mapper::Gap
Exceptions : none
Caller : Bio::EnsEMBL::Mapper
Status : Stable
=cut
sub new {
my ( $proto, $start, $end ) = @_;
my $class = ref($proto) || $proto;
return bless( { 'start' => $start, 'end' => $end }, $class );
}
=head2 start
Arg [1] : (optional) int $start
start coordinate of gap region
Example : $start = $gap->start();
Description: Getter/Setter for the start attribute
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub start {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'start'} = $value;
}
return $self->{'start'};
}
=head2 end
Arg [1] : (optional) int $newval
The new value to set the end coordinate to
Example : $end = $gap->end()
Description: Getter/Setter for the end coordinate of the gap region
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub end {
my ( $self, $value ) = @_;
if ( defined($value) ) {
$self->{'end'} = $value;
}
return $self->{'end'};
}
=head2 length
Arg [1] : none
Example : $len = $gap->length();
Description: Getter for the length of this gap region
Returntype : int
Exceptions : none
Caller : general
Status : Stable
=cut
sub length {
my ($self) = @_;
return $self->{'end'} - $self->{'start'} + 1;
}
1;
]]>