Raw content of Bio::EnsEMBL::Map::MapLocation
<![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::Map::MapLocation
=head1 SYNOPSIS
=head1 DESCRIPTION
Represents a location on a genetic map, yac map, radition hybrid map,
etc.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::MapLocation;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Exception qw(deprecate);
=head2 new
Arg [1] : (optional) string $name
Arg [2] : (optional) string $map_name
Arg [3] : (optional) string $chromosome_name
Arg [4] : (optional) string $position
Arg [5] : (optional) float $lod_score
Example : $map_location = Bio::EnsEMBL::Map::MapLocation('DS1234',
'genethon',
'X',
'12.39',
50.12);
Description: Creates a new MapLocation
Returntype : Bio::EnsEMBL::Map::MapLocation
Exceptions : none
Caller : general
Status : stable
=cut
sub new {
my ($caller, $name, $map_name, $chromosome_name, $position, $lod_score) = @_;
my $class = ref($caller) || $caller;
return bless( {'map_name' => $map_name,
'name' => $name,
'chromosome_name' => $chromosome_name,
'position' => $position,
'lod_score' => $lod_score}, $class );
}
=head2 map_name
Arg [1] : string $map_name
Example : $map_name = $map_location->map_name;
Description: Getter/Setter for the map name
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub map_name {
my $self = shift;
$self->{'map_name'} = shift if(@_);
return $self->{'map_name'};
}
=head2 name
Arg [1] : (optional) string $name
Example : $name = $map_location->name;
Description: A name associated with the marker at this position. For
example if this is a genethon map location the name will be
the synonym of source genethon.
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub name {
my $self = shift;
$self->{'name'} = shift if(@_);
return $self->{'name'};
}
=head2 chromosome_name
Arg [1] : (optional) string $chromosome_name
Example : $chr_name = $map_location->chromosome_name;
$map_location->chromosome_name('X');
Description: The name of the chromosome associated with this map location
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub chromosome_name{
my $self = shift;
$self->{'chromosome_name'} = shift if(@_);
return $self->{'chromosome_name'};
}
=head2 position
Arg [1] : (optional) string $position
Example : $pos = $map_location->position;
Description: Getter/Setter for the position of this map location
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub position {
my $self = shift;
$self->{'position'} = shift if(@_);
return $self->{'position'};
}
=head2 lod_score
Arg [1] : (optional) float $lod
Example : $lod = $map_location->lod_score;
Description: Getter/Setter for lod score of this map location
Returntype : float
Exceptions : none
Caller : general
Status : stable
=cut
sub lod_score {
my $self = shift;
$self->{'lod_score'} = shift if(@_);
return $self->{'lod_score'};
}
=head2 chromosome
Description: DEPRECATED use chromosome_name() instead
=cut
sub chromosome {
my $self = shift;
deprecate('use chromosome_name instead');
if(@_) {
my $chr = shift;
if(ref($chr)) {
$self->chromosome_name($chr->seq_region_name());
} else {
$self->chromosome_name($chr);
}
}
#this object has no way to talk to db and thus no way to
#get a chromosome object
return $self->chromosome_name();
}
1;
]]>