————————=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
=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;
$Bio::EnsEMBL::Map::MapLocation::VERSION
=
'113.0.0'
;
use
strict;
=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->
new('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'
};
}
1;