Raw content of Bio::EnsEMBL::Map::MarkerFeature
<![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::MarkerFeature
=head1 SYNOPSIS
=head1 DESCRIPTION
Represents a marker feature in the EnsEMBL database. A marker feature
is a marker which has been mapped to the genome by ePCR. Each marker
has one marker feature per mapped location.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::MarkerFeature;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Feature;
@ISA = qw(Bio::EnsEMBL::Feature);
=head2 new
Arg [1] : (optional) int $dbID
Arg [2] : (optional) Bio::EnsEMBL::Adaptor $adaptor
Arg [3] : (optional) int $start
Arg [4] : (optional) int $end
Arg [5] : (optional) Bio::EnsEMBL::Slice $slice
Arg [6] : (optional) Bio::EnsEMBL::Analysis
Arg [7] : (optional) int $marker_id
Arg [8] : (optional) int $map_weight
Arg [9] : (optional) Bio::EnsEMBL::Map::Marker $marker
Example : $marker = Bio::EnsEMBL::Map::MarkerFeature->new(123, $adaptor,
100, 200,
$ctg, 123);
Description: Creates a new MarkerFeature
Returntype : Bio::EnsEMBL::Map::MarkerFeature
Exceptions : none
Caller : general
Status : stable
=cut
sub new {
my ($caller, $dbID, $adaptor, $start, $end, $slice, $analysis,
$marker_id, $map_weight, $marker) = @_;
my $class = ref($caller) || $caller;
return bless( {
'dbID' => $dbID,
'adaptor' => $adaptor,
'start' => $start,
'end' => $end,
'strand' => 0,
'slice' => $slice,
'analysis' => $analysis,
'marker_id' => $marker_id,
'marker' => $marker,
'map_weight' => $map_weight }, $class);
}
=head2 _marker_id
Arg [1] : (optional) int $marker_id
Example : none
Description: PRIVATE Getter/Setter for the internal identifier of the marker
associated with this marker feature
Returntype : int
Exceptions : none
Caller : internal
Status : stable
=cut
sub _marker_id {
my $self = shift;
if(@_) {
$self->{'marker_id'} = shift;
}
return $self->{'marker_id'};
}
=head2 marker
Arg [1] : (optional) Bio::EnsEMBL::Map::Marker $marker
Example : $marker = $marker_feature->marker;
Description: Getter/Setter for the marker associated with this marker feature
If the marker has not been set and the database is available
the marker will automatically be retrieved (lazy-loaded).
Returntype : Bio::EnsEMBL::Map::Marker
Exceptions : none
Caller : general
Status : stable
=cut
sub marker {
my $self = shift;
if(@_) {
$self->{'marker'} = shift;
} elsif(!$self->{'marker'} && $self->{'adaptor'} && $self->{'marker_id'}) {
#lazy load the marker if it is not already loaded
my $ma = $self->{'adaptor'}->db->get_MarkerAdaptor;
$self->{'marker'} = $ma->fetch_by_dbID($self->{'marker_id'});
}
return $self->{'marker'};
}
=head2 map_weight
Arg [1] : (optional) int $map_weight
Example : $map_weight = $marker_feature->map_weight;
Description: Getter/Setter for the map weight of this marker. This is the
number of times that this marker has been mapped to the genome.
E.g. a marker iwth map weight 3 has been mapped to 3 locations
in the genome.
Returntype : int
Exceptions : none
Caller : general
Status : stable
=cut
sub map_weight {
my $self = shift;
if(@_) {
$self->{'map_weight'} = shift;
}
return $self->{'map_weight'};
}
=head2 display_id
Arg [1] : none
Example : print $mf->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For marker features this is the
name of the display synonym or '' if it is not defined.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : stable
=cut
sub display_id {
my $self = shift;
my $marker = $self->{'marker'};
return '' if(!$marker);
my $ms = $marker->display_MarkerSynonym();
return '' if(!$ms);
return $ms->name() || '';
}
1;
]]>