Raw content of Bio::EnsEMBL::Map::Qtl
<![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::Qtl
=head1 SYNOPSIS
=head1 DESCRIPTION
Represents a Qtl in the EnsEMBL database. A quantitative trait locus is
defined by three markers, two flanking and one peak (optional) marker.
Its a region (or more often a group of regions) which is likely to
affect the phenotype (trait) described in this Qtl.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::Qtl;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [1] : int $dbID
Arg [2] : Bio::EnsEMBL::Map::DBSQL::QtlAdaptor $adaptor
Arg [3] : Bio::EnsEMBL::Map::Marker $flank_marker_1
Arg [4] : Bio::EnsEMBL::Map::Marker $peak_marker
Arg [5] : Bio::EnsEMBL::Map::Marker $flank_marker_2
Arg [6] : string $trait
Arg [7] : float $lod_score
Arg [8] : hashref $synonyms
A hashref with source keys and identifier values
Example : none
Description: Creates a new Qtl object. Usually done by Adaptor
Returntype : Bio::EnsEMBL::Map::Qtl
Exceptions : none
Caller : general, DBSQL::QtlAdaptor, DBSQL::QtlFeatureAdaptor
Status : stable
=cut
sub new {
my ( $class, $dbID, $adaptor, $flank_marker_1, $peak_marker,
$flank_marker_2, $trait, $lod_score,
$synonyms ) = @_;
$class = ref( $class ) ||$class;
my $self = bless( {
'dbID' => $dbID,
'adaptor' => $adaptor,
'flank_marker_1' => $flank_marker_1,
'flank_marker_2' => $flank_marker_2,
'peak_marker' => $peak_marker,
'trait' => $trait,
'lod_score' => $lod_score,
'synonyms' => $synonyms
}, $class );
return $self;
}
=head2 add_synonym
Arg [1] : string $source
The source of the synonym
Arg [2] : string $identifier
The identifier from this source
Example : $qtl->add_synonym('rat genome database', '65516');
Description: Adds a synonym to this qtl
Returntype : none
Exceptions : thrown if arguments are not provided
Caller : general
Status : stable
=cut
sub add_synonym {
my $self = shift;
my $source = shift;
my $identifier = shift;
unless($source && $identifier) {
throw('Source and identifier arguments are required');
}
$self->{'synonyms'}->{$source} = $identifier;
}
=head2 get_synonyms
Arg [1] : none
Example :
foreach my $source ($keys %{$qtl->get_synonyms}) {
print $source . ':'. $qtl->get_synonyms->{$source};
}
Description: Returns a hashref of synonyms keyed on their source name
Returntype : hashref of synonyms keyed on their source name
Exceptions : none
Caller : general
Status : stable
=cut
sub get_synonyms {
my $self = shift;
return $self->{'synonyms'} || {};
}
=head2 trait
Arg [1] : string $trait
Phenotype of this Qtl
Example : none
Description: Getter/Setter for the trait attribute
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub trait {
my $self = shift;
if(@_) {
$self->{'trait'} = shift;
}
return $self->{'trait'};
}
=head2 lod_score
Arg [1] : float $lod_score
A score for the Qtl
Example : none
Description: Getter/Setter for attribute lod_score
Returntype : float
Exceptions : none
Caller : general
Status : stable
=cut
sub lod_score {
my $self = shift;
if(@_) {
$self->{'lod_score'} = shift;
}
return $self->{'lod_score'};
}
=head2 peak_marker
Arg [1] : Bio::EnsEMBL::Map::Marker $peak_marker
an optional Marker which has the peak probablitity
for this traits occurence
Example : none
Description: Getter/Setter for attribute peak_marker
Returntype : Bio::EnsEMBL::Map::Marker
Exceptions : none
Caller : general
Status : stable
=cut
sub peak_marker {
my $self = shift;
if(@_) {
$self->{'peak_marker'} = shift;
}
return $self->{'peak_marker'};
}
=head2 flank_marker_1
Arg [1] : Bio::EnsEMBL::Map::Marker $flank_marker_1
One flanking marker of the interest region, the two flanking
markers define the region
Example : none
Description: Getter/Setter attribute flanking_marker_1
Returntype : Bio::EnsEMBL::Map::Marker
Exceptions : none
Caller : general
Status : stable
=cut
sub flank_marker_1 {
my $self = shift;
if(@_) {
$self->{'flank_marker_1'} = shift;
}
return $self->{'flank_marker_1'};
}
=head2 flank_marker_2
Arg [1] : Bio::EnsEMBL::Map::Marker $flank_marker_2
One flanking marker of the interest region, the two flanking
markers define the region
Example : none
Description: Getter/Setter attribute flanking_marker_2
Returntype : Bio::EnsEMBL::Map::Marker
Exceptions : none
Caller : general
Status : stable
=cut
sub flank_marker_2 {
my $self = shift;
if(@_) {
$self->{'flank_marker_2'} = shift;
}
return $self->{'flank_marker_2'};
}
=head2 get_QtlFeatures
Args : none
Example : none
Description: return the qtl feature which is associated with this
Qtl. It comes in chromosomal slice coordinates. There can
only be one.
Returntype : Bio::EnsEMBL::Map::QtlFeature
Exceptions : only works with adaptored Qtls
Caller : general
Status : stable
=cut
sub get_QtlFeature {
my $self = shift;
my $adaptor = $self->adaptor();
return undef unless $adaptor;
my $result = $adaptor->db()->get_QtlFeatureAdaptor()->
fetch_all_by_Qtl( $self );
if( @$result ) {
return $result->[0];
} else {
return;
}
}
=head2 source_database
This method is deprecated. Use get_synonyms or add_synonym instead.
=cut
sub source_database {
my $self = shift;
deprecate('Use get_synonyms or add_synonym instead');
my $syns = $self->get_synonyms;
my ($source) = keys %$syns;
return $source || '';
}
=head2 source_primary_id
This method is deprecated. Use get_synonyms or add_synonym instead.
=cut
sub source_primary_id {
my $self = shift;
deprecate('Use get_synonyms or add_synonym instead');
my $syns = $self->get_synonyms;
my ($source) = keys %$syns;
if($source) {
return $syns->{$source};
}
return '';
}
1;
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