Raw content of Bio::EnsEMBL::Map::Marker
<![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::Marker
=head1 SYNOPSIS
=head1 DESCRIPTION
Represents a marker in the EnsEMBL database. The marker object
is unpositioned on the genome. Markers which are positioned are
represented by the MarkerFeature object.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::Marker;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::Utils::Exception qw(throw);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [1] : (optional) int $dbID
Arg [2] : (optional) Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor $adaptor
Arg [3] : (optional) string $left_primer
Arg [4] : (optional) string $right_primer
Arg [5] : (optional) int $primer_distance
Arg [6] : (optional) int $priority
Arg [7] : (optional) string $type
Arg [8] : (optional) Bio::EnsEMBL::Map::MarkerSynonym $display_synonym
Arg [9] : (optional) listref of Bio::EnsEMBL::Map::MarkerSynonyms $syns
Arg [10] : (optional) listref of Bio::EnsEMBL::Map::MapLocations $locs
Example : $marker = Bio::EnsEMBL::Map::MarkerSynonym->new
(123, $adaptor,
$left_primer, $right_primer, 400,
80, $ms1, [$ms1, $ms2], [$mloc1, $mloc2]);
Description: Creates a new Marker
Returntype : Bio::EnsEMBL::Map::Marker
Exceptions : none
Caller : general
Status : stable
=cut
sub new {
my ($caller, $dbID, $adaptor, $left_primer, $right_primer,
$min_primer_dist, $max_primer_dist, $priority, $type, $display_synonym,
$syns, $mlocs) = @_;
my $class = ref($caller) || $caller;
my $self = bless( {'dbID' => $dbID,
'adaptor' => $adaptor,
'left_primer' => $left_primer,
'right_primer' => $right_primer,
'min_primer_dist' => $min_primer_dist,
'max_primer_dist' => $max_primer_dist,
'priority' => $priority,
'type' => $type,
'display_marker_synonym' => $display_synonym
}, $class);
#only load the marker synononyms if they were supplied, otherwise they
# will be lazy-loaded
if($syns && @$syns) {
$self->{'marker_synonyms'} = $syns;
}
#only load the map_locations if they were supplied, otherwise they will
# be lazy-loaded
if($mlocs) {
foreach my $ml (@$mlocs) {
$self->add_MapLocation($ml);
}
}
return $self;
}
=head2 left_primer
Arg [1] : (optional) string $left_primer
Example : $left_primer = $marker->left_primer;
Description: Getter/Setter for the left primer sequence of this marker
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub left_primer {
my $self = shift;
if(@_) {
$self->{'left_primer'} = shift;
}
return $self->{'left_primer'};
}
=head2 right_primer
Arg [1] : (optional) string $right_primer
Example : $right_primer = $marker->right_primer;
Description: Getter/Setter for the right primer sequence of this marker
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub right_primer {
my $self = shift;
if(@_) {
$self->{'right_primer'} = shift;
}
return $self->{'right_primer'};
}
=head2 min_primer_dist
Arg [1] : (optional) string $min
Example : $dist = $marker->min_primer_dist;
Description: Getter/Setter for the minimum seperation distance between the
left and right primers of this marker
Returntype : int
Exceptions : none
Caller : general
Status : stable
=cut
sub min_primer_dist {
my $self = shift;
if(@_) {
$self->{'min_primer_dist'} = shift;
}
return $self->{'min_primer_dist'};
}
=head2 max_primer_dist
Arg [1] : (optional) string $max
Example : $dist = $marker->max_primer_dist;
Description: Getter/Setter for the maximum seperation distance between the
left and right primers of this marker
Returntype : int
Exceptions : none
Caller : general
Status : stable
=cut
sub max_primer_dist {
my $self = shift;
if(@_) {
$self->{'max_primer_dist'} = shift;
}
return $self->{'max_primer_dist'};
}
=head2 priority
Arg [1] : (optional) int $priority
Example : $priority = $marker->priority;
Description: Getter/Setter for priority of this marker which can be used to
determine which markers are displayed.
Returntype : int
Exceptions : none
Caller : general
Status : stable
=cut
sub priority {
my $self = shift;
if(@_) {
$self->{'priority'} = shift;
}
return $self->{'priority'};
}
=head2 type
Arg [1] : (optional) string $type
Example : $type = $marker->type;
Description: Getter/Setter for type of this marker. Rat markers are typed
as 'est' or 'microsatellite'. Other markers may not have
defined types.
Returntype : string
Exceptions : none
Caller : general
Status : stable
=cut
sub type {
my $self = shift;
if(@_) {
$self->{'type'} = shift;
}
return $self->{'type'};
}
=head2 get_all_MarkerSynonyms
Arg [1] : none
Example : @synonyms = @{$marker->get_all_MarkerSynonyms};
Description: Retrieves a list of marker synonyms associated with this
marker. If this marker is connected to the datbase (i.e. it
has an adaptor and
Returntype : listref of Bio::EnsEMBL::Map::MarkerSynonyms
Exceptions : none
Caller : general
Status : stable
=cut
sub get_all_MarkerSynonyms {
my $self = shift;
#lazy-load the marker synonyms if they haven't been retrieved
if(!exists $self->{'marker_synonyms'} &&
$self->{'adaptor'} && $self->{'dbID'}) {
$self->adaptor->fetch_attributes($self);
}
return $self->{'marker_synonyms'} || [];
}
=head2 add_MarkerSynonym
Arg [1] : Bio::EnsEMBL::MarkerSynonym $ms
Example : $marker->add_MarkerSynonym($ms);
Description: Associates a new synonym with this marker. Adding marker
synonyms to a marker which has not yet retrieved its
synonyms from the database will prevent the loading of these
from the database at request time (unless flush_MarkerSynonyms
is called first).
Returntype : none
Exceptions : thrown if incorrect argument is passed
Caller : general
Status : stable
=cut
sub add_MarkerSynonyms {
my ($self, @ms) = @_;
#create the array if it does not exist it
$self->{'marker_synonyms'} ||= [];
push(@{$self->{'marker_synonyms'}}, @ms);
}
=head2 flush_MarkerSynonyms
Arg [1] : none
Example : $marker->flush_MarkerSynonyms;
Description: clears all of the marker sysnonyms which have been added to
this marker.
Returntype : none
Exceptions : none
Caller : general
Status : stable
=cut
sub flush_MarkerSynonyms {
my $self = shift;
delete $self->{'marker_synonyms'};
}
=head2 display_MarkerSynonym
Arg [1] : (optional) Bio::EnsEMBL::DBSQL::MarkerSynonym $ms
Example : none
Description: Getter/Setter for the 'display' synonym of this marker
Returntype : Bio::EnsEMBL::Map::MarkerSynonym
Exceptions : thrown if the argument is invalid
Caller : general
Status : stable
=cut
sub display_MarkerSynonym {
my $self = shift;
if(@_) {
my $ms = shift;
if($ms && !(ref $ms && $ms->isa('Bio::EnsEMBL::Map::MarkerSynonym'))) {
throw("ms arg must be Bio::EnsEMBL::Map::MarkerSynonym not [$ms]");
}
$self->{'display_marker_synonym'} = $ms;
}
return $self->{'display_marker_synonym'};
}
=head2 get_all_MarkerFeatures
Arg [1] : none
Example : @marker_features = @{$marker->get_all_MarkerFeatures};
Description: Retrieves the marker features which are associated with this
marker. I.e. locations where this marker has been mapped to
the genome via e-PCR
Returntype : listref of Bio::EnsEMBL::Map::MarkerFeatures
Exceptions : none
Caller : general
Status : stable
=cut
sub get_all_MarkerFeatures {
my $self = shift;
my $marker_feature_adaptor = $self->adaptor->db->get_MarkerFeatureAdaptor;
#these results are not cached to avoid a circular reference loop
return $marker_feature_adaptor->fetch_all_by_Marker($self);
}
=head2 get_all_MapLocations
Arg [1] : none
Example : @map_locations = @{$marker->get_all_MapLocations};
Description: Retrieves all map locations which are associated with this
marker.
Returntype : listref of Bio::EnsEMBL::Map::MapLocations
Exceptions : none
Caller : general
Status : stable
=cut
sub get_all_MapLocations {
my $self = shift;
#lazy-load the map locations if they have not been fetched yet
if(!exists $self->{'map_locations'} &&
$self->{'adaptor'} && $self->{'dbID'}) {
$self->adaptor->fetch_attributes($self);
}
my @out = values %{$self->{'map_locations'}};
return \@out;
}
=head2 get_MapLocation
Arg [1] : string $map_name
Example : $map_location = $marker->get_MapLocation('genethon');
Description: Retrieves the location of this marker in a specified map.
If this marker is not defined in the specified map then
undef is returned.
Returntype : Bio::EnsEMBL::Map::MapLocation
Exceptions : thrown if the map_name arg is not provided
Caller : general
Status : stable
=cut
sub get_MapLocation {
my $self = shift;
my $map_name = shift;
#lazy-load the map locations if they have not been fetched yet
if(!exists $self->{'map_locations'} &&
$self->{'adaptor'} && $self->{'dbID'}) {
$self->adaptor->fetch_attributes($self);
}
unless($map_name) {
throw('map_name argument is required, or use get_all_MapLocations');
}
return $self->{'map_locations'}->{$map_name};
}
=head2 add_MapLocations
Arg [1..n] : @mlocs list of Bio::EnsEMBL::MapLocations
Example : $marker->add_MapLocations(@mlocs);
Description: Associates 1 or more map locations with this marker
using this function to manually load map locations will prevent
lazy-loading of locations from the database.
Returntype : listref of Bio::EnsEMBL::MapLocations
Exceptions : throws if map location has no name
Caller : general
Status : stable
=cut
sub add_MapLocations {
my ($self, @mlocs) = @_;
foreach my $ml (@mlocs) {
unless($ml && ref $ml && $ml->isa('Bio::EnsEMBL::Map::MapLocation')) {
throw("args must be Bio::EnsEMBL::Map::MapLocations not [$ml]");
}
my $mname = $ml->map_name;
unless($mname) {
throw("map location arg [$ml] does not define a map name");
}
$self->{'map_locations'}->{$mname} = $ml;
}
}
=head2 flush_MapLocations
Arg [1] : none
Example : $marker->get_all_MapLocations;
Description: Removes map locations associated with this marker. Markers may
be lazy-loaded from the database (again) after this.
Returntype : none
Exceptions :
Caller :
Status : stable
=cut
sub flush_MapLocations{
my $self = shift;
delete $self->{'map_locations'};
}
1;
]]>