Raw content of Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor
<![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::DBSQL::MarkerAdaptor
=head1 SYNOPSIS
=head1 DESCRIPTION
Provides database interaction for the Bio::EnsEMBL::Map::Marker object
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor;
use strict;
use vars ('@ISA');
use Bio::EnsEMBL::Map::Marker;
use Bio::EnsEMBL::Map::MapLocation;
use Bio::EnsEMBL::Map::MarkerSynonym;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_all
Arg [1] : none
Example : @all_markers = @{$marker_adaptor->fetch_all};
Description: Retrieves all markers from the database
Returntype : listref of Bio::EnsEMBL::Map::Markers
Exceptions : none
Caller : general
Status : stable
=cut
sub fetch_all {
my $self = shift;
my $dbID = shift;
my $sth = $self->prepare("SELECT m.marker_id, m.priority, m.left_primer,
m.right_primer, m.type,
m.min_primer_dist, m.max_primer_dist,
ms.marker_synonym_id, ms.name, ms.source
FROM marker m
LEFT JOIN marker_synonym ms
ON ms.marker_synonym_id =
m.display_marker_synonym_id");
$sth->execute;
my( $marker_id, $priority, $left_primer, $right_primer, $type,
$min_pdist, $max_pdist, $ms_id, $ms_name, $ms_src);
$sth->bind_columns(\$marker_id, \$priority,
\$left_primer, \$right_primer, \$type, \$min_pdist, \$max_pdist,
\$ms_id, \$ms_name, \$ms_src);
my @out;
while($sth->fetch) {
#create a display marker synonym for each marker created, if one is defined
my $synonym;
if($ms_id) {
$synonym = Bio::EnsEMBL::Map::MarkerSynonym->new
($ms_id, $ms_src, $ms_name);
}
push @out, Bio::EnsEMBL::Map::Marker->new
($marker_id, $self, $left_primer, $right_primer, $min_pdist, $max_pdist,
$priority, $type, $synonym);
}
return \@out;
}
=head2 fetch_by_dbID
Arg [1] : int $dbID
The internal identifier of the Marker to retrieve
Example : $marker = $marker_adaptor->fetch_by_dbID(123);
Description: Retrieves a marker object from the database via its internal
identifier.
Returntype : Bio::EnsEMBL::Map::Marker
Exceptions : thrown if no marker with $dbID is present in the database
Caller : general
Status : stable
=cut
sub fetch_by_dbID {
my $self = shift;
my $dbID = shift;
$self->throw('dbID argument is required') unless($dbID);
my $sth = $self->prepare("SELECT m.marker_id, m.display_marker_synonym_id,
m.priority, m.left_primer, m.right_primer,
m.type,
m.min_primer_dist, m.max_primer_dist,
ms.marker_synonym_id,
ms.source, ms.name
FROM marker m, marker_synonym ms
WHERE m.marker_id = ?
AND ms.marker_id = m.marker_id");
$sth->execute($dbID);
my( $marker_id, $display_ms_id, $priority, $left_primer, $right_primer,
$type, $min_pdist, $max_pdist, $ms_id, $ms_src, $ms_name);
$sth->bind_columns(\$marker_id, \$display_ms_id, \$priority,
\$left_primer, \$right_primer, \$type,
\$min_pdist, \$max_pdist,
\$ms_id, \$ms_src, \$ms_name);
my $display_synonym;
my @synonyms;
while($sth->fetch) {
#create a new synonym for each row
my $s = new Bio::EnsEMBL::Map::MarkerSynonym->new($ms_id, $ms_src,
$ms_name);
$display_synonym = $s if($display_ms_id == $ms_id);
push @synonyms, $s;
}
$sth->finish;
unless($marker_id) {
$self-> warning("marker with dbID=[$dbID] not present in database");
return undef;
}
#now create the marker
return new Bio::EnsEMBL::Map::Marker->new(
$marker_id, $self, $left_primer, $right_primer,$min_pdist, $max_pdist,
$priority, $type,$display_synonym, \@synonyms);
}
=head2 fetch_all_by_synonym
Arg [1] : string $synonym
An name of this marker
Arg [2] : (opional) string $source
The source of this name
Example : @markers = @{$marker_adaptor->fetch_all_by_synonym($id)};
Description: Retrieves a list of markers with the synonym (alias) $synonym
and from source $source. In most cases the list will have a
single element, however it is possible that multiple markers
with the same synonym exist.
Returntype : listref of Bio::EnsEMBL::Map::Markers
Exceptions : none
Caller : general
Status : stable
=cut
sub fetch_all_by_synonym {
my ($self, $synonym, $source) = @_;
$self->throw("synonym argument is required") unless($synonym);
my $q = "SELECT marker_id
FROM marker_synonym ms
WHERE ms.name = ?";
my @bind_vals = ($synonym);
if($source) {
$q .= " AND ms.source = ?";
push(@bind_vals, $source);
}
my $sth = $self->prepare($q);
$sth->execute(@bind_vals);
my @out = ();
my $marker_id;
my %seen;
#fetch the markers and filter out duplictes
while(($marker_id) = $sth->fetchrow_array) {
next if $seen{$marker_id};
# some synonyms point to markers that don't exist, so only add genuine ones
my $marker = $self->fetch_by_dbID($marker_id);
push @out, $marker if ($marker);
$seen{$marker_id} = 1;
}
$sth->finish;
return \@out;
}
=head2 fetch_attributes
Arg [1] : Bio::EnsEMBL::Map::Marker $marker
Example : $marker_adaptor->fetch_attributes($marker);
Description: Fetches the marker_synonym and map_location attributes of
a marker. This is done so that these attributes can be
lazy-loaded on request.
Returntype : none
Exceptions : none
Caller : Bio::EnsEMBL::Map::Marker::marker
Status : stable
=cut
sub fetch_attributes {
my $self = shift;
my $marker = shift;
my $m_id = $marker->dbID;
$self->throw('Marker argument does not have a dbID') unless($m_id);
#
# First Retrieve synonyms for this marker
#
$marker->flush_MarkerSynonyms;
my $sth = $self->prepare("SELECT ms.marker_synonym_id, ms.source, ms.name
FROM marker_synonym ms
WHERE ms.marker_id = ?");
my @syns = ();
my ($ms_id, $ms_src, $ms_name);
$sth->execute($m_id);
$sth->bind_columns(\$ms_id, \$ms_src, \$ms_name);
while($sth->fetch) {
push @syns, Bio::EnsEMBL::Map::MarkerSynonym->new($ms_id,$ms_src,$ms_name);
}
$sth->finish;
$marker->add_MarkerSynonyms(@syns) if(@syns);
#
# Now retrieve map locations for this marker
#
$marker->flush_MapLocations;
$sth = $self->prepare("SELECT mloc.chromosome_name, mloc.position,
mloc.lod_score, map.map_name, ms.name
FROM marker_map_location mloc, map map,
marker_synonym ms
WHERE mloc.marker_id = ?
AND map.map_id = mloc.map_id
AND ms.marker_synonym_id = mloc.marker_synonym_id");
my($chr_name, $pos, $lod, $mname, $name);
my @mlocs;
$sth->execute($m_id);
$sth->bind_columns(\$chr_name, \$pos, \$lod, \$mname, \$name);
while($sth->fetch) {
push(@mlocs, Bio::EnsEMBL::Map::MapLocation->new($name, $mname,
$chr_name,$pos,$lod));
}
$sth->finish;
$marker->add_MapLocations(@mlocs);
}
=head2 store
Arg [1] : Bio::EnsEMBL::Map::Marker
Example : $marker_adaptor->store(@markers);
Description: Stores a list of markers in this database.
The dbID and adaptor of each marker will be set on successful
storing.
Returntype : 1 on success
Exceptions : thrown if not all data needed for storing is populated in the
marker
Caller : general
Status : stable
=cut
sub store {
my ($self, @markers) = @_;
MARKER:foreach my $marker( @markers ){
if($marker->dbID){
if($self->fetch_by_dbID($marker->dbID)){
next MARKER;
}
}
#
# Sanity check
#
if(!$marker ||
!ref($marker) ||
!$marker->isa('Bio::EnsEMBL::Map::Marker')) {
$self->throw('Incorrect argument [$marker] to store. Expected ' .
'Bio::EnsEMBL::Map::Marker');
}
# Don't store if already stored
if($marker->is_stored($self->db())) {
warning('Marker ['.$marker->dbID.'] is already stored in this DB.');
next;
}
# Get/test the display marker synonym
my $display_synonym = $marker->display_MarkerSynonym;
if(!$display_synonym || !ref($display_synonym) ||
!$display_synonym->isa('Bio::EnsEMBL::Map::MarkerSynonym')) {
$self->throw('Cannot store Marker without an associated '.
'display_MarkerSynonym');
}
# Store the Marker itself
my $q = qq(
INSERT INTO marker ( left_primer, right_primer,
min_primer_dist, max_primer_dist,
priority, type)
VALUES ( ?,?,?,?,?,?) );
my $sth = $self->prepare($q);
$sth->execute( $marker->left_primer || '',
$marker->right_primer || '',
$marker->min_primer_dist || 0,
$marker->max_primer_dist || 0,
$marker->priority,
$marker->type );
my $dbID = $sth->{'mysql_insertid'};
$marker->dbID($dbID);
$marker->adaptor($self);
if(!$display_synonym->dbID) {
# Store synonym
$self->_store_MarkerSynonym($marker,$display_synonym);
}
my $display_synonym_id = $display_synonym->dbID ||
$self->throw('display_MarkerSynonym must have dbID to store Marker');
# Update the marker with the display synonym
my $qup = qq(
UPDATE marker
SET display_marker_synonym_id = $display_synonym_id
WHERE marker_id = ? );
my $sthup = $self->prepare($qup);
$sthup->execute($dbID);
# Loop through all MarkerSynonyms and store if needed
foreach my $synonym( @{$marker->get_all_MarkerSynonyms} ){
if(!$synonym->dbID) {
$self->_store_MarkerSynonym($marker,$synonym);
}
}
# Loop through all MapLocations and store if needed
foreach my $loc( @{$marker->get_all_MapLocations} ){
# Dunno how to implement this :( Just bomb out
$self->throw( 'Storing of MapLocation objects is not yet implemented' )
}
}
return 1;
}
=head2 _store_MarkerSynonym
Arg [1] : Bio::EnsEMBL::Map::Marker
Arg [2] : Bio::EnsEMBL::Map::MarkerSynonym
Example : $marker_adaptor->_store_MarkerSynonym($marker,$ms);
Description: Stores a marker synonym attached to the marker in the database
The dbID of each MarkerSynonym will be set on successful
storing.
Returntype : dbID of the MarkerSynonym
Exceptions : thrown if not all data needed for storing is populated
Caller : $self->store
Status : stable
=cut
sub _store_MarkerSynonym{
my $self = shift;
my $marker = shift;
my $ms = shift;
# Sanity check
if(!$marker || !ref($marker) ||
!$marker->isa('Bio::EnsEMBL::Map::Marker')) {
$self->throw("Incorrect argument [$marker] to _store_MarkerSynonym." .
"Expected Bio::EnsEMBL::Map::Marker");
}
if(!$ms || !ref($ms) ||
!$ms->isa('Bio::EnsEMBL::Map::MarkerSynonym')) {
$self->throw("Incorrect argument [$ms] to _store_MarkerSynonym." .
"Expected Bio::EnsEMBL::Map::MarkerSynonym");
}
# Don't store if already stored
if($ms->dbID) {
warning('MarkerSynonym ['.$ms->dbID.'] is already stored in this DB.');
return;
}
my $marker_id = $marker->dbID ||
throw( "Marker has no dbID. Cannot store MarkerSynonym" );
# Store the synonym
my $q = qq(
INSERT INTO marker_synonym ( marker_id, source, name )
VALUES ( ?,?,?) );
my $sth = $self->prepare($q);
$sth->execute( $marker_id,
$ms->source,
$ms->name );
my $dbID = $sth->{'mysql_insertid'};
$ms->dbID($dbID);
return $dbID;
}
1;
]]>