Raw content of Bio::EnsEMBL::DBSQL::AffyProbeAdaptor
<![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::DBSQL::AffyProbeAdaptor - A database adaptor for fetching and
storing AffyProbe objects.
=head1 SYNOPSIS
my $apa = $db->get_AffyProbeAdaptor();
my $probe =
$opa->fetch_by_array_probeset_probe( 'Affy-1', 'Probeset-1',
'Probe-1' );
=head1 DESCRIPTION
The AffyProbeAdaptor is a database adaptor for storing and retrieving
AffyProbe objects.
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::DBSQL::AffyProbeAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::AffyProbe;
use Bio::EnsEMBL::DBSQL::OligoProbeAdaptor;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::OligoProbeAdaptor);
=head2 fetch_all_by_AffyArray
Arg [1] : Bio::EnsEMBL::AffyArray
Example : my @probes = @{$apa->fetch_all_by_AffyArray($array)};
Description: Fetch all probes on a particular array.
Returntype : Listref of Bio::EnsEMBL::AffyProbe objects.
Exceptions : None
Caller : General
Status : Medium Risk
=cut
sub fetch_all_by_AffyArray {
my $self = shift;
my $array = shift;
return $self->fetch_all_by_Array($array);
}
=head2 fetch_by_AffyArray
Arg [1] : Bio::EnsEMBL::AffyArray
Example : my @probes = @{$apa->fetch_by_AffyArray($array)};
Description: Fetch all probes on a particular array. This method was misnamed
and is deprecated.
Returntype : Listref of Bio::EnsEMBL::AffyProbe objects.
Exceptions : None
Caller : General
Status : At Risk
: Likely to be removed - use fetch_all_by_AffyArray instead
=cut
sub fetch_by_AffyArray {
my $self = shift;
my $array = shift;
deprecate('fetch_all_by_Array() should be used instead of the deprecated fetch_by_AffyArray().');
return $self->fetch_all_by_Array($array);
}
=head2 fetch_by_AffyFeature
Arg [1] : Bio::EnsEMBL::AffyFeature
Example : my $probe = $apa->fetch_by_AffyFeature($feature);
Description: Returns the probe that created a particular feature.
Returntype : Bio::EnsEMBL::AffyProbe
Exceptions : Throws if argument is not a Bio::EnsEMBL::AffyFeature object
Caller : General
Status : Medium Risk
=cut
sub fetch_by_AffyFeature {
my $self = shift;
my $feature = shift;
return $self->fetch_by_OligoFeature($feature);
}
=head2 _objs_from_sth
Arg [1] : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates OligoProbe objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::AffyProbe objects
Exceptions : None
Caller : Internal
Status : Medium Risk
=cut
sub _objs_from_sth {
my ($self, $sth) = @_;
my (@result, $current_dbid, $probe_id, $array_id, $probeset, $name, $description, $probelength);
my ($array, %array_cache);
$sth->bind_columns( \$probe_id, \$array_id, \$probeset, \$name, \$description, \$probelength );
my $probe;
while ( $sth->fetch() ) {
$array = $array_cache{$array_id} || $self->db->get_AffyArrayAdaptor()->fetch_by_dbID($array_id);
if (!$current_dbid || $current_dbid != $probe_id) {
# New probe
$probe = Bio::EnsEMBL::AffyProbe->new(
-name => $name,
-array => $array,
-probeset => $probeset,
-description => $description,
-probelength => $probelength,
-dbID => $probe_id,
-adaptor => $self,
);
push @result, $probe;
$current_dbid = $probe_id;
} else {
# Extend existing probe
$probe->add_Array_probename($array, $name);
}
}
return \@result;
}
=head2 list_dbIDs
Arg [1] : none
Example : my @probe_ids = @{$apa->list_dbIDs()};
Description: Gets an array of internal IDs for all AffyProbe objects
in the current database. NOTE: In a multi-species
database, this method will return the dbIDs of all
AffyProbe objects, not just the ones associated with
the current species.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk
=cut
sub list_dbIDs {
my ($self) = @_;
#return $self->_list_dbIDs('oligo_probe');
# Can't use _list_dbIDs because only want OligoProbe objects on arrays of type AFFY
my @out;
# FIXME: This SQL will not work as expected on multi-species
# databases. It needs to be anchored in a coord_system entry
# coord_system.species_id = $self->species_id(). /ak4@2008-07-15
my $sql = "
SELECT DISTINCT op.oligo_probe_id
FROM oligo_probe op, oligo_array oa
WHERE op.oligo_array_id=oa.oligo_array_id
AND oa.type='AFFY'
";
my $sth = $self->prepare($sql);
$sth->execute;
while (my ($id) = $sth->fetchrow() ) {
push @out, $id;
}
$sth->finish;
return \@out;
}
1;
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