Raw content of Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor
#
# You may distribute this module under the same terms as Perl itself
=head1 NAME
Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor - A database adaptor for fetching and
storing Funcgen Array objects.
=head1 SYNOPSIS
my $oaa = $db->get_ArrayAdaptor();
my $array = $oaa->fetch_by_name('Array-1');
my @arrays = @{$oaa->fetch_all()};
=head1 DESCRIPTION
The ArrayAdaptor is a database adaptor for storing and retrieving
Funcgen Array objects.
=head1 AUTHOR
This module was created by Nathan Johnson, but is almost entirely based on the
ArrayAdaptor modules written by Ian Sealy and Arne Stabenau.
This module is part of the Ensembl project: /
=head1 CONTACT
Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Funcgen::DBSQL::ArrayAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( warning throw );
use Bio::EnsEMBL::Funcgen::Array;
use Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor;
use vars qw(@ISA);
#May need to our this?
@ISA = qw(Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor);
=head2 fetch_by_array_chip_dbID
Arg [1] : int - dbID of array_chip
Example : my $array = $oaa->fetch_by_array_chip_dbID($ac_dbid);
Description: Retrieves a named Array object from the database.
Returntype : Bio::EnsEMBL::Funcgen::Array
Exceptions : None
Caller : General
Status : At Risk
=cut
sub fetch_by_array_chip_dbID {
my $self = shift;
my $ac_dbid = shift;
my $sth = $self->prepare("
SELECT a.array_id
FROM array a, array_chip ac
WHERE a.array_id = ac.array_id
AND ac.array_chip_id = $ac_dbid
");
$sth->execute();
my ($array_id) = $sth->fetchrow();
return $self->fetch_by_dbID($array_id);
}
=head2 fetch_by_name_vendor
Arg [1] : string - name of an array
Arg [2] : string - name of vendor e.g. NIMBLEGEN
Example : my $array = $oaa->fetch_by_name('Array-1');
Description: Retrieves a named Array object from the database.
Returntype : Bio::EnsEMBL::Funcgen::Array
Exceptions : None
Caller : General
Status : At Risk
=cut
sub fetch_by_name_vendor {
my ($self, $name, $vendor) = @_;
throw("Must provide and array and vendor name") if (! ($name && $vendor));
#unique key means this only returns one element
my ($result) = @{$self->generic_fetch("a.name = '$name' and a.vendor='".uc($vendor)."'")};
return $result;
}
=head2 fetch_by_name_class
Arg [1] : string - name of an array
Arg [2] : string - class of array e.g. AFFY_UTR
Example : my $array = $oaa->fetch_by_name_class('HuGene_1_0_st_v1', 'AFFY_ST');
Description: Retrieves Array object from the database based on name and class.
Returntype : Bio::EnsEMBL::Funcgen::Array
Exceptions : Throws is name and class not passed
Caller : General
Status : At Risk
=cut
sub fetch_by_name_class {
my ($self, $name, $class) = @_;
throw("Must provide and array and class e.g.'HuGene_1_0_st_v1', 'AFFY_ST'") if (! ($name && $class));
my ($result) = @{$self->generic_fetch("a.name = '$name' and a.class='".uc($class)."'")};
return $result;
}
=head2 fetch_all_by_class
Arg [1] : string - class
Example : my $array = $oaa->fetch_all_by_class(''AFFY_ST');
Description: Retrieves Array object from the database based class.
Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::Array objects
Exceptions : Throws if nor class passed
Caller : General
Status : At Risk
=cut
sub fetch_all_by_class {
my ($self, $class) = @_;
throw("Must provide and array class e.g.'AFFY_ST'") if (! defined $class);
return $self->generic_fetch("a.class='".uc($class)."'");
}
=head2 fetch_all_by_type
Arg [1] : List of strings - type(s) (e.g. OLIGO, PCR)
Example : my @arrays = @{$aa->fetch_all_by_type('OLIGO')};
Description: Fetch all arrays of a particular type.
Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
Exceptions : Throws if no type is provided
Caller : General
Status : at risk
=cut
sub fetch_all_by_type {
my ($self, @types) = @_;
throw('Need type as parameter') if ! @types;
my $constraint;
if (scalar @types == 1) {
$constraint = qq( a.type = '$types[0]' );
} else {
$constraint = join q(','), @types;
$constraint = qq( a.type IN ('$constraint') );
}
return $self->generic_fetch($constraint);
}
=head2 fetch_all_by_Experiment
Arg [1] : Bio::EnsEMBL::Funcgen::Experiement
Example : my @arrays = @{$aa->fetch_all_by_Experiment($exp)};
Description: Fetch all arrays associated with a given Experiment
This is a convenience method to hide the 3 adaptor required
for this call.
Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
Exceptions : none
Caller : General
Status : at risk
=cut
sub fetch_all_by_Experiment{
my ($self, $exp) = @_;
my %array_ids;
my $echips = $self->db->get_ExperimentalChipAdaptor->fetch_all_by_Experiment($exp);
foreach my $achip(@{$self->db->get_ArrayChipAdaptor->fetch_all_by_ExperimentalChips($echips)}){
$array_ids{$achip->array_id()} = 1;
}
return $self->generic_fetch('a.array_id IN ('.join(', ', keys %array_ids).')');
}
=head2 fetch_attributes
Arg [1] : Bio::EnsEMBL::Funcgen::Array - array to fetch attributes for
Example : None
Description: This function is solely intended to lazy load attributes into
empty Array objects. You should not need to call this.
Returntype : None
Exceptions : None
Caller : Bio::EnsEMBL::Funcgen::Array getters
Status : Medium Risk
=cut
sub fetch_attributes {
my $self = shift;
my $array = shift;
my $tmp_array = $self->fetch_by_dbID( $array->dbID() );
%$array = %$tmp_array;
}
=head2 _tables
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns the names and aliases of the tables to use for queries.
Returntype : List of listrefs of strings
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _tables {
my $self = shift;
return ['array', 'a'];
}
=head2 _columns
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns a list of columns to use for queries.
Returntype : List of strings
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _columns {
my $self = shift;
return qw( a.array_id a.name a.format a.vendor a.description a.type a.class);
}
=head2 _objs_from_sth
Arg [1] : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates Array objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
Exceptions : None
Caller : Internal
Status : At Risk
=cut
sub _objs_from_sth {
my ($self, $sth) = @_;
my (@result, $array_id, $name, $format, $vendor, $description, $type, $class);
$sth->bind_columns(\$array_id, \$name, \$format, \$vendor, \$description, \$type, \$class);
while ( $sth->fetch() ) {
my $array = Bio::EnsEMBL::Funcgen::Array->new
(
-dbID => $array_id,
-adaptor => $self,
-name => $name,
-format => $format,
-vendor => $vendor,
-description => $description,
-type => $type,
-class => $class,
);
push @result, $array;
}
return \@result;
}
=head2 store
Args : List of Bio::EnsEMBL::Funcgen::Array objects
Example : $oaa->store($array1, $array2, $array3);
Description: Stores given Array objects in the database. This
method checks for arrays previously stored and updates
and new array_chips accordingly.
Returntype : Listref of stored Array objects
Exceptions : None
Caller : General
Status : At Risk
=cut
#This works slightly differently as arary_chip are not stored as objects,
#yet we need to retrieve a dbID for the array before we know about all the array_chips
sub store {
my $self = shift;
my @args = @_;
my ($sarray);
my $sth = $self->prepare("
INSERT INTO array
(name, format, vendor, description, type, class)
VALUES (?, ?, ?, ?, ?, ?)");
foreach my $array (@args) {
if ( !$array->isa('Bio::EnsEMBL::Funcgen::Array') ) {
warning('Can only store Array objects, skipping $array');
next;
}
if (!( $array->dbID() && $array->adaptor() == $self )){
#try and fetch array here and set to array if valid
$sarray = $self->fetch_by_name_vendor($array->name(), $array->vendor());#this should be name_vendor?
if( ! $sarray){
#sanity check here
throw("Array name must not be longer than 30 characters") if (length($array->name) > 40);
$sth->bind_param(1, $array->name(), SQL_VARCHAR);
$sth->bind_param(2, $array->format(), SQL_VARCHAR);
$sth->bind_param(3, $array->vendor(), SQL_VARCHAR);
$sth->bind_param(4, $array->description(), SQL_VARCHAR);
$sth->bind_param(5, $array->type(), SQL_VARCHAR);
$sth->bind_param(6, $array->class(), SQL_VARCHAR);
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
$array->dbID($dbID);
$array->adaptor($self);
}
else{
#warn("Array already stored, using previously stored array\n");# validating array_chips\n");
$array = $sarray;
}
}
}
return \@args;
}
=head2 list_dbIDs
Args : None
Example : my @array_ids = @{$oaa->list_dbIDs()};
Description: Gets an array of internal IDs for all Array objects in the
current database.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk
=cut
sub list_dbIDs {
my ($self) = @_;
return $self->_list_dbIDs('array');
}
#New Funcgen methods
#fetch_all_by_group?
#fetch_by_channel_id?
#fetch_by_chip_id?
#fetch_by_probe_id
#fetch_by_probe_set_id
1;
]]>