Raw content of Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
<![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::DensityTypeAdaptor
=head1 SYNOPSIS
my $density_type_adaptor =
$registry->get_adaptor( 'Human', 'Core', 'DensityType' );
my @density_types = @{ $density_type_adaptor->fetch_all() };
my $dt = $density_type_adaptor->fetch_by_dbID(12);
=head1 DESCRIPTION
DensityTypeAdaptor - Performs database interaction for DensityType objects.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::DensityTypeAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::DensityType;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 new
Arg [1] : see superclass (Bio::EnsEMBL::DBSQL::BaseAdaptor) arguments
Example : #use this instead of the constructor directly:
my $dta = $db_adaptor->get_DensityTypeAdaptor();
Description: Constructor. Creates a new DensityTypeAdaptor
Returntype : Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
Exceptions : none
Caller : DBAdaptor
Status : Stable
=cut
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
$self->{'dbID_cache'} = {};
return $self;
}
=head2 fetch_all
Arg [1] : none
Example : my @density_types = @{$density_type_adaptor->fetch_all};
Description: Retrieves every density type in the database.
NOTE: In a multi-species database, this method will
return all the entries, not just the ones associated with
the current species.
Returntype : reference to list of Bio::EnsEMBL::DensityType objects
Exceptions : none
Caller : general, new
Status : Stable
=cut
sub fetch_all {
my $self = shift;
my @out;
my $sth = $self->prepare("SELECT density_type_id, analysis_id, block_size,".
" value_type, region_features " .
"FROM density_type");
$sth->execute();
my($dbID, $analysis_id, $blk_size, $vtype, $region_features );
$sth->bind_columns(\$dbID, \$analysis_id, \$blk_size, \$vtype, \$region_features );
my $analysis_adaptor = $self->db->get_AnalysisAdaptor();
while($sth->fetch()) {
my $analysis = $analysis_adaptor->fetch_by_dbID($analysis_id);
my $dt = Bio::EnsEMBL::DensityType->new(-ADAPTOR => $self,
-DBID => $dbID,
-ANALYSIS => $analysis,
-BLOCK_SIZE => $blk_size,
-REGION_FEATURES => $region_features,
-VALUE_TYPE => $vtype);
$self->{'dbID_cache'}->{$dbID} = $dt;
push @out, $dt;
}
return \@out;
}
=head2 fetch_by_dbID
Arg [1] : int $dbID
Example : my $dt = $density_type_adaptor->fetch_by_dbID($dbID);
Description: Retrieves a density type object via its internal identifier
Returntype : Bio::EnsEMBL::DensityType
Exceptions : throw if dbID argument not defined
Caller : general
Status : Stable
=cut
sub fetch_by_dbID {
my $self = shift;
my $dbID = shift;
if(!defined($dbID)) {
throw("dbID argument must be defined");
}
if($self->{'dbID_cache'}->{$dbID}) {
return $self->{'dbID_cache'}->{$dbID};
}
# go back to database and refill caches
$self->fetch_all();
return $self->{'dbID_cache'}->{$dbID};
}
=head2 fetch_all_by_logic_name
Arg [1] : string $logic_name
Example : my @dts = @{$dtype_adaptor->fetch_all('repeat_coverage')};
Description: Retrieves all density types with a given logic name.
NOTE: In a multi-species database, this method will
return all the entries matching the search criteria, not
just the ones associated with the current species.
Returntype : reference to list of Bio::EnsEMBL::DensityTypes
Exceptions : thrown if logic_name argument is not provided
Caller : general
Status : Stable
=cut
sub fetch_all_by_logic_name {
my $self = shift;
my $logic_name = shift;
if(!defined($logic_name)) {
throw("logic_name argument is required.");
}
my $analysis_adaptor = $self->db()->get_AnalysisAdaptor();
my $analysis = $analysis_adaptor->fetch_by_logic_name($logic_name);
return [] if(!$analysis);
my $sth = $self->prepare("SELECT density_type_id, block_size,".
" value_type, region_features " .
"FROM density_type " .
"WHERE analysis_id = ?");
$sth->bind_param(1,$analysis->dbID,SQL_INTEGER);
$sth->execute();
my($dbID, $blk_size, $vtype, $region_features );
$sth->bind_columns(\$dbID, \$blk_size, \$vtype, \$region_features);
my @out;
while($sth->fetch()) {
my $dt = Bio::EnsEMBL::DensityType->new(-ADAPTOR => $self,
-DBID => $dbID,
-ANALYSIS => $analysis,
-BLOCK_SIZE => $blk_size,
-REGION_FEATURES => $region_features,
-VALUE_TYPE => $vtype);
$self->{'dbID_cache'}->{$dbID} = $dt;
push @out, $dt;
}
return \@out;
}
=head2 store
Arg [1] : list of Bio::EnsEMBL::DensityType @dt
the density types to store in the database
Example : $density_type->store(@density_types);
Description: Stores a list of density type objects in the database
Returntype : none
Exceptions : thrown if @dt is not defined
or if any elements of @dt are not Bio::EnsEMBL::DensityType
Caller : general
Status : Stable
=cut
sub store {
my ($self,@dt) = @_;
if( scalar(@dt) == 0 ) {
throw("Must call store with list of Density Types");
}
my $sth = $self->prepare
("INSERT IGNORE INTO density_type (analysis_id,".
"block_size, value_type, region_features ) ".
"VALUES (?, ?, ?, ?)");
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
FEATURE: foreach my $dt ( @dt ) {
if( !ref $dt || !$dt->isa("Bio::EnsEMBL::DensityType") ) {
throw("Density Type must be an Ensembl DensityType, " .
"not a [".ref($dt)."]");
}
if($dt->is_stored($db)) {
next FEATURE;
}
if(!defined($dt->analysis())) {
throw("An analysis must be attached to the density type to be stored.");
}
#store the analysis if it has not been stored yet
if(!$dt->analysis->is_stored($db)) {
$analysis_adaptor->store($dt->analysis());
}
my $block_size = $dt->block_size();
$block_size |= 0;
my $region_features = $dt->region_features();
$region_features |= 0;
$sth->bind_param(1,$dt->analysis->dbID,SQL_INTEGER);
$sth->bind_param(2,$block_size,SQL_INTEGER);
$sth->bind_param(3,$dt->value_type,SQL_VARCHAR);
$sth->bind_param(4,$region_features, SQL_VARCHAR);
my $inserted = $sth->execute();
my $dbID;
# $inserted can be 0E0 which is true but equal to 0
if(!$inserted || $inserted == 0) {
# insert failed, presumably because was already stored in database
my @dts=@{$self->fetch_all_by_logic_name($dt->analysis()->logic_name())};
my ($stored_dt) = grep {$_->block_size() == $dt->block_size()} @dts;
if(!$stored_dt) {
throw("Could not retrieve or store DensityType from database.\n" .
"Incorrect db permissions or missing density_type table?\n");
}
$dbID = $stored_dt->dbID();
} else {
$dbID = $sth->{'mysql_insertid'};
}
# next two lines are to set the density type as stored
$dt->dbID($dbID);
$dt->adaptor($self);
$self->{'dbID_cache'}->{$dbID} = $dt;
}
}
1;
]]>