Raw content of Bio::EnsEMBL::DBSQL::MiscSetAdaptor
<![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::MiscSetAdaptor - Provides database interaction for
Bio::EnsEMBL::MiscSet objects.
=head1 SYNOPSIS
my $msa = $registry->get_adaptor( 'Human', 'Core', 'MiscSet' );
my $misc_set = $msa->fetch_by_dbID(1234);
$misc_set = $msa->fetch_by_code('clone');
=head1 DESCRIPTION
This class provides database interactivity for MiscSet objects.
MiscSets are used to classify MiscFeatures into groups.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::MiscSetAdaptor;
use strict;
use warnings;
use Bio::EnsEMBL::MiscSet;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 new
Arg [...] : Superclass args. See Bio::EnsEMBL::DBSQL::BaseAdaptor
Description: Instantiates a Bio::EnsEMBL::DBSQL::MiscSetAdaptor and
caches the contents of the MiscSet table.
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : MiscFeatureAdaptor
Status : Stable
=cut
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
$self->{'_id_cache'} = {};
$self->{'_code_cache'} = {};
# cache the entire contents of the misc set table
# the table is small and it removes the need to repeatedly query the
# table or join to the table
$self->fetch_all();
return $self;
}
=head2 fetch_all
Arg [1] : none
Example : foreach my $ms (@{$msa->fetch_all()}) {
print $ms->code(), ' ', $ms->name(), "\n";
}
Description: Retrieves every MiscSet defined in the DB.
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 : listref of Bio::EnsEMBL::MiscSets
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_all {
my $self = shift;
my $sth = $self->prepare
('SELECT misc_set_id, code, name, description, max_length FROM misc_set');
$sth->execute();
my ($dbID, $code, $name, $desc, $max_len);
$sth->bind_columns(\$dbID, \$code, \$name, \$desc, \$max_len);
my @all;
while($sth->fetch()) {
my $ms = Bio::EnsEMBL::MiscSet->new
(-DBID => $dbID,
-ADAPTOR => $self,
-CODE => $code,
-NAME => $name,
-DESCRIPTION => $desc,
-LONGEST_FEATURE => $max_len);
$self->{'_id_cache'}->{$dbID} = $ms;
$self->{'_code_cache'}->{lc($code)} = $ms;
push @all, $ms;
}
$sth->finish();
return \@all;
}
=head2 fetch_by_dbID
Arg [1] : int $dbID
The internal identifier of the misc set to retrieve
Example : my $ms = $msa->fetch_by_dbID($dbID);
Description: Retrieves a misc set via its internal identifier
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_dbID {
my $self = shift;
my $dbID = shift;
if(!$self->{'_id_cache'}->{$dbID}) {
# on a cache miss reread the whole table and reload the cache
$self->fetch_all();
}
return $self->{'_id_cache'}->{$dbID};
}
=head2 fetch_by_code
Arg [1] : string $code
The unique code of the MiscSet to retrieve
Example : my $ms = $msa->fetch_by_code('clone');
Description: Retrieves a MiscSet via its code
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_code {
my $self = shift;
my $code = shift;
if(!$self->{'_code_cache'}->{lc($code)}) {
# on cache miss, reread whole table and reload cache
$self->fetch_all();
}
return $self->{'_code_cache'}->{lc($code)};
}
=head2 store
Arg [1] : list of MiscSets @mist_sets
Example : $misc_set_adaptor->store(@misc_sets);
Description: Stores a list of MiscSets in the database, and sets the
dbID and adaptor attributes of the stored sets.
Returntype : none
Exceptions : throw on incorrect arguments
warning if a feature is already stored in this database
Caller : MiscFeatureAdaptor::store
Status : Stable
=cut
sub store {
my $self = shift;
my @misc_sets = @_;
# we use 'insert ignore' so that inserts can occur safely on the farm
# otherwise 2 processes could try to insert at the same time and one
# would fail
my $sth = $self->prepare
("INSERT IGNORE INTO misc_set " .
"SET code = ?, " .
" name = ?, " .
" description = ?, " .
" max_length = ?");
my $db = $self->db();
SET:
foreach my $ms (@misc_sets) {
if(!ref($ms) || !$ms->isa('Bio::EnsEMBL::MiscSet')) {
throw("List of MiscSet arguments expected.");
}
if($ms->is_stored($db)) {
warning("MiscSet [".$ms->dbID."] is already stored in this database.");
next SET;
}
$sth->bind_param(1,$ms->code,SQL_VARCHAR);
$sth->bind_param(2,$ms->name,SQL_VARCHAR);
$sth->bind_param(3,$ms->description,SQL_LONGVARCHAR);
$sth->bind_param(4,$ms->longest_feature,SQL_INTEGER);
my $num_inserted = $sth->execute();
my $dbID;
if($num_inserted == 0) {
# insert failed because set with this code already exists
my $sth2 = $self->prepare("SELECT misc_set_id from misc_set " .
"WHERE code = ?");
$sth2->bind_param(1,$ms->code,SQL_VARCHAR);
$sth2->execute();
if($sth2->rows() != 1) {
throw("Could not retrieve or store MiscSet, code=[".$ms->code."]\n".
"Wrong database user/permissions?");
}
($dbID) = $sth2->fetchrow_array();
} else {
$dbID = $sth->{'mysql_insertid'};
}
$ms->dbID($dbID);
$ms->adaptor($self);
# update the internal caches
$self->{'_id_cache'}->{$dbID} = $ms;
$self->{'_code_cache'}->{lc($ms->code())} = $ms;
}
return;
}
1;
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