Raw content of Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor
<![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::RepeatConsensusAdaptor
=head1 SYNOPSIS
$rca = $database_adaptor->get_RepeatConsensusAdaptor();
$repeat_consensus = $rca->fetch_by_dbID(132);
$repeat_consensus = $rca->fetch_by_name_class( 'AluSx', 'SINE/Alu' );
$rca->store( $rc1, $rc2, $rc3 );
=head1 DESCRIPTION
This is an adaptor for the retrieval and storage of RepeatConsensus
objects.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::RepeatConsensus;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
use vars qw(@ISA);
@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
=head2 fetch_by_dbID
Arg [1] : int $db_id
The database identifier for the RepeatConsensus to obtain
Example : $repeat_consensus = $repeat_consensus_adaptor->fetch_by_dbID(4);
Description: Obtains a RepeatConsensus object from the database via its
primary key.
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general, Bio::EnsEMBL::RepeatFeatureAdaptor
Status : Stable
=cut
sub fetch_by_dbID {
my( $self, $db_id ) = @_;
my ($rc) = @{$self->_generic_fetch("repeat_consensus_id = $db_id")};
return $rc;
}
=head2 fetch_by_name
Arg [1] : string $name
the name of the repeat consensus to obtain
Example : $rc = $repeat_consensus_adaptor->fetch_by_name('AluSx');
Description: Obtains a repeat consensus from the database via its name
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_name {
my( $self, $name ) = @_;
my ($rc) = @{$self->_generic_fetch("repeat_name = '$name'")};
return $rc;
}
=head2 fetch_by_name_class
Arg [1] : string $name
the name of the repeat consensus to obtain
Arg [2] : string $class
the class of the repeat consensus to obtain
Example : $rc = $repeat_consensus_adaptor->
fetch_by_name_class('AluSx', 'SINE/Alu');
Description: Obtains a repeat consensus from the database
via its name and class
Returntype : Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_by_name_class {
my( $self, $name, $class ) = @_;
my ($rc) = @{$self->_generic_fetch(qq{
repeat_name = '$name'
AND repeat_class = '$class'
})};
return $rc;
}
=head2 fetch_all_by_class_seq
Arg [1] : string $class
the class of the repeat consensus to obtain
Arg [2] : string $seq
the sequence of the repeat consensus to obtain
Example : $rc = $repeat_consensus_adaptor->
fetch_all_by_class_seq('trf', 'ATGGTGTCA');
Description: Obtains a repeat consensus from the database
via its class and sequence
Returntype : listREF of Bio::EnsEMBL::RepeatConsensus
Exceptions : none
Caller : general
Status : Stable
=cut
sub fetch_all_by_class_seq {
my( $self, $class, $seq ) = @_;
return $self->_generic_fetch(qq{
repeat_class = '$class'
AND repeat_consensus = '$seq'
});
}
sub fetch_by_class_seq {
deprecate('Use fetch_all_by_class_seq instead');
fetch_all_by_class_seq(@_);
}
=head2 _generic_fetch
Arg [1] : string $where_clause
Example : none
Description: PRIVATE used to create RepeatConsensus features from an
SQL constraint
Returntype : listref of Bio::EnsEMBL::RepeatConsensus objects
Exceptions : none
Caller : internal
Status : Stable
=cut
sub _generic_fetch {
my( $self, $where_clause ) = @_;
my( $repeat_consensus_id, $repeat_name, $repeat_class,$repeat_length,
$repeat_consensus, $repeat_type );
my $sth = $self->prepare(qq{
SELECT repeat_consensus_id
, repeat_name
, repeat_class
, repeat_type
, repeat_consensus
FROM repeat_consensus
WHERE }. $where_clause);
$sth->execute;
$sth->bind_columns(
\$repeat_consensus_id,
\$repeat_name,
\$repeat_class,
\$repeat_type,
\$repeat_consensus
);
my @consensi;
while ($sth->fetch) {
if ($repeat_consensus =~ /^(\d+)\(N\)$/) {
$repeat_length = $1;
} else {
$repeat_length = CORE::length($repeat_consensus);
}
push @consensi, Bio::EnsEMBL::RepeatConsensus->new
(-DBID => $repeat_consensus_id,
-NAME => $repeat_name,
-REPEAT_CLASS => $repeat_class,
-REPEAT_TYPE => $repeat_type,
-LENGTH => $repeat_length,
-ADAPTOR => $self,
-REPEAT_CONSENSUS => $repeat_consensus);
}
return \@consensi;
}
=head2 store
Arg [1] : list of Bio::EnsEMBL::RepeatConsensus @consensi
Example : $repeat_consensus_adaptor->store(@consensi);
Description: stores a list of RepeatConsensus objects in the database
Returntype : none
Exceptions : none
Caller : ?
Status : Stable
=cut
sub store {
my( $self, @consensi ) = @_;
my $sth = $self->prepare(q{
INSERT into repeat_consensus( repeat_consensus_id
, repeat_name
, repeat_class
, repeat_type
, repeat_consensus )
VALUES (NULL, ?,?,?,?)
});
foreach my $rc (@consensi) {
my $name = $rc->name
or throw("name not set");
my $class = $rc->repeat_class
or throw("repeat_class not set");
my $type = $rc->repeat_type();
$type = "" unless defined $type;
my $seq = $rc->repeat_consensus
or throw("repeat_consensus not set");
$sth->bind_param(1,$name,SQL_VARCHAR);
$sth->bind_param(2,$class,SQL_VARCHAR);
$sth->bind_param(3,$type,SQL_VARCHAR);
$sth->bind_param(4,$seq,SQL_LONGVARCHAR);
$sth->execute();
my $db_id = $sth->{'mysql_insertid'}
or throw("Didn't get an insertid from the INSERT statement");
$rc->dbID($db_id);
$rc->adaptor($self);
}
}
1;
__END__
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