Raw content of Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor
<![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::UnconventionalTranscriptAssociationAdaptor
=head1 SYNOPSIS
$utaa = $registry->get_adaptor( 'Human', 'Core',
'UnconventionalTranscriptAssociation' );
my $uta = $utaa->fetch_all_by_type('antisense');
=head1 DESCRIPTION
This is an adaptor for the retrieval and storage of
UnconventionalTranscriptAssociation objects from the database. Most of
the implementation is in the superclass BaseFeatureAdaptor.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::UnconventionalTranscriptAssociation;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_all_by_interaction_type
Arg [1] : String type
the type of associations to obtain
Example : $utas = $utaa->fetch_all_by_type('antisense');
Description: Obtains all unconventional transcript associations that
have a particular interaction type.
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::UnconventionalTranscriptAssociations
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub fetch_all_by_interaction_type {
my( $self, $type) = @_;
my $sth = $self->prepare("SELECT transcript_id, gene_id, interaction_type " .
"FROM unconventional_transcript_association " .
"WHERE interaction_type = ?");
$sth->bind_param(1, $type, SQL_VARCHAR);
$sth->execute();
my $results = $self->_objs_from_sth($sth);
$sth->finish();
return $results;
}
=head2 fetch_all_by_gene
Arg [1] : String gene the gene of associations to obtain
Arg [2] : (optional) An interaction type; if set, only associations of this type will be returned.
Example : $utas = $utaa->fetch_all_by_gene($gene, 'antisense');
Description: Obtains all unconventional transcript associations that involve
a particular gene.
Returntype : listREF of Bio::EnsEMBL::UnconventionalTranscriptAssociations
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub fetch_all_by_gene {
my( $self, $gene, $type) = @_;
if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
throw('$gene must be a Bio::EnsEMBL::Gene');
}
my $sql = "SELECT transcript_id, gene_id, interaction_type FROM unconventional_transcript_association WHERE gene_id = ?";
$sql .= " AND interaction_type = ?" if ($type);
my $sth = $self->prepare($sql);
$sth->bind_param(1, $gene->dbID(), SQL_INTEGER);
$sth->bind_param(2, $type, SQL_VARCHAR) if ($type);
$sth->execute();
my $results = $self->_objs_from_sth($sth);
$sth->finish();
return $results;
}
=head2 fetch_all_by_transcript
Arg [1] : String transcript the transcript of associations to obtain
Arg [2] : (optional) An interaction type; if set, only associations of this type will be returned.
Example : $utas = $utaa->fetch_all_by_transcript($transcript, 'antisense');
Description: Obtains all unconventional transcript associations that involve
a particular transcript.
Returntype : listREF of Bio::EnsEMBL::UnconventionalTranscriptAssociations
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub fetch_all_by_transcript {
my( $self, $transcript, $type) = @_;
if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
throw('$transcript must be a Bio::EnsEMBL::Transcript');
}
my $sql = "SELECT transcript_id, gene_id, interaction_type FROM unconventional_transcript_association WHERE transcript_id = ?";
$sql .= " AND interaction_type = ?" if ($type);
my $sth = $self->prepare($sql);
$sth->bind_param(1, $transcript->dbID(), SQL_INTEGER);
$sth->bind_param(2, $type, SQL_VARCHAR) if ($type);
$sth->execute();
my $results = $self->_objs_from_sth($sth);
$sth->finish();
return $results;
}
=head2 store
Arg [1] : Bio::EnsEMBL::UnconventionalTranscriptAssociation
the unconventional transcript association to store in the database
Example : $utaa_adaptor->store($uta);
Description: stores unconventional transcript associations in the database
Returntype : none
Exceptions :
Caller : general
Status : At Risk
: under development
=cut
sub store {
my( $self, $uta ) = @_;
if(!ref($uta) || !$uta->isa('Bio::EnsEMBL::UnconventionalTranscriptAssociation')) {
throw('$uta must be a Bio::EnsEMBL::UnconventionalTranscriptAssociation');
}
my $sth = $self->prepare(qq {INSERT into unconventional_transcript_association
(transcript_id, gene_id, interaction_type) VALUES (?,?,?)});
$sth->bind_param(1, $uta->transcript()->dbID(), SQL_INTEGER);
$sth->bind_param(2, $uta->gene()->dbID, SQL_INTEGER);
$sth->bind_param(3, $uta->interaction_type(), SQL_VARCHAR);
$sth->execute();
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
my $gene_adaptor = $self->db()->get_GeneAdaptor();
my ($gene_id, $transcript_id, $type);
$sth->bind_columns(\$transcript_id, \$gene_id, \$type);
my @results;
while($sth->fetch()) {
my $gene = $gene_adaptor->fetch_by_dbID($gene_id);
my $transcript = $transcript_adaptor->fetch_by_dbID($transcript_id);
my $obj = Bio::EnsEMBL::UnconventionalTranscriptAssociation->new($transcript, $gene, $type);
push @results, $obj;
}
return \@results;
}
1;
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