Bio::EnsEMBL::DBSQL
UnconventionalTranscriptAssociationAdaptor
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Summary
Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$utaa = $registry->get_adaptor( 'Human', 'Core',
'UnconventionalTranscriptAssociation' );
my $uta = $utaa->fetch_all_by_type('antisense');
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.
Methods
Methods description
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 |
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 |
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 |
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 |
Methods code
| _objs_from_sth | description | prev | next | Top |
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;} | 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;} | 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;} | 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;} | 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();} | General documentation
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
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