From d1f1115b7498cb8a3383b85defc49dfacb48e4bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 10 Feb 2011 09:54:08 +0000
Subject: [PATCH] Remove accidentally re-added new() and ontology() methods.
Make fetch_by_name() take an optional second argument (ontology name).
Make fetch_by_name() also look at synonyms.
---
.../Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm | 127 ++++++------------
1 file changed, 38 insertions(+), 89 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
index 180990c079..4fa253839d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
@@ -60,82 +60,25 @@ use Bio::EnsEMBL::OntologyTerm;
use base qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
-=head2 new
-
- Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
- Argument required for parent class
- Bio::EnsEMBL::DBSQL::BaseAdaptor.
-
- Arg [2] : String
- The particular ontology that this ontology adaptor
- deals with.
-
- Caller : Bio::EnsEMBL::DBSQL::GOTermAdaptor
- Bio::EnsEMBL::DBSQL::SOTermAdaptor
-
- Description : Creates an ontology term adaptor.
-
- Example :
-
- my $ot_adaptor =
- Bio::EnsEMBL::DBSQL::OntologyTermAdaptor->new( $dba, 'GO' );
-
- Return type : Bio::EnsEMBL::DBSQL::OntologyTermAdaptor
-
-=cut
-
-sub new {
- my ( $proto, $dba, $ontology ) = @_;
-
- if ( !ref($dba) || !$dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
- throw('First argument needs to be a '
- . 'Bio::EnsEMBL::DBSQL::DBAdaptor object' );
- }
-
- my $this = $proto->SUPER::new($dba);
-
- $this->{'ontology'} = $ontology;
-
- return $this;
-}
-
-=head2 ontology
-
- Arg : None
-
- Description : Returns the name of the ontology which this
- adaptor is used to retrieve terms for.
-
- Example :
-
- my $ontology = $ot_adaptor->ontology();
-
- Return type : String
-
-=cut
-
-sub ontology {
- my ($this) = @_;
- return $this->{'ontology'};
-}
-
=head2 fetch_all_by_name
- Arg [1] : String - Name of term
+ Arg [1] : String, name of term, or SQL pattern
+ Arg [2] : (optional) String, name of ontology
- Description : Fetches an ontology term(s) given a name, which may
- contain MySQL wildcards i.e. _ or %
+ Description : Fetches ontology term(s) given a name, a synonym, or a
+ SQL pattern like "%splice_site"
Example :
- my ($term) = @{$ot_adaptor->fetch_by_name('DNA_binding_site')};
+ my ($term) =
+ @{ $ot_adaptor->fetch_by_name( 'DNA_binding_site', 'SO' ) };
- Return type : ARRAYREF of Bio::EnsEMBL::OntologyTerm Objects
+ Return type : listref of Bio::EnsEMBL::OntologyTerm
=cut
sub fetch_all_by_name {
- my ( $this, $name) = @_;
+ my ( $this, $pattern, $ontology ) = @_;
my $statement = q(
SELECT term.term_id,
@@ -145,43 +88,49 @@ SELECT term.term_id,
term.subsets,
ontology.namespace
FROM ontology,
- term
-WHERE ontology.name = ?
- AND ontology.ontology_id = term.ontology_id
- AND term.name like ?);
+ term,
+ synonym
+WHERE ontology.ontology_id = term.ontology_id
+ AND synonym.term_id = term.term_id
+ AND ( term.name LIKE ? OR synonym.name LIKE ? )
+ );
+
+ if ( defined($ontology) ) {
+ $statement .= "AND ontology.name = ?";
+ }
my $sth = $this->prepare($statement);
- $sth->bind_param( 1, $this->{'ontology'}, SQL_VARCHAR );
- $sth->bind_param( 2, $name, SQL_VARCHAR );
+ $sth->bind_param( 1, $pattern, SQL_VARCHAR );
+ $sth->bind_param( 2, $pattern, SQL_VARCHAR );
+
+ if ( defined($ontology) ) {
+ $sth->bind_param( 3, $this->{'ontology'}, SQL_VARCHAR );
+ }
$sth->execute();
- my ( $dbid, $accession, $term_name, $definition, $subsets, $namespace );
+ my ( $dbid, $accession, $name, $definition, $subsets, $namespace );
$sth->bind_columns(
- \( $dbid, $accession, $term_name, $definition, $subsets, $namespace ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $namespace ) );
my @terms;
+ while ( $sth->fetch ) {
+ $subsets ||= '';
- while($sth->fetch){
-
- $subsets ||= '';
- push @terms, Bio::EnsEMBL::OntologyTerm->new
- (
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
- '-namespace' => $namespace,
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $term_name,
- '-definition' => $definition
- );
+ push @terms,
+ Bio::EnsEMBL::OntologyTerm->new(
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
+ '-namespace' => $namespace,
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition );
}
- $sth->finish();
-
return \@terms;
-} ## end sub fetch_by_name
+} ## end sub fetch_all_by_name
=head2 fetch_by_accession
--
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