From 0f1a101cad0c940140fc914792dd41a2e80bcfab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 15 Feb 2011 14:03:57 +0000
Subject: [PATCH] Add helper method _fetch_synonyms_by_dbID() to fetch the
synonyms for a term.
---
.../Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm | 65 ++++++++++++++-----
1 file changed, 47 insertions(+), 18 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
index 24a7aa872f..8b3d5a4475 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
@@ -127,7 +127,7 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
- '-definition' => $definition );
+ '-definition' => $definition, );
}
return \@terms;
@@ -176,14 +176,16 @@ WHERE term.accession = ?);
my $term =
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
- '-ontology' => $ontology,
- '-namespace' => $namespace,
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition );
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
+ '-ontology' => $ontology,
+ '-namespace' => $namespace,
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ );
$sth->finish();
return $term;
@@ -510,6 +512,31 @@ ORDER BY closure.distance, parent_term.accession);
return \@terms;
} ## end sub fetch_all_by_descendant_term
+sub _fetch_synonyms_by_dbID {
+ my ( $this, $dbID ) = @_;
+
+ my $statement = q(
+SELECT synonym.name
+FROM synonym
+WHERE synonym.term_id = ?);
+
+ my $sth = $this->prepare($statement);
+ $sth->bind_param( 1, $dbID, SQL_INTEGER );
+
+ $sth->execute();
+
+ my $synonym;
+ $sth->bind_col( 1, \$synonym );
+
+ while ( $sth->fetch() ) {
+ push( @synonyms, $synonym );
+ }
+
+ return \@synonyms;
+}
+
+
+
=head2 _fetch_ancestor_chart
Arg [1] : Bio::EnsEMBL::OntologyTerm
@@ -636,14 +663,16 @@ WHERE term.term_id = ?);
my $term =
Bio::EnsEMBL::OntologyTerm->new(
- '-dbid' => $dbid,
- '-adaptor' => $this,
- '-accession' => $accession,
- '-ontology' => $ontology,
- '-namespace' => $namespace,
- '-subsets' => [ split( /,/, $subsets ) ],
- '-name' => $name,
- '-definition' => $definition );
+ '-dbid' => $dbid,
+ '-adaptor' => $this,
+ '-accession' => $accession,
+ '-ontology' => $ontology,
+ '-namespace' => $namespace,
+ '-subsets' => [ split( /,/, $subsets ) ],
+ '-name' => $name,
+ '-definition' => $definition,
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ );
$sth->finish();
return $term;
@@ -697,7 +726,7 @@ WHERE term.term_id IN (%s));
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
- '-definition' => $definition ) );
+ '-definition' => $definition, ) );
}
return \@terms;
--
GitLab