From c391111c3e7a683d5b95c2eb3e0208c481246a6a Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 12 Mar 2013 17:07:34 +0000
Subject: [PATCH] now supporting is_root method
---
.../Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm | 64 ++++++++++++-------
modules/Bio/EnsEMBL/OntologyTerm.pm | 23 ++++++-
2 files changed, 63 insertions(+), 24 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
index 2f264896af..b557645345 100644
--- a/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm
@@ -90,6 +90,7 @@ SELECT DISTINCT
term.name,
term.definition,
term.subsets,
+ term.is_root,
ontology.name,
ontology.namespace
FROM ontology
@@ -111,9 +112,9 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $namespace );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $namespace );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $ontology, $namespace ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology, $namespace ) );
my @terms;
@@ -125,12 +126,13 @@ WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
'-name' => $name,
'-definition' => $definition,
- '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
+ '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
);
}
@@ -162,6 +164,7 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
+ term.is_root,
ontology.name,
ontology.namespace
FROM ontology
@@ -173,9 +176,9 @@ WHERE term.accession = ?);
$sth->execute();
- my ( $dbid, $name, $definition, $subsets, $ontology, $namespace );
+ my ( $dbid, $name, $definition, $subsets, $is_root, $ontology, $namespace );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $ontology, $namespace ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology, $namespace ) );
$sth->fetch();
@@ -189,6 +192,7 @@ WHERE term.accession = ?);
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
@@ -232,6 +236,7 @@ SELECT child_term.term_id,
child_term.name,
child_term.definition,
child_term.subsets,
+ child_term.is_root,
rt.name
FROM term child_term
JOIN relation ON (relation.child_term_id = child_term.term_id)
@@ -251,9 +256,9 @@ WHERE relation.parent_term_id = ?
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $relation );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $relation ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation ) );
while ( $sth->fetch() ) {
$subsets ||= '';
@@ -263,6 +268,7 @@ WHERE relation.parent_term_id = ?
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
@@ -315,7 +321,8 @@ SELECT DISTINCT
child_term.accession,
child_term.name,
child_term.definition,
- child_term.subsets
+ child_term.subsets,
+ child_term.is_root
FROM term child_term
JOIN closure ON (closure.child_term_id = child_term.term_id)
JOIN ontology ON (closure.ontology_id = ontology.ontology_id)
@@ -333,9 +340,9 @@ ORDER BY closure.distance, child_term.accession);
$sth->bind_param( 2, $ontology, SQL_VARCHAR );
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root ) );
my @terms;
@@ -347,6 +354,7 @@ ORDER BY closure.distance, child_term.accession);
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
@@ -389,6 +397,7 @@ SELECT parent_term.term_id,
parent_term.name,
parent_term.definition,
parent_term.subsets,
+ parent_term.is_root,
rt.name
FROM term parent_term
JOIN relation ON (relation.parent_term_id = parent_term.term_id)
@@ -407,9 +416,9 @@ WHERE relation.child_term_id = ?
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $relation );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $relation ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $relation ) );
while ( $sth->fetch() ) {
$subsets ||= '';
@@ -419,6 +428,7 @@ WHERE relation.child_term_id = ?
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
@@ -495,6 +505,7 @@ SELECT DISTINCT
parent_term.name,
parent_term.definition,
parent_term.subsets,
+ parent_term.is_root,
closure.distance
FROM term parent_term
JOIN closure ON (closure.parent_term_id = parent_term.term_id)
@@ -532,9 +543,9 @@ ORDER BY closure.distance, parent_term.accession);
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $distance );
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $distance );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $distance ) );
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $distance ) );
my @terms;
my $min_distance;
@@ -549,6 +560,7 @@ ORDER BY closure.distance, parent_term.accession);
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $term->{'ontology'},
'-namespace' => $term->{'namespace'},
'-subsets' => [ split( /,/, $subsets ) ],
@@ -703,6 +715,7 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
+ term.is_root,
ontology.name,
ontology.namespace
FROM ontology
@@ -714,10 +727,10 @@ WHERE term.term_id = ?);
$sth->execute();
- my ( $accession, $name, $definition, $subsets, $ontology,
+ my ( $accession, $name, $definition, $subsets, $is_root, $ontology,
$namespace );
$sth->bind_columns(
- \( $dbid, $accession, $name, $definition, $subsets, $ontology, $namespace
+ \( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology, $namespace
) );
$sth->fetch();
@@ -731,6 +744,7 @@ WHERE term.term_id = ?);
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
@@ -754,6 +768,7 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
+ term.is_root,
ontology.name,
ontology.namespace
FROM ontology
@@ -772,10 +787,10 @@ WHERE term.term_id IN (%s));
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
- $subsets, $ontology, $namespace ) );
+ $subsets, $is_root, $ontology, $namespace ) );
my @terms;
@@ -787,6 +802,7 @@ WHERE term.term_id IN (%s));
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
@@ -828,6 +844,7 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
+ term.is_root,
ontology.name,
ontology.namespace
FROM ontology
@@ -844,10 +861,10 @@ FROM ontology
}
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
- $subsets, $ontology, $namespace ) );
+ $subsets, $is_root, $ontology, $namespace ) );
my @terms;
@@ -859,6 +876,7 @@ FROM ontology
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
@@ -882,6 +900,7 @@ SELECT term.term_id,
term.name,
term.definition,
term.subsets,
+ term.is_root,
ontology.name,
ontology.namespace
FROM ontology
@@ -890,10 +909,10 @@ FROM ontology
my $sth = $this->prepare($statement);
$sth->execute();
- my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
+ my ( $dbid, $accession, $name, $definition, $subsets, $is_root, $ontology,
$namespace );
$sth->bind_columns( \( $dbid, $accession, $name, $definition,
- $subsets, $ontology, $namespace ) );
+ $subsets, $is_root, $ontology, $namespace ) );
my @terms;
@@ -905,6 +924,7 @@ FROM ontology
'-dbid' => $dbid,
'-adaptor' => $this,
'-accession' => $accession,
+ '-is_root' => $is_root,
'-ontology' => $ontology,
'-namespace' => $namespace,
'-subsets' => [ split( /,/, $subsets ) ],
diff --git a/modules/Bio/EnsEMBL/OntologyTerm.pm b/modules/Bio/EnsEMBL/OntologyTerm.pm
index 1b24c99e94..49ff17f59c 100644
--- a/modules/Bio/EnsEMBL/OntologyTerm.pm
+++ b/modules/Bio/EnsEMBL/OntologyTerm.pm
@@ -99,9 +99,9 @@ sub new {
my $this = $proto->SUPER::new(@_);
- my ( $accession, $ontology, $namespace, $name, $definition, $subsets )
+ my ( $accession, $ontology, $namespace, $name, $definition, $is_root, $subsets )
= rearrange( [ 'ACCESSION', 'ONTOLOGY', 'NAMESPACE', 'NAME',
- 'DEFINITION', 'SUBSETS' ],
+ 'DEFINITION', 'IS_ROOT', 'SUBSETS' ],
@_ );
$this->{'accession'} = $accession;
@@ -109,6 +109,7 @@ sub new {
$this->{'namespace'} = $namespace;
$this->{'name'} = $name;
$this->{'definition'} = $definition;
+ $this->{'is_root'} = $is_root;
$this->{'subsets'} = [ @{$subsets} ];
$this->{'child_terms_fetched'} = 0;
@@ -202,6 +203,24 @@ sub definition {
return $this->{'definition'};
}
+=head2 is_root
+
+ Arg : None
+
+ Description : Returns true if the term is root of its ontology
+
+ Example : my $is_root = $term->is_root();
+
+ Return type : Boolean (TRUE if it is a root, else FALSE)
+
+=cut
+
+sub is_root {
+ my ($this) = @_;
+ return $this->{'is_root'};
+}
+
+
=head2 synonyms
Arg : None
--
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