From 64b686c262ed40e6f502e48df38cf188db43a0b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 25 Mar 2009 14:17:19 +0000
Subject: [PATCH] Make children() and parents() take a list of strings
representing the relationship types to consider, e.g. qw(is_a part_of).
---
modules/Bio/EnsEMBL/OntologyTerm.pm | 46 +++++++++++++++--------------
1 file changed, 24 insertions(+), 22 deletions(-)
diff --git a/modules/Bio/EnsEMBL/OntologyTerm.pm b/modules/Bio/EnsEMBL/OntologyTerm.pm
index 7a6ae0e7d1..1944a02855 100644
--- a/modules/Bio/EnsEMBL/OntologyTerm.pm
+++ b/modules/Bio/EnsEMBL/OntologyTerm.pm
@@ -181,28 +181,29 @@ sub defintion {
=head2 children
- Arg : (optional) String
- The type of relation to retrieve children for.
+ Args : (optional) List of strings
+ The type of relations to retrieve children for.
Description : Returns the children terms of this ontology term.
- Example : my @children = @{ $term->children('is_a') };
+ Example : my @children =
+ @{ $term->children( 'is_a', 'part_of' ) };
Return type : listref of Bio::EnsEMBL::OntologyTerm
=cut
sub children {
- my ( $this, $relation ) = @_;
+ my ( $this, @relations ) = @_;
- my @terms;
+ my @terms = @{ $this->adaptor()->fetch_by_parent_term($this) };
- @terms = @{ $this->adaptor()->fetch_by_parent_term($this); };
- if ( defined($relation) ) {
- if ( exists( $this->{'children'}{$relation} ) ) {
- @terms = @{ $this->{'children'}{$relation} };
- } else {
- @terms = ();
+ if (@relations) {
+ @terms = ();
+ foreach my $relation (@relations) {
+ if ( exists( $this->{'children'}{$relation} ) ) {
+ push( @terms, @{ $this->{'children'}{$relation} } );
+ }
}
}
@@ -230,28 +231,29 @@ sub descendants {
=head2 parents
- Arg : (optional) String
- The type of relation to retrieve parents for.
+ Args : (optional) List of strings
+ The type of relations to retrieve parents for.
Description : Returns the parent terms of this ontology term.
- Example : my @parents = @{ $term->parents('is_a')) };
+ Example : my @parents =
+ @{ $term->parents( 'is_a', 'part_of' ) };
Return type : listref of Bio::EnsEMBL::OntologyTerm
=cut
sub parents {
- my ( $this, $relation ) = @_;
+ my ( $this, @relations ) = @_;
- my @terms;
+ my @terms = @{ $this->adaptor()->fetch_by_child_term($this) };
- @terms = @{ $this->adaptor()->fetch_by_child_term($this); };
- if ( defined($relation) ) {
- if ( exists( $this->{'parents'}{$relation} ) ) {
- @terms = @{ $this->{'parents'}{$relation} };
- } else {
- @terms = ();
+ if (@relations) {
+ @terms = ();
+ foreach my $relation (@relations) {
+ if ( exists( $this->{'parents'}{$relation} ) ) {
+ push( @terms, @{ $this->{'parents'}{$relation} } );
+ }
}
}
--
GitLab