From 8b406953396dd1532a1c6ddeb9e8dd6bae8790e9 Mon Sep 17 00:00:00 2001
From: James Gilbert <jgrg@sanger.ac.uk>
Date: Fri, 29 Aug 2003 13:02:11 +0000
Subject: [PATCH] changed Gene so that $gene->adaptor(undef) removes adaptor
---
modules/Bio/EnsEMBL/Exon.pm | 3 +--
modules/Bio/EnsEMBL/Gene.pm | 20 +++++++++++---------
modules/Bio/EnsEMBL/Transcript.pm | 4 +---
modules/Bio/EnsEMBL/Translation.pm | 3 +--
4 files changed, 14 insertions(+), 16 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 0e9659949d..4e9d761104 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -199,8 +199,7 @@ sub temporary_id {
sub adaptor {
my $self = shift;
if( @_ ) {
- my $value = shift;
- $self->{'adaptor'} = $value;
+ $self->{'adaptor'} = shift;
}
return $self->{'adaptor'};
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 5b5c21313b..a0baffc3b0 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -276,7 +276,8 @@ sub is_known{
=head2 adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::GeneAdaptor $adaptor
- Example : none
+ Example : $gene->adaptor($gene_adaptor);
+ $gene->adaptor(undef); # to drop adaptor
Description: get/set for attribute adaptor
Returntype : Bio::EnsEMBL::DBSQL::GeneAdaptor
Exceptions : none
@@ -286,17 +287,18 @@ sub is_known{
sub adaptor {
- my ($self, $arg) = @_;
-
- if ( defined $arg ) {
- $self->{'_adaptor'} = $arg ;
- }
- return $self->{'_adaptor'};
+ my $self = shift;
+
+ if (@_) {
+ # Testing for any arguments allows undef to be
+ # passed as an argument to unset the adaptor
+ $self->{'_adaptor'} = shift;
+ }
+ return $self->{'_adaptor'};
}
-
=head2 analysis
Arg [1] : Bio::EnsEMBL::Analysis $analysis
@@ -514,7 +516,7 @@ sub get_all_DBEntries {
my $self = shift;
#if not cached, retrieve all of the xrefs for this gene
- if(!defined $self->{'dbentries'} && $self->adaptor()) {
+ if(!defined $self->{'dbentries'} && $self->adaptor()z) {
$self->{'dbentries'} =
$self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Gene($self);
}
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 6af64c7ae8..25d7278fb6 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -313,11 +313,9 @@ sub adaptor {
my $self = shift;
if( @_ ) {
- my $value = shift;
- $self->{'adaptor'} = $value;
+ $self->{'adaptor'} = shift;
}
return $self->{'adaptor'};
-
}
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index e1133f096a..e8cd6ccfbe 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -287,8 +287,7 @@ sub dbID {
sub adaptor {
my $self = shift;
if( @_ ) {
- my $value = shift;
- $self->{'adaptor'} = $value;
+ $self->{'adaptor'} = shift;
}
return $self->{'adaptor'};
--
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