From 2131d21a9d31c3966c0fd2c6991d8055ad4fa3ab Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 12 Aug 2013 10:05:57 +0000
Subject: [PATCH] removed 3 lines of commented out code replaced reg with
registry for more explicit code
---
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm | 16 ++++++----------
1 file changed, 6 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index 8719b52cb4..8374f8378a 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -64,7 +64,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::ConfigRegistry;
-my $reg = "Bio::EnsEMBL::Registry";
+my $registry = "Bio::EnsEMBL::Registry";
=head2 new
@@ -147,10 +147,6 @@ sub new {
$self = Bio::EnsEMBL::Utils::ConfigRegistry::gen_load($self);
-# if(!defined($species) ){
-# $reg->find_and_add_aliases($self);
-# }
-
$self->species_id( $species_id || 1 );
$self->is_multispecies( defined($is_multispecies)
@@ -555,7 +551,7 @@ sub add_ExternalFeatureFactory{
sub get_adaptor {
my ($self, $canonical_name, @other_args) = @_;
- return $reg->get_adaptor($self->species(),$self->group(),$canonical_name);
+ return $registry->get_adaptor($self->species(),$self->group(),$canonical_name);
}
@@ -580,7 +576,7 @@ sub get_adaptor {
sub set_adaptor {
my ($self, $canonical_name, $module) = @_;
- $reg->add_adaptor($self->species(),$self->group(),$canonical_name,$module);
+ $registry->add_adaptor($self->species(),$self->group(),$canonical_name,$module);
return $module;
}
@@ -895,11 +891,11 @@ sub dnadb {
if(@_) {
my $arg = shift;
- $reg->add_DNAAdaptor($self->species(),$self->group(),$arg->species(),$arg->group());
+ $registry->add_DNAAdaptor($self->species(),$self->group(),$arg->species(),$arg->group());
}
# return $self->{'dnadb'} || $self;
- return $reg->get_DNAAdaptor($self->species(),$self->group()) || $self;
+ return $registry->get_DNAAdaptor($self->species(),$self->group()) || $self;
}
@@ -917,7 +913,7 @@ sub AUTOLOAD {
throw( sprintf( "Could not work out type for %s\n", $AUTOLOAD ) );
}
- my $ret = $reg->get_adaptor( $self->species(), $self->group(), $type );
+ my $ret = $registry->get_adaptor( $self->species(), $self->group(), $type );
return $ret if $ret;
--
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