From 35bde354d18ce33ce33243572599bdd96edde2c2 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 9 Mar 2006 14:17:11 +0000
Subject: [PATCH] fix case sensitivity in species name
---
modules/Bio/EnsEMBL/Registry.pm | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 56c5b79fb1..931ff9ab8e 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -123,6 +123,7 @@ my $API_VERSION = 38;
Arg [1] : (optional) string $arg file to load the registry from
Arg [2] : (optional) string if set prints out messages about conf file used.
+ Arg [3] : (optional) string if not 0 will print out all information
Example : Bio::EnsEMBL::Registry->load_all();
Returntype : none
Exceptions : none
@@ -389,7 +390,7 @@ sub get_all_DBAdaptors{
$species = $class->get_alias($species);
}
foreach my $dba (@{$registry_register{'_DBA'}}){
- if(!defined($species) || $species eq $dba->species){
+ if(!defined($species) || lc($species) eq lc($dba->species)){
if(!defined($group) || lc($group) eq lc($dba->group)){
push @ret, $dba;
}
@@ -432,8 +433,9 @@ sub get_all_DBAdaptors_by_connection{
Arg [1] : name of the species to add the adaptor to in the registry.
Arg [2] : name of the group to add the adaptor to in the registry.
- Arg [3] : The adaptor to be added to the registry as a DNA adaptor.
- Example : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "core", $dnaAdap);
+ Arg [3] : name of the species to get the dna from
+ Arg [4] : name of the group to get the dna from
+ Example : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "estgene", "Human", "core");
Returntype : none
Exceptions : none
Status : Stable
@@ -511,7 +513,7 @@ sub add_adaptor{
# which should be a warning for now
#
- if(defined($reset)){ # JUST REST THE HASH VLAUE NO MORE PROCESSING NEEDED
+ if(defined($reset)){ # JUST REST THE HASH VALUE NO MORE PROCESSING NEEDED
$registry_register{$species}{lc($group)}{lc($type)} = $adap;
return;
}
@@ -711,7 +713,6 @@ sub get_alias{
=head2 alias_exists
Arg [1] : name of the possible alias to get species for
- Arg [2] : if set will not throw if not found.
Example : Bio::EnsEMBL::Registry->alias_exists("Human");
Description: does the species name exist.
Returntype : 1 if exists else 0
--
GitLab