From 2b1a1e6dbec93a8a7735d3a603fa12eee3312466 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 1 Dec 2010 11:39:11 +0000
Subject: [PATCH] Allow for using 'regulation' as a group name alias for
'funcgen'.
---
modules/Bio/EnsEMBL/Registry.pm | 35 +++++++++++++++++++--------------
1 file changed, 20 insertions(+), 15 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 4814aa2038..12d24892f5 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -133,20 +133,21 @@ use vars qw(%registry_register);
# This is a map from group names to Ensembl DB adaptors. Used by
# load_all() and reset_DBAdaptor().
my %group2adaptor = (
- 'blast' => 'Bio::EnsEMBL::External::BlastAdaptor',
- 'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
- 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
- 'estgene' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
- 'funcgen' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
- 'haplotype' => 'Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor',
- 'hive' => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor',
- 'lite' => 'Bio::EnsEMBL::Lite::DBAdaptor',
- 'ontology' => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor',
- 'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
- 'pipeline' => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
- 'snp' => 'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
- 'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
- 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ 'blast' => 'Bio::EnsEMBL::External::BlastAdaptor',
+ 'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
+ 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ 'estgene' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ 'funcgen' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
+ 'regulation' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
+ 'haplotype' => 'Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor',
+ 'hive' => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor',
+ 'lite' => 'Bio::EnsEMBL::Lite::DBAdaptor',
+ 'ontology' => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor',
+ 'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+ 'pipeline' => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
+ 'snp' => 'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
+ 'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
+ 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor'
);
@@ -938,10 +939,14 @@ sub get_adaptor {
'assemblyexceptionfeature' => 1
);
- ## warn "$species, $group, $type";
+ # warn "$species, $group, $type";
$type = lc($type);
+ # For historical reasons, allow use of group 'regulation' to refer to
+ # group 'funcgen'.
+ if ( lc($group) eq 'regulation' ) { $group = 'funcgen' }
+
my $dnadb_group =
$registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA'};
--
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