diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm index 4814aa2038c196f5b6bfa4a277076644fd5d3af6..12d24892f5f039ae4d3de59c87d2ae7eba90b8e2 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'};