diff --git a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm index abee10241ed7ad8b1e63cfb80bbf9039c28b9ee7..4a6ec357fd3106d95842ea41f9bc2600acb3bdcf 100644 --- a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm +++ b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm @@ -188,48 +188,9 @@ sub load_core{ my ($dba) = @_; - my %pairs = ( 'Analysis' => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor', - 'ArchiveStableId' => 'Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor', - 'Attribute' => 'Bio::EnsEMBL::DBSQL::AttributeAdaptor', - 'AssemblyExceptionFeature' => 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', - 'AssemblyMapper' => 'Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor', - 'Blast' => 'Bio::EnsEMBL::External::BlastAdaptor', - 'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer', - 'CoordSystem' => 'Bio::EnsEMBL::DBSQL::CoordSystemAdaptor', - 'CompressedSequence' => 'Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor', - 'DBEntry' => 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor', - 'DnaAlignFeature' => 'Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor', - 'DensityFeature' => 'Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor', - 'DensityType' => 'Bio::EnsEMBL::DBSQL::DensityTypeAdaptor', - 'Exon' => 'Bio::EnsEMBL::DBSQL::ExonAdaptor', - 'Gene' => 'Bio::EnsEMBL::DBSQL::GeneAdaptor', - 'KaryotypeBand' => 'Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor', - 'Marker' => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor', - 'MarkerFeature' => - 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor', - 'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer', - 'MiscSet' => 'Bio::EnsEMBL::DBSQL::MiscSetAdaptor', - 'MiscFeature' => 'Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor', - 'PredictionTranscript' => 'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor', - 'PredictionExon' => 'Bio::EnsEMBL::DBSQL::PredictionExonAdaptor', - 'ProteinFeature' => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor', - 'ProteinAlignFeature' => - 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor', - 'SNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor', - 'QtlFeature' => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor', - 'Qtl' => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor', - 'RepeatConsensus' => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor', - 'RepeatFeature' => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor', - 'Sequence' => 'Bio::EnsEMBL::DBSQL::SequenceAdaptor', - 'SimpleFeature' => 'Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor', - 'Slice' => 'Bio::EnsEMBL::DBSQL::SliceAdaptor', - 'SupportingFeature' => - 'Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor', - 'Transcript' => 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor', - 'Translation' => 'Bio::EnsEMBL::DBSQL::TranslationAdaptor'); + my %pairs = $dba->get_available_adaptors(); foreach my $key (keys %pairs){ - Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key}); } @@ -314,46 +275,7 @@ sub add_blast_link{ sub load_estgene{ my ($dba) = @_; - my %pairs = ( 'Analysis' => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor', - 'ArchiveStableId' => 'Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor', - 'Attribute' => 'Bio::EnsEMBL::DBSQL::AttributeAdaptor', - 'AssemblyExceptionFeature' => 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', - 'AssemblyMapper' => 'Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor', - 'Blast' => 'Bio::EnsEMBL::External::BlastAdaptor', - 'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer', - 'CoordSystem' => 'Bio::EnsEMBL::DBSQL::CoordSystemAdaptor', - 'CompressedSequence' => 'Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor', - 'DBEntry' => 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor', - 'DnaAlignFeature' => 'Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor', - 'DensityFeature' => 'Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor', - 'DensityType' => 'Bio::EnsEMBL::DBSQL::DensityTypeAdaptor', - 'Exon' => 'Bio::EnsEMBL::DBSQL::ExonAdaptor', - 'Gene' => 'Bio::EnsEMBL::DBSQL::GeneAdaptor', - 'KaryotypeBand' => 'Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor', - 'Marker' => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor', - 'MarkerFeature' => - 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor', - 'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer', - 'MiscSet' => 'Bio::EnsEMBL::DBSQL::MiscSetAdaptor', - 'MiscFeature' => 'Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor', - 'PredictionTranscript' => - 'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor', - 'PredictionExon' => 'Bio::EnsEMBL::DBSQL::PredictionExonAdaptor', - 'ProteinFeature' => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor', - 'ProteinAlignFeature' => - 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor', - 'ProxySNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor', - 'QtlFeature' => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor', - 'Qtl' => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor', - 'RepeatConsensus' => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor', - 'RepeatFeature' => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor', - 'Sequence' => 'Bio::EnsEMBL::DBSQL::SequenceAdaptor', - 'SimpleFeature' => 'Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor', - 'Slice' => 'Bio::EnsEMBL::DBSQL::SliceAdaptor', - 'SupportingFeature' => - 'Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor', - 'Transcript' => 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor', - 'Translation' => 'Bio::EnsEMBL::DBSQL::TranslationAdaptor' ); + my %pairs = $dba->get_available_adaptors(); #calls SUPER class so same as core adaptors foreach my $key (keys %pairs){ @@ -376,47 +298,7 @@ sub load_estgene{ sub load_est{ my ($dba) = @_; - my %pairs = ( 'Analysis' => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor', - 'ArchiveStableId' => 'Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor', - 'Attribute' => 'Bio::EnsEMBL::DBSQL::AttributeAdaptor', - 'AssemblyExceptionFeature' => 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', - 'AssemblyMapper' => 'Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor', - 'Blast' => 'Bio::EnsEMBL::External::BlastAdaptor', - 'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer', - 'CoordSystem' => 'Bio::EnsEMBL::DBSQL::CoordSystemAdaptor', - 'CompressedSequence' => 'Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor', - 'DBEntry' => 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor', - 'DnaAlignFeature' => 'Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor', - 'DensityFeature' => 'Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor', - 'DensityType' => 'Bio::EnsEMBL::DBSQL::DensityTypeAdaptor', - 'Exon' => 'Bio::EnsEMBL::DBSQL::ExonAdaptor', - 'Gene' => 'Bio::EnsEMBL::DBSQL::GeneAdaptor', - 'KaryotypeBand' => 'Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor', - 'Marker' => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor', - 'MarkerFeature' => - 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor', - 'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer', - 'MiscSet' => 'Bio::EnsEMBL::DBSQL::MiscSetAdaptor', - 'MiscFeature' => 'Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor', - 'PredictionTranscript' => - 'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor', - 'PredictionExon' => 'Bio::EnsEMBL::DBSQL::PredictionExonAdaptor', - 'ProteinFeature' => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor', - 'ProteinAlignFeature' => - 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor', - 'ProxySNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor', - 'QtlFeature' => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor', - 'Qtl' => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor', - 'RepeatConsensus' => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor', - 'RepeatFeature' => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor', - 'Sequence' => 'Bio::EnsEMBL::DBSQL::SequenceAdaptor', - 'SimpleFeature' => 'Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor', - 'Slice' => 'Bio::EnsEMBL::DBSQL::SliceAdaptor', - 'SupportingFeature' => - 'Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor', - 'Transcript' => 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor', - 'Translation' => 'Bio::EnsEMBL::DBSQL::TranslationAdaptor' ); - + my %pairs = $dba->get_available_adaptors(); #calls SUPER class so same as core adaptors foreach my $key (keys %pairs){ Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key}); @@ -436,46 +318,7 @@ sub load_est{ sub load_vega{ my ($dba) = @_; - my %pairs = ( 'Analysis' => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor', - 'ArchiveStableId' => 'Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor', - 'Attribute' => 'Bio::EnsEMBL::DBSQL::AttributeAdaptor', - 'AssemblyExceptionFeature' => 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', - 'AssemblyMapper' => 'Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor', - 'Blast' => 'Bio::EnsEMBL::External::BlastAdaptor', - 'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer', - 'CoordSystem' => 'Bio::EnsEMBL::DBSQL::CoordSystemAdaptor', - 'CompressedSequence' => 'Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor', - 'DBEntry' => 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor', - 'DnaAlignFeature' => 'Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor', - 'DensityFeature' => 'Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor', - 'DensityType' => 'Bio::EnsEMBL::DBSQL::DensityTypeAdaptor', - 'Exon' => 'Bio::EnsEMBL::DBSQL::ExonAdaptor', - 'Gene' => 'Bio::EnsEMBL::DBSQL::GeneAdaptor', - 'KaryotypeBand' => 'Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor', - 'Marker' => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor', - 'MarkerFeature' => - 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor', - 'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer', - 'MiscSet' => 'Bio::EnsEMBL::DBSQL::MiscSetAdaptor', - 'MiscFeature' => 'Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor', - 'PredictionTranscript' => - 'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor', - 'PredictionExon' => 'Bio::EnsEMBL::DBSQL::PredictionExonAdaptor', - 'ProteinFeature' => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor', - 'ProteinAlignFeature' => - 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor', - 'ProxySNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor', - 'QtlFeature' => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor', - 'Qtl' => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor', - 'RepeatConsensus' => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor', - 'RepeatFeature' => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor', - 'Sequence' => 'Bio::EnsEMBL::DBSQL::SequenceAdaptor', - 'SimpleFeature' => 'Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor', - 'Slice' => 'Bio::EnsEMBL::DBSQL::SliceAdaptor', - 'SupportingFeature' => - 'Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor', - 'Transcript' => 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor', - 'Translation' => 'Bio::EnsEMBL::DBSQL::TranslationAdaptor' ); + my %pairs = $dba->get_available_adaptors(); #calls SUPER class so same as core adaptors foreach my $key (keys %pairs){ Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key}); @@ -490,23 +333,7 @@ sub load_vega{ sub load_compara{ my ($dba) = @_; - my %pairs = ( "MetaContainer" => "Bio::EnsEMBL::DBSQL::MetaContainer", - 'SyntenyRegion' => 'Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor', - "DnaAlignFeature" => "Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor", - "Synteny" => "Bio::EnsEMBL::Compara::DBSQL::SyntenyAdaptor", - "GenomeDB" => "Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor", - "DnaFrag" => "Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor", - "GenomicAlign" => "Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor", - "Homology" => "Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor", - "Family" => "Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor", - "Domain" => "Bio::EnsEMBL::Compara::DBSQL::DomainAdaptor", - "Subset" => "Bio::EnsEMBL::Compara::DBSQL::SubsetAdaptor", - "Member" => "Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor", - "Attribute" => "Bio::EnsEMBL::Compara::DBSQL::AttributeAdaptor", - "Taxon" => "Bio::EnsEMBL::Compara::DBSQL::TaxonAdaptor", - "PeptideAlignFeature" => "Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor", - "Analysis" => "Bio::EnsEMBL::DBSQL::AnalysisAdaptor" - ); + my %pairs = $dba->get_available_adaptors(); foreach my $key (keys %pairs){ @@ -518,15 +345,7 @@ sub load_compara{ sub load_hive{ my ($dba) = @_; - my %pairs = ( - "MetaContainer" => 'Bio::EnsEMBL::DBSQL::MetaContainer', - "Analysis" => "Bio::EnsEMBL::DBSQL::AnalysisAdaptor", - "Queen" => "Bio::EnsEMBL::Hive::Queen", - "AnalysisJob" => "Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor", - "AnalysisStats" => "Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor", - "AnalysisCtrlRule" => "Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor", - "DataflowRule" => "Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor", - "SimpleRule" => "Bio::EnsEMBL::Hive::DBSQL::SimpleRuleAdaptor"); + my %pairs = $dba->get_available_adaptors(); foreach my $key (keys %pairs){ @@ -560,48 +379,13 @@ sub load_haplotype{ sub load_pipeline{ my ($dba) = @_; - my %pairs = ( 'ArchiveStableId' => 'Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor', - 'Attribute' => 'Bio::EnsEMBL::DBSQL::AttributeAdaptor', - 'AssemblyExceptionFeature' => 'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor', - 'AssemblyMapper' => 'Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor', - 'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer', - 'CoordSystem' => 'Bio::EnsEMBL::DBSQL::CoordSystemAdaptor', - 'CompressedSequence' => 'Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor', - 'DBEntry' => 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor', - 'DnaAlignFeature' => 'Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor', - 'DensityFeature' => 'Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor', - 'DensityType' => 'Bio::EnsEMBL::DBSQL::DensityTypeAdaptor', - 'Exon' => 'Bio::EnsEMBL::DBSQL::ExonAdaptor', - 'Gene' => 'Bio::EnsEMBL::DBSQL::GeneAdaptor', - 'KaryotypeBand' => 'Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor', - 'Marker' => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor', - 'MarkerFeature' => - 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor', - 'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer', - 'MiscSet' => 'Bio::EnsEMBL::DBSQL::MiscSetAdaptor', - 'MiscFeature' => 'Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor', - 'PredictionTranscript' => 'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor', - 'PredictionExon' => 'Bio::EnsEMBL::DBSQL::PredictionExonAdaptor', - 'ProteinFeature' => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor', - 'ProteinAlignFeature' => - 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor', - 'ProxySNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor', - 'QtlFeature' => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor', - 'Qtl' => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor', - 'RepeatConsensus' => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor', - 'RepeatFeature' => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor', - 'Sequence' => 'Bio::EnsEMBL::DBSQL::SequenceAdaptor', - 'SimpleFeature' => 'Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor', - 'Slice' => 'Bio::EnsEMBL::DBSQL::SliceAdaptor', - 'SupportingFeature' => - 'Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor', - 'Transcript' => 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor', - 'Translation' => 'Bio::EnsEMBL::DBSQL::TranslationAdaptor', - 'Analysis' => 'Bio::EnsEMBL::Pipeline::DBSQL::AnalysisAdaptor', - 'Job' => 'Bio::EnsEMBL::Pipeline::DBSQL::JobAdaptor', - 'PmatchFeature' => 'Bio::EnsEMBL::Pipeline::DBSQL::PmatchFeatureAdaptor', - 'Rule' => 'Bio::EnsEMBL::Pipeline::DBSQL::RuleAdaptor', - 'StateInfoContainer' => 'Bio::EnsEMBL::Pipeline::DBSQL::StateInfoContainer'); + my %pairs = $dba->get_available_adaptors(); #calls pipeline DBAdaptor (NOT implementred yet) +# core + these ones:- +# 'Analysis' => 'Bio::EnsEMBL::Pipeline::DBSQL::AnalysisAdaptor', +# 'Job' => 'Bio::EnsEMBL::Pipeline::DBSQL::JobAdaptor', +# 'PmatchFeature' => 'Bio::EnsEMBL::Pipeline::DBSQL::PmatchFeatureAdaptor', +# 'Rule' => 'Bio::EnsEMBL::Pipeline::DBSQL::RuleAdaptor', +# 'StateInfoContainer' => 'Bio::EnsEMBL::Pipeline::DBSQL::StateInfoContainer'); foreach my $key (keys %pairs){ Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key});