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Commit 1e3b6c2a authored by Ian Longden's avatar Ian Longden
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pairs no longer hard coded here but got from DBAdaptor with get_available_adaptors call

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modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
+ 13
− 229
View file @ 1e3b6c2a
......@@ -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});
......
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