From ff0713ae154909e33d0659ab75d3afcdc21a442e Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 29 Jul 2004 08:21:31 +0000
Subject: [PATCH] Registry modifications
---
modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm | 31 +-
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 2 +-
modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm | 1261 ++++++-----------
modules/Bio/EnsEMBL/DBSQL/DBConnection.pm | 388 ++---
modules/Bio/EnsEMBL/DBSQL/ProxyAdaptor.pm | 37 +-
modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm | 32 +-
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 2 +-
modules/Bio/EnsEMBL/External/BlastAdaptor.pm | 18 +-
modules/Bio/EnsEMBL/Lite/DBAdaptor.pm | 8 +-
modules/Bio/EnsEMBL/Registry.pm | 766 ++++++++++
modules/Bio/EnsEMBL/Slice.pm | 18 +-
modules/Bio/EnsEMBL/Storable.pm | 5 +-
modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm | 2 +-
13 files changed, 1464 insertions(+), 1106 deletions(-)
create mode 100644 modules/Bio/EnsEMBL/Registry.pm
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
index 4d912e9995..bead6dfa63 100755
--- a/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
@@ -124,12 +124,13 @@ sub new {
throw("Don't have a db [$dbobj] for new adaptor");
}
- if($dbobj->isa('Bio::EnsEMBL::Container')) {
- #avoid a circular reference loop!
- $self->db($dbobj->_obj);
- } else {
- $self->db($dbobj);
- }
+ if( ref($dbobj) =~ /DBAdaptor$/){
+ $self->db($dbobj);
+ $self->dbc($dbobj->db);
+ }
+ else{
+ throw("Don't have a DBAdaptor [$dbobj] for new adaptor");
+ }
return $self;
}
@@ -152,7 +153,7 @@ sub new {
sub prepare{
my ($self,$string) = @_;
- return $self->db->prepare($string);
+ return $self->dbc->prepare($string);
}
@@ -170,15 +171,19 @@ sub prepare{
=cut
sub db{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'db'} = $value;
- }
- return $obj->{'db'};
+ my $self = shift;
+ $self->{'db'} = shift if(@_);
+
+ return $self->{'db'};
}
+sub dbc{
+ my $self = shift;
+ $self->{'dbc'} = shift if(@_);
+
+ return $self->{'dbc'};
+}
=head2 deleteObj
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index ad58cb3b5b..01065b9133 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -170,7 +170,7 @@ sub generic_fetch {
#append additional clauses which may have been defined
$sql .= "\n$final_clause";
- my $sth = $db->prepare($sql);
+ my $sth = $db->db->prepare($sql);
$sth->execute;
my $res = $self->_objs_from_sth($sth, $mapper, $slice);
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index 4da0879a92..a4d542b03f 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -37,25 +37,21 @@ methods are usually preceded with a _
=cut
-
package Bio::EnsEMBL::DBSQL::DBAdaptor;
+
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::Utils::SeqRegionCache;
-
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
+#use Bio::EnsEMBL::Utils::Exception qw(warning throw deprecate stack_trace_dump);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-
-@ISA = qw(Bio::EnsEMBL::DBSQL::DBConnection);
-
-
-
-#Override constructor inherited by Bio::EnsEMBL::DBSQL::DBConnection
-
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::Utils::ConfigRegistry;
+my $reg = "Bio::EnsEMBL::Registry";
=head2 new
@@ -69,6 +65,9 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-dbname => 'pog',
-host => 'caldy',
-driver => 'mysql' );
+ Exmaple2 : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+ -species => 'Homo_sapiens',
+ -group => 'core');
Description: Constructor for DBAdaptor.
Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
Exceptions : none
@@ -80,861 +79,341 @@ sub new {
my($class, @args) = @_;
#call superclass constructor
- my $self = $class->SUPER::new(@args);
-
- my ( $dnadb ) = rearrange([qw(DNADB)],@args);
-
- if(defined $dnadb) {
- $self->dnadb($dnadb);
- }
-
- # $self here is actually a Container object
- # so need to call _obj to get the DBAdaptor
- $self->_obj->{'default_module'} =
- { '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',
- 'Chromosome' => 'Bio::EnsEMBL::DBSQL::ChromosomeAdaptor',
- 'Clone' => 'Bio::EnsEMBL::DBSQL::CloneAdaptor',
- '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',
- 'MapFrag' => 'Bio::EnsEMBL::DBSQL::MapFragAdaptor',
- 'Marker' => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor',
- 'MarkerFeature' =>
- 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor',
- 'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer',
- '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',
- 'Protein' => 'Bio::EnsEMBL::DBSQL::ProteinAdaptor',
- 'ProteinAlignFeature' =>
- 'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor',
- 'ProxySNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor',
- 'QtlFeature' => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor',
- 'Qtl' => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor',
- 'RawContig' => 'Bio::EnsEMBL::DBSQL::RawContigAdaptor',
- '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',
-
- };
-
-
- # initialise storage for hash of names of current modules
- %{$self->_obj->{'current_module'}} = %{$self->_obj->{'default_module'}};
-
- # keep a hash of objects representing objects of each adaptor type
- # instantiated as required in get adaptor
- $self->_obj->{'current_objects'} = {};
-
- # initialise generic feature adaptor storage
- $self->_obj->{'generic_feature_adaptors'} = {};
-
-
-
- return $self;
-}
-
-
-
-=head2 get_ArchiveStableIdAdaptor
-
- Args : none
- Example : none
- Description: ...
- Returntype : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_ArchiveStableIdAdaptor {
- my( $self ) = @_;
-
- return
- $self->get_adaptor("ArchiveStableId");
-}
-
-
-=head2 get_QtlFeatureAdaptor
-
- Args : none
- Example : none
- Description: ...
- Returntype : Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_QtlFeatureAdaptor {
- my $self = shift;
- return $self->get_adaptor("QtlFeature");
-}
-
-=head2 get_QtlAdaptor
-
- Args : none
- Example : none
- Description: ...
- Returntype : Bio::EnsEMBL::Map::DBSQL::QtlAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_QtlAdaptor {
- my $self = shift;
- return $self->get_adaptor("Qtl");
-}
-
-=head2 get_MetaContainer
-
- Args : none
- Example : $meta_container = $db_adaptor->get_MetaContainer();
- Description: Gets a MetaContainer object for this database
- Returntype : Bio::EnsEMBL::DBSQL::MetaContainer
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_MetaContainer {
- my $self = shift;
- return $self->get_adaptor('MetaContainer');
-}
-
-
-
-=head2 get_MetaCoordContainer
-
- Arg [1] : none
- Example : $meta_coord_container = $db_adaptor->get_MetaCoordContainer();
- Description: Gets a MetaCoordContainer object for this database.
- Returntype : Bio::EnsEMBL::DBSQL::MetaCoordContainer
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_MetaCoordContainer {
- my $self = shift;
- return $self->get_adaptor('MetaCoordContainer');
-}
-
-=head2 get_ProteinFeatureAdaptor
-
- Args : none
- Example : $pfa = $database_adaptor->get_ProteinFeatureAdaptor();
- Description: Gets a ProteinFeatureAdaptor for this database.
- Formerly named get_Protfeat_Adaptor()
- Returntype : Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_ProteinFeatureAdaptor {
- my $self = shift;
- return $self->get_adaptor("ProteinFeature");
-}
-
-
-=head2 get_SNPAdaptor
-
- Args : none
- Example : $snp_adaptor = $db_adaptor->get_SNPAdaptor();
- Description: Gets a SNPAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::SNPAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_SNPAdaptor {
- my ($self) = @_;
-
- my $lite = $self->get_db_adaptor('lite');
- my $primary_adaptor;
-
- if($lite) {
- $primary_adaptor = $lite->get_SNPAdaptor();
- } else {
- my $snp = $self->get_db_adaptor('SNP');
-
- unless($snp) {
- warning("No lite or SNP database, cannot get snp adaptor\n");
- return undef;
- }
-
- $primary_adaptor = $snp->get_SNPAdaptor();
- $primary_adaptor->ensembl_db( $self );
- }
-
- #return a proxy adaptor which can use the lite or the core database
- return $self->get_adaptor("ProxySNP",
- $primary_adaptor);
-}
-
-
-=head2 get_BlastAdaptor
-
- Args : none
- Example : $blast_adaptor = $db_adaptor->get_BlastAdaptor();
- Description: Gets a BlastAdaptor for retrieving stored blast hits
- Returntype : Bio::EnsEMBL::External::BlastAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_BlastAdaptor {
- my ($self) = @_;
-
- my $db_apt = $self->get_db_adaptor('blast');
-
- return $self->get_adaptor("Blast",
- $db_apt);
-}
-
-
-=head2 get_PredictionTranscriptAdaptor
-
- Args : none
- Example : $pta = $db_adaptor->get_PredictionTranscriptAdaptor();
- Description: Gets a PredictionTranscriptAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_PredictionTranscriptAdaptor {
- my ($self) = @_;
-
- return $self->get_adaptor("PredictionTranscript");
-}
-
-
-=head2 get_PredictionExonAdaptor
-
- Args : none
- Example : $pea = $db_adaptor->get_PredictionExonAdaptor();
- Description: Gets a PredictionExonAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::PredictionExonAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_PredictionExonAdaptor {
- my ($self) = @_;
-
- return $self->get_adaptor("PredictionExon");
-}
-
-
-=head2 get_SequenceAdaptor
-
- Args : none
- Example : $sequence_adaptor = $db_adaptor->get_SequenceAdaptor();
- Description: Gets a SequenceAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::SequenceAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_SequenceAdaptor {
- my $self = shift;
-
- my $mc = $self->dnadb->get_MetaContainer();
-
- my ($use_compressed) = @{$mc->list_value_by_key('sequence.compression')};
-
- if($use_compressed) {
- return $self->dnadb->get_adaptor("CompressedSequence");
- } else {
- #return the sequence adaptor for the dnadb (which may be this db)
- return $self->dnadb->get_adaptor("Sequence");
- }
-}
-
-
-=head2 get_CompressedSequenceAdaptor
-
- Args : none
- Example : $seq_adaptor = $db_adaptor->get_CompressedSequenceAdaptor();
- Description: Gets a CompressedSequenceAdaptor for this database.
- A compressed sequence adaptor behaves like a normal
- SequenceAdaptor except that it stores and retrieves compressed
- sequence from the dnac table (rather than the dna table).
- Normally if you want to use compressed sequence you should
- convert your database to a compressed database with a script
- and then set the 'sequence.compression' meta_key to a value
- of '1' in the meta table. This way the compressed sequence
- adaptor will be used instead of the normal sequence adaptor.
- Returntype : Bio::EnsEMBL::DBSQL::SequenceAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_CompressedSequenceAdaptor {
- my $self = shift;
-
- #return the sequence adaptor for the dnadb (which may be this db)
- return $self->dnadb->get_adaptor("CompressedSequence");
-}
-
-
-
-=head2 get_GeneAdaptor
-
- Args : none
- Example : $gene_adaptor = $db_adaptor->get_GeneAdaptor();
- Description: Gets a GeneAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::GeneAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_GeneAdaptor {
- my( $self ) = @_;
- #get a core db adaptor
- return $self->get_adaptor("Gene");
-}
-
-
-=head2 get_ExonAdaptor
-
- Args : none
- Example : $exon_adaptor = $db_adaptor->get_ExonAdaptor();
- Description: Gets an ExonAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::ExonAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_ExonAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("Exon");
-}
-
-
-=head2 get_TranscriptAdaptor
-
- Args : none
- Example : $transcript_adaptor = $db_adaptor->get_TranscriptAdaptor();
- Description: Gets a TranscriptAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::TranscriptAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_TranscriptAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("Transcript");
-}
-
-
-=head2 get_TranslationAdaptor
-
- Args : none
- Example : $translation_adaptor = $db_adaptor->get_TranslationAdaptor();
- Description: Gets a TranslationAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::TranslationAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_TranslationAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("Translation");
-}
-
-
-
-=head2 get_SliceAdaptor
-
- Args : none
- Example : $slice_adaptor = $db_adaptor->get_SliceAdaptor();
- Description: Gets a SliceAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::SliceAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_SliceAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("Slice");
-}
-
-
-=head2 get_AnalysisAdaptor
-
- Args : none
- Example : $analysis_adaptor = $db_adaptor->get_AnalysisAdaptor();
- Description: Gets an AnalysisAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::AnalysisAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_AnalysisAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("Analysis");
-}
-
-
-=head2 get_SimpleFeatureAdaptor
-
- Args : none
- Example : $sfa = $db_adaptor->get_SimpleFeatureAdaptor();
- Description: Gets a SimpleFeatureAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_SimpleFeatureAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("SimpleFeature");
-}
-
-
-=head2 get_RepeatConsensusAdaptor
-
- Args : none
- Example : $rca = $db_adaptor->get_RepeatConsensusAdaptor();
- Description: Gets a RepeatConsensusAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_RepeatConsensusAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("RepeatConsensus");
-}
-
-
-=head2 get_RepeatFeatureAdaptor
-
- Args : none
- Example : $rfa = $db_adaptor->get_RepeatFeatureAdaptor();
- Description: Gets a RepeatFeatureAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_RepeatFeatureAdaptor {
- my( $self ) = @_;
-
- return $self->dnadb->get_adaptor("RepeatFeature");
-}
-
-
-=head2 get_ProteinAlignFeatureAdaptor
-
- Args : none
- Example : $pafa = $db_adaptor->get_ProteinAlignFeatureAdaptor();
- Description: Gets a ProteinAlignFeatureAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_ProteinAlignFeatureAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("ProteinAlignFeature");
-}
-
-
-=head2 get_DnaAlignFeatureAdaptor
-
- Args : none
- Example : $dafa = $db_adaptor->get_DnaAlignFeatureAdaptor();
- Description: Gets a DnaAlignFeatureAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_DnaAlignFeatureAdaptor {
- my $self = shift;
-
- return $self->get_adaptor("DnaAlignFeature");
-}
-
-
-=head2 get_AssemblyMapperAdaptor
-
- Args : none
- Example : $asma = $db_adaptor->get_AssemblyMapperAdaptor();
- Description: Gets an AsemblyMapperAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_AssemblyMapperAdaptor {
- my( $self ) = @_;
-
- return
- $self->dnadb->get_adaptor("AssemblyMapper");
-}
-
-
-=head2 get_DBEntryAdaptor
-
- Args : none
- Example : $dbentry_adaptor = $db_adaptor->get_DBEntryAdaptor();
- Description: Gets a DBEntryAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::DBEntryAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_DBEntryAdaptor {
- my( $self ) = @_;
-
- return $self->get_adaptor("DBEntry");
-}
-
-
-
-
-=head2 get_DensityFeatureAdaptor
-
- Arg [1] : none
- Example : $density_feature_adaptor = $db_adaptor->get_DBEntryAdaptor();
- Description: Gets a DensityFeatureAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_DensityFeatureAdaptor {
- my $self = shift;
- return $self->get_adaptor('DensityFeature');
-}
-
-=head2 get_DensityTypeAdaptor
-
- Arg [1] : none
- Example : $density_feature_adaptor = $db_adaptor->get_DBEntryAdaptor();
- Description: Gets a DensityTypeAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
- Exceptions : none
- Caller : general
-
-=cut
-
-sub get_DensityTypeAdaptor {
- my $self = shift;
- return $self->get_adaptor('DensityType');
-}
-
+ my $self ={};
+ bless $self,$class;
+ my ($species, $group, $dbname) =
+ rearrange([qw(SPECIES GROUP DBNAME)], @args);
-=head2 get_KaryotypeBandAdaptor
- Args : none
- Example : $kba = $db_adaptor->get_KaryotypeBandAdaptor();
- Description: Gets a KaryotypeBandAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor
- Exceptions : none
- Caller : general
+ my ($spec,$gro) = $reg->check_if_already_there(@args);
+ if($spec){
+ $self = $reg->get_DBAdaptor($spec,$gro);
+ $self->species($species);
+ $self->group($group);
+ return $self;
+ }
+ my $config_sub;
+ if(defined($species)and defined($group)){ # NEW style usage of registry
+ $self = $reg->get_DBAdaptor($species,$group);
+ $self->species($species);
+ $self->group($group);
+ }
+ else{ # OLD style, so mimic by adding to registry
+ my $free=0;
+ if(!defined($species)){
+ $species= "DEFAULT";
+ }
+ if($class->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor')){
+ $group = "compara";
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_compara;
+ }
+ elsif($class->isa('Bio::EnsEMBL::Lite::DBAdaptor')){
+ $group = 'lite';
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_lite;
+ }
+ elsif($class->isa('Bio::EnsEMBL::External::BlastAdaptor')){
+ $group = 'blast';
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_blast;
+ }
+ elsif($class->isa('Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor')){
+ $group = "SNP";
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_SNP;
+ }
+ elsif($class->isa('Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor')){
+ $group = "pipeline";
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_pipeline;
+ }
+ elsif($class->isa('Bio::EnsEMBL::Hive::DBSQL::DBAdaptor')){
+ $group = "hive";
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_hive;
+ }
+ elsif($class->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
+ $group = "core";
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_core;
+ }
+ else{
+ throw("Unknown DBAdaptor type $class\n");
+ }
-=cut
+ $reg->add_alias($species,$species);
-sub get_KaryotypeBandAdaptor {
- my( $self ) = @_;
+ my $i = 0;
+ while(!$free){
+ if($i == 0){
+ if(!defined($reg->get_DBAdaptor($species, $group))){
+ $free =1;
+ $i ="";
+ }
+ else{
+ $i = 1;
+ }
+ }
+ else{
+ $reg->add_alias($species.$i,$species.$i); #set needed self alias
+ if(!defined($reg->get_DBAdaptor($species.$i, $group))){
+ $free =1;
+ }
+ else{
+ $i++;
+ }
+ }
+ }
- return
- $self->dnadb->get_adaptor("KaryotypeBand");
-}
+ $species .= $i;
+ push (@args, '-species');
+ push (@args, $species);
-=head2 get_SupportingFeatureAdaptor
+ &{$config_sub}($class,@args);
- Arg [1] : none
- Example : $sfa = $db_adaptor->get_SupportingFeatureAdaptor();
- Description: Gets a SupportingFeatreAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor
- Exceptions : none
- Caller : Bio::EnsEMBL::Exon
+ $self = $reg->get_DBAdaptor($species,$group);
-=cut
+ }
-sub get_SupportingFeatureAdaptor {
- my $self = shift;
+ my ( $dnadb ) = rearrange([qw(DNADB)],@args);
- return $self->get_adaptor("SupportingFeature");
+ if(defined $dnadb) {
+ $self->dnadb($dnadb);
+ }
+ return $self;
}
+=head2 new_fast
+ Arg [-CON]: Bio::EnsEMBL::DBSQL::DBConnection
-=head2 get_MarkerFeatureAdaptor
-
- Arg [1] : none
- Example : $mfa = $db_adaptor->get_MarkerFeatureAdaptor;
- Description: Gets a MarkerFeatureAdaptor for this database
- Returntype : Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor
+ Exmaple : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor( -con => $dbc);
+ Description: Constructor for DBAdaptor.
+ Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
Exceptions : none
Caller : general
=cut
-sub get_MarkerFeatureAdaptor {
- my $self = shift;
+sub new_fast{
+ my($class, @args) = @_;
+ my ( $con ) = rearrange([qw(CON)],@args);
- return $self->get_adaptor('MarkerFeature');
-}
+ #call superclass constructor
+ my $self ={};
+ bless $self,$class;
+ unless($con && ref $con &&
+ $con->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
+ throw("$con passed is not of type Bio::EnsEMBL::DBSQL::DBConnection");
+ }
+ $self->db($con);
+ $self->species($con->species());
+ $self->group($con->group());
+ return $self;
+}
-=head2 get_MarkerAdaptor
- Arg [1] : none
- Example : $ma = $db_adaptor->get_MarkerAdaptor;
- Description: Gets a MarkerAdaptor for this database
- Returntype : Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor
- Exceptions : none
- Caller : general
+sub new_merged{
+ my($class, $species, @args) = @_;
-=cut
+ my $self ={};
+ bless $self,$class;
-sub get_MarkerAdaptor {
- my $self = shift;
+ $self->species($species);
+ $self->group("_MERGED_");
- return $self->get_adaptor('Marker');
+ return $self;
}
-=head2 get_CoordSystemAdaptor
+=head2 db
- Arg [1] : none
- Example : $csa = $db_adaptor->get_CoordSystemAdaptor();
- Description: Gets a CoordSystemAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
+ Arg[1] : (optional) Bio::EnsEMBL::DBSQL::DBConnection
+
+ Exmaple : $dbc = $dba->db();
+ Description: Getter/Setter for DBConnection.
+ Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : none
Caller : general
=cut
-sub get_CoordSystemAdaptor {
- my $self = shift;
-
- return $self->dnadb()->get_adaptor('CoordSystem');
+sub db{
+ my ($self, $arg ) = @_;
+ ( defined $arg ) &&
+ ( $self->{_db} = $arg );
+ $self->{_db};
}
+sub DESTROY{
+ my ($self)= @_;
+ $self->{'_db'} = undef;
+}
-=head2 get_MiscSetAdaptor
+=head2 deleteObj
Arg [1] : none
- Example : $msa = $db_adaptor->get_MiscSetAdaptor();
- Description: Gets a MiscSet adaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::MiscSetAdaptor
+ Example : none
+ Description: Cleans up circular reference loops so proper garbage collection
+ can occur.
+ Returntype : none
Exceptions : none
- Caller : general
+ Caller : DBAdaptorContainer::DESTROY
=cut
-sub get_MiscSetAdaptor {
+sub deleteObj {
my $self = shift;
+ #print "called deleteObj on DBAdaptor\n";
- return $self->get_adaptor('MiscSet');
-}
-
-
-
-=head2 get_MiscFeatureAdaptor
+ #clean up external feature adaptor references
+ if(exists $self->{'_xf_adaptors'}) {
+ foreach my $key (keys %{$self->{'_xf_adaptors'}}) {
+ delete $self->{'_xf_adaptors'}->{$key};
+ }
+ }
- Arg [1] : none
- Example : $mfa = $db_adaptor->get_MiscFeatureAdaptor();
- Description: Gets a MiscFeature adaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor
- Exceptions : none
- Caller : general
+ if(exists $self->{'generic_feature_adaptors'}) {
+ foreach my $name (keys %{$self->{'generic_feature_adaptors'}}) {
+ my $adaptor = $self->{'generic_feature_adaptors'}->{$name};
+ if(ref($adaptor) && $adaptor->can('deleteObj')) {
+ $adaptor->deleteObj();
+ }
-=cut
+ delete $self->{'generic_feature_adaptors'}->{$name};
+ }
-sub get_MiscFeatureAdaptor {
- my $self = shift;
+ delete $self->{'generic_feature_adaptors'};
+ }
- return $self->get_adaptor('MiscFeature');
}
-=head2 get_AssemblyExceptionFeatureAdaptor
+=head2 add_db_adaptor
- Arg [1] : none
- Example : $aefa = $db_adaptor->get_AssemblyExceptionFeatureAdaptor();
- Description: Gets a AssemblyExceptionFeature adaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor
+ Arg [1] : string $name
+ the name of the database to attach to this database
+ Arg [2] : Bio::EnsEMBL::DBSQL::DBConnection
+ the db adaptor to attach to this database
+ Example : $db->add_db_adaptor('lite', $lite_db_adaptor);
+ Description: Attaches another database instance to this database so
+ that it can be used in instances where it is required.
+ Returntype : none
Exceptions : none
- Caller : general
+ Caller : EnsWeb
=cut
-sub get_AssemblyExceptionFeatureAdaptor {
- my $self = shift;
+sub add_db_adaptor {
+ my ($self, $name, $adaptor) = @_;
- return $self->dnadb->get_adaptor('AssemblyExceptionFeature');
-}
+ unless($name && $adaptor && ref $adaptor) {
+ throw('adaptor and name arguments are required');
+ }
+
+ Bio::EnsEMBL::Registry->add_db($self, $name, $adaptor);
+}
-=head2 get_AttributeAdaptor
+=head2 remove_db_adaptor
- Arg [1] : none
- Example : $aa = $db_adaptor->get_AttributeAdaptor()
- Description: Gets an AttributeAdaptor for this database
- Returntype : Bio::EnsEMBL::DBSQL::AttributeAdaptor
+ Arg [1] : string $name
+ the name of the database to detach from this database.
+ Example : $lite_db = $db->remove_db_adaptor('lite');
+ Description: Detaches a database instance from this database and returns
+ it.
+ Returntype : none
Exceptions : none
- Caller : general
+ Caller : ?
=cut
-sub get_AttributeAdaptor {
- my $self = shift;
- return $self->get_adaptor('Attribute');
+sub remove_db_adaptor {
+ my ($self, $name) = @_;
+
+ return Bio::EnsEMBL::Registry->remove_db($self, $name);
}
-=head2 dnadb
+=head2 get_all_db_adaptors
- Title : dnadb
- Usage : my $dnadb = $db->dnadb;
- Function: returns the database adaptor where the dna lives
- Useful if you only want to keep one copy of the dna
- on disk but have other databases with genes and features in
- Returns : dna database adaptor
- Args : Bio::EnsEMBL::DBSQL::DBAdaptor
+ Arg [1] : none
+ Example : @attached_dbs = values %{$db->get_all_db_adaptors()};
+ Description: returns all of the attached databases as
+ a hash reference of key/value pairs where the keys are
+ database names and the values are the attached databases
+ Returntype : hash reference with Bio::EnsEMBL::DBSQL::DBConnection values
+ Exceptions : none
+ Caller : Bio::EnsEMBL::DBSQL::ProxyAdaptor
=cut
-sub dnadb {
- my $self = shift;
+sub get_all_db_adaptors {
+ my ($self) = @_;
- if(@_) {
- my $arg = shift;
- if(ref($arg) && (($arg->isa('Bio::EnsEMBL::Container') &&
- $arg->_obj == $self) || $arg == $self)) {
- #we don't want to store a circular reference to our self
- return;
- }
+ my %ret = %{Bio::EnsEMBL::Registry->get_all_db_adaptors($self)};
- $self->{'dnadb'} = $arg;
- }
+# foreach my $key (%ret){
+# print $key."\n";
+# }
+# print %ret."\n";
+ return \%ret;
+# unless(defined $self->{'_db_adaptors'}) {
+# return {};
+# }
- return $self->{'dnadb'} || $self;
+# return $self->{'_db_adaptors'};
}
-=head2 deleteObj
+=head2 get_db_adaptor
- Arg [1] : none
- Example : none
- Description: Cleans up circular reference loops so proper garbage collection
- can occur.
- Returntype : none
+ Arg [1] : string $name
+ the name of the attached database to retrieve
+ Example : $lite_db = $db->get_db_adaptor('lite');
+ Description: returns an attached db adaptor of name $name or undef if
+ no such attached database exists
+ Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : none
- Caller : DBAdaptorContainer::DESTROY
+ Caller : ?
=cut
-sub deleteObj {
- my $self = shift;
- #print "called deleteObj on DBAdaptor\n";
-
- #clean up external feature adaptor references
- if(exists $self->{'_xf_adaptors'}) {
- foreach my $key (keys %{$self->{'_xf_adaptors'}}) {
- delete $self->{'_xf_adaptors'}->{$key};
- }
- }
-
- if(exists $self->{'current_objects'}) {
- foreach my $adaptor_name (keys %{$self->{'current_objects'}}) {
- my $adaptor = $self->{'current_objects'}->{$adaptor_name};
+sub get_db_adaptor {
+ my ($self, $name) = @_;
- if(ref($adaptor) && $adaptor->can('deleteObj')) {
- $adaptor->deleteObj();
- }
+ return Bio::EnsEMBL::Registry->get_db($self, $name);
+}
- delete $self->{'current_objects'}->{$adaptor_name};
- }
- }
+sub get_SNPAdaptor {
+ my ($self) = @_;
+
+ my $lite = $self->get_db_adaptor('lite'); #### use register directly here
- if(exists $self->{'generic_feature_adaptors'}) {
- foreach my $name (keys %{$self->{'generic_feature_adaptors'}}) {
- my $adaptor = $self->{'generic_feature_adaptors'}->{$name};
- if(ref($adaptor) && $adaptor->can('deleteObj')) {
- $adaptor->deleteObj();
- }
+ my $primary_adaptor;
- delete $self->{'generic_feature_adaptors'}->{$name};
+ if($lite) {
+ $primary_adaptor = $lite->get_SNPAdaptor();
+ } else {
+ my $snp = $self->get_db_adaptor('SNP');
+
+ unless($snp) {
+ warn("No lite or SNP database, cannot get snp adaptor");
+ return undef;
}
- delete $self->{'generic_feature_adaptors'};
+ $primary_adaptor = $snp->get_SNPAdaptor();
+ $primary_adaptor->ensembl_db( $self );
}
-
- delete $self->{'_meta_container'};
- delete $self->{'dnadb'};
-
- #call the superclass deleteObj method
- $self->SUPER::deleteObj;
+ #return a proxy adaptor which can use the lite or the core database
+ my $ret = $self->get_adaptor("ProxySNP");
+ $ret->set_primary($primary_adaptor);
+ return $ret;
+# return $self->get_adaptor("ProxySNP", $primary_adaptor);
}
@@ -1115,36 +594,79 @@ sub add_ExternalFeatureFactory{
Arg [1] : Canonical data type for which an adaptor is required.
Example : $db_adaptor->get_adaptor("Protein")
Description: Gets an adaptor object for a standard data type.
- Returntype : Adaptor Object of arbitrary type
- Exceptions : thrown if there is no associated module
+ Returntype : Adaptor Object of arbitrary type or undef
+ Exceptions : none
Caller : external
=cut
sub get_adaptor {
- my ($self, $canonical_name, @other_args) = @_;
+ my ($self, $canonical_name, @other_args) = @_;
- if ($self->isa('Bio::EnsEMBL::Container')) {
- $self = $self->_obj;
- }
+ return $reg->get_adaptor($self->db->species(),$self->db->group(),$canonical_name);
+}
- # throw if module for $canonical_name does not exist
- throw("No such data type $canonical_name")
- if (!exists($self->{'current_module'}->{$canonical_name}));
- # get module name for $canonical_name
- my $module_name = $self->{'default_module'}->{$canonical_name};
- # create and store a new one if necessary
- if (!exists($self->{'current_objects'}->{$canonical_name})) {
- $self->{'current_objects'}->{$canonical_name} =
- $self->_get_adaptor($module_name, @other_args);
- }
+sub prepare{
+ my ($self, @args) = @_;
+
+ deprecate("prepare Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->prepare(@args);
+}
+
+sub dbname{
+ my ($self, @args) = @_;
+
+ deprecate("dbname Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->dbname(@args);
+}
- return $self->{'current_objects'}->{$canonical_name};
+sub disconnect_when_inactive{
+ my ($self, @args) = @_;
+ deprecate("disconnect_when_inactive Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->disconnect_when_inactive(@args);
}
+sub host{
+ my ($self, @args) = @_;
+
+ deprecate("host Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->host(@args);
+}
+sub username{
+ my ($self, @args) = @_;
+
+ deprecate("username Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->username(@args);
+}
+sub password{
+ my ($self, @args) = @_;
+
+ deprecate("password Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->password(@args);
+}
+sub driver{
+ my ($self, @args) = @_;
+
+ deprecate("driver Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->driver(@args);
+}
+sub port{
+ my ($self, @args) = @_;
+
+ deprecate("port Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->port(@args);
+}
+
+sub db_handle{
+ my ($self, @args) = @_;
+
+
+ deprecate("db_handle Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
+ $self->db->db_handle(@args);
+}
=head2 set_adaptor
@@ -1155,34 +677,61 @@ sub get_adaptor {
Description: Stores the object which represents the adaptor for the
arg1 data type.
Returntype : none
- Exceptions : If arg2 is not a subclass of the default module for this
- data type.
+ Exceptions : none
Caller : external
=cut
sub set_adaptor {
- my ($self, $canonical_name, $new_object) = @_;
+ my ($self, $canonical_name, $module) = @_;
- if ($self->isa('Bio::EnsEMBL::Container')) {
- $self = $self->_obj;
- }
+ my $adaptor = $self->_get_adaptor($module);
- # throw if an unrecognised canonical_name is used
- throw("No such data type $canonical_name")
- if(!exists($self->{'default_module'}->{$canonical_name}));
+ $reg->add_adaptor($self->species(), $self->group(), $canonical_name, $adaptor);
- my $default_module = $self->{'default_module'}->{$canonical_name};
+ return $adaptor;
+}
+
+=head2 _get_adaptor
+
+ Arg [1] : string $module
+ the fully qualified of the adaptor module to be retrieved
+ Arg [2..n] : (optional) arbitrary list @args
+ list of arguments to be passed to adaptors constructor
+ Example : $adaptor = $self->_get_adaptor("full::adaptor::name");
+ Description: PROTECTED Used by subclasses to obtain adaptor objects
+ for this database connection using the fully qualified
+ module name of the adaptor. If the adaptor has not been
+ retrieved before it is created, otherwise it is retreived
+ from the adaptor cache.
+ Returntype : Adaptor Object of arbitrary type
+ Exceptions : thrown if $module can not be instantiated
+ Caller : Bio::EnsEMBL::DBAdaptor
+
+=cut
+
+sub _get_adaptor {
+ my( $self, $module) = @_;
+
+ my( $adaptor);
+
+ eval "require $module";
- # Check that $new_module is a subclass of $default_module
- if (!$new_object->isa($default_module)) { # polymorphism should work
- throw("ref($new_object) is not a subclass of $default_module");
+ if($@) {
+ warning("$module cannot be found.\nException $@\n");
+ return undef;
}
- # set the value in current_module
- $self->{'current_objects'}->{$canonical_name} = $new_object;
+ $adaptor = "$module"->new($self);
+
+ return $adaptor;
}
+
+
+
+
+
#
# GENERIC FEATURE ADAPTORS
#
@@ -1214,6 +763,8 @@ sub get_GenericFeatureAdaptors {
if (!exists($self->{'generic_feature_adaptors'}->{$name})) {
throw("No generic feature adaptor has been defined for $name" );
}
+
+
$adaptors{$name} = $self->{'generic_feature_adaptors'}->{$name};
}
}
@@ -1248,8 +799,50 @@ sub add_GenericFeatureAdaptor {
$self->{'generic_feature_adaptors'}->{$name} = $adaptor_obj;
}
+=head2 species
+ Arg [1] : (optional) string $arg
+ The new value of the species used by this DBAdaptor.
+ Example : $species = $dba->species()
+ Description: Getter/Setter for the species of to use for
+ this connection. There is currently no point in setting
+ this value after the connection has already been established
+ by the constructor.
+ Returntype : string
+ Exceptions : none
+ Caller : new
+
+=cut
+
+sub species {
+ my ($self, $arg ) = @_;
+ ( defined $arg ) &&
+ ( $self->{_species} = $arg );
+ $self->{_species};
+}
+
+
+=head2 group
+
+ Arg [1] : (optional) string $arg
+ The new value of the group used by this DBAdaptor.
+ Example : $group = $dba->group()
+ Description: Getter/Setter for the group of to use for
+ this connection. There is currently no point in setting
+ this value after the connection has already been established
+ by the constructor.
+ Returntype : string
+ Exceptions : none
+ Caller : new
+
+=cut
+sub group {
+ my ($self, $arg ) = @_;
+ ( defined $arg ) &&
+ ( $self->{_group} = $arg );
+ $self->{_group};
+}
=head2 get_SeqRegionCache
@@ -1278,6 +871,64 @@ sub get_SeqRegionCache {
}
+=head2 dnadb
+
+ Title : dnadb
+ Usage : my $dnadb = $db->dnadb();
+ Function: returns the database adaptor where the dna lives
+ Useful if you only want to keep one copy of the dna
+ on disk but have other databases with genes and features in
+ Returns : dna database adaptor
+ Args : Bio::EnsEMBL::DBSQL::BaseAdaptor
+
+=cut
+
+sub dnadb {
+ my $self = shift;
+
+ if(@_) {
+ my $arg = shift;
+ $reg->add_DNAAdaptor($self->species(),$self->group(),$arg);
+ }
+
+# return $self->{'dnadb'} || $self;
+ return $reg->get_DNAAdaptor($self->species(),$self->group()) || $self;
+}
+
+
+use vars '$AUTOLOAD';
+
+sub AUTOLOAD {
+ my ($self,@args) = @_;
+
+ my $type;
+ if($AUTOLOAD =~ /^.*::get_(\w+)Adaptor$/){
+ $type = $1;
+ }
+ elsif($AUTOLOAD =~ /^.*::get_(\w+)$/){
+ $type = $1;
+ }
+ else{
+ throw("Could not work out type for $AUTOLOAD \n");
+ }
+
+ my $ret = undef;
+ if($self->group() eq "_MERGED_"){
+ $ret = $reg->get_MergedAdaptor($self->species(),$type);
+ }
+ else{
+ $ret = $reg->get_adaptor($self->species(),$self->group(),$type);
+ }
+ if($ret){
+ return $ret;
+ }
+ else{
+ warning("Could not find $type adaptor in the registry for ".$self->species." ".$self->group."\n");
+ return $ret;
+ }
+ die("No such method: $AUTOLOAD\n");
+}
+
#########################
# sub DEPRECATED METHODS
#########################
@@ -1356,20 +1007,22 @@ sub source {
=head2 assembly_type
- Description: DEPRECATED - Use CoordSystemAdaptor to obtain coordinate
- systems instead.
+ Description: DEPRECATED - Use CoordSystemAdaptor to obtain default coordinate
+ system instead.
=cut
sub assembly_type{
my $self = shift;
- deprecate("Use version of coordinate system you are interested in instead.\n"
- . "Example:\n".
- ' ($cs) = @{$coord_system_adaptor->fetch_all()};'."\n" .
- ' $assembly = $cs->version();');
+
+ deprecate('Use CoordSystemAdaptor::fetch_top_level instead');
+
my $csa = $self->get_CoordSystemAdaptor();
- my $cs = @{$csa->fetch_all()};
- return $cs->version();
+
+ #get the default top-level coord system
+ my ($dbID,$name,$version) = $csa->fetch_top_level();
+
+ return $version;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
index 0edc89d5fc..e1e1ff2ee7 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
@@ -3,10 +3,12 @@
=head1 SYNOPSIS
$db = Bio::EnsEMBL::DBSQL::DBConnection->new(
- -user => 'anonymous',
- -dbname => 'homo_sapiens_core_20_34c',
- -host => 'ensembldb.ensembl.org',
- -driver => 'mysql',
+ -user => 'anonymous',
+ -dbname => 'homo_sapiens_core_20_34c',
+ -host => 'ensembldb.ensembl.org',
+ -driver => 'mysql',
+ -species => 'Homo Sapiens',
+ -group => 'core'
);
@@ -40,7 +42,9 @@ package Bio::EnsEMBL::DBSQL::DBConnection;
use vars qw(@ISA);
use strict;
-use Bio::EnsEMBL::Container;
+#use Bio::EnsEMBL::Container; ## Container no longer needed here
+use Bio::EnsEMBL::Registry;
+my $reg = "Bio::EnsEMBL::Registry";
use Bio::EnsEMBL::Root;
use DBI;
@@ -80,33 +84,65 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
which would otherwise keep open a lot of connections to the
database. Database connections are automatically reopened
when required.
+ Arg [DNADB] : (optional) Bio::EnsEMBL::DBSQL::DBConnection
+ The dbconnection to get the dna from.
+ Arg [SPECIES]: (optional) string
+ Name of the species to be labelled as.
+ Arg [GROUP]: (optional) string
+ Name of the group to be labelled as. (e.g. core, estgene, vega etc)
Example : $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new
(-user => 'anonymous',
-dbname => 'homo_sapiens_core_20_34c',
-host => 'ensembldb.ensembl.org',
- -driver => 'mysql');
+ -driver => 'mysql'
+ -species => 'Homo Sapiens',
+ -group => 'core');
Description: Constructor for a DatabaseConenction. Any adaptors that require
database connectivity should inherit from this class.
Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : thrown if USER or DBNAME are not specified, or if the database
cannot be connected to.
- Caller : Bio::EnsEMBL::DBSQL::DBAdaptor
+ Caller : Bio::EnsEMBL::::Utils::ConfigRegistry ( for newer code using the registry)
+ Bio::EnsEMBL::DBSQL::DBAdaptor ( for old style code)
=cut
sub new {
my $class = shift;
- my ($db,$host,$driver,$user,$password,$port, $inactive_disconnect, $dbconn) =
+ my ($db,$host,$driver,$user,$password,$port, $inactive_disconnect, $dbconn, $species, $group, $dnadb) =
rearrange([qw(DBNAME HOST DRIVER USER PASS PORT
- DISCONNECT_WHEN_INACTIVE DBCONN)], @_);
+ DISCONNECT_WHEN_INACTIVE DBCONN SPECIES GROUP DNADB)], @_);
my $self = {};
bless $self, $class;
+ # make sure the register can find the species name in the alias list as itself.
+
+ if(!defined($species)){
+ $species= "DEFAULT";
+ $group = "core";
+
+ Bio::EnsEMBL::Registry->add_alias($species,$species); #set needed self alias
+
+ my $free=0;
+ my $i = 1;
+ while(!$free){
+ Bio::EnsEMBL::Registry->add_alias($species.$i,$species.$i); #set needed self alias
+ if(!defined(Bio::EnsEMBL::Registry->get_DBAdaptor($species.$i, $group))){
+ $free =1;
+ }
+ else{
+ $i++;
+ }
+ }
+ $species .= $i;
+ }
+
if($dbconn) {
- if($db || $host || $driver || $password || $port || $inactive_disconnect) {
+ if($db || $host || $driver || $password || $port || $inactive_disconnect
+ || $dnadb) {
throw("Cannot specify other arguments when -DBCONN argument used.");
}
@@ -116,14 +152,20 @@ sub new {
$self->password($dbconn->password());
$self->port($dbconn->port());
$self->driver($dbconn->driver());
+ $self->species($dbconn->species());
+ $self->group($dbconn->group());
- $self->connect();
+# $self->connect();
if($dbconn->disconnect_when_inactive()) {
$self->disconnect_when_inactive(1);
}
+ else{
+ $self->connect();
+ }
} else {
+
$db || throw("-DBNAME argument is required.");
$user || throw("-USER argument is required.");
@@ -140,18 +182,37 @@ sub new {
$self->port($port);
$self->driver($driver);
- $self->connect();
+
+# $self->connect();
+
+
+ if($species){
+# print "setting species to $species\n";
+ Bio::EnsEMBL::Registry->add_alias($species,$species);
+ $self->species($species);
+# print "setting species to $species\n";
+ }
+ else{
+ throw("No species specified\n");
+ }
+ if($group){
+ $self->group($group);
+ }
+
if($inactive_disconnect) {
$self->disconnect_when_inactive($inactive_disconnect);
}
+ else{
+ $self->connect();
+ }
- # be very sneaky and actually return a container object which is outside
- # of the circular reference loops and will perform cleanup when all
- # references to the container are gone.
}
- return new Bio::EnsEMBL::Container($self);
+ if(defined $dnadb) {
+ $self->dnadb($dnadb);
+ }
+ return $self;
}
@@ -183,6 +244,9 @@ sub connect {
};
if(!$dbh || $@) {
+ warn("Could not connect to database " . $self->dbname() .
+ " as user " . $self->username() .
+ " using [$dsn] as a locator:\n" . $DBI::errstr);
throw("Could not connect to database " . $self->dbname() .
" as user " . $self->username() .
" using [$dsn] as a locator:\n" . $DBI::errstr);
@@ -332,6 +396,53 @@ sub password {
$self->{_password};
}
+=head2 species
+
+ Arg [1] : (optional) string $arg
+ The new value of the species used by this connection.
+ Example : $host = $db_connection->species()
+ Description: Getter/Setter for the species of to use for
+ this connection. There is currently no point in setting
+ this value after the connection has already been established
+ by the constructor.
+ Returntype : string
+ Exceptions : none
+ Caller : new
+
+=cut
+
+sub species {
+ my ($self, $arg ) = @_;
+ ( defined $arg ) &&
+ ( $self->{_species} = $arg );
+ return $self->{_species};
+}
+
+
+=head2 group
+
+ Arg [1] : (optional) string $arg
+ The new value of the group used by this connection.
+ Example : $host = $db_connection->group()
+ Description: Getter/Setter for the group of to use for
+ this connection. There is currently no point in setting
+ this value after the connection has already been established
+ by the constructor.
+ Returntype : string
+ Exceptions : none
+ Caller : new
+
+=cut
+
+sub group {
+ my ($self, $arg ) = @_;
+ ( defined $arg ) &&
+ ( $self->{_group} = $arg );
+ return $self->{_group};
+}
+
+
+
=head2 disconnect_when_inactive
@@ -356,7 +467,10 @@ sub disconnect_when_inactive {
$self->{'disconnect_when_inactive'} = $val;
if($val) {
$self->disconnect_if_idle();
- } elsif(!$self->db_handle->ping()) {
+ }
+ elsif(!defined($self->db_handle)){
+ $self->connect();
+ }elsif(!$self->db_handle->ping()) {
# reconnect if the connect went away
$self->connect();
}
@@ -433,8 +547,11 @@ sub prepare {
if( ! $string ) {
throw("Attempting to prepare an empty SQL query.");
}
- if( ! defined($self->db_handle) ) {
- throw("Database object has lost its database handle.");
+ if( ! defined($self->db_handle) ) { # No connection to star with now so need to try again.
+ $self->connect();
+ if( ! defined($self->db_handle) ) {
+ throw("Database object has lost its database handle.");
+ }
}
if($self->disconnect_when_inactive() && !$self->db_handle->ping()) {
@@ -476,7 +593,10 @@ sub do {
throw("Attempting to do an empty SQL query.");
}
if( ! defined($self->db_handle) ) {
- throw("Database object has lost its database handle.");
+ $self->connect();
+ if( ! defined($self->db_handle) ) {
+ throw("Database object has lost its database handle.");
+ }
}
if($self->disconnect_when_inactive() && !$self->db_handle->ping()) {
@@ -519,233 +639,13 @@ sub do {
sub disconnect_if_idle {
my $self = shift;
- if($self->db_handle()->{'Kids'} == 0 &&
- !$self->db_handle()->{'InactiveDestroy'}) {
- $self->db_handle->disconnect();
- }
-}
-
-
-=head2 _get_adaptor
-
- Arg [1] : string $module
- the fully qualified of the adaptor module to be retrieved
- Arg [2..n] : (optional) arbitrary list @args
- list of arguments to be passed to adaptors constructor
- Example : $adaptor = $self->_get_adaptor("full::adaptor::name");
- Description: PROTECTED Used by subclasses to obtain adaptor objects
- for this database connection using the fully qualified
- module name of the adaptor. If the adaptor has not been
- retrieved before it is created, otherwise it is retreived
- from the adaptor cache.
- Returntype : Adaptor Object of arbitrary type
- Exceptions : thrown if $module can not be instantiated
- Caller : Bio::EnsEMBL::DBAdaptor
-
-=cut
-
-sub _get_adaptor {
- my( $self, $module, @args) = @_;
-
- my( $adaptor, $internal_name );
-
- #Create a private member variable name for the adaptor by replacing
- #:: with _
-
- $internal_name = $module;
-
- $internal_name =~ s/::/_/g;
-
- unless (defined $self->{'_adaptors'}->{$internal_name}) {
- eval "require $module";
-
- if($@) {
- warning("$module cannot be found.\nException $@\n");
- return undef;
+ if(defined($self->db_handle())){
+ if($self->db_handle()->{'Kids'} == 0 &&
+ !$self->db_handle()->{'InactiveDestroy'}) {
+ $self->db_handle->disconnect();
}
-
- $adaptor = "$module"->new($self, @args);
-
- $self->{'_adaptors'}->{$internal_name} = $adaptor;
}
-
- return $self->{'_adaptors'}->{$internal_name};
}
-
-=head2 add_db_adaptor
-
- Arg [1] : string $name
- the name of the database to attach to this database
- Arg [2] : Bio::EnsEMBL::DBSQL::DBConnection
- the db adaptor to attach to this database
- Example : $db->add_db_adaptor('lite', $lite_db_adaptor);
- Description: Attaches another database instance to this database so
- that it can be used in instances where it is required.
- Returntype : none
- Exceptions : none
- Caller : EnsWeb
-
-=cut
-
-sub add_db_adaptor {
- my ($self, $name, $adaptor) = @_;
-
- unless($name && $adaptor && ref $adaptor) {
- throw('adaptor and name arguments are required');
- }
-
- #avoid circular references and memory leaks
- if($adaptor->isa('Bio::EnsEMBL::Container')) {
- $adaptor = $adaptor->_obj;
- }
-
- $self->{'_db_adaptors'}->{$name} = $adaptor;
-}
-
-
-=head2 remove_db_adaptor
-
- Arg [1] : string $name
- the name of the database to detach from this database.
- Example : $lite_db = $db->remove_db_adaptor('lite');
- Description: Detaches a database instance from this database and returns
- it.
- Returntype : none
- Exceptions : none
- Caller : ?
-
-=cut
-
-sub remove_db_adaptor {
- my ($self, $name) = @_;
-
- my $adaptor = $self->{'_db_adaptors'}->{$name};
- delete $self->{'_db_adaptors'}->{$name};
-
- unless($adaptor) {
- return undef;
- }
-
- return $adaptor;
-}
-
-
-=head2 get_all_db_adaptors
-
- Arg [1] : none
- Example : @attached_dbs = values %{$db->get_all_db_adaptors()};
- Description: returns all of the attached databases as
- a hash reference of key/value pairs where the keys are
- database names and the values are the attached databases
- Returntype : hash reference with Bio::EnsEMBL::DBSQL::DBConnection values
- Exceptions : none
- Caller : Bio::EnsEMBL::DBSQL::ProxyAdaptor
-
-=cut
-
-sub get_all_db_adaptors {
- my ($self) = @_;
-
- unless(defined $self->{'_db_adaptors'}) {
- return {};
- }
-
- return $self->{'_db_adaptors'};
-}
-
-
-
-=head2 get_db_adaptor
-
- Arg [1] : string $name
- the name of the attached database to retrieve
- Example : $lite_db = $db->get_db_adaptor('lite');
- Description: returns an attached db adaptor of name $name or undef if
- no such attached database exists
- Returntype : Bio::EnsEMBL::DBSQL::DBConnection
- Exceptions : none
- Caller : ?
-
-=cut
-
-sub get_db_adaptor {
- my ($self, $name) = @_;
-
- unless($self->{'_db_adaptors'}->{$name}) {
- return undef;
- }
-
- return $self->{'_db_adaptors'}->{$name};
-}
-
-
-#
-# This method is automatically called by the Container DESTROY method to
-# break circular references. Do not call it directly.
-#
-sub deleteObj {
- my $self = shift;
-
- #print STDERR "DBConnection::deleteObj : Breaking circular references:\n";
-
- if(exists($self->{'_adaptors'})) {
- foreach my $adaptor_name (keys %{$self->{'_adaptors'}}) {
- my $adaptor = $self->{'_adaptors'}->{$adaptor_name};
-
- #call each of the adaptor deleteObj methods
- if($adaptor && $adaptor->can('deleteObj')) {
- #print STDERR "\t\tdeleting adaptor\n";
- $adaptor->deleteObj();
- }
-
- #break dbadaptor -> object adaptor references
- delete $self->{'_adaptors'}->{$adaptor_name};
- }
- }
-
- #print STDERR "Cleaning up attached databases\n";
-
- #break dbadaptor -> dbadaptor references
- foreach my $db_name (keys %{$self->get_all_db_adaptors()}) {
- #print STDERR "\tbreaking reference to $db_name database\n";
- $self->remove_db_adaptor($db_name);
- }
-}
-
-
-=head2 DESTROY
-
- Arg [1] : none
- Example : none
- Description: Called automatically by garbage collector. Should
- never be explicitly called. The purpose of this destructor
- is to disconnect any active database connections.
- Returntype : none
- Exceptions : none
- Caller : Garbage Collector
-
-=cut
-
-sub DESTROY {
- my ($obj) = @_;
-
- #print STDERR "DESTROYING DBConnection\n";
-
- my $dbh = $obj->db_handle();
-
- if($dbh) {
- # don't disconnect if InactiveDestroy flag is set, this can really
- # screw up forked processes
- if(!$dbh->{'InactiveDestroy'}) {
- $dbh->disconnect();
- }
- }
-
- $obj->db_handle(undef);
-}
-
-
-
1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProxyAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProxyAdaptor.pm
index 40b227736d..60bcd4e00b 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProxyAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProxyAdaptor.pm
@@ -74,18 +74,6 @@ sub new {
#invoke superclass constructor
my $self = $class->SUPER::new($db);
- unless($primary_adaptor) {
- throw("The primary_adaptor argument is required\n");
- return undef;
- }
-
- #determine the type of adaptor the proxy is filling in for
- $self->{'_proxy_type'} = ref($primary_adaptor);
-
- #strip out fully qualified package name
- $self->{'_proxy_type'} =~ s/.*:://;
-
- $self->{'_primary_adaptor'} = $primary_adaptor;
return $self;
}
@@ -112,7 +100,7 @@ sub new {
sub AUTOLOAD {
my ($self, @args) = @_;
-
+
#determine the method which was called
my $method = $AUTOLOAD;
@@ -128,30 +116,29 @@ sub AUTOLOAD {
return $adaptor->$method(@args);
}
-
+
#
# The request could not be filled by the primary adaptor
# try the same request using all of the attached databases
#
my @databases = values %{$self->db()->get_all_db_adaptors()};
- foreach my $database (@databases) {
-
+ foreach my $adaptor (@databases) {
+
#Try to get the appropriate adaptor from the database
- my $get_adaptor = "get_" . $self->{'_proxy_type'};
- if($database->can($get_adaptor)) {
-
- #Try to invoke the request on the database's adaptor
- my $adaptor = eval "\$database->$get_adaptor";
- if($adaptor->can($method)) {
- return $adaptor->$method(@args);
- }
+ # my $get_adaptor = "get_" . $self->{'_proxy_type'};
+ # if($database->can($get_adaptor)) {
+
+ #Try to invoke the request on the database's adaptor
+ # my $adaptor = eval "\$database->$get_adaptor";
+ if($adaptor->can($method)) {
+ return $adaptor->$method(@args);
}
}
#none of the attached adaptors could fulfill the request either
throw("The requested method $method could not be found in the "
. $self->{'_proxy_type'} . " of the attached databases:" .
- @databases);
+ @databases);
return undef;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm
index 9956afa9d8..f0d8794c6a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm
@@ -39,6 +39,26 @@ use vars '@ISA';
@ISA = qw(Bio::EnsEMBL::DBSQL::ProxyAdaptor);
+sub set_primary{
+ my ($self, $primary_adaptor) = @_;
+
+#
+# For old style code i will have to add primary db later when get is called
+#
+ unless($primary_adaptor) {
+ throw("The primary_adaptor argument is required\n");
+ return undef;
+ }
+#
+# #determine the type of adaptor the proxy is filling in for
+ $self->{'_proxy_type'} = ref($primary_adaptor);
+#
+ #strip out fully qualified package name
+ $self->{'_proxy_type'} =~ s/.*:://;
+
+ $self->{'_primary_adaptor'} = $primary_adaptor;
+#
+}
=head2 fetch_by_Slice
@@ -56,15 +76,19 @@ use vars '@ISA';
sub fetch_all_by_Slice {
my ($self, @args) = @_;
- my $lite_db = $self->db()->get_db_adaptor('lite');
- my $snp_db = $self->db()->get_db_adaptor('SNP');
+ my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');#$self->db()->get_db_adaptor('lite');
+ my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP'); #$self->db()->get_db_adaptor('SNP');
if(defined $lite_db) {
#use the Lite database if it is available
- return $lite_db->get_SNPAdaptor()->fetch_all_by_Slice(@args);
+ my $lite_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
+ $lite_db->species, $lite_db->group ,"lite");
+ return $lite_adaptor->fetch_all_by_Slice(@args);
} elsif(defined $snp_db) {
#use the snp database if it is available
- return $snp_db->get_SNPAdaptor()->fetch_all_by_Slice(@args);
+ my $snp_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
+ $snp_db->species, $snp_db->group ,"SNP");
+ return $snp_adaptor->fetch_all_by_Slice(@args);
}
#There is no core SNPAdaptor so throw an exception if lite and SNP
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 12a87941d3..4c75fedd6c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -1267,7 +1267,7 @@ sub prepare {
my $self = shift;
my $sql = shift;
- return $self->db()->dnadb()->prepare( $sql );
+ return $self->db()->dnadb()->db->prepare( $sql );
}
sub _build_exception_cache {
diff --git a/modules/Bio/EnsEMBL/External/BlastAdaptor.pm b/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
index 7d803c9b76..670de48c82 100644
--- a/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
+++ b/modules/Bio/EnsEMBL/External/BlastAdaptor.pm
@@ -182,6 +182,13 @@ SET chr_name = NULL,
WHERE hsp_id = ?";
+
+sub new_fast{
+ my ($caller,$connection) = @_;
+ my $self = $caller->SUPER::new($connection);
+ return $self;
+}
+
#----------------------------------------------------------------------
=head2 new
@@ -197,7 +204,16 @@ WHERE hsp_id = ?";
sub new {
my $caller = shift;
- my $connection = Bio::EnsEMBL::DBSQL::DBConnection->new(@_);
+ my @tmp = @_;
+ my $con = shift;
+ my $connection;
+
+ if(ref($con) and $con->isa("Bio::EnsEMBL::DBSQL::DBConnection")){
+ $connection = new_fast Bio::EnsEMBL::DBSQL::DBAdaptor('-con' => $con);
+ }
+ else{
+ $connection = Bio::EnsEMBL::DBSQL::DBAdaptor->new(@tmp);
+ }
my $self = $caller->SUPER::new($connection);
return $self;
}
diff --git a/modules/Bio/EnsEMBL/Lite/DBAdaptor.pm b/modules/Bio/EnsEMBL/Lite/DBAdaptor.pm
index 725bab413e..fdd4f366bc 100755
--- a/modules/Bio/EnsEMBL/Lite/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Lite/DBAdaptor.pm
@@ -35,11 +35,14 @@ package Bio::EnsEMBL::Lite::DBAdaptor;
use vars qw(@ISA);
use strict;
+use Bio::EnsEMBL::Registry;
+my $reg = "Bio::EnsEMBL::Registry";
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::Utils::Exception qw(deprecate);
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-@ISA = qw(Bio::EnsEMBL::DBSQL::DBConnection);
+@ISA = qw(Bio::EnsEMBL::DBSQL::DBAdaptor);
@@ -58,7 +61,8 @@ use Bio::EnsEMBL::Utils::Exception qw(deprecate);
sub get_SNPAdaptor {
my $self = shift;
- return $self->_get_adaptor("Bio::EnsEMBL::Lite::SNPAdaptor");
+# return $self->_get_adaptor("Bio::EnsEMBL::Lite::SNPAdaptor");
+ return Bio::EnsEMBL::Registry->get_adaptor($self->db->species(), "lite", "ProxySNP");
}
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
new file mode 100644
index 0000000000..dcb224195f
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -0,0 +1,766 @@
+#
+# Ensembl module for Registry
+#
+# Copyright EMBL/EBI
+##
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::Registry
+
+=head1 SYNOPSIS
+
+$gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Homo Sapiens","core","Gene"))
+
+
+=head1 DESCRIPTION
+
+All Adaptors are stored/registered using this module. This module should then
+be used to get the adaptors needed.
+
+The registry can be loaded from a configuration file. If the enviroment
+variable ENSEMBL_REGISTRY is set then the file pointed to by it is executed.
+If not set then if the file ~/.ensembl_init exists then this will be executed.
+For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm.
+
+The four types of registrys are for db adaptors, dba adaptors, dna adaptors
+and the standard type.
+
+=head2 db
+
+These are registrys for backwards compatibillity and enable the subroutines
+to add other adaptors to connections.
+
+e.g. get_all_db_adaptors, get_db_adaptor, add_db_adaptor, remove_db_adaptor
+are the old DBAdaptor subroutines which are now redirected to the Registry.
+
+So if before we had
+ my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
+
+We now want to change this to
+ my $sfa = Bio::EnsEMBL::Registry->get_db($self->adaptor->db,'blast');
+
+OR preferably if the blast adaptor was set up in configure
+ my $sfa = Bio::EnsEMBL::Registry->get_adaptor("Human","core","blast");
+
+
+=head2 DBA
+
+These are the stores for the DBAdaptors
+
+The Registry will create all the DBConnections needed now if you set up the
+configuration correctly. So instead of the old commands like
+
+my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(....)
+my $exon_adaptor = $db->get_ExonAdaptor;
+
+we should now have just
+
+my $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");
+
+
+=head2 DNA
+
+This is an internal Registry and allows the configuration of a dnadb.
+An example here is to set the est database to get it's dna data from the core database.
+
+## set the est db to use the core for getting dna data.
+#Bio::EnsEMBL::Utils::ConfigRegistry->
+# dnadb_add("Homo Sapiens","core","Homo Sapiens","est");
+
+
+=head2 adaptors
+
+This is the registry for all the general types of adaptors like GeneAdaptor, ExonAdaptor,
+Slice Adaptor etc.
+
+These are accessed by the get_adaptor subroutine i.e.
+
+my $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");
+
+=head1 CONTACT
+
+Post questions to the Ensembl developer list: <ensembl-dev@ebi.ac.uk>
+
+
+=head1 METHODS
+
+=cut
+
+
+package Bio::EnsEMBL::Registry;
+
+use strict;
+
+use Bio::EnsEMBL::DBSQL::MergedAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+
+use vars qw(%registry_register);
+
+$registry_register{'_WARN'} = 0;
+
+
+
+=head2 load_all
+ Will load the registry with the configuration file which is obtained from
+ the first in the following and in that order.
+
+ 1) if an argument is passed to this method this is used as the conf file.
+ 2) If the enviroment variable ENSEMBL_REGISTRY is set this is used.
+ 3) If the file .ensembl_init exist in the home directory it is used
+
+ Arg [1] : (optional) string $arg file to load the registry from
+ Example : Bio::EnsEMBL::Registry->load_all();
+ Returntype : none
+ Exceptions : none
+
+
+=cut
+
+sub load_all{
+ my $class = shift;
+ my $web_reg = shift;
+
+ #$registry_register{'_WARN'} = 0; # default report overwriting
+ if(!defined($registry_register{'seen'})){
+ $registry_register{'seen'}=1;
+ if(defined($web_reg)){
+# print STDERR "Loading conf from site defs file ".$web_reg."\n";
+ unless (my $return = do $web_reg ){
+ throw "Error in Configuration\n $!\n";
+ }
+ # other wise it gets done again by the web initialisation stuff
+ delete $INC{$web_reg};
+ }
+ elsif(defined($ENV{ENSEMBL_REGISTRY}) and -e $ENV{ENSEMBL_REGISTRY}){
+# print STDERR "Loading conf from ".$ENV{ENSEMBL_REGISTRY}."\n";
+ unless (my $return = do $ENV{ENSEMBL_REGISTRY}){
+ throw "Error in Configuration\n $!\n";
+ }
+ }
+ elsif(-e $ENV{HOME}."/.ensembl_init"){
+ do($ENV{HOME}."/.ensembl_init");
+ }
+# else{
+# print STDERR "NO default configuration to load\n";
+# }
+ }
+# else{
+# print STDERR "Already configured???\n";
+# }
+}
+
+=head2 check_if_already_there
+
+ Arg [DBNAME] : string
+ The name of the database to check for.
+ Arg [HOST] : (optional) string
+ The domain name of the database host to check for
+ Arg [PORT] : int
+ The port to check for when connecting to the database
+ Arg [DRIVER] : (optional) string
+ The type of database driver to check for
+
+ Description: Check to see if the database is already stored.
+ Returntype : 0 if not found else the species and group.
+ Exceptions : none
+
+
+=cut
+
+
+sub check_if_already_there{
+ my ($class) = shift;
+
+ my ($dbname,$host,$driver,$port ) =
+ rearrange([qw(DBNAME HOST DRIVER PORT )], @_);
+
+ if(defined($registry_register{'_DBA'})){
+ foreach my $db (@{$registry_register{'_DBA'}}){
+ my $dbc= $db->db();
+ if($dbc->host() eq $host and $dbc->dbname() eq $dbname
+ and $dbc->driver() eq $driver and $dbc->port() eq $port){
+ return ($db->species(),$db->group());
+ }
+ }
+ }
+ return 0;
+}
+
+
+#
+# add ons.
+#
+
+=head2 add_db
+
+ Arg [1] : db to add adaptor to.
+ Arg [2] : name of the name to add the adaptor to in the registry.
+ Arg [3] : The adaptor to be added to the registry.
+ Example : Bio::EnsEMBL::Registry->add_db($db, "lite", $dba);
+ Returntype : none
+ Exceptions : none
+
+=cut
+
+sub add_db{
+ my ($class, $db, $name, $adap) = @_;
+
+ $registry_register{$db->species()}{$db->group()}{'_special'}{$name} = $adap;
+
+}
+
+=head2 remove_db
+
+ Arg [1] : db to remove adaptor from.
+ Arg [2] : name to remove the adaptor from in the registry.
+ Example : my $db = Bio::EnsEMBL::Registry->remove_db($db, "lite");
+ Returntype : adaptor
+ Exceptions : none
+
+=cut
+
+sub remove_db{
+ my ($class, $db, $name) = @_;
+
+ my $ret = $registry_register{$db->species()}{$db->group()}{'_special'}{$name};
+ $registry_register{$db->species()}{$db->group()}{'_special'}{$name} = undef;
+
+ return $ret;
+}
+
+=head2 get_db
+
+ Arg [1] : db to get adaptor from.
+ Arg [2] : name to get the adaptor for in the registry.
+ Example : my $db = Bio::EnsEMBL::Registry->get_db("Human", "core", "lite");
+ Returntype : adaptor
+ Exceptions : none
+
+=cut
+
+sub get_db{
+ my ($class, $db, $name) = @_;
+
+ return $registry_register{$db->species()}{$db->group()}{'_special'}{$name};
+}
+
+=head2 get_all_db_adaptors
+
+ Arg [1] : db to get all the adaptor from.
+ Example : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
+ Returntype : adaptor
+ Exceptions : none
+
+=cut
+
+sub get_all_db_adaptors{
+ my ($class,$db) = @_;
+ my %ret=();
+
+ foreach my $key (keys %{$registry_register{$db->species()}{$db->group()}{'_special'}}){
+ $ret{$key} = $registry_register{$db->species()}{$db->group()}{'_special'}{$key};
+ }
+
+ return \%ret;
+}
+
+
+#
+# DBAdaptors
+#
+
+=head2 add_DBAdaptor
+
+ 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 DBAaptor to be added to the registry.
+ Example : Bio::EnsEMBL::Registry->add_DBAdaptor("Human", "core", $dba);
+ Returntype : none
+ Exceptions : none
+
+=cut
+
+sub add_DBAdaptor{
+ my ($class, $species, $group, $adap) = @_;
+
+ $species = $class->get_alias($species);
+# if(defined($registry_register{$species}{$group}{'_DB'}) && warn_on_duplicates()){
+# warning("Overwriting DBAdaptor in Registry for $species $group $adap\n");
+# }
+
+ $registry_register{$species}{$group}{'_DB'} = $adap;
+
+ if(!defined($registry_register{'_DBA'})){
+ my @list =();
+ push(@list,$adap);
+ $registry_register{'_DBA'}= \@list;
+ }
+ else{
+ push(@{$registry_register{'_DBA'}},$adap);
+ }
+
+}
+
+
+
+=head2 get_DBAdaptor
+
+ Arg [1] : name of the species to get the adaptor for in the registry.
+ Arg [2] : name of the group to get the adaptor for in the registry.
+ Example : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
+ Returntype : DBAdaptor
+ Exceptions : none
+
+=cut
+
+sub get_DBAdaptor{
+ my ($class, $species, $group) = @_;
+
+ $species = $class->get_alias($species);
+
+ if(defined($group)){ # group defined so return standard DB Adaptor
+ return $registry_register{$species}{$group}{'_DB'};
+ }
+ else{ #return a merged db adaptor
+ return new_merged Bio::EnsEMBL::DBSQL::DBAdaptor($species);
+ }
+}
+
+=head2 get_all_DBAdaptors
+
+ Example : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors();
+ Returntype : list of DBAdaptors
+ Exceptions : none
+
+=cut
+
+sub get_all_DBAdaptors{
+ my ($class)=@_;
+
+ return @{$registry_register{'_DBA'}};
+}
+
+#
+# DNA Adaptors
+#
+
+=head2 add_DNAAdaptor
+
+ 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", $dnaAdap);
+ Returntype : none
+ Exceptions : none
+
+=cut
+
+sub add_DNAAdaptor{
+ my ($class, $species, $group, $adap) = @_;
+
+ $species = $class->get_alias($species);
+# if(defined($registry_register{$species}{$group}{'_DNA'}) && warn_on_duplicates()){
+# warning("Overwriting DNAAdaptor in Registry for $species $group $adap\n");
+# }
+
+ $registry_register{$species}{$group}{'_DNA'} = $adap;
+
+}
+
+=head2 get_DNAAdaptor
+
+ Arg [1] : name of the species to get the adaptor for in the registry.
+ Arg [2] : name of the group to get the adaptor for in the registry.
+ Example : $dnaAdap = Bio::EnsEMBL::Registry->get_DNAAdaptor("Human", "core");
+ Returntype : adaptor
+ Exceptions : none
+
+=cut
+
+sub get_DNAAdaptor{
+ my ($class, $species, $group) = @_;
+
+ $species = $class->get_alias($species);
+ return $registry_register{$species}{$group}{'_DNA'};
+}
+
+#
+# General Adaptors
+#
+
+=head2 add_adaptor
+
+ 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] : name of the type to add the adaptor to in the registry.
+ Arg [4] : The DBAaptor to be added to the registry.
+ Arg [5] : (optional) if set okay to overwrite.
+ Example : Bio::EnsEMBL::Registry->add_adaptor("Human", "core", "Gene", $adap);
+ Returntype : none
+ Exceptions : none
+
+
+=cut
+
+sub add_adaptor{
+ my ($class,$species,$group,$type,$adap, $reset)= @_;
+
+ $species = $class->get_alias($species);
+
+#
+# Becouse the adaptors are not stored initially only there class paths when
+# the adaptors are obtained we need to store these instead.
+# It is not necessarily an error if the registry is overwritten without
+# the reset set but it is an indication that we are overwriting a database
+# which should be a warning for now
+#
+
+ if(defined($reset)){ # JUST REST THE HASH VLAUE NO MORE PROCESSING NEEDED
+ $registry_register{$species}{$group}{$type} = $adap;
+ return;
+ }
+ if(defined($registry_register{$species}{$group}{$type})){
+ print STDERR ("Overwriting Adaptor in Registry for $species $group $type\n");
+ $registry_register{$species}{$group}{$type} = $adap;
+ return;
+ }
+ $registry_register{$species}{$group}{$type} = $adap;
+
+
+ if(!defined ($registry_register{$species}{'list'})){
+ my @list =();
+ push(@list,$adap);
+ $registry_register{$species}{'list'}= \@list;
+ }
+ else{
+ push(@{$registry_register{$species}{'list'}},$adap);
+ }
+
+# print STDERR "REGADD $species \t $group \t $type\t to the registry\n";
+
+ if(!defined ($registry_register{$type}{$species})){
+ my @list =();
+ push(@list,$adap);
+ $registry_register{$type}{$species}= \@list;
+ }
+ else{
+ push(@{$registry_register{$type}{$species}},$adap);
+ }
+
+}
+
+
+=head2 set_get_via_dnadb_if_set
+
+ set the flag so that for this type of adaptor the data is obtained
+ from the dna source and not centrally i.e. estgenes where the sequence
+ data is held in the core.
+
+ Arg [1] : name of the species to set flag for.
+ Arg [2] : name of the type to set flag for. (i.e. Sequence)
+ Example : Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set("Human","Sequence");
+ Returntype : none
+ Exceptions : none
+
+
+
+=cut
+
+sub set_get_via_dnadb_if_set{
+ my ($class,$species,$type) = @_;
+
+ $registry_register{$species}{$type}{'DNADB'} = 1;
+}
+
+=head2 get_adaptor
+
+ 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] : name of the type to add the adaptor to in the registry.
+ Example : $adap = Bio::EnsEMBL::Registry->get_adaptor("Human", "core", "Gene");
+ Returntype : adaptor
+ Exceptions : none
+
+=cut
+
+sub get_adaptor{
+ my ($class,$species,$group,$type)= @_;
+
+ $species = $class->get_alias($species);
+
+ #throw in a check to see if we should get the dnadb one and not the normal
+ if(defined($registry_register{$species}{$type}{'DNADB'}) && $class->get_DNAAdaptor($species,$group)){
+ my $dna = $class->get_DNAAdaptor($species,$group);
+ $species = $dna->species();
+ $group = $dna->group();
+ }
+
+ my $ret = $registry_register{$species}{$group}{$type};
+ if(!defined($ret)){
+ throw("COULD NOT FIND ADAPTOR species=$species\tgroup=$group\ttype=$type\n");
+ }
+ if(!ref($ret)){ # not instantiated yet
+ my $dba = $registry_register{$species}{$group}{'_DB'};
+ my $module = $ret;
+ eval "require $module";
+
+ if($@) {
+ warning("$module cannot be found.\nException $@\n");
+ return undef;
+ }
+ my $adap = "$module"->new($dba);
+ Bio::EnsEMBL::Registry->add_adaptor($species, $group, $type, $adap, "reset");
+ $ret = $adap;
+ }
+
+ return $ret;
+}
+
+=head2 get_all_adaptors
+
+ Arg [1] : name of the species to get the adaptors for.
+ Example : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
+ Returntype : list of adaptors
+ Exceptions : none
+
+=cut
+
+sub get_all_adaptors{
+ my ($class,$species)= @_;
+
+ $species = get_alias($species);
+ return $registry_register{$species}{'list'};
+}
+
+
+=head2 get_MergedAdaptor
+
+ Arg [1] : name of the species to get the adaptors for in the registry.
+ Arg [2] : name of the type to get the adaptors for in the registry.
+ Example : $merged = Bio::EnsEMBL::Registry->get_MergedAdaptor("Mouse","Gene");
+ Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
+ Exceptions : none
+
+=cut
+
+sub get_MergedAdaptor{
+ my ($class,$species,$type)=@_;
+
+ $species = $class->get_alias($species);
+ my $ret = new Bio::EnsEMBL::DBSQL::MergedAdaptor();
+ $ret->add_list(@{$registry_register{$type}{$species}});
+
+ return $ret;
+}
+
+=head2 add_alias
+
+ Arg [1] : name of the species to add alias for
+ Arg [2] : name of the alias
+ Example : Bio::EnsEMBL::Registry->add_alias("Homo Sapiens","Human");
+ Description: add alternative name for the species.
+ Returntype : none
+ Exceptions : none
+
+=cut
+
+sub add_alias{
+ my ($class, $species,$key) = @_;
+
+ $registry_register{'_ALIAS'}{$key} = $species;
+}
+
+=head2 get_alias
+
+ Arg [1] : name of the possible alias to get species for
+ Arg [2] : if set will not throw if not found.
+ Example : Bio::EnsEMBL::Registry->get_alias("Human");
+ Description: get proper species name.
+ Returntype : species name
+ Exceptions : if not found and second argument
+
+=cut
+
+sub get_alias{
+ my ($class, $key, $no_throw) = @_;
+
+ if(!defined($registry_register{'_ALIAS'}{$key})){
+ if(defined($no_throw)){
+ return undef;
+ }
+ else{
+ throw("Unknown species $key has it been mistyped??\n");
+ }
+ }
+ return $registry_register{'_ALIAS'}{$key};
+}
+
+#
+# Web specific routines
+#
+
+
+=head2 load_registry_with_web_adaptors
+ Will load the registry with all the Adaptors used in the Web server.
+ Providing Sitedefs and SpeciesDefs can be found on PERL5LIB path.
+
+ Example : Bio::EnsEMBL::Registry->load_registry_with_web_adaptors();
+ Returntype : none
+ Exceptions : Will die if Sitedefs or SpeciesDefs is not found on the
+ PERL5LIB path.
+
+=cut
+
+sub load_registy_with_web_adaptors{
+ my $class = shift;
+
+
+ eval{ require SiteDefs };
+ if ($@){ die "Can't use SiteDefs.pm - $@\n"; }
+ SiteDefs->import(qw(:ALL));
+
+ eval{ require SpeciesDefs };
+ if ($@){ die "Can't use SpeciesDefs.pm - $@\n"; }
+ my $conf = new SpeciesDefs();
+
+}
+
+=head2 set_default_track
+ Sets a flag to say that that this species/group are a default track and do not
+ need to be added as another web track.
+
+ Arg [1] : name of the species to get the adaptors for in the registry.
+ Arg [2] : name of the type to get the adaptors for in the registry.
+ Example : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
+ Returntype : none
+ Exceptions : none
+
+=cut
+
+sub set_default_track{
+ my ($class, $species, $group) = @_;
+
+ $registry_register{'def_track'}{$species}{$group} = 1;
+}
+
+=head2 default_track
+ Check flag to see if this is a default track
+
+ Arg [1] : name of the species to get the adaptors for in the registry.
+ Arg [2] : name of the type to get the adaptors for in the registry.
+ Example : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
+ Returntype : int
+ Exceptions : none
+
+=cut
+
+sub default_track{
+ my ($class, $species, $group) = @_;
+
+ if(defined($registry_register{'def_track'}{$species}{$group})){
+ return 1;
+ }
+
+ return 0;
+}
+
+
+=head2 add_new_tracks
+ Will add new gene tracks to the configuration of the WEB server if they are
+ not of the type default and the configuration already has genes in the display.
+
+ Arg [1] : hash of the default configuration of the web page
+ Returntype : none
+ Exceptions : none
+ Called by : UserConfig.pm
+
+=cut
+
+sub add_new_tracks{
+ my($class, $conf) = @_;
+
+ my $start = 0;
+ my $reg = $class;
+ my $species_reg = $reg->get_alias($conf->{'species'},"nothrow");
+ my $view = $conf->{'type'};
+ if(defined($species_reg)){
+ my $config = $conf->{'general'}->{$view};
+ foreach my $dba ($reg->get_all_DBAdaptors()){
+ # if($dba->species eq $species_reg and !$reg->default_track($dba->species,$dba->group)){
+ if(!$reg->default_track($dba->species,$dba->group)){
+ if($start == 0){
+ if(exists($config->{'vega_transcript_lite'}) and defined($config->{'vega_transcript_lite'}->{'pos'})){
+ $start = $config->{'vega_transcript_lite'}->{'pos'};
+ }
+ elsif(exists($config->{'transcript_lite'}) and defined($config->{'transcript_lite'}->{'pos'})){
+ $start = $config->{'transcript_lite'}->{'pos'};
+ }
+ else{ # no transcripts on this view so do not add track here
+ # print STDERR "no transcript options on this display \n";
+ next;
+ }
+ $start ++;
+ }
+ else{
+ if(exists($config->{'vega_transcript_lite'}) and defined($config->{'vega_transcript_lite'}->{'pos'})){
+ $start++;
+ }
+ elsif(exists($config->{'transcript_lite'}) and defined($config->{'transcript_lite'}->{'pos'})){
+ $start++;
+ }
+ else{ # no transcripts on this view so do not add track here
+ # print STDERR "no transcript options on this display \n";
+ next;
+ }
+ }
+ $reg->_add_new_track( $conf->{'general'}->{$view}, $dba, $start);
+ }
+ }
+ }
+}
+
+
+=head2 _add_new_track
+
+ Arg [1] : hash of the configuration
+ Arg [2] : dbadaptor to use to get track info from
+ Arg [3] : start index to place track in the right place
+ Returntype : none
+ Exceptions : none
+ Called by : add_new_tracks
+
+=cut
+
+sub _add_new_track{
+ my ($class, $config, $dba, $start ) = @_;
+
+
+ my $KEY = $dba->group();
+
+ $config->{$KEY} ={
+ 'on' => "on",
+ 'compact' => 'yes',
+ 'pos' => $start,
+ 'str' => 'b',
+ 'src' => 'all', # 'ens' or 'all'
+ 'available'=> 'species '.$dba->species(),
+ 'dba' => $dba,
+# 'colours' => {$config->{'_colourmap'}->colourSet( 'vega_gene' )},
+ 'glyphset' => 'generic_transcript',
+ 'dep' => 6,
+ };
+
+ push @{ $config->{'_artefacts'} }, $KEY;
+ push @{ $config->{'_settings'}->{'features'}}, [$KEY => $KEY] ;
+
+# [ 'transcript_lite' => "Ensembl Trans." ],
+ return;
+}
+
+
+1;
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index b884541a46..8f8458264c 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -73,6 +73,8 @@ use Bio::EnsEMBL::RepeatMaskedSlice;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::ProjectionSegment;
+use Bio::EnsEMBL::Registry;
+my $reg = "Bio::EnsEMBL::Registry";
# inheritance to Bio::EnsEMBL::Root will eventually be removed
@ISA = qw(Bio::EnsEMBL::Root Bio::PrimarySeqI);
@@ -1307,20 +1309,18 @@ sub get_all_Genes{
return [];
}
- my $db;
+ my $ga;
if($dbtype) {
- $db = $self->adaptor->db->get_db_adaptor($dbtype);
- if(!$db) {
- warning("Don't have db $dbtype returning empty list\n");
+ $ga = $reg->get_adaptor( $self->adaptor()->db()->species(), $dbtype, "Gene" );
+ if(!defined $ga) {
+ warning( "$dbtype genes not available" );
return [];
}
- } else {
- $db = $self->adaptor->db;
+ } else {
+ $ga = $self->adaptor->db->get_GeneAdaptor();
}
- my $ga = $db->get_GeneAdaptor();
-
- return $ga->fetch_all_by_Slice( $self, $logic_name, $load_transcripts);
+ return $ga->fetch_all_by_Slice( $self, $logic_name, $load_transcripts);
}
=head2 get_all_Genes_by_type
diff --git a/modules/Bio/EnsEMBL/Storable.pm b/modules/Bio/EnsEMBL/Storable.pm
index 17f4b62ad9..d1709be997 100644
--- a/modules/Bio/EnsEMBL/Storable.pm
+++ b/modules/Bio/EnsEMBL/Storable.pm
@@ -129,6 +129,9 @@ sub is_stored {
my $self = shift;
my $db = shift;
+ if($db and $db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
+ $db = $db->db();
+ }
if(!$db || !ref($db) || !$db->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
throw('db argument must be a Bio::EnsEMBL::DBSQL::DBConnection');
}
@@ -148,7 +151,7 @@ sub is_stored {
return 0 if (!$adaptor && !$dbID);
- my $cur_db = $adaptor->db();
+ my $cur_db = $adaptor->dbc();
#
# Databases are the same if they share the same port, host and username
diff --git a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
index e40de04da1..82664e603d 100644
--- a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
@@ -726,6 +726,6 @@ sub get_alias{
#
eval{ require Bio::EnsEMBL::Utils::User_defined_load };
-if ($@){ print STDERR "No user defined loads\n"; }
+#if ($@){ print STDERR "No user defined loads\n"; }
1;
--
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