Bio::EnsEMBL::Utils::ConfigRegistry->load_core($dba);

  my ( $class, @args ) = @_;

  my ( $species, $aliases ) = rearrange( [qw(SPECIES ALIAS)], @args );

  # Make sure it exists itself
  Bio::EnsEMBL::Registry->add_alias( $species, $species );

  if ( defined($aliases) ) {
    foreach my $ali (@$aliases) {
      Bio::EnsEMBL::Registry->add_alias( $species, $ali );
    }
  }
}

#
# overwrite/load new types. Done this way to enable no changes to CVS for
# external users. External users should add there own "GROUPS" in the file
# User_defined_load.
#

eval{ require Bio::EnsEMBL::Utils::User_defined_load };

1;

  my ( $species, $group ) = @_;

  $reg->add_alias( $species, $species );

  my $i    = 0;
  my $free = 0;

  while ( !$free ) {
    if ( $i == 0 ) {
      if ( !defined( $reg->get_DBAdaptor( $species, $group ) ) ) {
        $free = 1;
        $i    = "";
      } else {
        $i = 1;
      }
    } else {
      # set needed self alias
      $reg->add_alias( $species . $i, $species . $i );

      if ( !defined( $reg->get_DBAdaptor( $species . $i, $group ) ) ) {
        $free = 1;
      } else {
        $i++;
      }
    }
  }

  $species .= $i;
  return ($species);
} ## end sub find_unique_species

  my ($dba) = @_;
  my $config_sub;

# at some point we hope to set the group in the DBadaptor
# hence this long check etc should be simpler

  if($dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('compara');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_compara; 
  }
  elsif($dba->isa('Bio::EnsEMBL::Lite::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('lite');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_lite;
  }
  elsif($dba->isa('Bio::EnsEMBL::External::BlastAdaptor')){
    if(!defined($dba->group())){
      $dba->group('blast');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_blast;
  }
  elsif($dba->isa('Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('SNP');
    } 
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_SNP;
  }
  elsif($dba->isa('Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('pipeline');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_pipeline;
  }
  elsif($dba->isa('Bio::EnsEMBL::Hive::DBSQL::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('hive');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_hive;
  }
  elsif($dba->isa('Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('haplotype');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_haplotype;    
  }
  elsif($dba->isa('Bio::EnsEMBL::Variation::DBSQL::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('variation');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_variation;
  }
  elsif($dba->isa('Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor')){
    if(!defined($dba->group())){
      $dba->group('funcgen');
  }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen;
  }
  elsif ( $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('ontology');
    }
    $config_sub =\& Bio::EnsEMBL::Utils::ConfigRegistry::load_ontology;
  }
  elsif($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
    #vega uses the core DBAdaptor so test if vega is in the dbname
    if(!defined($dba->group())){
      $dba->group('core');
    }
    if($dba->group eq "estgene"){
      $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_estgene;
     }
    elsif($dba->group eq "otherfeatures"){
      $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_otherfeatures;
     }
    elsif($dba->group eq "vega"){
      $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_vega;
     }
    else{
      $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_core;
    }
  }
  else{
    # none standard DBA adaptor 
    if(!defined($dba->group())){
      $dba->group('none_standard');
    }
    $config_sub =\&  Bio::EnsEMBL::Utils::ConfigRegistry::load_and_attach_dnadb_to_core;
    #    throw("Unknown DBAdaptor type $dba\n");
  }


  # return if the connection and species, group are the same


  if(defined($dba->species)){
    my $db_reg = $reg->get_DBAdaptor($dba->species,$dba->group);
    if(defined($db_reg)){
      if($dba->dbc->equals($db_reg->dbc)){
	return $db_reg;
      }
      else{
	warn "WARN: Species and group same for two seperate databases\nModify species name for one of these\n";
	$dba->species(find_unique_species($dba->species,$dba->group));
      }
    }
  }
  else{  # no species 
    my @db_reg = @{$reg->get_all_DBAdaptors_by_connection($dba->dbc)};
    foreach my $db_adaptor (@db_reg){
      if($db_adaptor->group eq $dba->group){ # found same db connection and group
	return $db_adaptor;
      }
    }
    $dba->species(find_unique_species("DEFAULT",$dba->group));      
    if($dba->species ne "DEFAULT"){
      warn "WARN: For multiple species use species attribute in DBAdaptor->new\n" 
    }
  }


  Bio::EnsEMBL::Registry->add_DBAdaptor($dba->species(), $dba->group(), $dba);

  #call the loading subroutine. (add the adaptors to the DBAdaptor)
  &{$config_sub}($dba);
   
  return $dba;

 load_adaptors(@_)

  my ($dba) = @_;

  my %pairs = %{ $dba->get_available_adaptors() };

  while ( my ( $key, $value ) = each(%pairs) ) {
    Bio::EnsEMBL::Registry->add_adaptor( $dba->species(), $dba->group(),
      $key, $value );
  }

  my ($dba) = @_;

  load_adaptors($dba);
  $reg->add_DNAAdaptor( $dba->species(), $dba->group(), $dba->species(),
    'core' );

 load_adaptors(@_)

 load_and_attach_dnadb_to_core(@_)

 load_and_attach_dnadb_to_core(@_)

 load_adaptors(@_)

 load_adaptors(@_)

 load_adaptors(@_)

 load_adaptors(@_)

 load_and_attach_dnadb_to_core(@_)

 load_adaptors(@_)

 load_and_attach_dnadb_to_core(@_)

 load_and_attach_dnadb_to_core(@_)

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

  Arg [1]    : DBAdaptor with DBConnection alredy attached
  Returntype : DBAdaptor;
  Exceptions : none