Bio::EnsEMBL Registry
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Summary
Bio::EnsEMBL::Registry
Package variables
Privates (from "my" definitions)
%group2adaptor = ( 'blast' => 'Bio::EnsEMBL::External::BlastAdaptor', 'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor', 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'estgene' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'funcgen' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor', 'haplotype' => 'Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor', 'hive' => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor', 'lite' => 'Bio::EnsEMBL::Lite::DBAdaptor', 'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'pipeline' => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor', 'snp' => 'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor', 'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor', 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', )
$API_VERSION = 54
Included modules
Bio::EnsEMBL::DBSQL::DBAdaptor
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::ConfigRegistry
Bio::EnsEMBL::Utils::Exception qw ( deprecate throw warning )
DBI
Synopsis
  use Bio::EnsEMBL::Registry;

  my $registry = 'Bio::EnsEMBL::Registry';

  $registry->load_all("configuration_file");

  $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
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 using the load_all
method.
If a filename is passed to load_all then this is used. Else if the
enviroment variable ENSEMBL_REGISTRY is set to the name on an existing
configuration file, then this is used. Else if the file .ensembl_init
in your home directory exist, it is used.
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm. This
will then be passed on to load_all.
The registry can also be loaded via the method load_registry_from_db
which given a database host will load the latest versions of the Ensembl
databases from it.
The four types of registries are for db adaptors, dba adaptors, dna
adaptors and the standard type. These are registries for backwards compatibility 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_adaptor( "human", "core", "blast" );
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" );
This is an internal Registry and allows the configuration of a dnadb.
An example here is to set the est database to get its 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" );
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" );
Methods
add_DBAdaptorDescriptionCode
add_DNAAdaptorDescriptionCode
add_adaptorDescriptionCode
add_aliasDescriptionCode
add_dbDescriptionCode
add_new_tracksDescriptionCode
alias_existsDescriptionCode
change_accessDescriptionCode
clearDescriptionCode
default_trackDescriptionCode
disconnect_allDescriptionCode
find_and_add_aliasesDescriptionCode
get_DBAdaptorDescriptionCode
get_DNAAdaptorDescriptionCode
get_adaptorDescriptionCode
get_aliasDescriptionCode
get_all_DBAdaptorsDescriptionCode
get_all_DBAdaptors_by_connectionDescriptionCode
get_all_DBAdaptors_by_dbnameDescriptionCode
get_all_adaptorsDescriptionCode
get_all_db_adaptorsDescriptionCode
get_dbDescriptionCode
get_species_and_object_typeDescriptionCode
load_allDescriptionCode
load_registry_from_dbDescriptionCode
load_registry_from_urlDescriptionCode
load_registry_with_web_adaptors
No description
Code
no_version_checkDescriptionCode
remove_DBAdaptorDescriptionCode
remove_dbDescriptionCode
reset_DBAdaptorDescriptionCode
set_default_trackDescriptionCode
set_disconnect_when_inactiveDescriptionCode
software_versionDescriptionCode
version_checkDescriptionCode
Methods description
add_DBAdaptorcode    nextTop
  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
  caller     : internal
  Status     : Stable
add_DNAAdaptorcodeprevnextTop
  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 species to get the dna from
  Arg [4]    : name of the group to get the dna from
  Example    : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "estgene", "Human", "core");
  Returntype : none
  Exceptions : none
  Status     : Stable
add_adaptorcodeprevnextTop
  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", $adap);
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable
add_aliascodeprevnextTop
  Arg [1]    : name of the species to add alias for
  Arg [2]    : name of the alias
  Example    : Bio::EnsEMBL::Registry->add_alias("Homo Sapiens","Human");
  Description: add alternative name for the species.
  Returntype : none
  Exceptions : none
  Status     : Stable
add_dbcodeprevnextTop
  Arg [1]    : db (DBAdaptor) to add adaptor to.
  Arg [2]    : name of the name to add the adaptor to in the registry.
  Arg [3]    : The adaptor to be added to the registry.
  Example    : Bio::EnsEMBL::Registry->add_db($db, "lite", $dba);
  Returntype : none
  Exceptions : none
  Status     : At Risk.
             : This is here for backwards compatibility only and may
             : be removed eventually.  Solution is to make sure the
             : db and the adaptor have the same species and the call
             : is then no longer needed.
add_new_trackscodeprevnextTop
  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
  Status     : At Risk.
alias_existscodeprevnextTop
  Arg [1]    : name of the possible alias to get species for
  Example    : Bio::EnsEMBL::Registry->alias_exists("Human");
  Description: does the species name exist.
  Returntype : 1 if exists else 0
  Exceptions : none
  Status     : Stable
change_accesscodeprevnextTop
  Will change the username and password for a set of databases.
  if host,user or database names are missing then these are not checked.
  So for example if you do not specify a database then ALL databases on
  the specified  host and port will be changed.

  Arg [1]    : name of the host to change access on
  Arg [2]    : port number to change access on
  Arg [3]    : name of the user to change access on
  Arg [4]    : name of the database to change access on
  Arg [5]    : name of the new user
  Arg [6]    : new password

  Example    : Bio::EnsEMBL::Registry->get_alias("Human");
  Description: change username and password on one or more databases
  Returntype : none
  Exceptions : none
  Status     : Stable
clearcodeprevnextTop
 Will clear the registry and disconnect from all databases.

  Example    : Bio::EnsEMBL::Registry->clear();
  Returntype : none
  Exceptions : none
  Status     : Stable
default_trackcodeprevnextTop
  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
  Status     : At Risk.
disconnect_allcodeprevnextTop
  Example    : Bio::EnsEMBL::Registry->disconnect_all();
  Description: disconnect from all the databases.
  Returntype : none
  Exceptions : none
  Status     : Stable
find_and_add_aliasescodeprevnextTop
  Arg [DBH]     : (optional) DBI handle
                  A connected DBI database handle.  Used instead
                  of the database handles stored in the DBAdaptor
                  objects.  Bypasses the use of MetaContainer.

  Arg [ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor
                  The adaptor to use to retrieve aliases from.

  Arg [GROUP]   : (optional) string
                  The group you want to find aliases for. If not
                  given assumes all types.

  Arg [HANDLE]  : (optional) DBI database handle
                  A connected database handle to use instead of the
                  database handles stored in the DBAdaptors.  Bypasses
                  the use of MetaContainer.

  Example       : Bio::EnsEMBL::Registry->find_and_add_aliases(
                    -ADAPTOR => $dba,
                    -GROUP   => 'core'
                  );

  Description   : Looks in the meta container for each database for
                  an entry called "species.alias".  If any are found
                  then the species adaptor is registered to that
                  set of aliases.  This can work across any adaptor
                  which has a MetaContainer.  If no MetaContainer
                  can be returned from a given adaptor then no alias
                  searching is performed.

  Return type   : none
  Exceptions    : none
  Status        : Stable
get_DBAdaptorcodeprevnextTop
  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
  Status     : Stable
get_DNAAdaptorcodeprevnextTop
  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
  Status     : Stable
get_adaptorcodeprevnextTop
  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
  Status     : Stable
get_aliascodeprevnextTop
  Arg [1]    : name of the possible alias to get species for
  Example    : Bio::EnsEMBL::Registry->get_alias("Human");
  Description: get proper species name.
  Returntype : species name
  Exceptions : none
  Status     : Stable
get_all_DBAdaptorscodeprevnextTop
  Arg [SPECIES]: (optional) string 
                  species name to get adaptors for
  Arg [GROUP]  : (optional) string 
                  group name to get adaptors for
  Example      : 
                @dba =
                  @{ Bio::EnsEMBL::Registry->get_all_DBAdaptors() };

                @human_dbas =
                  @{ Bio::EnsEMBL::Registry->get_all_DBAdaptors(
                    -species => 'human'
                  ) };

  Returntype   : list of DBAdaptors
  Exceptions   : none
  Status       : Stable
get_all_DBAdaptors_by_connectioncodeprevnextTop
  Arg [1]    : DBConnection used to find DBAdaptors
  Returntype : reference to list of DBAdaptors
  Exceptions : none
  Example    : @dba = @{ Bio::EnsEMBL::Registry
                  ->get_all_DBAdaptors_by_connection($dbc) };
  Status     : Stable
get_all_DBAdaptors_by_dbnamecodeprevnextTop
  Arg [1]    : string, name of database
  Returntype : reference to list of DBAdaptors
  Exceptions : none
  Example    : @dba = @{ Bio::EnsEMBL::Registry
                  ->get_all_DBAdaptors_by_dbname($dbname) };
  Status     : Stable
get_all_adaptorscodeprevnextTop
  Arg [SPECIES] : (optional) string 
                  species name to get adaptors for
  Arg [GROUP] : (optional) string 
                  group name to get adaptors for
  Arg [TYPE] : (optional) string 
                  type to get adaptors for
  Example    : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
  Returntype : ref to list of adaptors
  Exceptions : none
  Status     : Stable
get_all_db_adaptorscodeprevnextTop
  Arg [1]    : db (DBAdaptor) to get all the adaptors from.
  Example    : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
  Returntype : adaptor
  Exceptions : none
  Status     : At Risk.
             : This is here for backwards compatibility only and
             : may be removed eventually.  Solution is to make
             : sure the dbs all have the same species then call
             : get_all_DBAdaptors(-species => "human");
get_dbcodeprevnextTop
  Arg [1]    : db (DBAdaptor) 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
  Status     : At Risk.
             : This is here for backwards compatibility only and may
             : be removed eventually.  Solution is to make sure the
             : db and the adaptor have the same species then call
             : get_DBAdaptor instead.
get_species_and_object_typecodeprevnextTop
  
  get the species, ensembl type (Gene, Transcript , Translation or Exon) 
  and database type (core, vega, otherfeatures) for a given stable_id
  
  Arg[1]     : stable_id to find species and ensembl type for.
  Arg[2]     : (optional) integer. force searching of other databases that do not have a set format
               for the stable_id by connecting to the databases and trying to retrieve each of the
               ensembl object fetching using the stabke_id.
  Example    : my ($species, $type, $db_type) = Bio::EnsEMBL::Registry->get_species_and_object_type(ENST00000326632);
  Returntype : array. consisting of the species name, ensembl type and database type (core,vega,otherfeatures). undef, undef, undef returned if not found
  Exceptions : none
  Status     : At Risk.
load_allcodeprevnextTop
 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
     name of the configuration file to read.

  2) If the enviroment variable ENSEMBL_REGISTRY is set, this is
     used as the name of the configuration file to read.

  3) If the file .ensembl_init exist in the home directory, it is
     used as the configuration file.

  Arg [1]    : (optional) string
               Name of file to load the registry from.

  Arg [2]    : (optional) integer
               If not 0, will print out all information.

  Arg [3]    : (optional) integer
               If not 0, the database connection will not be
               cleared, if 0 or if not set the database connections
               will be cleared (this is the default).

  Arg [4]:     (optional) boolean
               This option will turn off caching for slice features,
               so, every time a set of features is retrieved,
               they will come from the database instead of the
               cache.  This option is only recommended for advanced
               users, specially if you need to store and retrieve
               features.  It might reduce performance when querying
               the database if not used properly.  If in doubt, do
               not use it or ask in ensembl-dev.

  Example    : Bio::EnsEMBL::Registry->load_all();
  Returntype : none
  Exceptions : none
  Status     : Stable
load_registry_from_dbcodeprevnextTop
  Arg [HOST] : string
                The domain name of the database host to connect to.

  Arg [USER] : string
                The name of the database user to connect with.

  Arg [PASS] : (optional) string
                The password to be used to connect to the database.

  Arg [PORT] : (optional) integer
                The port to use when connecting to the database.

  Arg [VERBOSE]: (optional) boolean
                Whether to print database messages.

  Arg [DB_VERSION]: (optional) integer
                By default, only databases corresponding to this API
                version are loaded. This allows the script to use
                databases from another version although it might not
                work properly.  This option should only be used for
                production or testing purposes and if you really
                know what you are doing.

  Arg [WAIT_TIMEOUT]: (optional) integer
                Time in seconds for the wait timeout to happen.
                Time after which the connection is deleted if not
                used.  By default this is 28800 (8 hours), so set
                this to greater than this if your connection are
                getting deleted.  Only set this if you are having
                problems and know what you are doing.

   Arg [-NO_CACHE]: (optional) int 1
                This option will turn off caching for slice
                features, so, every time a set of features is
                retrieved, they will come from the database instead
                of the cache.  This option is only recommended for
                advanced users, specially if you need to store and
                retrieve features.  It might reduce performance when
                querying the database if not used properly.  If in
                doubt, do not use it or ask in ensembl-dev.

  Example : load_registry_from_db(
              -host    => 'ensembldb.ensembl.org',
              -user    => 'anonymous',
              -verbose => '1'
            );

  Description: Will load the correct versions of the ensembl
               databases for the software release it can find on a
               database instance into the registry.  Also adds a set
               of standard aliases.

  Exceptions : None.
  Status     : Stable
load_registry_from_urlcodeprevnextTop
  Arg [1] : string $url
  Arg [2] : (optional) integer
            If not 0, will print out all information.
  Arg [3] : (optional) integer
          This option will turn off caching for slice features,
          so, every time a set of features is retrieved, they
          will come from the database instead of the cache. This
          option is only recommended for advanced users, specially
          if you need to store and retrieve features. It might
          reduce performance when querying the database if not used
          properly. If in doubt, do not use it or ask in ensembl-dev

  Example : load_registry_from_url(
            'mysql://anonymous@ensembldb.ensembl.org:3306');

  Description: Will load the correct versions of the ensembl
               databases for the software release it can find on
               a database instance into the registry. Also adds
               a set of standard aliases. The url format is:
               mysql://[[username][:password]@]hostname[:port].  You
               can also request a specific version for the databases
               by adding a slash and the version number but your
               script may crash as the API version won't match the
               DB version.

  Exceptions : None.
  Status     : Stable
no_version_checkcodeprevnextTop
  
  getter/setter for whether to run the version checking
  
  Arg[0]     : (optional) int
  Returntype : int or undef if not set
  Exceptions : none
  Status     : At Risk.
remove_DBAdaptorcodeprevnextTop
  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->remove_DBAdaptor("Human", "core");
  Returntype : none
  Exceptions : none
  Status     : At risk
remove_dbcodeprevnextTop
  Arg [1]    : db (DBAdaptor) 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
  Status     : At Risk.
             : This is here for backwards compatibility only and may
             : be removed eventually.  Solution is to make sure the
             : db and the adaptor have the same species and the call
             : is then no longer needed.
reset_DBAdaptorcodeprevnextTop
  Arg [1]:     string - species e.g. homo_sapiens
  Arg [2]:     string - DB group e.g. core
  Arg [3]:     string - new dbname
  Args [4-7]:  string - optional DB parameters, defaults to current db params if omitted
  Arg [8]:     hashref - Hash ref of additional parameters e.g. eFG dnadb params for auto selecting dnadb
  Usage :      $reg->reset_registry_db( 'homo_sapiens', 'core',
                  'homo_sapiens_core_37_35j' );
  Description: Resets a DB within the registry.
  Exceptions:  Throws if mandatory params not supplied
               Throws if species name is not already seen by the registry
               Throws if no current DB for species/group available
  Status :     At risk
set_default_trackcodeprevnextTop
  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
  Status     : At Risk.
set_disconnect_when_inactivecodeprevnextTop
  Example    : Bio::EnsEMBL::Registry->set_disconnect_when_inactive();
  Description: Set the flag to make sure that the database connection is dropped if
               not being used on each database.
  Returntype : none
  Exceptions : none
  Status     : Stable
software_versioncodeprevnextTop
  
  get the software version.
  
  Args       : none
  ReturnType : int
  Status     : At Risk
version_checkcodeprevnextTop
  
  run the database/API code version check for a DBAdaptor
  
  Arg[0]     : DBAdaptor to check
  Returntype : int 1 if okay, 0 if not the same 
  Exceptions : none
  Status     : At Risk.
Methods code
add_DBAdaptordescriptionprevnextTop
sub add_DBAdaptor {
  my ( $class, $species, $group, $adap ) = @_;

  if ( !( $class->alias_exists($species) ) ) {
    $class->add_alias( $species, $species );
  }

  $species = $class->get_alias($species);

  $registry_register{$species}{ lc($group) }{'_DB'} = $adap;

  if ( !defined( $registry_register{'_DBA'} ) ) {
    my @list = ();
    push( @list, $adap );
    $registry_register{'_DBA'} =\@ list;
  } else {
    push( @{ $registry_register{'_DBA'} }, $adap );
  }
}
add_DNAAdaptordescriptionprevnextTop
sub add_DNAAdaptor {
  my ( $class, $species, $group, $dnadb_species, $dnadb_group ) = @_;

  $species       = $class->get_alias($species);
  $dnadb_species = $class->get_alias($dnadb_species);
  if ( $dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
    deprecated("");
  } else {
    $registry_register{$species}{ lc($group) }{'_DNA'} = $dnadb_group;
    $registry_register{$species}{ lc($group) }{'_DNA2'} =
      $dnadb_species;
  }
}
add_adaptordescriptionprevnextTop
sub add_adaptor {
  my ( $class, $species, $group, $type, $adap, $reset ) = @_;

  $species = $class->get_alias($species);

  # Since the adaptors are not stored initially, only their 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 VALUE NO MORE PROCESSING NEEDED
    $registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
    return;
  }
  if (
    defined( $registry_register{$species}{ lc($group) }{ lc($type) } ) )
  {
  # print STDERR (
  #      "Overwriting Adaptor in Registry for $species $group $type\n");
    $registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
    return;
  }
  $registry_register{$species}{ lc($group) }{ lc($type) } = $adap;

  if ( !defined( $registry_register{$species}{'list'} ) ) {
    $registry_register{$species}{'list'} = [$type];
  } else {
    push( @{ $registry_register{$species}{'list'} }, $type );
  }

  if ( !defined( $registry_register{ lc($type) }{$species} ) ) {
    $registry_register{ lc($type) }{$species} = [$type];
  } else {
    push( @{ $registry_register{ lc($type) }{$species} }, $adap );
  }

} ## end sub add_adaptor
}
add_aliasdescriptionprevnextTop
sub add_alias {
  my ($class, $species,$key) = @_;

  $registry_register{'_ALIAS'}{lc($key)} = lc($species);
}
add_dbdescriptionprevnextTop
sub add_db {
  my ( $class, $db, $name, $adap ) = @_;

  if ( lc( $db->species() ) ne lc( $adap->species ) ) {
    $registry_register{ lc( $db->species() ) }{ lc( $db->group() ) }
      {'_special'}{ lc($name) } = $adap;
  }
}
add_new_tracksdescriptionprevnextTop
sub add_new_tracks {
  my($class, $conf, $pos) = @_;

  my $start = 0;
  my $reg = $class;
  my $species_reg = $reg->get_alias($conf->{'species'},"nothrow");
  my %pars;
#  print STDERR "Species $species_reg check for default tracks\n";
  if(defined($species_reg)){
    foreach my $dba (@{$reg->get_all_DBAdaptors()}){
      if(!$reg->default_track($dba->species,$dba->group)){
	$pars{'available'} = "species ".$reg->get_alias($dba->species());
	$pars{'db_alias'} = $dba->group();
#	print STDERR "Adding new track for ".$dba->species."\t".$dba->group."\n";
	$conf->add_new_track_generictranscript('',$dba->group(), "black",$pos,%pars);
	$pos++;
      }
    }
  }
  return $pos;
}
alias_existsdescriptionprevnextTop
sub alias_exists {
  my ($class, $key) = @_;

  if(defined($registry_register{'_ALIAS'}{lc($key)})){
    return 1;
  }
  return 0;
}
change_accessdescriptionprevnextTop
sub change_access {
my $self = shift;
    my ($host,$port,$user,$dbname,$new_user,$new_pass) = @_;
    foreach my $dba ( @{$registry_register{'_DBA'}}){
	my $dbc = $dba->dbc;
	if((!defined($host) or $host eq $dbc->host) and
	   (!defined($port) or $port eq $dbc->port) and
	   (!defined($user) or $user eq $dbc->username) and
	   (!defined($dbname) or $dbname eq $dbc->dbname)){
	    if($dbc->connected()){
		$dbc->db_handle->disconnect();
		$dbc->connected(undef);
	    }
	    # over write the username and password
	    $dbc->username($new_user);
	    $dbc->password($new_pass);
	}
    }
}
cleardescriptionprevnextTop
sub clear {
  my ($self);
  
  foreach my $dba (@{$registry_register{'_DBA'}}){
    if($dba->dbc->connected){
      $dba->dbc->db_handle->disconnect();
    }
  }
  %registry_register = ();
}

#
# db adaptors. (for backwards compatibility)
#
}
default_trackdescriptionprevnextTop
sub default_track {
  my ($class, $species, $group) = @_;  

  $species = get_alias($species);
  if(defined($registry_register{'def_track'}{$species}{lc($group)})){
    return 1;
  }
  
  return 0;
}
disconnect_alldescriptionprevnextTop
sub disconnect_all {
  foreach my $dba ( @{get_all_DBAdaptors()||[]} ){
    my $dbc = $dba->dbc;
    next unless $dbc;
    # Disconnect if connected
    $dbc->disconnect_if_idle() if $dbc->connected();
  }
}
find_and_add_aliasesdescriptionprevnextTop
sub find_and_add_aliases {
  my $class = shift @_;

  my ( $adaptor, $group, $dbh ) =
    rearrange( [qw(ADAPTOR GROUP HANDLE)], @_ );

  my @dbas;
  if ( defined($adaptor) ) {
    @dbas = ($adaptor);
  } else {
    @dbas = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) };
  }

  foreach my $dba (@dbas) {
    my @aliases;
    my $species = $dba->species();

    if ( defined($dbh) ) {
      my $dbname = $dba->dbc()->dbname();
      my $sth    = $dbh->prepare(
        sprintf(
          "SELECT meta_value FROM %s.meta "
            . "WHERE meta_key = 'species.alias' "
            . "AND species_id = ?",
          $dbh->quote_identifier($dbname) ) );

      # Execute, and don't care about errors (there will be errors for
      # databases without a 'meta' table, such as ensembl_ontology_NN).
      $sth->{'PrintError'} = 0;
      $sth->{'RaiseError'} = 0;
      if ( !$sth->execute( $dba->species_id() ) ) { next }
      $sth->{'PrintError'} = $dbh->{'PrintError'};
      $sth->{'RaiseError'} = $dbh->{'RaiseError'};

      my $alias;
      $sth->bind_columns(\$ alias );
      while ( $sth->fetch() ) {
        push( @aliases, $alias );
      }
    } else {
      my $meta_container = eval { $dba->get_MetaContainer() };

      if ( defined($meta_container) ) {
        @aliases =
          @{ $meta_container->list_value_by_key('species.alias') };
      }

      # Need to disconnect so we do not spam the MySQL servers trying to
      # get aliases.  Can only call disonnect if dbc was defined.
      if ( defined( $dba->dbc() ) ) {
        $dba->dbc()->disconnect_if_idle();
      }
    }

    foreach my $alias (@aliases) {
      $class->add_alias( $species, $alias );
    }
  } ## end foreach my $dba (@dbas)

} ## end sub find_and_add_aliases


#
# Web specific routines
#
}
get_DBAdaptordescriptionprevnextTop
sub get_DBAdaptor {
  my ( $class, $species, $group ) = @_;

  $species = $class->get_alias($species);

  return $registry_register{$species}{ lc($group) }{'_DB'};
}
get_DNAAdaptordescriptionprevnextTop
sub get_DNAAdaptor {
  my ( $class, $species, $group ) = @_;

  $species = $class->get_alias($species);
  my $new_group   = $registry_register{$species}{ lc($group) }{'_DNA'};
  my $new_species = $registry_register{$species}{ lc($group) }{'_DNA2'};

  if ( defined $new_group ) {
    return $class->get_DBAdaptor( $new_species, $new_group );
  }

  return undef;
}

#
# General Adaptors
#
}
get_adaptordescriptionprevnextTop
sub get_adaptor {
  my ( $class, $species, $group, $type ) = @_;

  $species = $class->get_alias($species);

  my %dnadb_adaptors = (
    'sequence'                 => 1,
    'assemblymapper'           => 1,
    'karyotypeband'            => 1,
    'repeatfeature'            => 1,
    'coordsystem'              => 1,
    'assemblyexceptionfeature' => 1
  );

  ## warn "$species, $group, $type";

  $type = lc($type);

  my $dnadb_group = $registry_register{$species}{ lc($group) }{'_DNA'};

  if ( defined($dnadb_group)
    && defined( $dnadb_adaptors{ lc($type) } ) )
  {
    $species = $registry_register{$species}{ lc($group) }{'_DNA2'};
    $group   = $dnadb_group;
  }

  my $ret = $registry_register{$species}{ lc($group) }{ lc($type) };
  if ( !defined($ret) ) { return undef }
  if ( ref($ret) )      { return $ret }

  # Not instantiated yet

  my $dba    = $registry_register{$species}{ lc($group) }{'_DB'};
  my $module = $ret;

  eval "require $module";
  if ($@) {
    warning("'$module' cannot be found.\nException $@\n");
    return undef;
  }

  if (
    !defined( $registry_register{$species}{ lc($group) }{'CHECKED'} ) )
  {
    $registry_register{$species}{ lc($group) }{'CHECKED'} = 1;
    $class->version_check($dba);
  }

  my $adap = "$module"->new($dba);
  Bio::EnsEMBL::Registry->add_adaptor( $species, $group, $type, $adap,
    'reset' );
  $ret = $adap;

  return $ret;
} ## end sub get_adaptor
}
get_aliasdescriptionprevnextTop
sub get_alias {
  my ($class, $key) = @_;

  if(!defined($registry_register{'_ALIAS'}{lc($key)})){
    return $key;
  }
  return $registry_register{'_ALIAS'}{lc($key)};
}
get_all_DBAdaptorsdescriptionprevnextTop
sub get_all_DBAdaptors {
  my ( $class, @args ) = @_;

  my ( $species, $group ) = rearrange( [qw(SPECIES GROUP)], @args );

  if ( defined($species) ) { $species = $class->get_alias($species) }

  my @ret;
  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
    if ( ( !defined($species) || lc($species) eq lc( $dba->species() ) )
      && ( !defined($group) || lc($group) eq lc( $dba->group() ) ) )
    {
      push( @ret, $dba );
    }
  }

  return\@ ret;
}
get_all_DBAdaptors_by_connectiondescriptionprevnextTop
sub get_all_DBAdaptors_by_connection {
  my ( $self, $dbc_orig ) = @_;

  my @return;

  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
    my $dbc = $dba->dbc();

    if (    defined($dbc)
         && $dbc->can('equals')
         && $dbc->equals($dbc_orig) )
    {
      push( @return, $dba );
    }
  }

  return\@ return;
}
get_all_DBAdaptors_by_dbnamedescriptionprevnextTop
sub get_all_DBAdaptors_by_dbname {
  my ( $self, $dbname ) = @_;

  my @return;

  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
    my $dbc = $dba->dbc();

    if ( defined($dbc) && $dbc->dbname() eq $dbname ) {
      push( @return, $dba );
    }
  }

  return\@ return;
}
get_all_adaptorsdescriptionprevnextTop
sub get_all_adaptors {
  my ($class,@args)= @_;
  my ($species, $group, $type);
  my @ret=();
  my (%species_hash, %group_hash, %type_hash);


  if(@args == 1){ # Old species only one parameter
    warn("-SPECIES argument should now be used to get species adaptors");
    $species = $args[0];
  }
  else{
    # new style -SPECIES, -GROUP, -TYPE
    ($species, $group, $type) =
      rearrange([qw(SPECIES GROUP TYPE)], @args);
  }

  if(defined($species)){
    $species_hash{$species} = 1;
  }
  else{
    # get list of species
    foreach my $dba (@{$registry_register{'_DBA'}}){
      $species_hash{lc($dba->species())} = 1;
    }
  }
  if(defined($group)){
    $group_hash{$group} = 1;
  }
  else{
    foreach my $dba (@{$registry_register{'_DBA'}}){
      $group_hash{lc($dba->group())} = 1;
    }
  }
  if(defined($type)){
    $type_hash{$type} =1;
  }
  else{
    foreach my $dba (@{$registry_register{'_DBA'}}){ 
	foreach my $ty (@{$registry_register{lc($dba->species)}{'list'}}){
	  $type_hash{lc($ty)} = 1;
	}
      }
  }
  
  ### NOW NEED TO INSTANTIATE BY CALLING get_adaptor
  foreach my $sp (keys %species_hash){
    foreach my $gr (keys %group_hash){
      foreach my $ty (keys %type_hash){
	my $temp = $class->get_adaptor($sp,$gr,$ty);
	if(defined($temp)){
	  push @ret, $temp;
	}
      }
    }
  }
  return (\@ret);
}
get_all_db_adaptorsdescriptionprevnextTop
sub get_all_db_adaptors {
  my ( $class, $db ) = @_;
  my %ret = ();

  # we now also want to add all the DBAdaptors for the same species.
  # as add_db_adaptor does not add if it is from the same species.

  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
    if ( lc( $dba->species() ) eq lc( $db->species() ) ) {
      $ret{ $dba->group() } = $dba;
    }
  }

  foreach my $key (
    keys %{
      $registry_register{ $class->get_alias( $db->species() ) }
        { lc( $db->group() ) }{'_special'} } )
  {
    $ret{$key} =
      $registry_register{ $class->get_alias( $db->species() ) }
      { lc( $db->group() ) }{'_special'}{$key};
  }

  return\% ret;
} ## end sub get_all_db_adaptors


#
# DBAdaptors
#
}
get_dbdescriptionprevnextTop
sub get_db {
  my ( $class, $db, $name ) = @_;

  my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor( lc( $db->species ),
    lc($name) );

  if ( defined($ret) ) { return $ret }

  return $registry_register{ lc( $db->species() ) }
    { lc( $db->group() ) }{'_special'}{ lc($name) };
}
get_species_and_object_typedescriptionprevnextTop
sub get_species_and_object_type {
  my ($self, $stable_id, $force) = @_;
 
## Check for Ensembl/Vega style identifiers...
  if( $stable_id =~ /(\w+?)(EST)?([GTPE])\d/ ) {
      return $ensembl_species{$1},$ensembl_type{$3}, $ensembl_db_type{$2} ||'core' if $ensembl_species{$1};
      return $vega_species{$1}, $ensembl_type{$3}, 'vega' if $vega_species{$1};
  }
## Check for Vector base style identifiers
  if( $stable_id =~ /^([A-Z]+)\d+-?(RP)?\w?/ && $vectorbase_species{$1} ) {
      return $vectorbase_species{$1}, $vectorbase_type{$2}||'Gene','core';
  }
  if( $stable_id =~ /^([A-Z]+)?(\.e|E)\d+$/ && ($1 eq '' || $vectorbase_species{$1}) ) {
      return $vectorbase_species{$1||'AGAP'}, 'Exon', 'core';
  }
  return unless defined($force) && $force;
## Finally if "force" is passed see if we can find a non-standard string...
  foreach my $species (qw(saccharomyces_cerevisiae tetraodon_nigroviridis
                          drosophila_melanogaster caenorhabditis_elegans)){
      foreach my $type (qw(Transcript Gene Translation Exon)){
	  my $adaptor = $self->get_adaptor($species, 'core', $type);
	  next unless defined($adaptor);
	  my $entity = $adaptor->fetch_by_stable_id($stable_id);
	  return ucfirst( $species ), $type,'core' if defined $entity;
      }
  }
  return;

}

1;
}
load_alldescriptionprevnextTop
sub load_all {
    my $class = shift;
    my ( $config_file, $verbose, $no_clear, $no_cache ) = @_;

    $config_file ||= $ENV{ENSEMBL_REGISTRY}
      || $ENV{HOME} . "/.ensembl_init";

    $verbose  ||= 0;
    $no_clear ||= 0;
    $no_cache ||= 0;

    if ( !defined($config_file) ) {
        if ($verbose) {
            print( STDERR
                   "No default registry configuration to load.\n" );
        }
    } elsif ( !-e $config_file ) {
        if ($verbose) {
            printf( STDERR "Configuration file '%s' does not exist. "
                      . "Registry configuration not loaded.\n",
                    $config_file );
        }
    } else {
        if ( defined( $registry_register{'seen'} ) ) {
            if ( !$no_clear ) {
                if ($verbose) {
                    print( STDERR "Clearing previously loaded "
                           . "registry configuration\n" );
                }
                $class->clear();
            }
        }
        $registry_register{'seen'} = 1;

        if ($verbose) {
            printf( STDERR
                      "Loading registry configuration from '%s'.\n",
                    $config_file );
        }

        my $cfg;

        eval { require Config::IniFiles };
        if ($@) {
          # The user does not have the 'Config::IniFiles' module.
          if ($verbose) {
            print( STDERR "No Config::IniFiles module found, "
                   . "assuming this is not an ini-file\n" );
          }
          # If the configuration file *is* an ini-file, we can expect a
          # load of compilation errors from the next eval...
        } else {
          # The user has the 'Config::IniFiles' module installed.  See
          # if this is an ini-file or not...
          $cfg = Config::IniFiles->new( -file => $config_file );
        }

        if ( defined $cfg ) {
		  my %default_adaptor_args = ();

            if ( $cfg->SectionExists('default') ) {
                # The 'default' section is special.  It contain default
                # values that should be implicit to all other section in
                # this configuration file.  Aliases are added if there
                # is also a 'species' setting.

                my $alias = $cfg->val( 'default', 'alias' );
                $cfg->delval( 'default', 'alias' );

                my $species = $cfg->val( 'default', 'species' );

                if ( defined($alias) && defined($species) ) {
                    Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                     -species => $species,
                                     -alias => [ split( /\n/, $alias ) ]
                    );
                }

                %default_adaptor_args =
                  map { '-' . $_ => $cfg->val( 'default', $_ ) }
                  $cfg->Parameters('default');
            }

            foreach my $section ( $cfg->Sections() ) {
                if ( $section eq 'default' )
                {    # We have already done the 'default' section.
                    next;
                }

                my $group = $cfg->val( $section, 'group' )
                  || $cfg->val( 'default', 'group' );

                if ( !defined($group) ) {
                    printf( STDERR "Key 'group' is undefined "
                              . "for configuration section '%s', "
                              . "skipping this section.\n",
                            $section );
                    next;
                }

                my $adaptor = $group2adaptor{ lc($group) };
                if ( !defined($adaptor) ) {
                    printf( STDERR "Unknown group '%s' "
                              . "for configuration section '%s', "
                              . "skipping this section.\n",
                            $group, $section );
                    next;
                }

                # Handle aliases.  A section must have both an 'alias'
                # setting and a 'species' setting for aliases to be
                # added.  The 'species' setting might be inherited from
                # the 'default' section.

                my $alias = $cfg->val( $section, 'alias' );
                $cfg->delval( $section, 'alias' );

                my $species = $cfg->val( $section, 'species' )
                  || $cfg->val( 'default', 'species' );

                if ( defined($alias) && defined($species) ) {
                    Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                     -species => $species,
                                     -alias => [ split( /\n/, $alias ) ]
                    );
                }

                # Fill in the adaptor initialization arguments.
                # We trust the user to provide sensible key-value pairs.
                my %adaptor_args = %default_adaptor_args;
                foreach my $parameter ( $cfg->Parameters($section) ) {
                  $adaptor_args{ '-' . $parameter } =
                    $cfg->val( $section, $parameter );

                  # when set, do not use the feature cache in the
                  # different adaptors
                  if ($no_cache) {
                    $adaptor_args{'-no_cache'} = 1;
                  }
                }

                if ($verbose) {
                    printf( "Configuring adaptor '%s' "
                              . "for configuration section '%s'...\n",
                            $adaptor, $section );
                }

                eval "require $adaptor";
                if ($@) { die($@) }

                $adaptor->new(%adaptor_args);

            } ## end foreach my $section ( $cfg->Sections...
        } else {
            # This is probably no ini-file but an old style piece
            # of configuration written in Perl.  We need to try to
            # require() it.

            eval { require($config_file) };
            if ($@) { die($@) }

            # To make the web code avoid doing this again:
            delete $INC{$config_file};
        }
    } ## end else [ if ( !defined($config_file...
} ## end sub load_all
}
load_registry_from_dbdescriptionprevnextTop
sub load_registry_from_db {
  my ( $self, @args ) = @_;

  my ( $host, $port, $user, $pass, $verbose, $db_version, $wait_timeout,
    $no_cache )
    = rearrange( [
      'HOST',    'PORT',       'USER',         'PASS',
      'VERBOSE', 'DB_VERSION', 'WAIT_TIMEOUT', 'NO_CACHE'
    ],
    @args
    );

  my $go_version       = 0;
  my $ontology_version = 0;

  $user ||= "ensro";
  if ( !defined($port) ) {
    $port = 3306;
    if ( $host eq "ensembldb.ensembl.org" ) {
      if ( !defined($db_version) or $db_version >= 48 ) {
        $port = 5306;
      }
    }
  }

  $wait_timeout ||= 0;

  my $dbh =
    DBI->connect( "DBI:mysql:host=$host;port=$port", $user, $pass );

  my $res = $dbh->selectall_arrayref('SHOW DATABASES');
  my @dbnames = map { $_->[0] } @$res;

  my %temp;
  my $software_version = $self->software_version();

  if ( defined($db_version) ) {
    $software_version = $db_version;
  }

  if ($verbose) {
    printf( "Will only load v%d databases\n", $software_version );
  }

  for my $db (@dbnames) {
    if ( $db =~ /^(\w+)_(collection_core_(?:\d+_)?(\d+)_(\w+))/ )
    {    # NEEDS TO BE FIRST
      if ( $3 eq $software_version ) {
        $temp{$1} = $2;
      }
    } elsif ( $db =~ /^(.+)_(userdata)$/ ) {
      $temp{$1} = $2;
    } elsif ( $db =~ /^(ensembl_compara(?:_\w+)*?)_(\d+)$/ ) {
      if ( $2 eq $software_version ) {
        $temp{$1} = $2;
      }
    } elsif ( $db =~ /^(ensembl_ancestral(?:_\w+?)*?)_(\d+)$/ ) {
      if ( $2 eq $software_version ) {
        $temp{$1} = $2;
      }
    } elsif ( $db =~ /^ensembl_go_(\d+)/ ) {
      if ( $1 eq $software_version ) {
        $go_version = $1;
      }
    } elsif ( $db =~ /^(ensembl_ontology)_(\d+)/ ) {
      if ( $2 eq $software_version ) {
        $ontology_version = $2;
      }
    } elsif (
      $db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\w+)/ )
    {
      if ( $2 eq $software_version ) {
        $temp{$1} = $2 . "_" . $3;
      }
    } else {
      # warn( sprintf( "Skipping database '%s'\n", $db ) );
    }
  } ## end for my $db (@dbnames)

  @dbnames = ();

  foreach my $key ( keys %temp ) {
    push @dbnames, $key . "_" . $temp{$key};
  }

  # Register Core databases

  my @core_dbs = grep { /^[a-z]+_[a-z]+_core_(?:\d+_)?\d+_/ } @dbnames;

  foreach my $coredb (@core_dbs) {
    next if ($coredb =~ /collection/);  # Skip multi-species databases

    my ( $species, $num ) =
      ( $coredb =~ /(^[a-z]+_[a-z]+)_core_(?:\d+_)?(\d+)/ );

    my $dba =
      Bio::EnsEMBL::DBSQL::DBAdaptor->new(
                                         -group        => "core",
                                         -species      => $species,
                                         -host         => $host,
                                         -user         => $user,
                                         -pass         => $pass,
                                         -port         => $port,
                                         -dbname       => $coredb,
                                         -wait_timeout => $wait_timeout,
                                         -no_cache     => $no_cache );

    ( my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );

    if ($verbose) {
      printf( "Species '%s' loaded from database '%s'\n",
              $species, $coredb );
    }
  }

  # Register multi-species databases
  my @multi_dbs = grep { /^\w+_collection_core_\w+$/ } @dbnames;

  foreach my $multidb (@multi_dbs) {
    my $sth =
      $dbh->prepare(
                 sprintf( 'SELECT species_id, meta_value FROM %s.meta ',
                          $dbh->quote_identifier($multidb) )
                   . "WHERE meta_key = 'species.db_name'" );

    $sth->execute();

    my ( $species_id, $species );
    $sth->bind_columns(\(  $species_id, $species ) );

    while ( $sth->fetch() ) {
      my $dba =
        Bio::EnsEMBL::DBSQL::DBAdaptor->new(
                                         -group      => "core",
                                         -species    => $species,
                                         -species_id => $species_id,
                                         -multispecies_db => 1,
                                         -host            => $host,
                                         -user            => $user,
                                         -pass            => $pass,
                                         -port            => $port,
                                         -dbname          => $multidb,
                                         -wait_timeout => $wait_timeout,
                                         -no_cache     => $no_cache );

      ( my $sp = $species ) =~ s/_/ /g;
      $self->add_alias( $species, $sp );

      if ($verbose) {
        printf( "Species '%s' (id:%d) loaded from database '%s'\n",
                $species, $species_id, $multidb );
      }
    }
  } ## end foreach my $multidb (@multi_dbs)

  # register cdna databases

  my @cdna_dbs = grep { /^[a-z]+_[a-z]+_cdna_(?:\d+_)?\d+_/ } @dbnames;

  for my $cdnadb (@cdna_dbs) {
    my ( $species, $num ) =
      ( $cdnadb =~ /(^[a-z]+_[a-z]+)_cdna_(?:\d+_)?(\d+)_/ );
    my $dba =
      Bio::EnsEMBL::DBSQL::DBAdaptor->new(
                                         -group        => "cdna",
                                         -species      => $species,
                                         -host         => $host,
                                         -user         => $user,
                                         -pass         => $pass,
                                         -port         => $port,
                                         -dbname       => $cdnadb,
                                         -wait_timeout => $wait_timeout,
                                         -no_cache     => $no_cache );
    ( my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );

    if ($verbose) {
      printf( "%s loaded\n", $cdnadb );
    }
  }

  my @vega_dbs = grep { /^[a-z]+_[a-z]+_vega_\d+_/ } @dbnames;

  for my $vegadb (@vega_dbs) {
    my ( $species, $num ) =
      ( $vegadb =~ /(^[a-z]+_[a-z]+)_vega_(\d+)/ );
    my $dba =
      Bio::EnsEMBL::DBSQL::DBAdaptor->new(
                                         -group        => "vega",
                                         -species      => $species,
                                         -host         => $host,
                                         -user         => $user,
                                         -pass         => $pass,
                                         -port         => $port,
                                         -wait_timeout => $wait_timeout,
                                         -dbname       => $vegadb,
                                         -no_cache     => $no_cache );
    ( my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );

    if ($verbose) {
      printf( "%s loaded\n", $vegadb );
    }
  }

  # Otherfeatures

  my @other_dbs = grep { /^[a-z]+_[a-z]+_otherfeatures_(?:\d+_)?\d+_/ } @dbnames;

  for my $other_db (@other_dbs) {
    my ( $species, $num ) =
      ( $other_db =~ /(^[a-z]+_[a-z]+)_otherfeatures_(?:\d+_)?(\d+)_/ );
    my $dba =
      Bio::EnsEMBL::DBSQL::DBAdaptor->new(
                                         -group   => "otherfeatures",
                                         -species => $species,
                                         -host    => $host,
                                         -user    => $user,
                                         -pass    => $pass,
                                         -port    => $port,
                                         -wait_timeout => $wait_timeout,
                                         -dbname       => $other_db,
                                         -no_cache     => $no_cache );
    ( my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );

    if ($verbose) {
      printf( "%s loaded\n", $other_db );
    }
  }

  # User upload DBs

  my @userupload_dbs = grep { /_userdata$/ } @dbnames;
  for my $userupload_db (@userupload_dbs) {
    my ($species) = ( $userupload_db =~ /(^.+)_userdata$/ );
    my $dba =
      Bio::EnsEMBL::DBSQL::DBAdaptor->new(
                                         -group        => "userupload",
                                         -species      => $species,
                                         -host         => $host,
                                         -user         => $user,
                                         -pass         => $pass,
                                         -port         => $port,
                                         -wait_timeout => $wait_timeout,
                                         -dbname   => $userupload_db,
                                         -no_cache => $no_cache );
    ( my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );

    if ($verbose) {
      printf( "%s loaded\n", $userupload_db );
    }
  }

  # Variation

  eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor";
  if ($@) {
    # Ignore variations as code required not there for this
    if ($verbose) {
      print(
           "Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found "
             . "so variation databases will be ignored if found\n" );
    }
  } else {
    my @variation_dbs =
      grep { /^[a-z]+_[a-z]+_variation_(?:\d+_)?\d+_/ } @dbnames;

    for my $variation_db (@variation_dbs) {
      my ( $species, $num ) =
        ( $variation_db =~ /(^[a-z]+_[a-z]+)_variation_(?:\d+_)?(\d+)_/ );
      my $dba =
        Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(
                                         -group        => "variation",
                                         -species      => $species,
                                         -host         => $host,
                                         -user         => $user,
                                         -pass         => $pass,
                                         -port         => $port,
                                         -wait_timeout => $wait_timeout,
                                         -dbname       => $variation_db,
                                         -no_cache     => $no_cache );

      if ($verbose) {
        printf( "%s loaded\n", $variation_db );
      }
    }
  }

  eval "require Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor";
  if ($@) {
    if ($verbose) {
      # Ignore funcgen DBs as code required not there for this
      print( "Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found "
         . "so functional genomics databases will be ignored if found\n"
      );
    }
  } else {
    my @funcgen_dbs = grep { /^[a-z]+_[a-z]+_funcgen_(?:\d+_)?\d+_/ } @dbnames;

    for my $funcgen_db (@funcgen_dbs) {
      my ( $species, $num ) =
        ( $funcgen_db =~ /(^[a-z]+_[a-z]+)_funcgen_(?:\d+_)?(\d+)_/ );
      my $dba =
        Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(
                                         -group        => "funcgen",
                                         -species      => $species,
                                         -host         => $host,
                                         -user         => $user,
                                         -pass         => $pass,
                                         -port         => $port,
                                         -wait_timeout => $wait_timeout,
                                         -dbname       => $funcgen_db,
                                         -no_cache     => $no_cache );

      if ($verbose) {
        printf( "%s loaded\n", $funcgen_db );
      }
    }
  }

  # Compara

  my @compara_dbs = grep { /^ensembl_compara/ } @dbnames;

  if (@compara_dbs) {
    eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
    if ($@) {
      # Ignore Compara as code required not there for this
      if ($verbose) {
        printf(
          "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor "
            . "not found so the following compara "
            . "databases will be ignored: %s\n",
          join( ', ', @compara_dbs ) );
      }
    } else {
      foreach my $compara_db (@compara_dbs) {
        # Looking for EnsEMBL Genomes Comparas.
        # ensembl_compara_bacteria_2_53 is registered as
        # 'bacteria', ensembl_compara_pan_homology_2_53 is
        # registered as 'pan_homology', ensembl_compara_53 is
        # registered as 'multi', and the alias 'compara' still
        # operates.

        my ($species) =
          $compara_db =~ /^ensembl_compara_(\w+)(?:_\d+){2}$/xm;

        $species ||= 'multi';

        my $dba = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(
          -group        => 'compara',
          -species      => $species,
          -host         => $host,
          -user         => $user,
          -pass         => $pass,
          -port         => $port,
          -wait_timeout => $wait_timeout,
          -dbname       => $compara_db,
          -no_cache     => $no_cache
        );

        if ($verbose) {
          printf( "%s loaded\n", $compara_db );
        }
      } ## end foreach my $compara_db (@compara_dbs)
    } ## end else [ if ($@)
  } elsif ($verbose) {
    print("No Compara databases found\n");
  }

  # Ancestral sequences

  my @ancestral_dbs =
    sort grep { /^ensembl_ancestral/ } @dbnames;

  if (@ancestral_dbs) {
    my $ancestral_db = shift @ancestral_dbs;

    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
      -group        => 'core',
      -species      => 'Ancestral sequences',
      -host         => $host,
      -user         => $user,
      -pass         => $pass,
      -port         => $port,
      -wait_timeout => $wait_timeout,
      -dbname       => $ancestral_db,
      -no_cache     => $no_cache
    );

    if ($verbose) {
      printf( "%s loaded\n", $ancestral_db );

      if (@ancestral_dbs) {
        # If we still had some more then report the problem.
        printf(
          "Multiple ancestral databases found.\n"
            . "Ignoring the following: %s\n",
          join( ', ', @ancestral_dbs ) );
      }
    }
  } elsif ($verbose) {
    print("No ancestral database found\n");
  }

  # GO

  if ($go_version) {
    eval "require Bio::EnsEMBL::ExternalData::GO::GOAdaptor";
    if ($@) {
      #ignore go as code required not there for this
      #      print $@;
      if ($verbose) {
        print "GO software not installed "
          . "so GO database ensembl_go_$go_version will be ignored\n";
      }
    } else {
      my $go_db = "ensembl_go_" . $go_version;
      my $dba =
        Bio::EnsEMBL::ExternalData::GO::GOAdaptor->new(
                                                  -group    => "go",
                                                  -species  => "multi",
                                                  -host     => $host,
                                                  -user     => $user,
                                                  -pass     => $pass,
                                                  -port     => $port,
                                                  -dbname   => $go_db,
                                                  -no_cache => $no_cache
        );

      if ($verbose) {
        printf( "%s loaded\n", $go_db );
      }
    }
  } elsif ($verbose) {
    print("No GO database found\n");
  }

  # Ontology

  if ( $ontology_version != 0 ) {
    require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;

    my $ontology_db =
      sprintf( "ensembl_ontology_%d", $ontology_version );

    my $dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
      '-species' => 'multi',
      '-group'   => 'ontology',
      '-host'    => $host,
      '-port'    => $port,
      '-user'    => $user,
      '-pass'    => $pass,
      '-dbname'  => $ontology_db,
    );

    if ($verbose) {
      printf( "%s loaded\n", $ontology_db );
    }
  } elsif ($verbose) {
    print("No ontology database found\n");
  }

  # Hard coded aliases for the different species

  my @aliases = ( 'chimp', 'PanTro1', 'Pan', 'P_troglodytes' );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Pan_troglodytes",
    -alias   =>\@ aliases
  );

  @aliases = ( 'elegans', 'worm' );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Caenorhabditis_elegans",
    -alias   =>\@ aliases
  );

  @aliases = ('tetraodon');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Tetraodon_nigroviridis",
    -alias   =>\@ aliases
  );

  @aliases = (
    'H_Sapiens', 'homo sapiens', 'Homo_Sapiens', 'Homo',
    'human',     'Hg17',         'ensHS',        '9606'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Homo_sapiens",
    -alias   =>\@ aliases
  );

  @aliases = (
    'M_Musculus', 'mus musculus', 'Mus_Musculus', 'Mus',
    'mouse',      'Mm5',          'ensMM',        '10090'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Mus_musculus",
    -alias   =>\@ aliases
  );

  @aliases = (
    'R_Norvegicus',      'rattus norvegicus',
    'Rattus_Norvegicus', 'Rattus',
    'rat',               'Rn3',
    '10116'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Rattus_norvegicus",
    -alias   =>\@ aliases
  );

  @aliases = ( 'T_Rubripes', 'Fugu', 'takifugu' );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Takifugu_rubripes",
    -alias   =>\@ aliases
  );

  @aliases = ( 'G_Gallus', 'gallus gallus', 'Chicken', 'GalGal2' );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Gallus_Gallus",
    -alias   =>\@ aliases
  );

  @aliases = (
    'D_Rerio',   'danio rerio', 'Danio_Rerio', 'Danio',
    'zebrafish', 'zfish'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Danio_rerio",
    -alias   =>\@ aliases
  );

  @aliases = (
    'X_Tropicalis',       'xenopus tropicalis',
    'Xenopus_tropicalis', 'Xenopus'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Xenopus_tropicalis",
    -alias   =>\@ aliases
  );

  @aliases = (
    'A_Gambiae',         'Anopheles Gambiae',
    'Anopheles_gambiae', 'Anopheles',
    'mosquito'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Anopheles_gambiae",
    -alias   =>\@ aliases
  );

  @aliases = (
    'D_Melanogaster',          'drosophila melanogaster',
    'Drosophila_melanogaster', 'drosophila',
    'fly'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Drosophila_melanogaster",
    -alias   =>\@ aliases
  );

  @aliases = (
    'S_Cerevisiae',             'Saccharomyces Cerevisiae',
    'Saccharomyces_cerevisiae', 'Saccharomyces',
    'yeast'
  );
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Saccharomyces_cerevisiae",
    -alias   =>\@ aliases
  );

  @aliases = (
    'C_Familiaris',     'Canis Familiaris',
    'Canis_familiaris', 'Canis',
    'dog'
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Canis_familiaris",
    -alias   =>\@ aliases
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Ciona_intestinalis",
    -alias   => [ 'ciona', 'Ciona intestinalis' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Bos_taurus",
    -alias   => [ 'cow', 'bos_taurus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Macaca_mulatta",
    -alias => [ 'rhesus', 'rhesus_monkey', 'macaque', 'macaca mulatta' ]
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Otolemur_garnettii",
    -alias   => [ 'bushbaby', 'galago', 'Otolemur garnettii' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Oryctolagus_cuniculus",
    -alias   => [ 'rabbit', 'Oryctolagus cuniculus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Felis_catus",
    -alias   => [ 'cat', 'felis catus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Sus_scrofa",
    -alias   => [ 'pig', 'sus scrofa' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Sorex_araneus",
    -alias =>
      [ 'shrew', 'ground_shrew', 'european_shrew', 'Sorex araneus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Erinaceus_europaeus",
    -alias   => [ 'western_european_hedgehog', 'Erinaceus europaeus' ]
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Myotis_lucifugus",
    -alias   => [ 'microbat', 'little_brown_bat' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Dasypus_novemcinctus",
    -alias   => [ 'armadillo', 'arma', 'Dasypus novemcinctu' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Loxodonta_africana",
    -alias   => [ 'african_elephant', 'elephant', 'Loxodonta africana' ]
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Echinops_telfairi",
    -alias   => [
      'tenrec',          'madagascar_hedgehog',
      'lesser_hedgehog', 'Echinops telfairi'
    ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Monodelphis_domestica",
    -alias   => [ 'opossum', 'Monodelphis domestica' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Ornithorhynchus_anatinus",
    -alias   => [ 'platypus', 'Ornithorhynchus anatinus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Gasterosteus_aculeatus",
    -alias   => [ 'stickleback', 'Gasterosteus aculeatus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Oryzias_latipes",
    -alias   => [ 'medaka', 'Oryzias latipes' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Cavia_porcellus",
    -alias   => [ 'guinea_pig', '"Cavia porcellus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Aedes_aegypti",
    -alias   => [ 'aedes', 'Aedes aegypti' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Spermophilus_tridecemlineatus",
    -alias   => [ 'squirrel', 'Spermophilus tridecemlineatus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Tupaia_belangeri",
    -alias   => [ 'tree_shrew', 'Tupaia belangeri' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Culex_pipiens",
    -alias   => [ 'culex', 'Culex Pipiens' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Ochotona_princeps",
    -alias   => [ 'pika', 'Ochotona princeps' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Anolis_carolinensis",
    -alias   => [ 'anolis', 'anolis_lizard', 'Anolis carolinensis' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Microcebus_murinus",
    -alias   => [ 'mouse_lemur', 'Microcebus murinus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Pongo_pygmaeus",
    -alias   => [ 'orang', 'orang_utan', 'orangutan', 'Pongo pygmaeus' ]
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Equus_caballus",
    -alias   => [ 'horse', 'Equuscaballus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Tursiops_truncatus",
    -alias   => [ 'dolphin', 'Tursiopstruncatus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Procavia_capensis",
    -alias   => [ 'rock_hyrax', 'hyrax', 'Procaviacapensis' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Dipodomys_ordii",
    -alias   => [ 'kangaroo_rat', 'Dipodomysordii' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Pteropus_vampyrus",
    -alias   => [ 'megabat', 'Pteropusvampyrus' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Tarsius_syrichta",
    -alias   => [ 'philippine tarsier', 'tarsier', 'Tarsiussyrichta' ]
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Vicugna_pacos",
    -alias   => [ 'alpaca', 'vicugnapacos' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Gorilla_gorilla",
    -alias   => [ 'gorilla', 'gorillagorilla' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Anolis_carolinensis",
    -alias   => [ 'anolis', 'anoliscarolinensis' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Choloepus_hoffmanni",
    -alias   => [ 'sloth', 'choloepus', 'choloepushoffmanni' ] );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "Taeniopygia_guttata",
    -alias =>
      [ 'finch', 'zebrafinch', 'taeniopygia', 'taeniopygiaguttata' ] );

  @aliases = ('compara');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "multi",
    -alias   =>\@ aliases
  );

  @aliases = ('go');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => "multi",
    -alias   =>\@ aliases
  );

  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
    -species => 'multi',
    -alias   => ['ontology'] );

  # Register aliases as found in adaptor meta tables.
  $self->find_and_add_aliases( '-handle' => $dbh );
  $dbh->disconnect();

} ## end sub load_registry_from_db
}
load_registry_from_urldescriptionprevnextTop
sub load_registry_from_url {
  my ($self, $url, $verbose, $no_cache) = @_;

  if ($url =~ /mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?/) {
    my $user_pass = $1;
    my $host = $2;
    my $port = $3;
    my $version = $4;

    $user_pass =~ s/\@$//;
    my ($user, $pass) = $user_pass =~ m/([^\:]+)(\:.+)?/;
    $pass =~ s/^\:// if ($pass);
    $port =~ s/^\:// if ($port);
    $version =~ s/^\/// if ($version);

    $self->load_registry_from_db(
        -host=> $host,
        -user => $user,
        -pass => $pass,
        -port => $port,
        -db_version => $version,
        -verbose => $verbose,
	-no_cache => $no_cache);
  } else {
    throw("Only MySQL URLs are accepted at the moment");
  }
}
load_registry_with_web_adaptorsdescriptionprevnextTop
sub load_registry_with_web_adaptors {
  my $class = shift;

  deprecate('Use the load_registry_from_db instead'); 
  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();
  
  my %species_alias = %{$SiteDefs::ENSEMBL_SPECIES_ALIASES};

  foreach my $spec (keys %species_alias){
    Bio::EnsEMBL::Registry->add_alias($species_alias{$spec},$spec);
  }
}
no_version_checkdescriptionprevnextTop
sub no_version_check {
  my ($self, $arg ) = @_;
  ( defined $arg ) && ( $registry_register{'_no_version_check'} = $arg );
  return $registry_register{'_no_version_check'};
}
remove_DBAdaptordescriptionprevnextTop
sub remove_DBAdaptor {
  my ($class, $species, $group) = @_;

  $species = $class->get_alias($species);
  
 
  delete $registry_register{$species}{$group};
  # This will remove the DBAdaptor and all the other adaptors

  # Now remove if from the _DBA array
  my $index;


  foreach my $i(0..$#{$registry_register{'_DBA'}}){
    my $dba = $registry_register{'_DBA'}->[$i];

    if(($dba->species eq $species) &&
       $dba->group eq $group){
      $index = $i;

      last;
    }
  }
  
  
  # Now remove from _DBA cache
  splice(@{$registry_register{'_DBA'}}, $index, 1) if defined $index;

  return;
}
remove_dbdescriptionprevnextTop
sub remove_db {
  my ( $class, $db, $name ) = @_;

  my $ret =
    $registry_register{ lc( $db->species() ) }{ lc( $db->group() ) }
    {'_special'}{ lc($name) };

  $registry_register{ lc( $db->species() ) }{ lc( $db->group() ) }
    {'_special'}{ lc($name) } = undef;

  return $ret;
}
reset_DBAdaptordescriptionprevnextTop
sub reset_DBAdaptor {
  my (
    $self, $species, $group, $dbname, $host,
    $port, $user,    $pass,  $params
  ) = @_;

  # Check mandatory params
  if ( !( defined $species && defined $group && defined $dbname ) ) {
    throw(
      'Must provide at least a species, group, and dbname parameter '
        . 'to redefine a DB in the registry' );
  }

  # Validate species here
  my $alias = $self->get_alias($species);
  throw("Could not find registry alias for species:\t$species")
    if ( !defined $alias );

  # Get all current defaults if not defined

  my $db = $self->get_DBAdaptor( $alias, $group );
  my $class;

  if ($db) {
    $class = ref($db);
    $host ||= $db->dbc->host;
    $port ||= $db->dbc->port;
    $user ||= $db->dbc->username;
    $pass ||= $db->dbc->password;
  } else {
    #Now we need to test mandatory params
    $class = $group2adaptor{ lc($group) };

    if ( !( $host && $user ) ) {
      throw("No comparable $alias $group DB present in Registry. "
          . "You must pass at least a dbhost and dbuser" );
    }
  }

  $self->remove_DBAdaptor( $alias, $group );

  #my @adaptors = @{$self->get_all_adaptors};
  #This is causing a loop as it was constantly trying to reset the db
  #and never getting there.
  #I think this was left over from testing

  # ConfigRegistry should automatically add this to the Registry

  $db = $class->new(
    -user    => $user,
    -host    => $host,
    -port    => $port,
    -pass    => $pass,
    -dbname  => $dbname,
    -species => $alias,
    -group   => $group,
    %{$params} );

  return $db;
} ## end sub reset_DBAdaptor


#
# DNA Adaptors
#
}
set_default_trackdescriptionprevnextTop
sub set_default_track {
  my ($class, $species, $group) = @_;  

  $species = get_alias($species);
  $registry_register{'def_track'}{$species}{lc($group)} = 1;
}
set_disconnect_when_inactivedescriptionprevnextTop
sub set_disconnect_when_inactive {
  foreach my $dba ( @{get_all_DBAdaptors()}){
    my $dbc = $dba->dbc;
    # Disconnect if connected
    $dbc->disconnect_if_idle() if $dbc->connected();
    $dbc->disconnect_when_inactive(1);
  }
}
software_versiondescriptionprevnextTop
sub software_version {
  my ($self) = @_;
  return $API_VERSION;
}
version_checkdescriptionprevnextTop
sub version_check {
  my ( $self, $dba ) = @_;

  # Check the datbase and versions match
  # give warning if they do not.
  my $check = no_version_check();

  if ( (
      defined( $ENV{HOME} )
      and ( -e $ENV{HOME} . "/.ensemblapi_no_version_check" ) )
    or ( defined($check) and ( $check != 0 ) ) )
  {
    return 1;
  }

  my $mca =
    $self->get_adaptor( $dba->species(), $dba->group(),
    "MetaContainer" );

  my $database_version = 0;
  if ( defined($mca) ) {
    $database_version = $mca->get_schema_version();
  }

  if ( $database_version == 0 ) {
    # Try to work out the version
    if ( $dba->dbc()->dbname() =~ /^_test_db_/ ) {
      return 1;
    }
    if ( $dba->dbc()->dbname() =~ /(\d+)_\S+$/ ) {
      $database_version = $1;
    } elsif ( $dba->dbc()->dbname() =~ /ensembl_compara_(\d+)/ ) {
      $database_version = $1;
    } elsif ( $dba->dbc()->dbname() =~ /ensembl_go_(\d+)/ ) {
      $database_version = $1;
    } elsif ( $dba->dbc()->dbname() =~ /ensembl_help_(\d+)/ ) {
      $database_version = $1;
    } elsif ( $dba->dbc()->dbname() =~ /ensembl_ontology_(\d+)/ ) {
      $database_version = $1;
    } else {
      warn(
        sprintf(
          "No database version for database %s "
            . ". You must be using a pre version 34 database "
            . "with version 34 or later code.\n"
            . "You need to update your database "
            . "or use the appropriate Ensembl software release "
            . "to ensure your script does not crash\n",
          $dba->dbc()->dbname() ) );
    }
  } ## end if ( $database_version...

  if ( $database_version != $API_VERSION ) {
    warn(
      sprintf(
        "For %s there is a difference in the software release (%s) "
          . "and the database release (%s). "
          . "You should update one of these to ensure that your script "
          . "does not crash.\n",
        $dba->dbc()->dbname(),
        $API_VERSION, $database_version
      ) );
    return 0;
  }

  return 1;    # Ok
} ## end sub version_check
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.
DEPRECATED load_registry_with_web_adaptorsTop
  DEPRECATED: Use load_registry_from_db instead.