Registry.pm

=head1 LICENSE

  Copyright (c) 1999-2010 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

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  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>.

=cut

=head1 NAME

Bio::EnsEMBL::Registry

=head1 SYNOPSIS

  use Bio::EnsEMBL::Registry;

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

  $registry->load_all("configuration_file");

  $gene_adaptor = $registry->get_adaptor( 'Human', '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 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.

=head2 db

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" );


=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 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" );


=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 METHODS

=cut

package Bio::EnsEMBL::Registry;

use strict;

use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::ConfigRegistry;
use DBI;

use vars qw(%registry_register);

my $API_VERSION = 59;

# This is a map from group names to Ensembl DB adaptors.  Used by
# load_all() and reset_DBAdaptor().
my %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',
  'ontology'      => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor',
  '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',
);


=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
     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

=cut

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

=head2 clear

 Will clear the registry and disconnect from all databases.

  Example    : Bio::EnsEMBL::Registry->clear();
  Returntype : none
  Exceptions : none
  Status     : Stable

=cut

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)
#

=head2 add_db

  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.

=cut

sub add_db {
  my ( $class, $db, $name, $adap ) = @_;

  if ( lc( $db->species() ) ne lc( $adap->species ) ) {
    $registry_register{_SPECIES}{ lc( $db->species() ) }
      { lc( $db->group() ) }{'_special'}{ lc($name) } = $adap;
  }
}

=head2 remove_db

  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.

=cut

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

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

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

  return $ret;
}

=head2 get_db

  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.

=cut

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{_SPECIES}{ lc( $db->species() ) }
    { lc( $db->group() ) }{'_special'}{ lc($name) };
}

=head2 get_all_db_adaptors

  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");


=cut

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

  return \%ret;
} ## end sub get_all_db_adaptors


#
# 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
  caller     : internal
  Status     : Stable

=cut

sub add_DBAdaptor {
  my ( $class, $species, $group, $adap ) = @_;

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

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

  $registry_register{_SPECIES}{$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 );
  }

}



=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
  Status     : Stable

=cut

sub get_DBAdaptor {
  my ( $class, $species, $group ) = @_;

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

  return $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
}

=head2 get_all_DBAdaptors

  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

=cut

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;
}

=head2 get_all_DBAdaptors_by_connection

  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

=cut

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;
}

=head2 get_all_DBAdaptors_by_dbname

  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

=cut

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;
}

=head2 remove_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->remove_DBAdaptor("Human", "core");
  Returntype : none
  Exceptions : none
  Status     : At risk

=cut

sub remove_DBAdaptor {
  my ( $class, $species, $group ) = @_;

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

  delete $registry_register{_SPECIES}{$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
  if ( defined($index) ) {
    splice( @{ $registry_register{'_DBA'} }, $index, 1 );
  }

} ## end sub remove_DBAdaptor



=head2 reset_DBAdaptor

  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

=cut

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
#

=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]    : 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

=cut

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 {
    $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA'} =
      $dnadb_group;
    $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA2'} =
      $dnadb_species;
  }
}

=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
  Status     : Stable

=cut

sub get_DNAAdaptor {
  my ( $class, $species, $group ) = @_;

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

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

  return undef;
}

#
# 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
  Caller     : internal
  Status     : Stable

=cut

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
    $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) } =
      $adap;
    return;
  }

  if (
    defined(
      $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) }
    ) )
  {
  # print STDERR (
  #      "Overwriting Adaptor in Registry for $species $group $type\n");
    $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) } =
      $adap;
    return;
  }
  $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) } =
    $adap;

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

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

} ## end sub add_adaptor


=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
  Status     : Stable

=cut

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

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

  my $ret =
    $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) };

  if ( !defined($ret) ) { return undef }
  if ( ref($ret) )      { return $ret }

  # Not instantiated yet

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

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

  if (
    !defined(
      $registry_register{_SPECIES}{$species}{ lc($group) }{'CHECKED'} )
    )
  {
    $registry_register{_SPECIES}{$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

=head2 get_all_adaptors

  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

=cut

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{_SPECIES}{ 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);
}


=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
  Status     : Stable

=cut

sub add_alias{
  my ($class, $species,$key) = @_;

  $registry_register{'_ALIAS'}{lc($key)} = lc($species);
}

=head2 get_alias

  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

=cut

sub get_alias{
  my ($class, $key) = @_;

  if(!defined($registry_register{'_ALIAS'}{lc($key)})){
    return $key;
  }
  return $registry_register{'_ALIAS'}{lc($key)};
}

=head2 get_all_aliases

  Arg [1]    : Species name to retrieve aliases for
               (may be an alias as well).
  Example    : Bio::EnsEMBL::Registry->get_all_aliases('Homo sapiens');
  Description: Returns all known aliases for a given species (but not the
               species name/alias that was given).
  Returntype : ArrayRef of all known aliases
  Exceptions : none
  Status     : Development

=cut

sub get_all_aliases {
  my ( $class, $key ) = @_;

  my $species = $registry_register{_ALIAS}{ lc($key) };

  my @aliases;
  if ( defined($species) ) {
    foreach my $alias ( keys( %{ $registry_register{_ALIAS} } ) ) {
      if ( $species ne $alias
        && $species eq $registry_register{_ALIAS}{ lc($alias) } )
      {
        push( @aliases, $alias );
      }
    }
  }

  return \@aliases;
}

=head2 alias_exists

  Arg [1]    : name of the possible alias to get species for