ensemb_rep_gvl: variant_effect_predictor/Bio/EnsEMBL/Registry.pm comparison

comparison variant_effect_predictor/Bio/EnsEMBL/Registry.pm @ 0:2bc9b66ada89 draft default tip

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author	mahtabm
date	Thu, 11 Apr 2013 06:29:17 -0400
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+:2bc9b66ada89
+=head1 LICENSE
+Copyright (c) 1999-2012 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 <dev@ensembl.org>.
+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
+environment 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 warnings;
+our $NEW_EVAL = 0;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::ConfigRegistry;
+use Bio::EnsEMBL::ApiVersion;
+use Bio::EnsEMBL::Utils::URI qw/parse_uri/;
+use DBI qw(:sql_types);
+use vars qw(%registry_register);
+# 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',
+'regulation' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
+'haplotype' => 'Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor',
+'hive'      => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor',
+'ontology'  => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor',
+'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+'pipeline'      => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
+'snp'       => 'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
+'stable_ids' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
+'vega'      => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+'vega_update' => '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 environment 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 the developer mailing list.
+Example    : Bio::EnsEMBL::Registry->load_all();
+Returntype : Int count of the DBAdaptor instances which can be found in the
+registry due to this method being called. Will never be negative
+Exceptions : none
+Status     : Stable
+=cut
+sub load_all {
+my ($class, $config_file, $verbose, $no_clear, $no_cache ) = @_;
+if ( !defined($config_file) ) {
+if ( defined( $ENV{ENSEMBL_REGISTRY} ) ) {
+$config_file = $ENV{ENSEMBL_REGISTRY};
+} elsif ( defined( $ENV{HOME} ) ) {
+$config_file = $ENV{HOME} . "/.ensembl_init";
+}
+}
+$verbose  ||= 0;
+$no_clear ||= 0;
+$no_cache ||= 0;
+my $original_count = $class->get_DBAdaptor_count();
+if ( !defined($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;
+my $test_eval = eval { require Config::IniFiles };
+if ($@ or (!$test_eval)) {
+# The user does not have the 'Config::IniFiles' module.
+if ($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 );
+}
+my $test_eval = eval "require $adaptor";
+if ($@ or (!$test_eval)) { die($@) }
+$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.
+my $test_eval;
+if($NEW_EVAL) {
+require Bio::EnsEMBL::Utils::IO;
+my $contents = Bio::EnsEMBL::Utils::IO::slurp($config_file);
+$test_eval = eval $contents;
+}
+else {
+$test_eval = eval { require($config_file) };
+# To make the web code avoid doing this again we delete first
+delete $INC{$config_file};
+}
+#Now raise the exception just in case something above is
+#catching this
+if ($@ or (!$test_eval)) { die($@) }
+}
+} ## end else [ if ( !defined($config_file...
+my $count = $class->get_DBAdaptor_count() - $original_count;
+return $count >= 0 ? $count : 0;
+} ## end sub load_all
+=head2 clear
+Will clear the registry and disconnect from all databases.
+Example    : Bio::EnsEMBL::Registry->clear();
+Returntype : none
+Exceptions : none
+Status     : Stable
+=cut
+sub clear{
+my ($self);
+foreach my $dba (@{$registry_register{'_DBA'}}){
+if($dba->dbc->connected){
+$dba->dbc->db_handle->disconnect();
+}
+}
+%registry_register = ();
+return;
+}
+#
+# 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;
+}
+return;
+}
+=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 : See get_DBAdaptor()
+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]    : DBAdaptor 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( $registry_register{'_DBA'} ) ) {
+$registry_register{'_DBA'} = [$adap];
+} else {
+push( @{ $registry_register{'_DBA'} }, $adap );
+}
+return;
+}
+=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.
+Arg [3]    : if set will not give warnings when looking for alias.
+Example    : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
+Returntype : DBAdaptor
+Exceptions : If $species is not defined and if no valid internal name
+could be found for $species. If thrown check your API and DB
+version
+Status     : Stable
+=cut
+sub get_DBAdaptor {
+my ( $class, $species, $group, $no_alias_check ) = @_;
+if ( !defined($species) ) {
+throw('Species not defined.');
+}
+my $ispecies = $class->get_alias( $species, $no_alias_check );
+if ( !defined($ispecies) ) {
+if(! $no_alias_check) {
+throw("Can not find internal name for species '$species'");
+}
+}
+else { $species = $ispecies }
+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 );
+}
+return;
+} ## 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, $group );
+# ConfigRegistry should automatically add this to the Registry
+$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;
+}
+return;
+}
+=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;
+}
+#
+# 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 DBAdaptor to be added to the registry.
+Arg [5]    : (optional) Set to allow overwrites of existing adaptors.
+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($reset) )
+{    # JUST RESET THE HASH VALUE NO MORE PROCESSING NEEDED
+$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 );
+}
+return;
+} ## 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 : Thrown if a valid internal name cannot be found for the given
+name. If thrown check your API and DB version. Also thrown if
+no type or group was given
+Status     : Stable
+=cut
+sub get_adaptor {
+my ( $class, $species, $group, $type ) = @_;
+my $ispecies = $class->get_alias($species);
+if ( !defined($ispecies) ) {
+throw("Can not find internal name for species '$species'");
+}
+else { $species = $ispecies }
+throw 'No adaptor group given' if ! defined $group;
+throw 'No adaptor type given' if ! defined $type;
+if($type =~ /Adaptor$/i) {
+warning("Detected additional Adaptor string in given the type '$type'. Removing it to avoid possible issues. Alter your type to stop this message");
+$type =~ s/Adaptor$//i;
+}
+my %dnadb_adaptors = (
+'sequence'                 => 1,
+'assemblymapper'           => 1,
+'karyotypeband'            => 1,
+'repeatfeature'            => 1,
+'coordsystem'              => 1,
+'assemblyexceptionfeature' => 1
+);
+# warn "$species, $group, $type";
+$type = lc($type);
+# For historical reasons, allow use of group 'regulation' to refer to
+# group 'funcgen'.
+if ( lc($group) eq 'regulation' ) { $group = 'funcgen' }
+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 }
+if ( ref($ret) )      { return $ret }
+# Not instantiated yet
+my $dba = $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
+my $module = $ret;
+my $test_eval = eval "require $module";
+if ($@ or (!$test_eval)) {
+warning("'$module' cannot be found.\nException $@\n");
+return;
+}
+if (
+!defined(
+$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($species);
+return;
+}
+=head2 remove_alias
+Arg [1]    : name of the species to remove alias for
+Arg [2]    : name of the alias
+Example    : Bio::EnsEMBL::Registry->remove_alias("Homo Sapiens","Human");
+Description: remove alternative name for the species.
+Returntype : none
+Exceptions : none
+Status     : Stable
+=cut
+sub remove_alias{
+my ($class, $species,$key) = @_;
+delete $registry_register{'_ALIAS'}{lc($key)};
+return;
+}
+=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, $no_warn ) = @_;
+if ( !defined( $registry_register{'_ALIAS'}{ lc($key) } ) ) {
+if ( ( !defined( $registry_register{_SPECIES}{ lc($key) } ) ) and
+( !defined( $registry_register{_ALIAS}{ lc($key) } ) ) )
+{
+if ( ( !defined($no_warn) ) or ( !$no_warn ) ) {
+warning( "$key is not a valid species name " .
+"(check DB and API version)" );
+}
+return;
+}
+else { 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
+Example    : Bio::EnsEMBL::Registry->alias_exists("Human");
+Description: does the species name exist.
+Returntype : 1 if exists else 0
+Exceptions : none
+Status     : Stable
+=cut
+sub alias_exists {
+my ( $class, $key ) = @_;
+return defined( $registry_register{'_ALIAS'}{ lc($key) } );
+}
+=head2 set_disconnect_when_inactive
+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
+=cut
+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);
+}
+return;
+}
+=head2 set_reconnect_when_lost
+Example    : Bio::EnsEMBL::Registry->set_reconnect_when_lost();
+Description: Set the flag to make sure that the database connection is not lost before it's used.
+This is useful for long running jobs (over 8hrs).
+Returntype : none
+Exceptions : none
+Status     : Stable
+=cut
+sub set_reconnect_when_lost{
+foreach my $dba ( @{get_all_DBAdaptors()}){
+my $dbc = $dba->dbc;
+$dbc->reconnect_when_lost(1);
+}
+return;
+}
+=head2 disconnect_all
+Example    : Bio::EnsEMBL::Registry->disconnect_all();
+Description: disconnect from all the databases.
+Returntype : none
+Exceptions : none
+Status     : Stable
+=cut
+sub disconnect_all {
+foreach my $dba ( @{get_all_DBAdaptors()||[]} ){
+my $dbc = $dba->dbc;
+next unless $dbc;
+# Disconnect if connected
+$dbc->disconnect_if_idle() if $dbc->connected();
+}
+return;
+}
+=head get_DBAdaptor_count
+Example     : Bio::EnsEMBL::Registry->get_DBAdaptor_count();
+Description : Returns the count of database adaptors currently held by
+the registry
+Returntype  : Int count of database adaptors currently known
+Exceptions  : None
+=cut
+sub get_DBAdaptor_count {
+return scalar(@{$registry_register{'_DBA'}}) if(defined $registry_register{'_DBA'});
+return 0;
+}
+=head2 change_access
+Will change the username and password for a set of databases.
+if host,user or database names are missing then these are not checked.
+So for example if you do not specify a database then ALL databases on
+the specified  host and port will be changed.
+Arg [1]    : name of the host to change access on
+Arg [2]    : port number to change access on
+Arg [3]    : name of the user to change access on
+Arg [4]    : name of the database to change access on
+Arg [5]    : name of the new user
+Arg [6]    : new password
+Example    : Bio::EnsEMBL::Registry->get_alias("Human");
+Description: change username and password on one or more databases
+Returntype : none
+Exceptions : none
+Status     : Stable
+=cut
+sub change_access{
+my ($self, $host,$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);
+}
+}
+return;
+}
+=head2 load_registry_from_url
+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 the developer mailing list.
+Example : load_registry_from_url(
+'mysql://anonymous@ensembldb.ensembl.org:3306');
+load_registry_from_url(
+'mysql://anonymous@ensembldb.ensembl.org:3306/homo_sapiens_core_65_37?group=core&species=homo_sapiens'
+);
+load_registry_from_url(
+'mysql://anonymous@ensembldb.ensembl.org:3306/homo_sapiens_core_65_37?group=core'
+);
+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.
+You can also specify a database name which will cause the
+loading of a single DBAdaptor instance. Parameters are
+mapped from a normal URL parameter set to their DBAdaptor
+equivalent. Group must be defined.
+Returntype : Int count of the DBAdaptor instances which can be found in the
+registry
+Exceptions : Thrown if the given URL does not parse according to the above
+scheme and if the specified database cannot be connected to
+(see L<load_registry_from_db> for more information)
+Status     : Stable
+=cut
+sub load_registry_from_url {
+my ( $self, $url, $verbose, $no_cache ) = @_;
+if ( $url =~ /^mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?\/?$/x ) {
+my $user_pass = $1;
+my $host      = $2;
+my $port      = $3;
+my $version   = $4;
+$user_pass =~ s/\@$//;
+my ( $user, $pass ) = $user_pass =~ m/([^\:]+)(\:.+)?/x;
+$pass    =~ s/^\://x if ($pass);
+$port    =~ s/^\://x if ($port);
+$version =~ s/^\///x if ($version);
+return $self->load_registry_from_db(
+-host       => $host,
+-user       => $user,
+-pass       => $pass,
+-port       => $port,
+-db_version => $version,
+-verbose    => $verbose,
+-no_cache   => $no_cache
+);
+}
+my $uri = parse_uri($url);
+if($uri) {
+if($uri->scheme() eq 'mysql') {
+my %params = $uri->generate_dbsql_params();
+if($params{-DBNAME}) {
+$params{-SPECIES} = $params{-DBNAME} unless $params{-SPECIES};
+$params{-NO_CACHE} = 1 if $no_cache;
+my $group = $params{-GROUP};
+my $class = $self->_group_to_adaptor_class($group);
+if($verbose) {
+printf("Loading database '%s' from group '%s' with DBAdaptor class '%s' from url %s\n", $params{-DBNAME}, $group, $class, $url);
+}
+$class->new(%params);
+return 1;
+}
+}
+}
+throw("Only MySQL URLs are accepted. Given URL was '${url}'");
+} ## end sub load_registry_from_url
+=head2 load_registry_from_db
+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 [SPECIES]: (optional) string
+By default, all databases that are found on the
+server and that corresponds to the correct release
+are probed for aliases etc.  For some people,
+depending on where they are in the world, this might
+be a slow operation.  With the '-species' argument,
+one may reduce the startup time by restricting the
+set of databases that are probed to those of a
+particular species.
+Note that the latin name of the species is required,
+e.g., 'homo sapiens', 'gallus gallus', 'callithrix
+jacchus' etc.  It may be the whole species name,
+or only the first part of the name, e.g. 'homo',
+'gallus', or 'callithrix'.  This will be used in
+matching against the name of the databases.
+Arg [DB_VERSION]: (optional) integer
+By default, only databases corresponding to the
+current API version are loaded.  This argument
+allows the script to use databases from another
+version although it might not work properly.  This
+argument 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) 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 the
+developer mailing list.
+Arg [SPECIES_SUFFIX]: (optional) string
+This option will append the string to the species name
+in the registry for all databases found on this server.
+Example :
+$registry->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.
+Returntype : Int count of the DBAdaptor instances which can be found in the
+registry due to this method call.
+Exceptions : Thrown if the given MySQL database cannot be connected to
+or there is any error whilst querying the database.
+Status     : Stable
+=cut
+sub load_registry_from_db {
+my ( $self, @args ) = @_;
+my ( $host,         $port,     $user,
+$pass,         $verbose,  $db_version,
+$wait_timeout, $no_cache, $species, $species_suffix )
+= rearrange( [ 'HOST',         'PORT',
+'USER',         'PASS',
+'VERBOSE',      'DB_VERSION',
+'WAIT_TIMEOUT', 'NO_CACHE',
+'SPECIES', 'SPECIES_SUFFIX' ],
+@args );
+if ( defined($species) ) {
+$species = lc($species);
+$species =~ tr/ -/__/;
+}
+if (!defined($species_suffix)) {
+$species_suffix = "";
+}
+my $ontology_db;
+my $ontology_version;
+my $stable_ids_db;
+my $stable_ids_version;
+$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 $original_count = $self->get_DBAdaptor_count();
+my $err_pattern = 'Cannot %s to the Ensembl MySQL server at %s:%d; check your settings & DBI error message: %s';
+my $dbh = DBI->connect( "DBI:mysql:host=$host;port=$port", $user, $pass ) or
+throw(sprintf($err_pattern, 'connect', $host, $port, $DBI::errstr));
+$dbh->ping() or
+throw(sprintf($err_pattern, 'ping', $host, $port, $DBI::errstr));
+my $res = $dbh->selectall_arrayref('SHOW DATABASES');
+my @dbnames = map { $_->[0] } @$res;
+my %temp;
+my $software_version = software_version();
+if ( defined($db_version) ) {
+$software_version = $db_version;
+}
+if ($verbose) {
+printf( "Will only load v%d databases\n", $software_version );
+}
+# From the list of all the databses create a tempory hash of those we
+# are interested in
+for my $db (@dbnames) {
+if ( $db =~ /^(\w+_collection_\w+(?:_\d+)?)_((\d+)_\w+)/ )
+{    # NEEDS TO BE FIRST TO PICK UP COLLECTION DBS
+if ( $3 eq $software_version ) {
+$temp{$1} = $2;
+}
+} elsif ( $db =~ /^(.+)_(userdata)$/x ) {
+$temp{$1} = $2;
+} elsif (
+$db =~ /^(ensembl_compara # compara database
+(?:_\w+)*?)     # optional ensembl genomes bit
+_
+(\d+)$/x )
+{    # db version
+if ( $2 eq $software_version ) {
+$temp{$1} = $2;
+}
+} elsif ( $db =~ /^(ensembl_ancestral(?:_\w+?)*?)_(\d+)$/x ) {
+if ( $2 eq $software_version ) {
+$temp{$1} = $2;
+}
+} elsif ( $db =~ /^ensembl(?:genomes)?_ontology_(?:\d+_)?(\d+)/x ) {
+if ( $1 eq $software_version ) {
+$ontology_db      = $db;
+$ontology_version = $1;
+}
+} elsif ( $db =~ /^ensembl(?:genomes)?_stable_ids_(?:\d+_)?(\d+)/x ) {
+if ( $1 eq $software_version ) {
+$stable_ids_db      = $db;
+$stable_ids_version = $1;
+}
+} elsif (
+$db =~ /^([a-z]+_[a-z0-9]+(?:_[a-z0-9]+)? # species name e.g. homo_sapiens or canis_lupus_familiaris
+_
+[a-z]+            # db type
+(?:_\d+)?)        # optional end bit for ensembl genomes databases
+_
+(\d+)             # database release
+_
+(\w+)$             # assembly number can have letters too e.g 37c
+/x
+)
+{
+# Species specific databases (core, cdna, vega etc.)
+my ( $sp_name, $db_rel, $assem ) = ( $1, $2, $3 );
+if ( !defined($species) || $sp_name =~ /^$species/ ) {
+if ( $db_rel eq $software_version ) {
+$temp{$sp_name} = $db_rel . "_" . $assem;
+}
+}
+} 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 like databases
+my $core_like_dbs_found = 0;
+foreach my $type (qw(core cdna vega vega_update otherfeatures rnaseq)) {
+my @dbs = grep { /^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?  # species name
+_
+$type            # the database type
+_
+(?:\d+_)?         # optional end bit for ensembl genomes
+\d+               # database release
+_
+/x } @dbnames;
+if(@dbs) {
+$core_like_dbs_found = 1;
+}
+foreach my $database (@dbs) {
+if ( index( $database, 'collection' ) != -1 ) {
+# Skip multi-species databases.
+next;
+}
+my ( $species, $num ) =
+( $database =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?)  # species name
+_
+$type                   # type
+_
+(?:\d+_)?               # optional endbit for ensembl genomes
+(\d+)                   # databases release
+_
+/x );
+if(!defined($species)){
+warn "Cannot extract species name from database '$database'";
+}
+my $dba =
+Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+-group        => $type,
+-species      => $species.$species_suffix,
+-host         => $host,
+-user         => $user,
+-pass         => $pass,
+-port         => $port,
+-dbname       => $database,
+-wait_timeout => $wait_timeout,
+-no_cache     => $no_cache );
+if ($verbose) {
+printf( "Species '%s' loaded from database '%s'\n",
+$species, $database );
+}
+}
+}
+# Register multi-species databases
+my @multi_dbs = grep { /^\w+_collection_core_\w+$/ } @dbnames;
+foreach my $multidb (@multi_dbs) {
+my $sth = $dbh->prepare(
+sprintf(
+"SELECT species_id, meta_value FROM %s.meta "
+. "WHERE meta_key = 'species.db_name'",
+$dbh->quote_identifier($multidb) ) );
+$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_suffix,
+-species_id      => $species_id,
+-multispecies_db => 1,
+-host            => $host,
+-user            => $user,
+-pass            => $pass,
+-port            => $port,
+-dbname          => $multidb,
+-wait_timeout    => $wait_timeout,
+-no_cache        => $no_cache
+);
+if ($verbose) {
+printf( "Species '%s' (id:%d) loaded from database '%s'\n",
+$species, $species_id, $multidb );
+}
+}
+} ## end foreach my $multidb (@multi_dbs)
+if(!$core_like_dbs_found && $verbose) {
+print("No core-like databases found. Check your DB_VERSION (used '$software_version')\n");
+}
+# User upload DBs
+my @userupload_dbs = grep { /_userdata$/ } @dbnames;
+for my $userupload_db (@userupload_dbs) {
+if ( index( $userupload_db, 'collection' ) != -1 ) {
+# Skip multi-species databases.
+next;
+}
+my ($species) = ( $userupload_db =~ /(^.+)_userdata$/ );
+my $dba =
+Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+-group        => "userupload",
+-species      => $species.$species_suffix,
+-host         => $host,
+-user         => $user,
+-pass         => $pass,
+-port         => $port,
+-wait_timeout => $wait_timeout,
+-dbname   => $userupload_db,
+-no_cache => $no_cache );
+if ($verbose) {
+printf( "%s loaded\n", $userupload_db );
+}
+}
+# Register multi-species userupload databases.
+my @userdata_multidbs = grep { /^.+_collection_userdata$/ } @dbnames;
+foreach my $multidb (@userdata_multidbs) {
+my $sth = $dbh->prepare(
+sprintf(
+"SELECT species_id, meta_value FROM %s.meta "
+. "WHERE meta_key = 'species.db_name'",
+$dbh->quote_identifier($multidb) ) );
+$sth->execute();
+my ( $species_id, $species );
+$sth->bind_columns( \( $species_id, $species ) );
+while ( $sth->fetch() ) {
+my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+-group           => "userupload",
+-species         => $species.$species_suffix,
+-species_id      => $species_id,
+-multispecies_db => 1,
+-host            => $host,
+-user            => $user,
+-pass            => $pass,
+-port            => $port,
+-dbname          => $multidb,
+-wait_timeout    => $wait_timeout,
+-no_cache        => $no_cache
+);
+if ($verbose) {
+printf( "Species '%s' (id:%d) loaded from database '%s'\n",
+$species, $species_id, $multidb );
+}
+}
+} ## end foreach my $multidb (@userdata_multidbs)
+# Variation
+my $test_eval = eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor";
+if ($@or (!$test_eval)) {
+# Ignore variations as code required not there for this
+if ($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-z0-9]+(?:_[a-z0-9]+)?_variation_(?:\d+_)?\d+_/ } @dbnames;
+if(! @variation_dbs && $verbose) {
+print("No variation databases found\n");
+}
+for my $variation_db (@variation_dbs) {
+if ( index( $variation_db, 'collection' ) != -1 ) {
+	  # Skip multi-species databases.
+	  next;
+}
+my ( $species, $num ) =
+( $variation_db =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?)_variation_(?:\d+_)?(\d+)_/ );
+my $dba =
+Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(
+-group        => "variation",
+-species      => $species.$species_suffix,
+-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", $variation_db );
+}
+}
+# Register variation multispecies databases
+my @variation_multidbs =
+grep { /^\w+_collection_variation_\w+$/ } @dbnames;
+foreach my $multidb (@variation_multidbs) {
+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::Variation::DBSQL::DBAdaptor->new(
+-group           => 'variation',
+-species         => $species.$species_suffix,
+-species_id      => $species_id,
+-multispecies_db => 1,
+-host            => $host,
+-user            => $user,
+-pass            => $pass,
+-port            => $port,
+-dbname          => $multidb,
+-wait_timeout    => $wait_timeout,
+-no_cache        => $no_cache
+);
+if ($verbose) {
+printf( "Species '%s' (id:%d) loaded from database '%s'\n",
+$species, $species_id, $multidb );
+}
+}
+} ## end foreach my $multidb (@variation_multidbs)
+}
+my $func_eval = eval "require Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor";
+if ($@ or (!$func_eval)) {
+if ($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-z0-9]+(?:_[a-z0-9]+)?_funcgen_(?:\d+_)?\d+_/ } @dbnames;
+if(! @funcgen_dbs && $verbose) {
+print("No funcgen databases found\n");
+}
+for my $funcgen_db (@funcgen_dbs) {
+if ( index( $funcgen_db, 'collection' ) != -1 ) {
+# Skip multi-species databases.
+next;
+}
+my ( $species, $num ) =
+( $funcgen_db =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?)_funcgen_(?:\d+_)?(\d+)_/ );
+my $dba = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(
+-group        => "funcgen",
+-species      => $species.$species_suffix,
+-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", $funcgen_db );
+}
+}
+# Register functional genomics multispecies databases
+my @funcgen_multidbs =
+grep { /^\w+_collection_funcgen_\w+$/ } @dbnames;
+foreach my $multidb (@funcgen_multidbs) {
+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::Funcgen::DBSQL::DBAdaptor->new(
+-group           => 'funcgen',
+-species         => $species.$species_suffix,
+-species_id      => $species_id,
+-multispecies_db => 1,
+-host            => $host,
+-user            => $user,
+-pass            => $pass,
+-port            => $port,
+-dbname          => $multidb,
+-wait_timeout    => $wait_timeout,
+-no_cache        => $no_cache
+);
+if ($verbose) {
+printf( "Species '%s' (id:%d) loaded from database '%s'\n",
+$species, $species_id, $multidb );
+}
+}
+} ## end foreach my $multidb (@funcgen_multidbs)
+} ## end else [ if ($@) ]
+# Compara
+my @compara_dbs = grep { /^ensembl_compara/ } @dbnames;
+if (@compara_dbs) {
+my $comp_eval = eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
+if ($@ or (!$comp_eval)) {
+# Ignore Compara as code required not there for this
+if ($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      => $species.$species_suffix,
+-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 $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+-group        => 'core',
+-species      => 'Ancestral sequences'.$species_suffix,
+-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");
+}
+# Ontology
+if ( defined($ontology_version) && $ontology_version != 0 ) {
+require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
+my $dba =
+Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
+'-species' => 'multi' . $species_suffix,
+'-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");
+}
+if ( defined($stable_ids_db) && $stable_ids_version != 0 ) {
+my $dba =
+Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+'-species' => 'multi' . $species_suffix,
+'-group'   => 'stable_ids',
+'-host'    => $host,
+'-port'    => $port,
+'-user'    => $user,
+'-pass'    => $pass,
+'-dbname'  => $stable_ids_db, );
+if ($verbose) {
+printf( "%s loaded\n", $stable_ids_db );
+}
+}
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+-species => 'multi'.$species_suffix,
+-alias   => ['compara'.$species_suffix] );
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+-species => 'multi'.$species_suffix,
+-alias   => ['ontology'.$species_suffix] );
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+-species => 'multi'.$species_suffix,
+-alias   => ['stable_ids'.$species_suffix] );
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+-species => 'Ancestral sequences'.$species_suffix,
+-alias   => ['ancestral_sequences'.$species_suffix] );
+# Register aliases as found in adaptor meta tables.
+$self->find_and_add_aliases( '-handle'         => $dbh,
+'-species_suffix' => $species_suffix );
+$self->_additional_aliases($species_suffix);
+$dbh->disconnect();
+my $count = $self->get_DBAdaptor_count() - $original_count;
+return $count >= 0 ? $count : 0;
+} ## end sub load_registry_from_db
+# Used as a place to push "hack" aliases
+sub _additional_aliases {
+my ($self, $species_suffix) = @_;
+#Adding branch-68 thirteen-lined ground squirrel "old" aliases
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+-species => 'ictidomys_tridecemlineatus'.$species_suffix,
+-alias   => ['spermophilus_tridecemlineatus'.$species_suffix] );
+Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+-species => 'ictidomys_tridecemlineatus'.$species_suffix,
+-alias   => ['spermophilus tridecemlineatus'.$species_suffix] );
+return;
+} # end sub _additional_aliases
+=head2 _group_to_adaptor_class
+Arg [1]       : The group you wish to decode to an adaptor class
+Example       : Bio::EnsEMBL::Registry->_group_to_adaptor_class('core');
+Description   : Has an internal lookup of groups to their adaptor classes
+Returntype    : String
+Exceptions    : Thrown if the group is unknown
+Status        : Stable
+=cut
+sub _group_to_adaptor_class {
+my ($self, $group) = @_;
+my $class = {
+core => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+cdna => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+otherfeatures => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+rnaseq => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+vega => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
+variation => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
+funcgen => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
+compara => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
+}->{$group};
+throw "Group '${group}' is unknown" if ! $class;
+return $class;
+}
+=head2 find_and_add_aliases
+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.
+Arg [SPECIES_SUFFIX]: (optional) string
+This option will append the string to the species
+name in the registry for all databases.
+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    : Throws if an alias is found in more than one species.
+Status        : Stable
+=cut
+sub find_and_add_aliases {
+my $class = shift ;
+my ($adaptor, $group, $dbh, $species_suffix ) =
+rearrange( [ 'ADAPTOR', 'GROUP', 'HANDLE', 'SPECIES_SUFFIX' ], @_ );
+#Can be undef; needs to be something to avoid warnings
+$species_suffix ||=  q{};
+my @dbas;
+if ( defined($adaptor) ) {
+@dbas = ($adaptor);
+} elsif ( defined($dbh) ) {
+if ( length($species_suffix) > 0 ) {
+my @full = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) };
+foreach my $db (@full) {
+if ( $db->species =~ /$species_suffix/ ) {
+push( @dbas, $db );
+}
+}
+} else {
+@dbas = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) };
+}
+} 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($dbname) ) );
+# Execute, and don't care about errors (there will be errors for
+# databases without a 'meta' table.
+$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) ) {
+push( @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) {
+my $alias_suffix = $alias.$species_suffix;
+#Lowercase because stored aliases are lowercased
+my $lc_species = lc($species);
+my $lc_alias_suffix = lc($alias_suffix);
+if (   !$class->alias_exists( $alias_suffix )
+&& $lc_species ne $lc_alias_suffix )
+{
+$class->add_alias( $species, $alias_suffix );
+} elsif (
+$lc_species ne $class->get_alias( $alias_suffix ) )
+{
+$class->remove_alias( $species, $alias_suffix );
+}
+}
+} ## end foreach my $dba (@dbas)
+return;
+} ## end sub find_and_add_aliases
+=head2 load_registry_from_multiple_dbs
+Arg [1]   : Array of hashes, each hash being a set of arguments to
+load_registry_from_db() (see above).
+Example   :
+$registry->load_registry_from_multiple_dbs( {
+'-host'    => 'ensembldb.ensembl.org',
+'-user'    => 'anonymous',
+'-verbose' => '1'
+},
+{
+'-host'     => 'server.example.com',
+'-user'     => 'anonymouse',
+'-password' => 'cheese',
+'-verbose'  => '1'
+} );
+Description:  Will call load_registry_from_db() (see above)
+multiple times and merge the resulting registries
+into one, effectively allowing a user to connect to
+databases on multiple database servers from within
+one program.
+If a database is found on more than one server, the
+first found instance of that database will be used.
+Returntype : Int count of the DBAdaptor instances which can be found in the
+registry
+=cut
+sub load_registry_from_multiple_dbs {
+my ( $self, @args ) = @_;
+my $original_count = $self->get_DBAdaptor_count();
+my %merged_register = %registry_register;
+foreach my $arg (@args) {
+local %registry_register = ();
+my $verbose;
+($verbose) = rearrange( ['VERBOSE'], %{$arg} );
+$self->load_registry_from_db( %{$arg} );
+#
+# Merge the localized %registry_register into %merged_register.
+#
+# Merge the _SPECIES and _ALIAS sections of %registry_register.
+foreach my $section ( 'Species', 'Alias' ) {
+my $section_key = '_' . uc($section);
+while ( my ( $key, $value ) =
+each( %{ $registry_register{$section_key} } ) )
+{
+if ( !exists( $merged_register{$section_key}{$key} ) ) {
+$merged_register{$section_key}{$key} = $value;
+} elsif ($verbose) {
+printf( "%s '%s' found on multiple servers, "
+. "using first found\n",
+$section, $key );
+}
+}
+}
+} ## end foreach my $arg (@args)
+# Add the DBAs from the _SPECIES section into the _DBA section.
+foreach my $species_hash ( values( %{ $merged_register{_SPECIES} } ) )
+{
+foreach my $group_hash ( values( %{$species_hash} ) ) {
+if ( ref($group_hash) eq 'HASH' && exists( $group_hash->{_DB} ) )
+{
+push( @{ $merged_register{_DBA} }, $group_hash->{_DB} );
+}
+}
+}
+%registry_register = %merged_register;
+my $count = $self->get_DBAdaptor_count() - $original_count;
+return $count >= 0 ? $count : 0;
+} ## end sub load_registry_from_multiple_dbs
+#
+# Web specific routines
+#
+=head2 DEPRECATED load_registry_with_web_adaptors
+DEPRECATED: Use load_registry_from_db instead.
+=cut
+sub load_registry_with_web_adaptors{
+my $class = shift;
+deprecate('Use the load_registry_from_db instead');
+my $site_eval = eval{ require SiteDefs };
+if ($@ or (!defined($site_eval))){ die "Can't use SiteDefs.pm - $@\n"; }
+SiteDefs->import(qw(:ALL));
+my $species_eval = eval{ require SpeciesDefs };
+if ($@ or (!defined($species_eval))){ 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);
+}
+return;
+}
+=head2 set_default_track
+Sets a flag to say that that this species/group are a default track and do not
+need to be added as another web track.
+Arg [1]    : name of the species to get the adaptors for in the registry.
+Arg [2]    : name of the type to get the adaptors for in the registry.
+Example    : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
+Returntype : none
+Exceptions : none
+Status     : At Risk.
+=cut
+sub set_default_track {
+my ( $class, $species, $group ) = @_;
+$species = get_alias($species);
+$registry_register{'def_track'}{$species}{ lc($group) } = 1;
+return;
+}
+=head2 default_track
+Check flag to see if this is a default track
+Arg [1]    : name of the species to get the adaptors for in the registry.
+Arg [2]    : name of the type to get the adaptors for in the registry.
+Example    : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
+Returntype : int
+Exceptions : none
+Status     : At Risk.
+=cut
+sub default_track {
+my ( $class, $species, $group ) = @_;
+$species = get_alias($species);
+if (
+defined( $registry_register{'def_track'}{$species}{ lc($group) } ) )
+{
+return 1;
+}
+return 0;
+}
+=head2 add_new_tracks
+Will add new gene tracks to the configuration of the WEB server if they are
+not of the type default and the configuration already has genes in the display.
+Arg [1]    : hash of the default configuration of the web page
+Returntype : none
+Exceptions : none
+Called by  : UserConfig.pm
+Status     : At Risk.
+=cut
+sub add_new_tracks{
+my($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;
+}
+=head2 no_version_check
+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.
+=cut
+sub no_version_check {
+my ( $self, $arg ) = @_;
+( defined $arg )
+&& ( $registry_register{'_no_version_check'} = $arg );
+return $registry_register{'_no_version_check'};
+}
+=head2 no_cache_warnings
+Arg[0]      : boolean for turning the flag on and off
+Description : Turns off any warnings about not using caching in all available
+adaptors.
+Returntype  : boolean Current status
+Exceptions  : None
+=cut
+sub no_cache_warnings {
+my ($self, $arg) = @_;
+if(defined $arg) {
+$Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::SILENCE_CACHE_WARNINGS = $arg;
+}
+return $Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::SILENCE_CACHE_WARNINGS;
+}
+=head2 version_check
+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.
+=cut
+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_/x ) {
+return 1;
+}
+if ( $dba->dbc()->dbname() =~ /(\d+)_\S+$/x ) {
+$database_version = $1;
+} elsif ( $dba->dbc()->dbname() =~ /ensembl_compara_(\d+)/x ) {
+$database_version = $1;
+} elsif ( $dba->dbc()->dbname() =~ /ensembl_help_(\d+)/x ) {
+$database_version = $1;
+} elsif ( $dba->dbc()->dbname() =~ /ensembl_ontology_(\d+)/x ) {
+$database_version = $1;
+} elsif ( $dba->dbc()->dbname() =~ /ensembl_stable_ids_(\d+)/x ) {
+$database_version = $1;
+} else {
+warn(
+sprintf(
+"No database version for database %s "
+. ". You must be using a post version 34 database "
+. "with version 34 or later code.\n"
+. "You need to update your database "
+. "or use the appropriate Ensembl software release "
+. "to ensure your script does not crash\n",
+$dba->dbc()->dbname() ) );
+}
+} ## end if ( $database_version...
+if ( $database_version != software_version() ) {
+warn(
+sprintf(
+"For %s there is a difference in the software release (%s) "
+. "and the database release (%s). "
+. "You should update one of these to ensure that your script "
+. "does not crash.\n",
+$dba->dbc()->dbname(),
+software_version(), $database_version
+) );
+return 0;
+}
+return 1;    # Ok
+} ## end sub version_check
+=head2 get_species_and_object_type
+Description:  Get the species name, object type (gene, transcript,
+translation, or exon etc.), and database type for a
+stable ID.
+Arg [1]    :  String stable_id
+The stable ID to find species and object type for.
+Arg [2]    :  String known_type (optional)
+The type of the stable ID, if it is known.
+Arg [3]    :  String known_species (optional)
+The species, if known
+Arg [4]    :  String known_db_type (optional)
+The database type, if known
+Example    :  my $stable_id = 'ENST00000326632';
+my ( $species, $object_type, $db_type ) =
+$registry->get_species_and_object_type($stable_id);
+my $adaptor =
+$registry->get_adaptor( $species, $db_type,
+$object_type );
+my $object = $adaptor->fetch_by_stable_id($stable_id);
+Return type:  Array consisting of the species name, object type,
+and database type.  The array may be empty if no
+match is found.
+Exceptions :  none
+Status     :  At Risk.
+=cut
+my %stable_id_stmts = (
+gene => 'SELECT m.meta_value '
+. 'FROM %1$s.gene '
+. 'JOIN %1$s.seq_region USING (seq_region_id) '
+. 'JOIN %1$s.coord_system USING (coord_system_id) '
+. 'JOIN %1$s.meta m USING (species_id) '
+. 'WHERE stable_id = ? '
+. 'AND m.meta_key = "species.production_name"',
+transcript => 'SELECT m.meta_value '
+. 'FROM %1$s.transcript '
+. 'JOIN %1$s.seq_region USING (seq_region_id) '
+. 'JOIN %1$s.coord_system USING (coord_system_id) '
+. 'JOIN %1$s.meta m USING (species_id) '
+. 'WHERE stable_id = ? '
+. 'AND m.meta_key = "species.production_name"',
+exon => 'SELECT m.meta_value '
+. 'FROM %1$s.exon '
+. 'JOIN %1$s.seq_region USING (seq_region_id) '
+. 'JOIN %1$s.coord_system USING (coord_system_id) '
+. 'JOIN %1$s.meta m USING (species_id) '
+. 'WHERE stable_id = ? '
+. 'AND m.meta_key = "species.production_name"',
+translation => 'SELECT m.meta_value '
+. 'FROM %1$s.translation tl '
+. 'JOIN %1$s.transcript USING (transcript_id) '
+. 'JOIN %1$s.seq_region USING (seq_region_id) '
+. 'JOIN %1$s.coord_system USING (coord_system_id) '
+. 'JOIN %1$s.meta m USING (species_id) '
+. 'WHERE tl.stable_id = ? '
+. 'AND m.meta_key = "species.production_name"',
+operon => 'SELECT m.meta_value '
+. 'FROM %1$s.operon '
+. 'JOIN %1$s.seq_region USING (seq_region_id) '
+. 'JOIN %1$s.coord_system USING (coord_system_id) '
+. 'JOIN %1$s.meta m USING (species_id) '
+. 'WHERE stable_id = ? '
+. 'AND m.meta_key = "species.production_name"',
+operontranscript => 'SELECT m.meta_value '
+. 'FROM %1$s.operon_transcript '
+. 'JOIN %1$s.seq_region USING (seq_region_id) '
+. 'JOIN %1$s.coord_system USING (coord_system_id) '
+. 'JOIN %1$s.meta m USING (species_id) '
+. 'WHERE stable_id = ? '
+. 'AND m.meta_key = "species.production_name"',
+);
+sub get_species_and_object_type {
+my ($self, $stable_id, $known_type, $known_species, $known_db_type, $force_long_lookup) = @_;
+#get the stable_id lookup database adaptor
+my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1);
+if ($stable_ids_dba && ! $force_long_lookup) {
+my $statement = 'SELECT name, object_type, db_type FROM stable_id_lookup join species using(species_id) WHERE stable_id = ?';
+if ($known_species) {
+	 $statement .= ' AND name = ?';
+}
+if ($known_db_type) {
+	 $statement .= ' AND db_type = ?';
+}
+if ($known_type) {
+	 $statement .= ' AND object_type = ?';
+}
+my $sth = $stable_ids_dba->dbc()->prepare($statement);
+$sth->bind_param(1, $stable_id, SQL_VARCHAR);
+my $param_count = 1;
+if ($known_species) {
+$known_species = $self->get_alias($known_species);
+	 $param_count++;
+	 $sth->bind_param($param_count, $known_species, SQL_VARCHAR);
+}
+if ($known_db_type) {
+	 $param_count++;
+	 $sth->bind_param($param_count, $known_db_type, SQL_VARCHAR);
+}
+if ($known_type) {
+	 $param_count++;
+	 $sth->bind_param($param_count, $known_type, SQL_VARCHAR);
+}
+$sth->execute();
+my ($species, $type, $db_type) = $sth->fetchrow_array();
+$sth->finish();
+return ($species ,$type, $db_type);
+} else {
+if (defined $known_type && !exists $stable_id_stmts{lc $known_type}) {
+	  return;
+}
+my @types = defined $known_type ? ($known_type) : ('Gene', 'Transcript', 'Translation', 'Exon', 'Operon', 'OperonTranscript');
+if(! $known_db_type) {
+$known_db_type = 'core';
+}
+my %get_adaptors_args;
+$get_adaptors_args{'-group'} = $known_db_type;
+if ($known_species) {
+	  $get_adaptors_args{'-species'} = $known_species;
+}
+my @dbas = sort { $a->dbc->host cmp $b->dbc->host || $a->dbc->port <=> $b->dbc->port }
+	  @{$self->get_all_DBAdaptors(%get_adaptors_args)};
+foreach my $dba (@dbas) {
+	  foreach my $type (@types) {
+	      my $statement = sprintf $stable_id_stmts{lc $type}, $dba->dbc->dbname;
+	      my $sth = $dba->dbc()->prepare($statement);
+	      $sth->bind_param(1, $stable_id, SQL_VARCHAR);
+	      $sth->execute;
+	      my $species = $sth->fetchall_arrayref->[0][0];
+	      $sth->finish;
+	      return ($species, $type, $known_db_type) if defined $species;
+	  }
+} ## end foreach my $dba ( sort { $a...})
+}
+return;
+} ## end sub get_species_and_object_type
+1;

Mercurial > repos > mahtabm > ensemb_rep_gvl

comparison variant_effect_predictor/Bio/EnsEMBL/Registry.pm @ 0:2bc9b66ada89 draft default tip