Public Member Functions
public	gen_load ()

public	find_unique_species ()

public	load_adaptors ()

public	load_and_attach_dnadb_to_core ()

public DBAdaptor	load_core ()

public DBAdaptor	load_compara ()

public DBAdaptor	load_hive ()

public DBAdaptor	load_pipeline ()

public DBAdaptor	load_SNP ()

public	load_haplotype ()

public	load_ontology ()

public	load_estgene ()

public	load_variation ()

public	load_funcgen ()

public DBAdaptor	load_otherfeatures ()

public	load_rnaseq ()

public DBAdaptor	load_vega ()

public	add_alias ()

public	pre_funcgen_hook ()

Detailed Description

Synopsis

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

Description

The ConfigRegistry will "Register" a set of adaptors based on the type
of database that is being loaded.

Definition at line 23 of file ConfigRegistry.pm.

Member Function Documentation

◆ add_alias()

public Bio::EnsEMBL::Utils::ConfigRegistry::add_alias ( )

Undocumented method

Code:

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◆ find_unique_species()

public Bio::EnsEMBL::Utils::ConfigRegistry::find_unique_species ( )

Undocumented method

Code:

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◆ gen_load()

public Bio::EnsEMBL::Utils::ConfigRegistry::gen_load ( )

Undocumented method

Code:

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sub gen_load {
  my ($dba) = @_;
  my $pre_hook;
  my $config_sub;
 
  # At some point we hope to set the group in the DBadaptor, hence this
  # long check etc. should be simpler.
 
  if ( $dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('compara');
    }
    $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_compara;
  } elsif ( $dba->isa('Bio::EnsEMBL::Lite::DBAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('lite');
    }
    $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_lite;
  } elsif ( $dba->isa('Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('pipeline');
    }
    $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_pipeline;
  } elsif ( $dba->isa('Bio::EnsEMBL::Hive::DBSQL::DBAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('hive');
    }
    $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_hive;
  } elsif ( $dba->isa('Bio::EnsEMBL::Variation::DBSQL::DBAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('variation');
    }
    $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_variation;
  } elsif ( $dba->isa('Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('funcgen');
    }
    $pre_hook = \&Bio::EnsEMBL::Utils::ConfigRegistry::pre_funcgen_hook;
    $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen;
  } elsif ( $dba->isa('Bio::EnsEMBL::DBSQL::OntologyDBAdaptor') || $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) {
    if ( !defined( $dba->group() ) ) {
      $dba->group('ontology');
    }
    $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_ontology;
  } elsif ( $dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
    #vega uses the core DBAdaptor so test if vega is in the dbname
    if ( !defined( $dba->group() ) ) {
      $dba->group('core');
    }
 
    if ( $dba->group eq "estgene" ) {
      $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_estgene;
    } elsif ( $dba->group eq "otherfeatures" ) {
      $config_sub =
        \&Bio::EnsEMBL::Utils::ConfigRegistry::load_otherfeatures;
    } elsif ( $dba->group eq "rnaseq" ) {
      $config_sub =
        \&Bio::EnsEMBL::Utils::ConfigRegistry::load_rnaseq;
    } elsif ( $dba->group eq 'vega' || $dba->group eq 'vega_update' ) {
      $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_vega;
    } else {
      $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_core;
    }
 
  } else {
    # none standard DBA adaptor
    if ( !defined( $dba->group() ) ) {
      $dba->group('none_standard');
    }
    $config_sub =
      \&Bio::EnsEMBL::Utils::ConfigRegistry::load_and_attach_dnadb_to_core;
    #    throw("Unknown DBAdaptor type $dba\n");
  }
  
  #Run the pre-hook if one was defined
  $pre_hook->($dba) if $pre_hook;
 
  # return if the connection and species, group are the same
 
  if ( defined( $dba->species ) ) {
    my $db_reg = $reg->get_DBAdaptor( $dba->species, $dba->group, 1 );
    if ( defined($db_reg) ) {
      if ( $dba->dbc->equals( $db_reg->dbc ) ) { return $db_reg }
      else {
        my $msg =
          sprintf( 'WARN: Species (%s) and group (%s) '
            . 'same for two seperate databases',
          $dba->species(), $dba->group() );
 
        warn "${msg}\nModify species name for one of these\n";
        $dba->species(
          find_unique_species( $dba->species, $dba->group ) );
      }
    }
  } else {    # no species
    
    my @db_reg =
      @{ $reg->get_all_DBAdaptors_by_connection( $dba->dbc ) };
 
    foreach my $db_adaptor (@db_reg) {
      if ( $db_adaptor->group eq $dba->group ) {
        # found same db connection and group
        return $db_adaptor;
      }
    }
 
    $dba->species( find_unique_species( "DEFAULT", $dba->group ) );
    if ( $dba->species ne "DEFAULT" ) {
      warn "WARN: For multiple species "
        . "use species attribute in DBAdaptor->new()\n";
    }
  }
 
  Bio::EnsEMBL::Registry->add_DBAdaptor( $dba->species(), $dba->group(),
    $dba );
 
  #call the loading subroutine. (add the adaptors to the DBAdaptor)
  &{$config_sub}($dba);
 
  return $dba;
} ## end sub gen_load

◆ load_adaptors()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_adaptors ( )

Undocumented method

Code:

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◆ load_and_attach_dnadb_to_core()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_and_attach_dnadb_to_core ( )

Undocumented method

Code:

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◆ load_compara()

public DBAdaptor Bio::EnsEMBL::Utils::ConfigRegistry::load_compara ( )

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

Code:

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◆ load_core()

public DBAdaptor Bio::EnsEMBL::Utils::ConfigRegistry::load_core ( )

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

Code:

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◆ load_estgene()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_estgene ( )

Undocumented method

Code:

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◆ load_funcgen()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen ( )

Undocumented method

Code:

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◆ load_haplotype()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_haplotype ( )

Undocumented method

Code:

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◆ load_hive()

public DBAdaptor Bio::EnsEMBL::Utils::ConfigRegistry::load_hive ( )

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

Code:

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◆ load_ontology()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_ontology ( )

Undocumented method

Code:

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◆ load_otherfeatures()

public DBAdaptor Bio::EnsEMBL::Utils::ConfigRegistry::load_otherfeatures ( )

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

Code:

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◆ load_pipeline()

public DBAdaptor Bio::EnsEMBL::Utils::ConfigRegistry::load_pipeline ( )

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

Code:

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◆ load_rnaseq()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_rnaseq ( )

Undocumented method

Code:

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◆ load_SNP()

public DBAdaptor Bio::EnsEMBL::Utils::ConfigRegistry::load_SNP ( )

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

Code:

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◆ load_variation()

public Bio::EnsEMBL::Utils::ConfigRegistry::load_variation ( )

Undocumented method

Code:

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◆ load_vega()

public DBAdaptor Bio::EnsEMBL::Utils::ConfigRegistry::load_vega ( )

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

Code:

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◆ pre_funcgen_hook()

public Bio::EnsEMBL::Utils::ConfigRegistry::pre_funcgen_hook ( )

Undocumented method

Code:

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The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ add_alias()

◆ find_unique_species()

◆ gen_load()

◆ load_adaptors()

◆ load_and_attach_dnadb_to_core()

◆ load_compara()

◆ load_core()

◆ load_estgene()

◆ load_funcgen()

◆ load_haplotype()

◆ load_hive()

◆ load_ontology()

◆ load_otherfeatures()

◆ load_pipeline()

◆ load_rnaseq()

◆ load_SNP()

◆ load_variation()

◆ load_vega()

◆ pre_funcgen_hook()