Bio::EnsEMBL::DBSQL::MetaContainer Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::MetaContainer:

Public Member Functions
public String	get_production_name ()
public String	get_display_name ()
public String	get_common_name ()
public String	get_scientific_name ()
public String	get_division ()
public String	get_taxonomy_id ()
public String	get_genebuild ()
public	get_classification ()
Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseMetaContainer
public Int	get_schema_version ()
public Listref	list_value_by_key ()
public Scalar	single_value_by_key ()
public void	store_key_value ()
public void	update_key_value ()
public void	delete_key ()
public void	delete_key_value ()
public Boolean	key_value_exists ()
protected	_species_specific_key ()
Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()
public DBI::StatementHandle	prepare ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public Boolean	is_multispecies ()
public Int	species_id ()
protected	_list_dbIDs ()
protected	_straight_join ()
protected	_can_straight_join ()
public Listref	bind_param_generic_fetch ()
protected	_bind_param_generic_fetch ()
public String	generate_in_constraint ()
public Listref	generic_fetch ()
public Int	generic_count ()
protected	_generate_sql ()
public Bio::EnsEMBL::Feature	fetch_by_dbID ()
protected	_uncached_fetch_by_dbID ()
public Listref	fetch_all_by_dbID_list ()
protected	_uncached_fetch_all_by_dbID_list ()
protected ArrayRef	_uncached_fetch_all_by_id_list ()
public	fetch_all ()
public Scalar	last_insert_id ()
public	insert_ignore_clause ()
protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()
protected Boolean	_no_id_cache ()
public Boolean	ignore_cache_override ()
public Int	schema_version ()
protected	_tables ()
protected	_columns ()
protected	_default_where_clause ()
protected	_left_join ()
protected	_final_clause ()
protected	_objs_from_sth ()
protected	_build_id_cache ()
protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

my $meta_container =
  $registry->get_adaptor( 'Human', 'Core', 'MetaContainer' );
 
my @mapping_info =
  @{ $meta_container->list_value_by_key('assembly.mapping') };
 
my $scientific_name = $meta_container->get_scientific_name();

Description

  An object that encapsulates specific access to core db meta data

Definition at line 22 of file MetaContainer.pm.

Member Function Documentation

get_classification()

public Bio::EnsEMBL::DBSQL::MetaContainer::get_classification

(

)

Undocumented method

Code:

get_common_name()

public String Bio::EnsEMBL::DBSQL::MetaContainer::get_common_name

(

)

  Args          : none
  Example       :

$species = $meta_container->get_common_name();

  Description   : Obtains the common name of the species.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

Code:

get_display_name()

public String Bio::EnsEMBL::DBSQL::MetaContainer::get_display_name

(

)

  Args          : none
  Example       :

$species = $meta_container->get_display_name();

  Description   : Obtains the name of the species in a form usable as, for
                  example, a short label in a GUI.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

Code:

get_division()

public String Bio::EnsEMBL::DBSQL::MetaContainer::get_division

(

)

  Args          : none
  Example       :

$div = $meta_container->get_division();

  Description   : Obtains the Ensembl Genomes division to which the species belongs.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

Code:

get_genebuild()

public ArrayRef Bio::EnsEMBL::DBSQL::MetaContainer::get_genebuild

(

)

  Arg [1]    : none
  Example    :

$tax_id = $meta_container->get_genebuild();

  Description: Retrieves the genebuild from the database meta table
  Returntype : string
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

  Example    :

$classification = $meta_container->get_classification();

  Description: Retrieves the classification held in the backing database minus
               any species specific levels. This means that the first element
               in the array will be subfamily/family level ascending to
               superkingdom
  Returntype : ArrayRef[String]
  Exceptions : none
  Caller     : ?
  Status     : Stable

/**

get_production_name()

public String Bio::EnsEMBL::DBSQL::MetaContainer::get_production_name

(

)

  Args          : none
  Example       :

$species = $meta_container->get_production_name();

  Description   : Obtains the name of the species in a form usable as, for
                  example, a table name, file name etc.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

Code:

get_scientific_name()

public String Bio::EnsEMBL::DBSQL::MetaContainer::get_scientific_name

(

)

  Args          : none
  Example       :

$species = $meta_container->get_scientific_name();

  Description   : Obtains the full scientific name of the species.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

Code:

get_taxonomy_id()

public String Bio::EnsEMBL::DBSQL::MetaContainer::get_taxonomy_id

(

)

  Arg [1]    : none
  Example    :

$tax_id = $meta_container->get_taxonomy_id();

  Description: Retrieves the taxonomy id from the database meta table
  Returntype : string
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm