Bio::EnsEMBL::Compara::DBSQL::DBAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::DBAdaptor:

List of all members.

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Class Summary

Description

This object represents the handle for a comparative DNA alignment database

Synopsis

    $db = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor-\>new(
        -user   =\> 'root',
        -host   =\> 'caldy',
        -dbname =\> 'pog',
        -species =\> 'Multi',
        );

    $db = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor-\>new(
        -url =\> 'mysql://user:pass@host:port/db_name');

Definition at line 27 of file DBAdaptor.pm.

Available Methods
protected Bio::EnsEMBL::ExternalFeatureFactory	_each_DASFeatureFactory ()
protected	_get_schema_build ()
public void	add_DASFeatureFactory ()
public void	add_db_adaptor ()
public void	add_ExternalFeatureAdaptor ()
public void	add_ExternalFeatureFactory ()
public void	add_GenericFeatureAdaptor ()
public Array	all_species ()
public	assembly_type ()
public	AUTOLOAD ()
public	db ()
public	db_handle ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public	dbname ()
public	DESTROY ()
public	disconnect_when_inactive ()
public Dna	dnadb ()
public	driver ()
public Adaptor	get_adaptor ()
public Hash	get_all_db_adaptors ()
public	get_available_adaptors ()
public Bio::EnsEMBL::DBSQL::DBConnection	get_db_adaptor ()
public Reference	get_ExternalFeatureAdaptors ()
public Reference	get_GenericFeatureAdaptors ()
public Bio::EnsEMBL::Utils::SeqRegionCache	get_SeqRegionCache ()
public String	group ()
public	host ()
public Boolean	is_multispecies ()
public	list_supported_assemblies ()
public Bio::EnsEMBL::Compara::DBSQL::DBAdaptor	new ()
public Int	no_cache ()
public	password ()
public	port ()
public	prepare ()
public	reconnect_when_lost ()
public	remove_all_DASFeatureFactories ()
public void	remove_db_adaptor ()
public void	set_adaptor ()
public	source ()
public String	species ()
public String	species_id ()
public	username ()

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Method Documentation

public Bio::EnsEMBL::Compara::DBSQL::DBAdaptor::get_available_adaptors

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::DBSQL::DBAdaptor.

Reimplemented in Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::DBAdaptor Bio::EnsEMBL::Compara::DBSQL::DBAdaptor::new

(

)

  Arg [..]   : list of named arguments.  See Bio::EnsEMBL::DBConnection.
               [-URL mysql://user:pass@host:port/db_name] alternative way to specify the
               connection parameters. Pass and port are optional. If none is speciefied,
               the species name will be equal to the db_name.
               [-GROUP] This option is *always* set to "compara". Use another DBAdaptor
               for other groups.
  Example    :  $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
                    -user   => 'root',
                    -pass => 'secret',
                    -host   => 'caldy',
                    -port   => 3306,
                    -dbname => 'ensembl_compara',
                    -species => 'Multi');
  Example    :  $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
                    -url => 'mysql://root:secret@caldy:3306/ensembl_compara'
                    -species => 'Multi');
  Description: Creates a new instance of a DBAdaptor for the compara database.
  Returntype : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : general

Code:

Reimplemented from Bio::EnsEMBL::DBSQL::DBAdaptor.

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

• Bio/EnsEMBL/Compara/DBSQL/DBAdaptor.pm