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Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor:

List of all members.


Class Summary

Synopsis

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

Description

This object represents the handle for a comparative DNA alignment database
 

Definition at line 24 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 ()

Method Documentation

public Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor::get_available_adaptors ( )

Undocumented method

Code:
click to view

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

public Bio::EnsEMBL::Compara::DBSQL::DBAdaptor Bio::EnsEMBL::Compara::DBSQL::DBAdaptor::new ( ) [inherited]
  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:
click to view

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


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