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

Class Summary

Synopsis

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

  $gene_adaptor = $db-\>get_GeneAdaptor();

  $gene = $gene_adaptor-\>fetch_by_stable_id($stable_id);

  $slice =
    $db-\>get_SliceAdaptor()-\>fetch_by_chr_start_end( 'X', 1, 10000 );

Description

Formerly this class provided database connectivity and a means
to retrieve object adaptors.  This class is now provided for
convenience and backwards compatibility, and delegates its connection
responsibilities to the DBConnection class (no longer inherited from)
and its object adaptor retrieval to the static Bio::EnsEMBL::Registry.

Please use Bio::EnsEMBL::Registry to retrieve object adaptors.

Definition at line 40 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 Reference	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::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

protected Bio::EnsEMBL::ExternalFeatureFactory Bio::EnsEMBL::DBSQL::DBAdaptor::_each_DASFeatureFactory ( )

  Args       : none
  Example    : none
  Description: Not sure if this is used, or if it should be removed.  It 
               does not seem to be used at the moment
  Returntype : Bio::EnsEMBL::ExternalFeatureFactory
  Exceptions : none
  Caller     : ??
  Status     : At Risk
             : with the new web code this may not be needed/supported

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protected Bio::EnsEMBL::DBSQL::DBAdaptor::_get_schema_build ( )

Undocumented method

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public void Bio::EnsEMBL::DBSQL::DBAdaptor::add_DASFeatureFactory ( )

  Arg [1]    : Bio::EnsEMBL::ExternalFeatureFactory $value 
  Example    : none
  Description: Attaches a DAS Feature Factory to this method.  
               ExternalFeatureFactory objects are not really used right now.
               They may be reintroduced or taken out completely.  The fate
               of this function is unknown (although it is presently needed).
  Returntype : none
  Exceptions : none
  Caller     : EnsWeb
  Status     : At Risk
             : with the new web code this may not be needed/supported

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public void Bio::EnsEMBL::DBSQL::DBAdaptor::add_db_adaptor ( )

Arg [1] : string $name the name of the database to attach to this database Arg [2] : Bio::EnsEMBL::DBSQL::DBConnection the db adaptor to attach to this database Example : $db->add_db_adaptor('lite', $lite_db_adaptor); Description: Attaches another database instance to this database so that it can be used in instances where it is required. Returntype : none Exceptions : none Caller : EnsWeb Status : At Risk : may get

Deprecated:: , please use add_db from the registry instead

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public void Bio::EnsEMBL::DBSQL::DBAdaptor::add_ExternalFeatureAdaptor ( )

  Arg [1]    : Bio::EnsEMBL::External::ExternalFeatureAdaptor
  Example    : $db_adaptor->add_ExternalFeatureAdaptor($xfa);
  Description: Adds an external feature adaptor to this database adaptor.
               Adding the external adaptor in this way allows external
               features to be obtained from Slices and from RawContigs.

               The external feature adaptor which is passed to this method
               will have its db attribuite set to this DBAdaptor object via 
               the db accessor method.

               ExternalFeatureAdaptors passed to this method are stored 
               internally in a hash keyed on the string returned by the 
               ExternalFeatureAdaptors track_name method.

               If the track name method is not implemented then the 
               a default key named 'External features' is assigned.  In the
               event of duplicate key names, a number is appended to the
               key name, and incremented for each subsequent adaptor with the
               same track name.  For example, if no track_names are specified 
               then the the external feature adaptors will be stored under the
               keys 'External features', 'External features2' 
               'External features3' etc.
  Returntype : none
  Exceptions : none
  Caller     : general

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public void Bio::EnsEMBL::DBSQL::DBAdaptor::add_ExternalFeatureFactory ( )

  Arg [1]    : Bio::EnsEMBL::DB::ExternalFeatureFactoryI $value
  Example    : $db_adaptor->add_ExternalFeatureFactory
  Description: It is recommended that add_ExternalFeatureAdaptor be used 
               instead.  See documentation for 
               Bio::EnsEMBL::External::ExternalFeatureAdaptor

               Adds an external feature factory to the core database
               so that features from external sources can be displayed in 
               ensembl. This method is still available mainly for legacy
               support for external EnsEMBL installations.
  Returntype : none
  Exceptions : none
  Caller     : external

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public void Bio::EnsEMBL::DBSQL::DBAdaptor::add_GenericFeatureAdaptor ( )

  Arg [1]    : The name of the feature.
  Arg [2]    : Adaptor object for a generic feature.
  Example    : $db->add_GenericFeatureAdaptor("SomeFeature",
                              "Bio::EnsEMBL::DBSQL::SomeFeatureAdaptor")
  Description: Stores the object which represents the adaptor for the
               named feature type.
  Returntype : none
  Exceptions :
  Caller     : external

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public Array Bio::EnsEMBL::DBSQL::DBAdaptor::all_species ( )

  Args       : NONE
  Example    : @all_species = @{$dba->all_species()};
  Description: Returns the names of all species contained in the
               database to which this DBAdaptor is connected.
  Returntype : array reference
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBAdaptor::assembly_type ( )

Description:

Deprecated:

Use CoordSystemAdaptor to obtain default coordinate system instead.

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public Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor::db ( )

Description:

Deprecated:

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public Bio::EnsEMBL::DBSQL::DBAdaptor::db_handle ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::DBAdaptor::dbc ( )

  Arg[1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection

  Example    : $dbc = $dba->dbc();
  Description: Getter/Setter for DBConnection.
  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
  Exceptions : throws if argument not a Bio::EnsEMBL::DBSQL::DBConnection
  Caller     : general
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBAdaptor::dbname ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor::DESTROY ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor::disconnect_when_inactive ( )

Undocumented method

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public Dna Bio::EnsEMBL::DBSQL::DBAdaptor::dnadb ( )

 Title   : dnadb
 Usage   : my $dnadb = $db->dnadb();
 Function: returns the database adaptor where the dna lives
           Useful if you only want to keep one copy of the dna
           on disk but have other databases with genes and features in
 Returns : dna database adaptor
 Args    : Bio::EnsEMBL::DBSQL::BaseAdaptor
 Status  : Medium Risk.
         : Use the Registry method add_DNAAdaptor/get_DNAAdaptor instead

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public Bio::EnsEMBL::DBSQL::DBAdaptor::driver ( )

Undocumented method

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public Adaptor Bio::EnsEMBL::DBSQL::DBAdaptor::get_adaptor ( )

  Arg [1]    : Canonical data type for which an adaptor is required.
  Example    : $db_adaptor->get_adaptor("Protein")
  Description: Gets an adaptor object for a standard data type.
  Returntype : Adaptor Object of arbitrary type or undef
  Exceptions : none
  Caller     : external
  Status     : Medium Risk
             : please use the Registry method, as at some time this
             : may no longer be supprted.

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public Hash Bio::EnsEMBL::DBSQL::DBAdaptor::get_all_db_adaptors ( )

Arg [1] : none Example : @attached_dbs = values %{$db->get_all_db_adaptors()}; Description: returns all of the attached databases as a hash reference of key/value pairs where the keys are database names and the values are the attached databases Returntype : hash reference with Bio::EnsEMBL::DBSQL::DBConnection values Exceptions : none Caller : Bio::EnsEMBL::DBSQL::ProxyAdaptor Status : At Risk : may get

Deprecated:: soon : please use Bio::EnsEMBL::Registry->get_all_db_adaptors

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public Reference Bio::EnsEMBL::DBSQL::DBAdaptor::get_available_adaptors ( )

  Example    : my %pairs = %{$dba->get_available_adaptors()};
  Description: gets a hash of the available adaptors
  ReturnType : reference to a hash
  Exceptions : none
  Caller     : Bio::EnsEMBL::Utils::ConfigRegistry
  Status     : Stable

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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyDBAdaptor.

public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::DBAdaptor::get_db_adaptor ( )

Arg [1] : string $name the name of the attached database to retrieve Example : $lite_db = $db->get_db_adaptor('lite'); Description: returns an attached db adaptor of name $name or undef if no such attached database exists Returntype : Bio::EnsEMBL::DBSQL::DBConnection Exceptions : none Caller : ? Status : At Risk : may get

Deprecated:: soon : please use Bio::EnsEMBL::Registry->get_db_adaptors

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public Reference Bio::EnsEMBL::DBSQL::DBAdaptor::get_ExternalFeatureAdaptors ( )

  Arg [1]    : none
  Example    : @xfas = values %{$db_adaptor->get_ExternalFeatureAdaptors}; 
  Description: Retrieves all of the ExternalFeatureAdaptors which have been
               added to this DBAdaptor.  The ExternalFeatureAdaptors are 
               returned in a reference to a hash keyed on the track names
               of the external adaptors
  Returntype : Reference to a hash of ExternalFeatureAdaptors keyed on 
               their track names.
  Exceptions : none
  Caller     : general

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public Reference Bio::EnsEMBL::DBSQL::DBAdaptor::get_GenericFeatureAdaptors ( )

  Arg [1]    : List of names of feature adaptors to get. If no
               adaptor names are given, all the defined adaptors are returned.
  Example    : $db->get_GenericFeature("SomeFeature", "SomeOtherFeature")
  Description: Returns a hash containing the named feature adaptors (or
               all feature adaptors).
  Returntype : reference to a Hash containing the named
               feature adaptors (or all feature adaptors).
  Exceptions : If any of the the named generic feature adaptors do not exist.
  Caller     : external

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public Bio::EnsEMBL::Utils::SeqRegionCache Bio::EnsEMBL::DBSQL::DBAdaptor::get_SeqRegionCache ( )

  Arg [1]    : none
  Example    : my $srcache = $dba->get_SeqRegionCache();
  Description: Retrieves a seq_region cache for this database
  Returntype : Bio::EnsEMBL::Utils::SeqRegionCache
  Exceptions : none
  Caller     : SliceAdaptor, AssemblyMapperAdaptor
  Status     : Stable

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public String Bio::EnsEMBL::DBSQL::DBAdaptor::group ( )

  Arg [1]    : (optional) string $arg
               The new value of the group used by this DBAdaptor. 
  Example    : $group = $dba->group()
  Description: Getter/Setter for the group of to use for 
               this connection.  There is currently no point in setting 
               this value after the connection has already been established 
               by the constructor.
  Returntype : string
  Exceptions : none
  Caller     : new
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBAdaptor::host ( )

Undocumented method

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public Boolean Bio::EnsEMBL::DBSQL::DBAdaptor::is_multispecies ( )

  Arg [1]    : (optional) boolean $arg
  Example    : if ($dba->is_multispecies()) { }
  Description: Getter/Setter for the is_multispecies boolean of
               to use for this connection.  There is currently no
               point in setting this value after the connection has
               already been established by the constructor.
  Returntype : boolean
  Exceptions : none
  Caller     : new
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBAdaptor::list_supported_assemblies ( )

Description:

Deprecated:

Use CoordSystemAdaptor to obtain list of top-level coordinate systems instead

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public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::DBAdaptor::new ( )

  Arg [-DNADB]: (optional) Bio::EnsEMBL::DBSQL::DBAdaptor DNADB 
               All sequence, assembly, contig information etc, will
               be retrieved from this database instead.

  Arg [-NO_CACHE]: (optional) int 1
               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 [..]   : Other args are passed to superclass
               Bio::EnsEMBL::DBSQL::DBConnection

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

  Example2   : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
                -species => 'Homo_sapiens',
                -group   => 'core',
                -user    => 'root',
                -dbname  => 'pog',
                -host    => 'caldy',
                -driver  => 'mysql'
              );

  Example3   : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
                -species         => 'staphylococcus_aureus',
                -group           => 'core',
                -user            => 'root',
                -dbname          => 'staphylococcus_collection_1_52_1a',
                -multispecies_db => 1,
                -host            => 'caldy',
                -driver          => 'mysql'
              );

  Description: Constructor for DBAdaptor.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : general
  Status     : Stable

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public Int Bio::EnsEMBL::DBSQL::DBAdaptor::no_cache ( )

  Arg [1]    : (optional) int $arg
               The new value of the no cache attribute used by this DBAdaptor. 
  Example    : $no_cache = $dba->no_cache();
  Description: Getter/Setter for the no_cache to use for 
               this connection.  There is currently no point in setting 
               this value after the connection has already been established 
               by the constructor.
  Returntype : int
  Exceptions : none
  Caller     : new
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBAdaptor::password ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor::port ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor::prepare ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor::reconnect_when_lost ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBAdaptor::remove_all_DASFeatureFactories ( )

Undocumented method

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public void Bio::EnsEMBL::DBSQL::DBAdaptor::remove_db_adaptor ( )

Arg [1] : string $name the name of the database to detach from this database. Example : $lite_db = $db->remove_db_adaptor('lite'); Description: Detaches a database instance from this database and returns it. Returntype : none Exceptions : none Caller : ? Status : At Risk : mey get

Deprecated:: , use remove_db instead from the Registry

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public void Bio::EnsEMBL::DBSQL::DBAdaptor::set_adaptor ( )

  Arg [1]    : Canonical data type for new adaptor.
	Arg [2]    : Object defining the adaptor for arg1.
  Example    : $aa = Bio::EnsEMBL::DBSQL::GeneAdaptor->new($db_adaptor);
             : $db_adaptor->set_adaptor("Gene", $ga)
  Description: Stores the object which represents the adaptor for the
               arg1 data type.
  Returntype : none
  Exceptions : none
  Caller     : external
  Status     : Medium Risk
             : please use the Registry method, as at some time this
             : may no longer be supprted.

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public Bio::EnsEMBL::DBSQL::DBAdaptor::source ( )

Undocumented method

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public String Bio::EnsEMBL::DBSQL::DBAdaptor::species ( )

  Arg [1]    : (optional) string $arg
               The new value of the species used by this DBAdaptor. 
  Example    : $species = $dba->species()
  Description: Getter/Setter for the species of to use for 
               this connection.  There is currently no point in setting 
               this value after the connection has already been established 
               by the constructor.
  Returntype : string
  Exceptions : none
  Caller     : new
  Status     : Stable

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public String Bio::EnsEMBL::DBSQL::DBAdaptor::species_id ( )

  Arg [1]    : (optional) string $arg
               The new value of the species_id used by this DBAdaptor
               when dealing with multi-species databases.
  Example    : $species_id = $dba->species_id()
  Description: Getter/Setter for the species_id of to use for this
               connection.  There is currently no point in setting
               this value after the connection has already been
               established by the constructor.
  Returntype : string
  Exceptions : none
  Caller     : new
  Status     : Stable

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public Bio::EnsEMBL::DBSQL::DBAdaptor::username ( )

Undocumented method

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

Bio/EnsEMBL/DBSQL/DBAdaptor.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation