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

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.
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 | ( | ) |
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