# metadata_db is an instance of MetaDataDBAdaptor
my $adaptor = $metadata_db->get_DatabaseInfoAdaptor();
$adaptor->fetch_databases($info);
Adaptor to handle DatabaseInfo objects associated with GenomeInfo or DataReleaseInfo objects. Uses delegate pattern to handle objects differently according to their subject objects.
Bio::EnsEMBL::MetaData::DatabaseInfo Bio::EnsEMBL::MetaData::DataReleaseInfo Bio::EnsEMBL::MetaData::GenomeInfo
Definition at line 30 of file DatabaseInfoAdaptor.pm.
Available Methods | |
protected String | _args_to_sql () |
protected void | _cache () |
protected void | _clear_cache () |
protected | _fetch_children () |
protected Arrayref | _fetch_generic () |
protected Arrayref | _fetch_generic_with_args () |
protected Arrayref | _first_element () |
protected | _get_base_sql () |
protected Object | _get_cached_obj () |
protected void | _get_division_id () |
protected String | _get_id_field () |
protected String | _get_obj_class () |
protected void | _store_cached_obj () |
public | fetch_all () |
public Bio::EnsEMBL::MetaData::GenomeInfo | fetch_by_dbID () |
public Bio::EnsEMBL::MetaData::GenomeInfo | fetch_by_dbIDs () |
public Arrayref | fetch_databases () |
public Arrayref | fetch_databases_DataReleaseInfo () |
public Arrayref | fetch_databases_GenomeInfo () |
public | store () |
public | store_DataReleaseInfo () |
public void | store_GenomeInfo () |
public void | update () |
public void | update_DataReleaseInfo () |
public void | update_GenomeInfo () |
protected String Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_args_to_sql | ( | ) | [inherited] |
Description: Add where clauses to SQL given arguments Arg : String - Base SQL Arg : Hashref - arguments Returntype : String Exceptions : none Caller : internal Status : Stable
Reimplemented in Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor, and Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor.
protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_cache | ( | ) | [inherited] |
Arg : type of object for cache Description: Return internal cache for given type Returntype : none Exceptions : none Caller : internal Status : Stable
protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_clear_cache | ( | ) | [inherited] |
Arg : (optional) type of object to clear Description: Clear internal cache (optionally just one type) Returntype : none Exceptions : none Caller : internal Status : Stable
protected Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_children | ( | ) | [inherited] |
Undocumented method
Reimplemented in Bio::EnsEMBL::MetaData::DBSQL::DataReleaseInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor, and Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor.
protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic | ( | ) | [inherited] |
Arg : SQL to use to fetch object Arg : arrayref of bind parameters Arg : (optional) if set to 1, all children will be fetched Description: Instantiate a GenomeInfo from the database using the specified SQL Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo Exceptions : none Caller : internal Status : Stable
protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_fetch_generic_with_args | ( | ) | [inherited] |
Arg : hashref of arguments by column Arg : (optional) if set to 1, all children will be fetched Description: Instantiate a GenomeInfo from the database using a generic method, with the supplied arguments Returntype : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo Exceptions : none Caller : internal Status : Stable
protected Arrayref Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_first_element | ( | ) | [inherited] |
Arg : arrayref Description: Utility method to return the first element in a list, undef if empty Returntype : arrayref element Exceptions : none Caller : internal Status : Stable
protected Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_base_sql | ( | ) | [inherited] |
Undocumented method
Reimplemented in Bio::EnsEMBL::MetaData::DBSQL::DataReleaseInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor, and Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor.
protected Object Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_cached_obj | ( | ) | [inherited] |
Arg : type of object to retrieve Arg : ID of object to retrieve Description: Retrieve object from internal cache Returntype : object Exceptions : none Caller : internal Status : Stable
protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_division_id | ( | ) | [inherited] |
Arg : division name Description: Return ID for division, storing if required Returntype : none Exceptions : none Caller : internal Status : Stable
protected String Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_id_field | ( | ) | [inherited] |
Description: Database column containing dbID - must be implemented Returntype : String Exceptions : none Caller : internal Status : Stable
Reimplemented in Bio::EnsEMBL::MetaData::DBSQL::DataReleaseInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor, and Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor.
protected Non Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_get_obj_class | ( | ) | [inherited] |
Description: Class of object retrieved - must be implemented Returntype : String Exceptions : none Caller : internal Status : Stable
Description: Load children of object - no-op implementation, can be overridden Arg : Object to retrieve children for Returntype : non Exceptions : none Caller : internal Status : Stable
/**
Reimplemented in Bio::EnsEMBL::MetaData::DBSQL::DataReleaseInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor, Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor, and Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor.
protected void Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::_store_cached_obj | ( | ) | [inherited] |
Arg : type of object to store Arg : object to store Description: Store object in internal cache Returntype : none Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_all | ( | ) | [inherited] |
Undocumented method
public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbID | ( | ) | [inherited] |
Arg : ID of genome info Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified ID Returntype : Bio::EnsEMBL::MetaData::GenomeInfo Exceptions : none Caller : internal Status : Stable
public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_by_dbIDs | ( | ) | [inherited] |
Arg : IDs of genome info Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified ID Returntype : Bio::EnsEMBL::MetaData::GenomeInfo Exceptions : none Caller : internal Status : Stable
public Arrayref Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::fetch_databases | ( | ) |
Arg : Bio::EnsEMBL::MetaData::DataReleaseInfo or Bio::EnsEMBL::MetaData::GenomeInfo Arg : String - Optional division Description: Find the databases associated with the supplied object Returntype : Arrayref of Bio::EnsEMBL::MetaData::DatabaseInfo Exceptions : none Caller : general Status : Stable
public Arrayref Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::fetch_databases_DataReleaseInfo | ( | ) |
Description: Implementation of fetch_databases for Bio::EnsEMBL::MetaData::DataReleaseInfo Arg : Bio::EnsEMBL::MetaData::DataReleaseInfo Description: Find the databases associated with the supplied object Returntype : Arrayref of Bio::EnsEMBL::MetaData::DatabaseInfo Exceptions : none Caller : general Status : Stable
public Arrayref Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::fetch_databases_GenomeInfo | ( | ) |
Description: Implementation of fetch_databases for Bio::EnsEMBL::MetaData::GenomeInfo Arg : Bio::EnsEMBL::MetaData::GenomeInfo Arg : String - Optional division Returntype : Arrayref of Bio::EnsEMBL::MetaData::DatabaseInfo Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::store | ( | ) |
Undocumented method
public Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::store_DataReleaseInfo | ( | ) |
Undocumented method
public void Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::store_GenomeInfo | ( | ) |
Description: Implementation of store for Bio::EnsEMBL::MetaData::GenomeInfo Arg : Bio::EnsEMBL::MetaData::DatabaseInfo Returntype : none Exceptions : none Caller : general Status : Stable
public void Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::update | ( | ) |
Arg : Bio::EnsEMBL::MetaData::DatabaseInfo Description: Update the supplied object (must be previously stored) Returntype : none Exceptions : none Caller : general Status : Stable
public void Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::update_DataReleaseInfo | ( | ) |
Description: Implementation of update for Bio::EnsEMBL::MetaData::DataReleaseInfo Arg : Bio::EnsEMBL::MetaData::DatabaseInfo Returntype : none Exceptions : none Caller : general Status : Stabl
public void Bio::EnsEMBL::MetaData::DBSQL::DatabaseInfoAdaptor::update_GenomeInfo | ( | ) |
Description: Implementation of update for Bio::EnsEMBL::MetaData::GenomeInfo Arg : Bio::EnsEMBL::MetaData::DatabaseInfo Returntype : none Exceptions : none Caller : general Status : Stabl