# metadata_db is an instance of MetaDataDBAdaptor my $adaptor = $metadata_db->get_GenomeAssemblyInfoAdaptor(); my $assembly = $adaptor->fetch_by_assembly_accession('GCA_000001405.15');
Adaptor for storing and retrieving GenomeAssemblyInfo objects from MySQL ensembl_metadata database
Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::GenomeOrganismInfo
Definition at line 29 of file GenomeAssemblyInfoAdaptor.pm.
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 void Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::_fetch_children | ( | ) |
Arg : Arrayref of Bio::EnsEMBL::MetaData::GenomeInfo Description: Fetch all children of specified genome info object Returntype : none Exceptions : none Caller : internal Status : Stable
Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.
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 Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::_fetch_organism | ( | ) |
Undocumented method
protected void Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::_fetch_sequences | ( | ) |
Arg : Bio::EnsEMBL::MetaData::GenomeInfo Description: Add sequences to supplied object Returntype : none 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::GenomeAssemblyInfoAdaptor::_get_base_sql | ( | ) |
Undocumented method
Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.
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 Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::_get_id_field | ( | ) |
Undocumented method
Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.
protected Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::_get_obj_class | ( | ) |
Undocumented method
Reimplemented from Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor.
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
protected Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::_store_sequences | ( | ) |
Undocumented method
public Bio::EnsEMBL::MetaData::DBSQL::BaseInfoAdaptor::fetch_all | ( | ) | [inherited] |
Undocumented method
public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::fetch_all_by_assembly_set_chain | ( | ) |
Arg : INSDC assembly set chain (unversioned accession) Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified assembly set chain Returntype : Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::fetch_all_by_organism | ( | ) |
Arg : GenomeOrganismInfo object Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified organism Returntype : Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::fetch_all_by_sequence_accession | ( | ) |
Arg : INSDC sequence accession e.g. U00096.1 or U00096 Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified sequence accession Returntype : Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::fetch_all_by_sequence_accession_unversioned | ( | ) |
Arg : INSDC sequence accession e.g. U00096 Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified sequence accession Returntype : Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::fetch_all_by_sequence_accession_versioned | ( | ) |
Arg : INSDC sequence accession e.g. U00096.1 Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified sequence accession Returntype : Bio::EnsEMBL::MetaData::GenomeInfo Exceptions : none Caller : general Status : Stable
public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::fetch_by_assembly_accession | ( | ) |
Arg : INSDC assembly accession Arg : (optional) if 1, expand children of genome info Description: Fetch genome info for specified assembly ID (versioned or unversioned) Returntype : Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Exceptions : none Caller : general Status : Stable
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 void Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::store | ( | ) |
Arg : Bio::EnsEMBL::MetaData::DatabaseInfo Description: Store the supplied object Returntype : none Exceptions : none Caller : general Status : Stable
public void Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor::update | ( | ) |
Arg : Bio::EnsEMBL::MetaData::DatabaseInfo Description: Update the supplied object (must be previously stored) Returntype : none Exceptions : none Caller : general Status : Stable