LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::DBSQL::BiotypeAdaptor - An adaptor which performs database
interaction relating to the storage and retrieval of Biotypes

SYNOPSIS

my $biotype = $db_adaptor->fetch_by_name_object_type('protein_coding', 'gene');

DESCRIPTION

This adaptor provides a means to retrieve and store information related
to Biotypes.  Primarily this involves the retrieval or storage of
Bio::EnsEMBL::Biotype objects from a database.

See Bio::EnsEMBL::Biotype for details of the Biotype class.

METHODS

_tables

Arg [1]    : none
Description: PROTECTED implementation of superclass abstract method.
             Returns the names, aliases of the tables to use for queries.
Returntype : list of arrays of strings
Exceptions : none

_columns

Arg [1]    : none
Example    : none
Description: PROTECTED implementation of superclass abstract method.
             Returns a list of columns to use for queries.
Returntype : list of strings
Exceptions : none

_objs_from_sth

Arg [1]    : StatementHandle $sth
Example    : none
Description: PROTECTED implementation of abstract superclass method.
             responsible for the creation of ProteinFeatures
Returntype : arrayref of Bio::EnsEMBL::Biotype objects
Exceptions : none

fetch_by_name_object_type

Arg [1]    : String $name
             The name of the biotype to retrieve
Arg [2]    : String $object_type
             The object type of the biotype to retrieve (gene or transcript)
Example    : $biotype = $biotype_adaptor->fetch_by_name_object_type('mRNA', 'gene');
Description: Retrieves a biotype object from the database via its combined key (name, object_type).
             If the Biotype requested does not exist in the database, a new Biotype object is
             created with the provided name and object_type to be returned.
Returntype : Bio::EnsEMBL::Biotype
Exceptions : none

fetch_all_by_object_type

Arg [1]    : String $object_type
             The object_type of the biotypes to retrieve (gene or transcript).
Example    : $biotypes = $biotype_adaptor->fetch_all_by_object_type('gene');
Description: Retrieves an array reference of biotype objects from the database.
Returntype : arrayref of Bio::EnsEMBL::Biotype objects or empty arrayref
Warning    : If empty arrayref is to be returned
Exceptions : none

fetch_all_by_name

Arg [1]    : String $name
             The name of the biotype to retrieve
Arg [2]    : (optional) String $object_type
             The object_type of the biotypes to retrieve (gene or transcript).
Example    : $biotypes = $biotype_adaptor->fetch_all_by_name('lincRNA');
Description: Retrieves an array reference of biotype objects from the database.
Returntype : arrayref of Bio::EnsEMBL::Biotype objects or empty arrayref
Warning    : If empty arrayref is to be returned
Exceptions : none

fetch_all_by_group_object_db_type

Arg [1]    : String $biotype_group
             The group of the biotypes to retrieve
Arg [2]    : String $object_type
             The object type of the biotypes to retrieve (gene or transcript)
Arg [3]    : (optional) String $db_type
             The db_type of the biotypes to retrieve. If not provided defaults to 'core'.
Example    : $biotype = $biotype_adaptor->fetch_all_by_group_object_db_type('coding', 'gene');
Description: Retrieves an array reference of biotype objects from the database of the provided
             biotype_group and object_type and core db_type.
Returntype : arrayref of Bio::EnsEMBL::Biotype objects or empty arrayref
Warning    : If empty arrayref is to be returned
Exceptions : none