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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::MiscSetAdaptor - Provides database interaction for Bio::EnsEMBL::MiscSet objects.

SYNOPSIS

my $msa = $registry->get_adaptor( 'Human', 'Core', 'MiscSet' );

my $misc_set = $msa->fetch_by_dbID(1234);

$misc_set = $msa->fetch_by_code('clone');

DESCRIPTION

This class provides database interactivity for MiscSet objects. MiscSets are used to classify MiscFeatures into groups.

METHODS

new

Arg [...]  : Superclass args.  See Bio::EnsEMBL::DBSQL::BaseAdaptor
Description: Instantiates a Bio::EnsEMBL::DBSQL::MiscSetAdaptor and
             caches the contents of the MiscSet table.
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller     : MiscFeatureAdaptor
Status     : Stable

fetch_all

Arg [1]    : none
Example    : foreach my $ms (@{$msa->fetch_all()}) {
               print $ms->code(), ' ', $ms->name(), "\n";
             }
Description: Retrieves every MiscSet defined in the DB.
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
Returntype : listref of Bio::EnsEMBL::MiscSets
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_dbID

Arg [1]    : int $dbID
             The internal identifier of the misc set to retrieve
Example    : my $ms = $msa->fetch_by_dbID($dbID);
Description: Retrieves a misc set via its internal identifier
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_code

Arg [1]    : string $code
             The unique code of the MiscSet to retrieve
Example    : my $ms = $msa->fetch_by_code('clone');
Description: Retrieves a MiscSet via its code
Returntype : Bio::EnsEMBL::MiscSet
Exceptions : none
Caller     : general
Status     : Stable

store

Arg [1]    : list of MiscSets @mist_sets
Example    : $misc_set_adaptor->store(@misc_sets);
Description: Stores a list of MiscSets in the database, and sets the
             dbID and adaptor attributes of the stored sets.
Returntype : none
Exceptions : throw on incorrect arguments
             warning if a feature is already stored in this database
Caller     : MiscFeatureAdaptor::store
Status     : Stable

update

Arg [1]    : Bio::EnsEMBL::MiscSet $miscset
Example    : $adaptor->update($miscset)
Description: Updates this misc_set in the database
Returntype : int 1 if update is performed, undef if it is not
Exceptions : throw if arg is not an misc_set object
Caller     : ?
Status     : Stable