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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     http://www.apache.org/licenses/LICENSE-2.0

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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