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

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NAME

Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor

SYNOPSIS

  $rca = $database_adaptor->get_RepeatConsensusAdaptor();

  $repeat_consensus = $rca->fetch_by_dbID(132);
  $repeat_consensus = $rca->fetch_by_name_class( 'AluSx', 'SINE/Alu' );

  $rca->store( $rc1, $rc2, $rc3 );

DESCRIPTION

This is an adaptor for the retrieval and storage of RepeatConsensus objects.

METHODS

fetch_all_repeat_types

  Example                       : my $types = $rca->fetch_all_repeat_types();
  Description   : Returns the distinct repeat types available from a database
  Returntype    : Array
  Exceptions    : -

fetch_by_dbID

  Arg [1]    : int $db_id
               The database identifier for the RepeatConsensus to obtain
  Example    : $repeat_consensus = $repeat_consensus_adaptor->fetch_by_dbID(4);
  Description: Obtains a RepeatConsensus object from the database via its
               primary key. 
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general, Bio::EnsEMBL::RepeatFeatureAdaptor
  Status     : Stable

fetch_by_name

  Arg [1]    : string $name
               the name of the repeat consensus to obtain
  Example    : $rc = $repeat_consensus_adaptor->fetch_by_name('AluSx');
  Description: Obtains a repeat consensus from the database via its name
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_by_name_class

  Arg [1]    : string $name
               the name of the repeat consensus to obtain
  Arg [2]    : string $class
               the class of the repeat consensus to obtain
  Example    : $rc = $repeat_consensus_adaptor->
                 fetch_by_name_class('AluSx', 'SINE/Alu');
  Description: Obtains a repeat consensus from the database
               via its name and class
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

fetch_all_by_class_seq

  Arg [1]    : string $class
               the class of the repeat consensus to obtain
  Arg [2]    : string $seq
               the sequence of the repeat consensus to obtain
  Example    : $rc = $repeat_consensus_adaptor->
                 fetch_all_by_class_seq('trf', 'ATGGTGTCA');
  Description: Obtains a repeat consensus from the database
               via its class and sequence
  Returntype : listREF of Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

_generic_fetch

  Arg [1]    : string $where_clause
  Example    : none
  Description: PRIVATE used to create RepeatConsensus features from an 
               SQL constraint
  Returntype : listref of Bio::EnsEMBL::RepeatConsensus objects
  Exceptions : none
  Caller     : internal
  Status     : Stable

store

  Arg [1]    : list of Bio::EnsEMBL::RepeatConsensus @consensi
  Example    : $repeat_consensus_adaptor->store(@consensi);
  Description: stores a list of RepeatConsensus objects in the database
  Returntype : none
  Exceptions : none
  Caller     : ?
  Status     : Stable