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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::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