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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::RepeatFeatureAdaptor

SYNOPSIS

  $rfa = $database_adaptor->get_RepeatFeatureAdaptor();

  my $repeat  = $rfa->fetch_by_dbID(1234);
  my @repeats = @{ $rfa->fetch_all_by_Slice($slice) };

DESCRIPTION

This is an adaptor for the retrieval and storage of RepeatFeature objects from the database. Most of the implementation is in the superclass BaseFeatureAdaptor.

METHODS

fetch_all_by_Slice

  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Arg [2]    : (optional) string $logic_name
               Limits RepeatFeatures obtained to those having an Analysis with
               of the specified logic_name.  If no logic name is specified
               Repeats of all analysis types are retrieved.
  Arg [3]    : (optional) string/array $repeat_type
               Limits RepeatFeatures obtained to those of specified 
               repeat_type
  Example    : @rfeats = @{$rfa->fetch_all_by_Slice($slice, undef, 'Type II Transposons')};
               @rfeats = @{$rfa->fetch_all_by_Slice($slice, undef, ['Type II Transposons', 'RNA repeats'])};
  Description: Retrieves repeat features overlapping the area designated by
               the provided slice argument.  Returned features will be in
               in the same coordinate system as the provided slice and will
               have coordinates relative to the slice start.
  Returntype : reference to a list of Bio::EnsEMBL::RepeatFeatures.
  Exceptions : throw on bad argument
  Caller     : Slice::get_all_RepeatFeatures
  Status     : Stable

store

  Arg [1]    : list of Bio::EnsEMBL::RepeatFeatures $repeat_feature_id
               the list of repeat features to store in the database
  Example    : $repeat_feature_adaptor->store(@repeat_features);
  Description: stores a repeat feature in the database
  Returntype : none
  Exceptions : if the repeat features do not have attached sequences 
               or if repeat_consensus are not present 
  Caller     : general
  Status     : Stable

list_dbIDs

  Arg [1]    : none
  Example    : @feature_ids = @{$repeat_feature_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all repeat features in the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable