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Bio-EnsEMBL-112.0_54
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor

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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