
Class Summary
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.
Definition at line 24 of file RepeatFeatureAdaptor.pm.
Method Documentation
protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_check_start_end_strand | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor::_columns | ( | ) |
protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_create_feature | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_create_feature_fast | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor::_default_where_clause | ( | ) |
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause | ( | ) | [inherited] |
Undocumented method

Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_left_join | ( | ) | [inherited] |
Undocumented method

Reimplemented in Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_list_seq_region_ids | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_logic_name_to_constraint | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_max_feature_length | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor::_objs_from_sth | ( | ) |
protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_pre_store | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_pre_store_userdata | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_remap | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Utils::Cache Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_feature_cache | ( | ) | [inherited] |
Description : Returns the feature cache if we are allowed to cache and will build it if we need to. We will never return a reference to the hash to avoid unintentional auto-vivfying caching Returntype : Bio::EnsEMBL::Utils::Cache Exceptions : None Caller : Internal

protected Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_fetch | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor::_tables | ( | ) |
public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch | ( | ) | [inherited] |
Arg [1] : (optional) scalar $param This is the parameter to bind Arg [2] : (optional) int $sql_type Type of the parameter (from DBI (:sql_types)) Example : $adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR); $adaptor->generic_fetch(); Description: When using parameters for the query, will call the bind_param to avoid some security issues. If there are no arguments, will return the bind_parameters ReturnType : listref Exceptions: if called with one argument

public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::clear_cache | ( | ) | [inherited] |
Args : None Example : my $sa = $registry->get_adaptor( 'Mus musculus', 'Core', 'Slice' ); my $ga = $registry->get_adaptor( 'Mus musculus', 'Core', 'Gene' );
my $slice = $sa->fetch_by_region( 'Chromosome', '1', 1e8, 1.05e8 );
my $genes = $ga->fetch_all_by_Slice($slice);
$ga->clear_cache();
Description : Empties the feature cache associated with this feature adaptor. Return type : None Exceptions : None Caller : General Status : At risk (under development)

public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db | ( | ) | [inherited] |
Arg [1] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj the database this adaptor is using. Example : $db = $adaptor->db(); Description: Getter/Setter for the DatabaseConnection that this adaptor is using. Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor Exceptions : none Caller : Adaptors inherited from BaseAdaptor Status : Stable

public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::BaseAdaptor::dbc | ( | ) | [inherited] |
Arg [1] : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj the database this adaptor is using. Example : $db = $adaptor->db(); Description: Getter/Setter for the DatabaseConnection that this adaptor is using. Returntype : Bio::EnsEMBL::DBSQL::DBConnection Exceptions : none Caller : Adaptors inherited from BaseAdaptor Status : Stable

public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all | ( | ) | [inherited] |
Undocumented method

Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::OntologyTermAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::SliceAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::TranslationAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlAdaptor.
public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list | ( | ) | [inherited] |
Arg [1] : listref of integers $id_list The unique database identifiers for the features to be obtained. Arg [2] : optional - Bio::EnsEMBL::Slice to map features onto. Example : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))}; Description: Returns the features created from the database defined by the the IDs in contained in the provided ID list $id_list. The features will be returned in their native coordinate system. That is, the coordinate system in which they are stored in the database. In order to convert the features to a particular coordinate system use the transfer() or transform() method. If none of the features are found in the database a reference to an empty list is returned. Returntype : listref of Bio::EnsEMBL::Features Exceptions : thrown if $id arg is not provided does not exist Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.
public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_logic_name | ( | ) | [inherited] |
Arg [3] : string $logic_name the logic name of the type of features to obtain Example : $fs = $a->fetch_all_by_logic_name('foobar'); Description: Returns a listref of features created from the database. only features with an analysis of type $logic_name will be returned. If the logic name is invalid (not in the analysis table), a reference to an empty list will be returned. Returntype : listref of Bio::EnsEMBL::SeqFeatures Exceptions : thrown if no $logic_name Caller : General Status : Stable

public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig | ( | ) | [inherited] |
public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_and_score | ( | ) | [inherited] |
public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_constraint | ( | ) | [inherited] |
public Reference Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor::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

Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.
public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_and_score | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Slice $slice the slice from which to obtain features Arg [2] : (optional) float $score lower bound of the the score of the features retrieved Arg [3] : (optional) string $logic_name the logic name of the type of features to obtain Example : $fts = $a->fetch_all_by_Slice_and_score($slice,90,'Swall'); Description: Returns a list of features created from the database which are are on the Slice defined by $slice and which have a score greater than $score. If $logic_name is defined, only features with an analysis of type $logic_name will be returned. Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates Exceptions : none Caller : Bio::EnsEMBL::Slice Status : Stable

Reimplemented in Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor.
public Listref Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_constraint | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Slice $slice the slice from which to obtain features Arg [2] : (optional) string $constraint An SQL query constraint (i.e. part of the WHERE clause) Arg [3] : (optional) string $logic_name the logic name of the type of features to obtain Example : $fs = $a->fetch_all_by_Slice_constraint($slc, 'perc_ident > 5'); Description: Returns a listref of features created from the database which are on the Slice defined by $slice and fulfill the SQL constraint defined by $constraint. If logic name is defined, only features with an analysis of type $logic_name will be returned. Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates Exceptions : thrown if $slice is not defined Caller : Bio::EnsEMBL::Slice Status : Stable

public Bio::EnsEMBL::Feature Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_by_dbID | ( | ) | [inherited] |
Arg [1] : int $id The unique database identifier for the feature to be obtained Example : $feat = $adaptor->fetch_by_dbID(1234)); $feat = $feat->transform('contig'); Description: Returns the feature created from the database defined by the the id $id. The feature will be returned in its native coordinate system. That is, the coordinate system in which it is stored in the database. In order to convert it to a particular coordinate system use the transfer() or transform() method. If the feature is not found in the database then undef is returned instead Returntype : Bio::EnsEMBL::Feature or undef Exceptions : thrown if $id arg is not provided does not exist Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DBEntryAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::OntologyTermAdaptor, Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor, Bio::EnsEMBL::DBSQL::TranslationAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlAdaptor.
public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_Iterator_by_Slice | ( | ) | [inherited] |
Arg [1] : Bio::EnsEMBL::Slice Arg [2] : Optional string: logic name of analysis Arg [3] : Optional int: Chunk size to iterate over. Default is 500000 Example : my $slice_iter = $feature_adaptor->fetch_Iterator_by_Slice($slice);
while(my $feature = $slice_iter->next && defined $feature){ #Do something here }
Description: Creates an Iterator which chunks the query Slice to facilitate large Slice queries which would have previously run out of memory Returntype : Bio::EnsEMBL::Utils::Iterator Exceptions : None Caller : general Status : at risk

public Bio::EnsEMBL::Utils::Iterator Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_Iterator_by_Slice_method | ( | ) | [inherited] |
Arg [1] : CODE ref of Slice fetch method Arg [2] : ARRAY ref of parameters for Slice fetch method Arg [3] : Optional int: Slice index in parameters array Arg [4] : Optional int: Slice chunk size. Default=500000 Example : my $slice_iter = $feature_adaptor->fetch_Iterator_by_Slice_method ($feature_adaptor->can('fetch_all_by_Slice_Arrays'), \@fetch_method_params, 0,#Slice idx );
while(my $feature = $slice_iter->next && defined $feature){ #Do something here }
Description: Creates an Iterator which chunks the query Slice to facilitate large Slice queries which would have previously run out of memory Returntype : Bio::EnsEMBL::Utils::Iterator Exceptions : Throws if mandatory params not valid Caller : general Status : at risk

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch | ( | ) | [inherited] |
Arg [1] : (optional) string $constraint An SQL query constraint (i.e. part of the WHERE clause) Arg [2] : (optional) Bio::EnsEMBL::AssemblyMapper $mapper A mapper object used to remap features as they are retrieved from the database Arg [3] : (optional) Bio::EnsEMBL::Slice $slice A slice that features should be remapped to Example : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall'); Description: Performs a database fetch and returns feature objects in contig coordinates. Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates Exceptions : none Caller : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch Status : Stable

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.
public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::get_seq_region_id_external | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::get_seq_region_id_internal | ( | ) | [inherited] |
Undocumented method

public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies | ( | ) | [inherited] |
Arg [1] : (optional) boolean $arg Example : if ($adaptor->is_multispecies()) { } Description: Getter/Setter for the is_multispecies boolean of to use for this adaptor. Returntype : boolean Exceptions : none Caller : general Status : Stable

public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id | ( | ) | [inherited] |
Arg [1] : (optional) $field the name of the field the inserted ID was pushed into Arg [2] : (optional) HashRef used to pass extra attributes through to the DBD driver Description : Delegating method which uses DBI to extract the last inserted identifier. If using MySQL we just call the DBI method DBI::last_insert_id() since MySQL ignores any extra arguments. See DBI for more information about this delegated method. Example : my $id = $self->last_insert_id('my_id'); my $other_id = $self->last_insert_id(); Returntype : Scalar or undef

public List Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor::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

public Bio::EnsEMBL::BaseFeatureAdaptor Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::new | ( | ) | [inherited] |
Arg [1] : list of args @args Superclass constructor arguments Example : none Description: Constructor which warns if caching has been switched off Returntype : Bio::EnsEMBL::BaseFeatureAdaptor Exceptions : none Caller : implementing subclass constructors Status : Stable

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.
Reimplemented in Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, and Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor.
public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare | ( | ) | [inherited] |
Arg [1] : string $string a SQL query to be prepared by this adaptors database Example : $sth = $adaptor->prepare("select yadda from blabla") Description: provides a DBI statement handle from the adaptor. A convenience function so you dont have to write $adaptor->db->prepare all the time Returntype : DBI::StatementHandle Exceptions : none Caller : Adaptors inherited from BaseAdaptor Status : Stable

Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.
public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove | ( | ) | [inherited] |
Arg [1] : A feature $feature Example : $feature_adaptor->remove($feature); Description: This removes a feature from the database. The table the feature is removed from is defined by the abstract method _tablename, and the primary key of the table is assumed to be _tablename() . '_id'. The feature argument must be an object implementing the dbID method, and for the feature to be removed from the database a dbID value must be returned. Returntype : none Exceptions : thrown if $feature arg does not implement dbID(), or if $feature->dbID is not a true value Caller : general Status : Stable

Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionExonAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, and Bio::EnsEMBL::DBSQL::TranscriptAdaptor.
public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_analysis_id | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_feature_id | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_RawContig | ( | ) | [inherited] |
public void Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_Slice | ( | ) | [inherited] |
Arg [1] : Bio::Ensembl::Slice $slice Example : $feature_adaptor->remove_by_Slice($slice); Description: This removes features from the database which lie on a region represented by the passed in slice. Only features which are fully contained by the slice are deleted; features which overlap the edge of the slice are not removed. The table the features are removed from is defined by the abstract method_tablename. Returntype : none Exceptions : thrown if no slice is supplied Caller : general Status : Stable

public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id | ( | ) | [inherited] |
Arg [1] : (optional) int $species_id The internal ID of the species in a multi-species database. Example : $db = $adaptor->db(); Description: Getter/Setter for the internal ID of the species in a multi-species database. The default species ID is 1. Returntype : Integer Exceptions : none Caller : Adaptors inherited from BaseAdaptor Status : Stable

public Boolean Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::start_equals_end | ( | ) | [inherited] |
Arg [1] : (optional) boolean $newval Example : $bfa->start_equals_end(1); Description: Getter/Setter for the start_equals_end flag. If set to true sub _slice_fetch will use a simplified sql to retrieve 1bp slices. Returntype : boolean Exceptions : none Caller : EnsemblGenomes variation DB build Status : Stable

public void Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor::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

Reimplemented from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor.
The documentation for this class was generated from the following file:
- Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm