
Class Summary
Synopsis
# base adaptor provides # SQL prepare function $adaptor-\>prepare("sql statement"); # get of root DBAdaptor object $adaptor-\>db(); # constructor, ok for inheritence $adaptor = Bio::EnsEMBL::DBSQL::SubClassOfBaseAdaptor-\>new($dbobj)
Description
This is a true base class for Adaptors in the Ensembl DBSQL system. Original idea from Arne
Adaptors are expected to have the following functions
$obj = $adaptor->fetch_by_dbID($internal_id);
which builds the object from the primary key of the object. This function is crucial because it allows adaptors to collaborate relatively independently of each other - in other words, we can change the schema under one adaptor without too many knock on changes through the other adaptors.
Most adaptors will also have
$dbid = $adaptor->store($obj);
which stores the object. Currently the storing of an object also causes the objects to set
$obj->dbID();
correctly and attach the adaptor.
Other fetch functions go by the convention of
@object_array = @{ $adaptor->fetch_all_by_XXXX($arguments_for_XXXX) };
sometimes it returns an array ref denoted by the 'all' in the name of the method, sometimes an individual object. For example
$gene = $gene_adaptor->fetch_by_stable_id($stable_id);
or
@fp = @{ $simple_feature_adaptor->fetch_all_by_Slice($slice) };
Occassionally adaptors need to provide access to lists of ids. In this case the convention is to go list_XXXX, such as
@gene_ids = @{ $gene_adaptor->list_geneIds() };
(note: this method is poorly named)
Definition at line 69 of file BaseAdaptor.pm.
Available Methods | |
protected | _columns () |
protected | _default_where_clause () |
protected | _final_clause () |
protected | _left_join () |
protected | _list_dbIDs () |
protected | _objs_from_sth () |
protected | _straight_join () |
protected | _tables () |
public Listref | bind_param_generic_fetch () |
public Bio::EnsEMBL::DBSQL::DBAdaptor | db () |
public Bio::EnsEMBL::DBSQL::DBConnection | dbc () |
public | dump_data () |
public | fetch_all () |
public Listref | fetch_all_by_dbID_list () |
public Bio::EnsEMBL::Feature | fetch_by_dbID () |
public Listref | generic_fetch () |
public | get_dumped_data () |
public Boolean | is_multispecies () |
public Scalar | last_insert_id () |
public Bio::EnsEMBL::DBSQL::BaseAdaptor | new () |
public DBI::StatementHandle | prepare () |
public Int | species_id () |
Method Documentation
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_columns | ( | ) |
Undocumented method

Reimplemented in Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionExonAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingTranscriptPairAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::QtlAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause | ( | ) |
Undocumented method

Reimplemented in Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause | ( | ) |
Undocumented method

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

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_objs_from_sth | ( | ) |
Undocumented method

Reimplemented in Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionExonAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join | ( | ) |
Undocumented method

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_tables | ( | ) |
Undocumented method

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor, Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::GeneAdaptor, Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, Bio::EnsEMBL::DBSQL::OperonAdaptor, Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor, Bio::EnsEMBL::DBSQL::PredictionExonAdaptor, Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor, Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor, Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventAdaptor, Bio::EnsEMBL::DBSQL::SplicingEventFeatureAdaptor, Bio::EnsEMBL::DBSQL::SplicingTranscriptPairAdaptor, Bio::EnsEMBL::DBSQL::TranscriptAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor.
public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch | ( | ) |
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 Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db | ( | ) |
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 | ( | ) |
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 | ( | ) |
Undocumented method

public Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all | ( | ) |
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 | ( | ) |
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 Bio::EnsEMBL::Feature Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_by_dbID | ( | ) |
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 Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch | ( | ) |
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 | ( | ) |
Undocumented method

public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies | ( | ) |
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 | ( | ) |
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 Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::new | ( | ) |
Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection $dbobj Example : $adaptor = new AdaptorInheritedFromBaseAdaptor($dbobj); Description: Creates a new BaseAdaptor object. The intent is that this constructor would be called by an inherited superclass either automatically or through $self->SUPER::new in an overridden new method. Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor Exceptions : none Caller : Bio::EnsEMBL::DBSQL::DBConnection Status : Stable

Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor, Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor, Bio::EnsEMBL::DBSQL::AttributeAdaptor, Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::GOTermAdaptor, Bio::EnsEMBL::DBSQL::MetaCoordContainer, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::SequenceAdaptor, Bio::EnsEMBL::DBSQL::SliceAdaptor, Bio::EnsEMBL::DBSQL::SOTermAdaptor, Bio::EnsEMBL::DBSQL::StrainSliceAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.
public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare | ( | ) |
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 Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id | ( | ) |
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

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