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Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor:

List of all members.


Class Summary

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.
 

Definition at line 24 of file RepeatConsensusAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _final_clause ()
protected Listref _generic_fetch ()
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_class_seq ()
public Listref fetch_all_by_dbID_list ()
public Array fetch_all_repeat_types ()
public fetch_by_class_seq ()
public
Bio::EnsEMBL::RepeatConsensus 
fetch_by_dbID ()
public
Bio::EnsEMBL::RepeatConsensus 
fetch_by_name ()
public
Bio::EnsEMBL::RepeatConsensus 
fetch_by_name_class ()
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 ()
public void store ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

protected Listref Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::_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
 
Code:
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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( ) [inherited]

Undocumented method

Code:
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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

Code:
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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
 
Code:
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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
 
Code:
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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
 
Code:
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public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

Code:
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public ListREF Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::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
 
Code:
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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
 
Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

public Array Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::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 	: -
 
Code:
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public Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::fetch_by_class_seq ( )

Undocumented method

Code:
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public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::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
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::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
 
Code:
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public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::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
 
Code:
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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
 
Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

Code:
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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
 
Code:
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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
 
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public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::new ( ) [inherited]
  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
 
Code:
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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 ( ) [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
 
Code:
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Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

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
 
Code:
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public void Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::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
 
Code:
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The documentation for this class was generated from the following file: