Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor Class Reference

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

Public Member Functions
public Array	fetch_all_repeat_types ()
public Bio::EnsEMBL::RepeatConsensus	fetch_by_dbID ()
public Bio::EnsEMBL::RepeatConsensus	fetch_by_name ()
public Bio::EnsEMBL::RepeatConsensus	fetch_by_name_class ()
public ListREF	fetch_all_by_class_seq ()
protected Listref	_generic_fetch ()
public void	store ()
Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()
public DBI::StatementHandle	prepare ()
public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()
public Boolean	is_multispecies ()
public Int	species_id ()
protected	_list_dbIDs ()
protected	_straight_join ()
protected	_can_straight_join ()
public Listref	bind_param_generic_fetch ()
protected	_bind_param_generic_fetch ()
public String	generate_in_constraint ()
public Listref	generic_fetch ()
public Int	generic_count ()
protected	_generate_sql ()
public Bio::EnsEMBL::Feature	fetch_by_dbID ()
protected	_uncached_fetch_by_dbID ()
public Listref	fetch_all_by_dbID_list ()
protected	_uncached_fetch_all_by_dbID_list ()
protected ArrayRef	_uncached_fetch_all_by_id_list ()
public	fetch_all ()
public Scalar	last_insert_id ()
public	insert_ignore_clause ()
protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()
protected Boolean	_no_id_cache ()
public Boolean	ignore_cache_override ()
public Int	schema_version ()
protected	_tables ()
protected	_columns ()
protected	_default_where_clause ()
protected	_left_join ()
protected	_final_clause ()
protected	_objs_from_sth ()
protected	_build_id_cache ()
protected	_logic_name_to_constraint ()

Detailed Description

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.

Member Function Documentation

_generic_fetch()

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:

fetch_all_by_class_seq()

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:

fetch_all_repeat_types()

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:

fetch_by_dbID()

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:

fetch_by_name()

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:

fetch_by_name_class()

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:

store()

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:

• ensembl/modules/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm