Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor:

List of all members.


Class Summary

Synopsis

Definition at line 15 of file DnaFragChunkAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _fetch_DnaFrag_by_dbID ()
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_dbID_list ()
public Listref fetch_all_for_genome_db_id ()
public
Bio::EnsEMBL::Compara::Production::DnaFragChunk 
fetch_by_dbID ()
public Listref fetch_by_dbIDs ()
public fetch_MaskingOptions_by_mlss_tag ()
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 ()
public update_sequence ()

Method Documentation

protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::_columns ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::_default_where_clause ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::_fetch_DnaFrag_by_dbID ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::_final_clause ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Listref Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::_generic_fetch ( )
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  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::Production::DnaFragChunk in contig coordinates
  Exceptions : none
  Caller     : internal
 
Code:
click to view
protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::_objs_from_sth ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::_tables ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::fetch_all ( )
  Arg        : None
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::fetch_all_for_genome_db_id ( )
  Arg [1]    : int $genome_db_id
  Example    : $chunks = $adaptor->fetch_all_for_genome_db_id(1);
  Description: Returns an array with all the DnaFragChunk objects for a given genome_db_id
  Returntype : listref of Bio::EnsEMBL::Compara::Production::DnaFragChunk objects
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
click to view
public Bio::EnsEMBL::Compara::Production::DnaFragChunk Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::fetch_by_dbID ( )
  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
  Example    : $dfc = $adaptor->fetch_by_dbID(1234);
  Description: Returns the DnaFragChunk created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Compara::Production::DnaFragChunk
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::fetch_by_dbIDs ( )
  Arg [1...] : int $id (multiple)
               the unique database identifier for the feature to be obtained
  Example    : $dfc = $adaptor->fetch_by_dbID(1234);
  Description: Returns an array of DnaFragChunk created from the database defined by the
               the id $id.
  Returntype : listref of Bio::EnsEMBL::Compara::Production::DnaFragChunk objects
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
click to view
public Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::fetch_MaskingOptions_by_mlss_tag ( )

Undocumented method

Code:
click to view
public void Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::store ( )
  Arg[1]     : one or many DnaFragChunk objects
  Example    : $adaptor->store($chunk);
  Description: stores DnaFragChunk objects into compara database
  Returntype : none
  Exceptions : none
  Caller     : general
 
Code:
click to view
public Bio::EnsEMBL::Compara::Production::DBSQL::DnaFragChunkAdaptor::update_sequence ( )

Undocumented method

Code:
click to view

The documentation for this class was generated from the following file: