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Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor:

List of all members.


Class Summary

Synopsis

Description

Adpter to DnaColelction objects/tables
DnaColelction is an object to hold a super-set of DnaFragChunk, and/or DnaFragChunkSet 
objects.  Used in production to encapsulate particular genome/region/chunk/group DNA set
from the others.  To allow system to blast against self, and isolate different 
chunk/group sets of the same genome from each other.
 

Definition at line 25 of file DnaCollectionAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _fetch_all_DnaFragChunk_by_ids ()
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 delete_link ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_dbID_list ()
public
Bio::EnsEMBL::Compara::Production::DnaCollection 
fetch_by_dbID ()
public fetch_by_set_description ()
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 Int store ()
public store_link ()

Method Documentation

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

Undocumented method

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

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

Undocumented method

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

protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::_fetch_all_DnaFragChunk_by_ids ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::_final_clause ( )

Undocumented method

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

protected Listref Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::_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::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch
 
Code:
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protected Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::_objs_from_sth ( )

Undocumented method

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

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

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::delete_link ( )
  Arg [1]    :  int $dna_collection_id
  Arg [2]    :  int $foreign_id
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 
public Bio::EnsEMBL::Compara::Production::DnaCollection Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::fetch_by_dbID ( )
  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234);
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Compara::Production::DnaCollection
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::fetch_by_set_description ( )
  Arg [1]    : string $set_description
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :
 
Code:
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public Int Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::store ( )
  Arg [1]    : Bio::EnsEMBL::Compara::Production::DnaCollection
  Example    :
  Description: stores the set of DnaFragChunk objects
  Returntype : int dbID of DnaCollection
  Exceptions :
  Caller     :
 
Code:
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public Bio::EnsEMBL::Compara::Production::DBSQL::DnaCollectionAdaptor::store_link ( )
  Arg [1]    :  int $dna_collection_id
  Arg [2]    :  int $foreign_id
  Example    :
  Description:
  Returntype :
  Exceptions :
  Caller     :
 

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