Bio::EnsEMBL::DBSQL::MiscSetAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::MiscSetAdaptor:

Public Member Functions
public Bio::EnsEMBL::MiscSet	new ()
public Listref	fetch_all ()
public Bio::EnsEMBL::MiscSet	fetch_by_dbID ()
public Bio::EnsEMBL::MiscSet	fetch_by_code ()
public void	store ()
public Int	update ()
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

my $msa = $registry->get_adaptor( 'Human', 'Core', 'MiscSet' );
 
my $misc_set = $msa->fetch_by_dbID(1234);
 
$misc_set = $msa->fetch_by_code('clone');

Description

This class provides database interactivity for MiscSet objects.
MiscSets are used to classify MiscFeatures into groups.

Definition at line 23 of file MiscSetAdaptor.pm.

Member Function Documentation

fetch_all()

public Listref Bio::EnsEMBL::DBSQL::MiscSetAdaptor::fetch_all

(

)

  Arg [1]    : none
  Example    :

foreach my $ms (@{$msa->fetch_all()}) {
                print $ms->code(), ' ', $ms->name(), "\n";
              }

  Description: Retrieves every MiscSet defined in the DB.
               NOTE:  In a multi-species database, this method will
               return all the entries matching the search criteria, not
               just the ones associated with the current species.
  Returntype : listref of Bio::EnsEMBL::MiscSets
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

fetch_by_code()

public Bio::EnsEMBL::MiscSet Bio::EnsEMBL::DBSQL::MiscSetAdaptor::fetch_by_code

(

)

  Arg [1]    : string $code
               The unique code of the MiscSet to retrieve
  Example    :

my $ms = $msa->fetch_by_code('clone');

  Description: Retrieves a MiscSet via its code
  Returntype : Bio::EnsEMBL::MiscSet
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

fetch_by_dbID()

public Bio::EnsEMBL::MiscSet Bio::EnsEMBL::DBSQL::MiscSetAdaptor::fetch_by_dbID

(

)

  Arg [1]    : int $dbID
               The internal identifier of the misc set to retrieve
  Example    :

my $ms = $msa->fetch_by_dbID($dbID);

  Description: Retrieves a misc set via its internal identifier
  Returntype : Bio::EnsEMBL::MiscSet
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::MiscSet Bio::EnsEMBL::DBSQL::MiscSetAdaptor::new

(

)

  Arg [...]  : Superclass args.  See Bio::EnsEMBL::DBSQL::BaseAdaptor
  Description: Instantiates a Bio::EnsEMBL::DBSQL::MiscSetAdaptor and
               caches the contents of the MiscSet table.
  Returntype : Bio::EnsEMBL::MiscSet
  Exceptions : none
  Caller     : MiscFeatureAdaptor
  Status     : Stable

Code:

store()

public void Bio::EnsEMBL::DBSQL::MiscSetAdaptor::store

(

)

  Arg [1]    : list of MiscSets @mist_sets
  Example    :

$misc_set_adaptor->store(@misc_sets);

  Description: Stores a list of MiscSets in the database, and sets the
               dbID and adaptor attributes of the stored sets.
  Returntype : none
  Exceptions : throw on incorrect arguments
               warning if a feature is already stored in this database
  Caller     : MiscFeatureAdaptor::store
  Status     : Stable

Code:

update()

public Int Bio::EnsEMBL::DBSQL::MiscSetAdaptor::update

(

)

  Arg [1]    : Bio::EnsEMBL::MiscSet $miscset
  Example    :

$adaptor->update($miscset)

  Description: Updates this misc_set in the database
  Returntype : int 1 if update is performed, undef if it is not
  Exceptions : throw if arg is not an misc_set object
  Caller     : ?
  Status     : Stable

Code:

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

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