Bio::EnsEMBL::DBSQL::Support::FullIdCache Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::Support::FullIdCache:

Public Member Functions
public Hash	build_cache ()
public	put ()
public	remove ()
public	clear_cache ()
public Object	get_by_additional_lookup ()
public ArrayRef	get_all_by_additional_lookup ()
public void	remove_from_additional_lookup ()
public HashRef	compute_keys ()
public void	add_to_additional_lookups ()
protected HashRef	_additional_lookup ()
Public Member Functions inherited from Bio::EnsEMBL::DBSQL::Support::BaseCache
public Bio::EnsEMBL::DBSQL::Support::BaseCache	new ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Hash	cache ()
public void	delete_cache ()
public Scalar	get ()
public ArrayRef	get_by_list ()
public ArrayRef	get_by_sql ()
public Scalar	put ()
public Scalar	remove ()
public void	clear_cache ()
public List	cache_keys ()
public List	cached_values ()
public Int	size ()
public Hash	build_cache ()

Detailed Description

Synopsis

my $cache = Bio::EnsEMBL::DBSQL::Support::FullIdCache->new($adaptor);
my $obj = $cache->get(21);

Description

An implementation of caching which uses a raw hash to hold all available
values from an adaptor. Useful for working with a controlled vocabulary
table where cardinality is low.

Provides extra functionality to compute additional lookup keys.

Definition at line 22 of file FullIdCache.pm.

Member Function Documentation

_additional_lookup()

protected HashRef Bio::EnsEMBL::DBSQL::Support::FullIdCache::_additional_lookup

(

)

  Description : Returns the additional lookup hash
  Example     :

Example of additional hash structure (key is 
               lookup name, second key is value to search for
               and value is an array of dbIDs)
               {
                 logic_name => {
                   xrefalignment => [1]
                 },
                 display_label => {
                   'Xref Alignment' => [1]
                 }
               }

  Returntype  : HashRef
  Exceptions  : none
  Caller      : BaseAdaptors
  Status      : Beta

Code:

add_to_additional_lookups()

public void Bio::EnsEMBL::DBSQL::Support::FullIdCache::add_to_additional_lookups

(

)

  Arg [1]     : String The key used in the primary lookup hash. Normally
                a DB identifier
  Arg [2]     : Object The object to add to the additional lookups
  Description : Internally calls the compute_keys() method and adds
                the object to the _additional_lookup() hash.
  Returntype  : None
  Exceptions  : Thrown if additional lookups are not supported
  Caller      : BaseAdaptors
  Status      : Beta

Code:

build_cache()

public Hash Bio::EnsEMBL::DBSQL::Support::FullIdCache::build_cache

(

)

  Description: Builds a cache keyed by dbID and populated from a call
               using generic_fetch()
  Returntype : Hash
  Exceptions : None
  Caller     : BaseAdaptors
  Status     : Beta

Code:

clear_cache()

public Bio::EnsEMBL::DBSQL::Support::FullIdCache::clear_cache

(

)

Undocumented method

Code:

compute_keys()

public HashRef Bio::EnsEMBL::DBSQL::Support::FullIdCache::compute_keys

(

)

  Arg [1]     : Object The object to compute keys from
  Description : Override to provide support for additional key lookup. The
                keys of the hash should represent the lookup name and the
                value is the computed key.
  Example     :

Example of returning hash not of its usage. Proposed Analysis encoding
               { logic_name => 'xrefalignment', display_label => 'Xref Alignment'}

  Returntype  : HashRef key is the lookup name and value is the computed key
  Exceptions  : none
  Caller      : BaseAdaptors
  Status      : Beta

Code:

get_all_by_additional_lookup()

public ArrayRef Bio::EnsEMBL::DBSQL::Support::FullIdCache::get_all_by_additional_lookup

(

)

  Arg [1]     : String key of the lookup to search for the value in
  Arg [2]     : String value to search for. We expect exact lookups in the hash
  Description : Returns an array of all the objects linked to the value
                in the specified lookup.
  Example     :

my $array = $cache->get_all_by_additional_lookup('logic_name', 'xrefchecksum');

  Returntype  : ArrayRef of objects keyed agains the second argument
  Exceptions  : Throws an exception if there are more than one ID linked to the
                value lookup. Also thrown if additional lookups are not supported
  Caller      : BaseAdaptors
  Status      : Beta

Code:

get_by_additional_lookup()

public Object Bio::EnsEMBL::DBSQL::Support::FullIdCache::get_by_additional_lookup

(

)

  Arg [1]     : String key of the lookup to search for the value in
  Arg [2]     : String value to search for. We expect exact lookups in the hash
  Description : Returns the object linked to the value in the specified lookup.
  Example     :

my $analysis = $cache->get_by_additional_lookup('logic_name', 'xrefchecksum');

  Returntype  : Object a single object
  Exceptions  : Throws an exception if there are more than one ID linked to the
                value lookup. Also thrown if additional lookups are not supported 
  Caller      : BaseAdaptors
  Status      : Beta

Code:

put()

public Bio::EnsEMBL::DBSQL::Support::FullIdCache::put

(

)

Undocumented method

Code:

remove()

public Bio::EnsEMBL::DBSQL::Support::FullIdCache::remove

(

)

Undocumented method

Code:

remove_from_additional_lookup()

public void Bio::EnsEMBL::DBSQL::Support::FullIdCache::remove_from_additional_lookup

(

)

  Arg [1]     : String The lookup key to remove from the additional lookup hash
  Arg [2]     : Object The object to remove from the additional lookup hash
  Description : Re-computes the additional keys for this object 
  Example     :

$cache->remove_Object_from_additional_lookup($lookup_key, $object);

  Returntype  : None
  Exceptions  : Thrown if we do not support additional lookups
  Caller      : BaseAdaptors
  Status      : Beta

Code:

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

• ensembl/modules/Bio/EnsEMBL/DBSQL/Support/FullIdCache.pm