LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::DBSQL::Support::FullIdCache - ID based caching using all available values

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.

METHODS

build_cache

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

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

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

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

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

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 C<compute_keys()> method and adds
                the object to the C<_additional_lookup()> hash.
  Returntype  : None
  Exceptions  : Thrown if additional lookups are not supported
  Caller      : BaseAdaptors
  Status      : Beta

_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