view variant_effect_predictor/Bio/EnsEMBL/Utils/SeqRegionCache.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::Utils::SeqRegionCache - A shared LRU cache of information about
seq_regions

=head1 SYNOPSIS

  use Bio::EnsEMBL::DBSQL::DBAdaptor;

  $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);

  $seq_region_cache = $db->get_SeqRegionCache();

  $key = "$seq_region_name:$coord_system_id";

  $array = $seq_region_cache->{$key};

  if ($array) {
    $name   = $array->[1];
    $length = $array->[3];
  } else {
    # cache miss, get the info from the database
    # ...

    # cache the retrieved information
    $seq_region_cache->{$key} = [
      $seq_region_id,   $seq_region_name,
      $coord_system_id, $seq_region_length
    ];
  }

=head1 DESCRIPTION

This module is simply a convenient place to put a cache of sequence
region information which is shared by several adaptors for a given
database.

=head1 METHODS

=cut

use strict;
use Bio::EnsEMBL::Utils::Cache;

package Bio::EnsEMBL::Utils::SeqRegionCache;

our $SEQ_REGION_CACHE_SIZE = 40000;



sub new {
  my $class = shift;

  my %id_cache;
  my %name_cache;

  #
  # the items to cache should be listrefs to
  # [ sr_id, sr_name, cs_id, sr_length ]
  #
  # The name cache key is "sr_name:cs_id"
  # The id cache is keyed on "sr_id"
  #

  tie(%name_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
  tie(%id_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);

  return bless {'name_cache' => \%name_cache, 
                'id_cache' => \%id_cache}, $class;
}


1;