diff variant_effect_predictor/Bio/EnsEMBL/Utils/SeqRegionCache.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Utils/SeqRegionCache.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,97 @@
+=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;
+
+
+
+