SeqRegionCache.pm

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=head1 LICENSE
 
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regarding copyright ownership.
 
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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distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
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=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
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  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=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;