Raw content of Bio::EnsEMBL::Utils::SeqRegionCache
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=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;
]]>