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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Utils::SeqRegionCache - A shared LRU cache of information about
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24 seq_regions
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25
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26 =head1 SYNOPSIS
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27
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28 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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29
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30 $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
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31
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32 $seq_region_cache = $db->get_SeqRegionCache();
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33
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34 $key = "$seq_region_name:$coord_system_id";
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35
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36 $array = $seq_region_cache->{$key};
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37
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38 if ($array) {
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39 $name = $array->[1];
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40 $length = $array->[3];
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41 } else {
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42 # cache miss, get the info from the database
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43 # ...
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44
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45 # cache the retrieved information
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46 $seq_region_cache->{$key} = [
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47 $seq_region_id, $seq_region_name,
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48 $coord_system_id, $seq_region_length
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49 ];
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50 }
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51
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52 =head1 DESCRIPTION
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53
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54 This module is simply a convenient place to put a cache of sequence
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55 region information which is shared by several adaptors for a given
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56 database.
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57
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58 =head1 METHODS
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59
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60 =cut
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61
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62 use strict;
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63 use Bio::EnsEMBL::Utils::Cache;
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64
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65 package Bio::EnsEMBL::Utils::SeqRegionCache;
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66
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67 our $SEQ_REGION_CACHE_SIZE = 40000;
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68
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69
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70
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71 sub new {
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72 my $class = shift;
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73
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74 my %id_cache;
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75 my %name_cache;
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76
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77 #
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78 # the items to cache should be listrefs to
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79 # [ sr_id, sr_name, cs_id, sr_length ]
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80 #
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81 # The name cache key is "sr_name:cs_id"
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82 # The id cache is keyed on "sr_id"
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83 #
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84
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85 tie(%name_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
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86 tie(%id_cache, 'Bio::EnsEMBL::Utils::Cache', $SEQ_REGION_CACHE_SIZE);
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87
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88 return bless {'name_cache' => \%name_cache,
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89 'id_cache' => \%id_cache}, $class;
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90 }
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91
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92
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93 1;
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94
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95
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96
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97
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