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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/ncbi/pnbrdb.vschema @ 3:38ad1130d077 draft

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author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 /*===========================================================================
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2 *
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3 * PUBLIC DOMAIN NOTICE
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4 * National Center for Biotechnology Information
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5 *
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6 * This software/database is a "United States Government Work" under the
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7 * terms of the United States Copyright Act. It was written as part of
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8 * the author's official duties as a United States Government employee and
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9 * thus cannot be copyrighted. This software/database is freely available
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10 * to the public for use. The National Library of Medicine and the U.S.
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11 * Government have not placed any restriction on its use or reproduction.
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12 *
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13 * Although all reasonable efforts have been taken to ensure the accuracy
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14 * and reliability of the software and data, the NLM and the U.S.
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15 * Government do not and cannot warrant the performance or results that
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16 * may be obtained by using this software or data. The NLM and the U.S.
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17 * Government disclaim all warranties, express or implied, including
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18 * warranties of performance, merchantability or fitness for any particular
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19 * purpose.
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20 *
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21 * Please cite the author in any work or product based on this material.
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22 *
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23 * ===========================================================================
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24 *
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25 */
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26
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27 version 1;
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28 include 'vdb/vdb.vschema';
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29
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30 /* PNBRDB
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31 * the original flat-file pnbrdb structure was divided into two forks:
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32 * 1 - "hsp" containing full blastp hsps
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33 * 2 - "nbr" containing only pig->pig relationships with max score
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34 *
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35 * each fork was organized into bin directories by "query" ( left-hand ) pig
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36 * each bin contained entries for up to 1M query pigs with a numeric
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37 * 4 digit 1-based name generated as "( ( qpig - 1 ) / 1024 ) / 1024 + 1".
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38 * this bin approach served as a primitive index.
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39 *
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40 * within each bin directory, there are 1024 data files, where each data file
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41 * represented 1024 query pigs. the file name incorporated a 4 digit 1-based
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42 * file id generated as "( ( qpig - 1 ) / 1024 ) % 1024 + 1" making it possible
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43 * to locate any entry by query pig within a 1024 entry neighborhood by using
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44 * filesystem path alone.
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45 *
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46 * within each data file, a fixed-size 1024-entry header gave the location of
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47 * entries ordered according to the most common queries.
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48 *
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49 * all basic data are contained within the "hsp" fork. the "nbr" fork served
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50 * as a pre-calculated result of the query selecting all unique pig->pig pairs
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51 * with their maximum score value.
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52 */
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53
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54 /* The vdb representation of the pnbrdb has two tables
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55 * 1. table with one row per qpig (i.e. qpig = row_id) and two columns:
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56 * offset and count. Offset indicates row_id in the second table where the
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57 * hsps for the qpig are stored and count indicates the number of these rows.
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58 * 2. table with these coulmns: spig, max_score and blob. The blob contains all
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59 * segments for given (qpig, spig) pair.
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60 */
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61
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62 table NCBI:pnbr:table:qpig #1
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63 {
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64 /* OFFSET
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65 * start position of hsps for qpig = row_id in the hsp table.
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66 */
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67 extern column <U64> izip_encoding OFFSET;
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68
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69 /* COUNT
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70 * number of hsps for qpig = row_id in the hsp table.
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71 */
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72 extern column <U64> izip_encoding COUNT;
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73 };
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74
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75 table NCBI:pnbr:table:hsp #1
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76 {
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77 /* SPIG
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78 * the subject pig column
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79 */
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80 extern column <U32> izip_encoding SPIG;
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81
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82 /* MAX_SCORE
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83 * max score between given query pig and subject pig
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84 */
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85 extern column <I32> izip_encoding MAX_SCORE;
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86
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87 /* SEGMENTS
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88 * blob for storing hsps for given qpig and spig.
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89 */
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90 extern column <B8> zip_encoding SEGMENTS;
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91 };
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92
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93 database NCBI:pnbr:db:pnbr #1
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94 {
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95 table NCBI:pnbr:table:qpig #1 QPIG_REFERENCE;
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96 table NCBI:pnbr:table:hsp #1 HSP;
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97 };
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98