Mercurial > repos > charles_s_test > seqsero2

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/vdb/built-in.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 /*==========================================================================
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28 * VDB built-in functions, formats and types
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29 */
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30 version 1;
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31
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32
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33 /*--------------------------------------------------------------------------
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34 * types
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35 */
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36
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37 // Row id range consist of row_id_start and row_id_stop
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38 typedef I64 vdb:row_id_range [ 2 ];
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39
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40
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41 /*--------------------------------------------------------------------------
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42 * typesets
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43 */
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44 typeset integer_set { I8, U8, I16, U16, I32, U32, I64, U64 };
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45 typeset float_set { F32, F64 };
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46 typeset numeric_set { integer_set, float_set };
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47 typeset text_set { utf8, utf16, utf32, ascii };
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48 typeset text8_set { utf8, ascii };
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49 typeset transpose_set { B8, B16, B32, B64 };
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50
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51
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52 /*--------------------------------------------------------------------------
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53 * formats
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54 */
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55 fmtdef merged_fmt;
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56 fmtdef transposed_fmt;
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57 fmtdef delta_averaged_fmt;
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58
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59
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60 /*--------------------------------------------------------------------------
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61 * constants
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62 */
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63 const U8 ALIGN_LEFT = 0;
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64 const U8 ALIGN_RIGHT = 1;
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65
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66 /*--------------------------------------------------------------------------
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67 * functions
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68 */
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69
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70
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71 /* cast
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72 * performs a "C++ reinterpret_cast" style cast
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73 * rewrites input as required to produce output
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74 *
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75 * legal operations include numeric_set -> numeric_set,
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76 * numeric <-> character, etc.
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77 */
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78 function
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79 any cast #1.0 ( any in )
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80 = vdb:cast;
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81
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82 /* bit_or
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83 * performs a bitwise operation 'OR' for every byte in A and B
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84 * A and B are not neccesarily have the same size
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85 * the resulting row will have the size of B while OR operation is done for portion of A overlapping B
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86 * For different sizes of A and B 'align' parameter provides what edge of A and B are aligned
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87 * possible values ALIGN_LEFT, ALIGN_RIGHT
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88 *
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89 */
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90 function < type T >
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91 T bit_or #1 < U8 align > ( T A, T B )
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92 = vdb:bit_or;
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93
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94 /* trim
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95 * performs trimming of value val from column A
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96 * align provides left- or right- trimming
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97 */
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98 function < type T >
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99 T trim #1 < U8 align, T val > ( T A )
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100 = vdb:trim;
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101
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102
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103 /* redimension
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104 * performs a change of dimension without changing bit pattern
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105 */
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106 function
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107 any redimension #1.0 ( any in )
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108 = vdb:redimension;
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109
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110
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111 /* row_id
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112 * returns the row id of a request
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113 */
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114 function
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115 I64 row_id #1.0 ()
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116 = vdb:row_id;
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117
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118
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119 /* row_len
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120 * returns the number of elements in a row
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121 *
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122 * "in" [ DATA ] - column supplying row. if row does not exist
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123 * in column, the resultant length is 0.
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124 */
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125 function
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126 U32 row_len #1.0 ( any in )
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127 = vdb:row_len;
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128
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129
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130 /* fixed_row_len
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131 * returns non-zero if the entire page
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132 * has a uniform row-length, zero otherwise
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133 *
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134 * "in" [ DATA ] - column to query
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135 */
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136 function
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137 U32 fixed_row_len #1.0 ( any in )
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138 = vdb:fixed_row_len;
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139
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140
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141 /* compare
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142 * evaluates src [ i ] == cmp [ i ]
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143 * causes writing exception if unequal.
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144 *
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145 * For whole types, equality is bitwise equal
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146 * for floating point types see below.
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147 *
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148 * "T" [ TYPE ] - base element type to be processed
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149 *
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150 * "sig_bits" [ OPTIONAL CONST >= 1 ] - for floating point types, ignored
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151 * otherwise, the number of significant binary digits in the mantissas to
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152 * compare such that |x - y| <= 1, for corresponding numbers x (in a) and
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153 * y (in b) both scaled according to sig_bits and their common magnitude.
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154 * "sig_bits" may be an array, if so "sel" is required (see below).
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155 *
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156 * "src" [ DATA ] - standard input data derived from source
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157 *
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158 * "cmp" [ DATA ] - feedback data after being written and re-read
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159 *
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160 */
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161 validate function < type T >
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162 void compare #1.0 < * U32 sig_bits > ( T src, T cmp )
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163 = vdb:compare;
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164
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165 validate function < type T >
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166 void no_compare #1.0 ( T src, T cmp )
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167 = vdb:no_compare;
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168
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169
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170 /* compare2f
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171 * evaluates src [ i ] == cmp [ i ]
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172 * causes writing exception if unequal.
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173 *
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174 * "T" [ TYPE ] - base element type to be processed
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175 *
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176 * "sig_bits" [ CONST >= 1 ] - for floating point types, ignored otherwise,
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177 * array containing the number of significant binary digits in the mantissas
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178 * to compare such that |x - y| <= 1, for corresponding numbers x (in a) and
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179 * y (in b) both scaled according to sig_bits and their common magnitude.
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180 *
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181 * "src" [ DATA ] - standard input data derived from source
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182 *
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183 * "cmp" [ DATA ] - feedback data after being written and re-read
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184 *
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185 * "sel" [ DATA ] - data to select which element of "sig_bits" to
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186 * use for the comparison. The valid values of "sel" are
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187 * [0 .. length sig_bits).
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188 *
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189 validate function < type T >
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190 void compare2f #1.0 < U32 sig_bits > ( float_set src, float_set cmp, T sel )
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191 = vdb:compare2f;
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192 */
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193
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194 /* range_validate
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195 * passes input through if all values fall between lower and
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196 * upper bounds, INCLUSIVE
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197 *
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198 * "T" [ TYPE ] - type to be validated
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199 *
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200 * "lower" [ CONST ] and "upper" [ CONST ] - inclusive
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201 * bounds on input values
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202 *
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203 * "in" [ DATA ] - data to be validated
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204 */
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205 function < type T >
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206 T range_validate #1.0 < T lower, T upper > ( T in )
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207 = vdb:range_validate;
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208
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209
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210 /* select
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211 * return first non-empty input for id
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212 * inputs are taken from first to last
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213 *
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214 * "T" [ TYPE ] - data type of selection
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215 *
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216 * "first" [ DATA ] - first of N inputs
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217 *
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218 * "second" [ DATA ] - second of N inputs
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219 * all other inputs are optional and must
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220 * be compatible with type "T"
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221 */
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222 function < type T >
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223 T select #1.0 ( T first, T second, ... )
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224 = vdb:select;
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225
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226
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227 /* transpose
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228 * transpose a page of unformatted data
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229 *
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230 * for example - convert a simple page of values,
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231 * where vertical scale is row id and horizontal element index:
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232 *
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233 * 1 2 3
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234 * +---+---+---+
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235 * 1 | a | b | c |
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236 * +---+---+---+
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237 * 2 | d | e | f |
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238 * +---+---+---+
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239 * 3 | g | h | i |
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240 * +---+---+---+
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241 * 4 | j | k | l |
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242 * +---+---+---+
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243 *
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244 * into:
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245 *
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246 * 1 2 3 4
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247 * +---+---+---+---+
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248 * 1 | a | d | g | j |
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249 * +---+---+---+---+
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250 * 2 | b | e | h | k |
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251 * +---+---+---+---+
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252 * 3 | c | f | i | l |
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253 * +---+---+---+---+
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254 *
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255 * variable row-lengths are supported. The output blob is
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256 * formatted, meaning that the result can no longer be addressed
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257 * as a matrix, but the transposition has be applied to data.
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258 *
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259 * "in" [ DATA ] - unformatted data to be transposed
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260 */
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261 function
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262 transposed_fmt transpose #1 ( transpose_set in )
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263 = vdb:transpose;
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264
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265
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266 /* detranspose
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267 * pardoning the awful name, apply a transposition on the result
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268 * of "transpose" to produce the original blob. "transpose"
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269 * itself cannot be reused because of its signature.
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270 */
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271 function
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272 transpose_set detranspose #1 ( transposed_fmt in )
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273 = vdb:detranspose;
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274
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275 /*
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276 * delta_average computes average representation of the maximium
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277 * lengh row and deltas every row against it
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278 */
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279 function
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280 delta_averaged_fmt delta_average #1 ( any in )
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281 = vdb:delta_average;
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282
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283 function
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284 any undelta_average #1 ( delta_averaged_fmt in )
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285 = vdb:undelta_average;
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286
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287 /* merge
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288 * merges all input blobs of any format/type into a single blob
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289 */
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290 function
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291 merged_fmt merge #1.0 ( any in, ... )
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292 = vdb:merge;
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293
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294
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295 /* split
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296 * extracts a single blob from a merged blob by index
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297 *
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298 * "idx" [ CONST ] - blob index
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299 */
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300
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301 function
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302 any split #1.0 < U32 idx > ( merged_fmt in )
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303 = vdb:split;
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304
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305
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306 /* meta:read
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307 * reads table metadata node as a row
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308 * meta:value
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309 * reads metadata node as single value,
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310 * performing size conversion if necessary,
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311 * e.g. I8 TO I64, I32 TO I16
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312 *
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313 * "T" [ TYPE ] - cast data type of metadata node
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314 *
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315 * "node" [ CONST ] - path to metadata node
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316 */
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317 function < type T >
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318 T meta:read #1.0 < ascii node, * bool deterministic > ();
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319
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320 function < type T >
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321 T meta:value #1.0 < ascii node, * bool deterministic > ();
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322
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323
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324 /* meta:write
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325 * writes row data to table metadata node
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326 *
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327 * "T" [ TYPE ] - cast data type of metadata node
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328 *
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329 * "node" [ CONST ] - path to metadata node
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330 *
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331 * "in" [ DATA ] - source of row data
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332 */
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333 function < type T >
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334 T meta:write #1.0 < ascii node > ( T in );
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335
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336
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337 /* meta:attr:read
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338 * reads table metadata attribute as a row
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339 *
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340 * "node" [ CONST ] - path to metadata node
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341 *
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342 * "attr" [ CONST ] - attribute name on node
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343 */
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344 function
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345 ascii meta:attr:read #1.0 < ascii node, ascii attr, * bool deterministic > ();
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346
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347
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348 /* meta:attr:write
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349 * write row data as table metadata attribute
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350 *
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351 * "node" [ CONST ] - path to metadata node
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352 *
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353 * "attr" [ CONST ] - attribute name on node
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354 */
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355 function
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356 ascii meta:attr:write #1.0 < ascii node, ascii attr > ( ascii in );
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357
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358
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359 /* parameter:read
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360 * reads named cursor parameter text
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361 *
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362 * "name" [ CONST ] - parameter name
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363 */
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364 function
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365 text8_set parameter:read #1.0 < ascii name, * bool deterministic > ();
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366
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367
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368 /* environment:read
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369 * reads named environment variable text
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370 *
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371 * "name" [ CONST ] - environment variable name
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372 */
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373 function
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374 text8_set environment:read #1.0 < ascii name > ();
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375
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376 // case sensivity mode
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377 const U8 CASE_SENSITIVE = 0;
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378 const U8 CASE_INSENSITIVE_LOWER = 1;
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379 const U8 CASE_INSENSITIVE_UPPER = 2;
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380
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381 /* idx:text:project
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382 * perform a reverse lookup in an index
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383 * if key not found then use substitute
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384 *
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385 * "index_name" [ CONST ] - name of text index
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386 *
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387 * "substitute" [ DATA, OPTIONAL ] - source
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388 * of values to substitute for values not
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389 * found in the index.
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390 *
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391 * Version 1.1: look into "substitute" (if available) first and then to the index,
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392 * added parameter "case_sensitivity"
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393 */
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394 function text8_set idx:text:project #1.1 < ascii index_name, * U8 case_sensitivity > ( * text8_set substitute );
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395
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396
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397 /* idx:text:insert
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398 * inserts "key" into index. returns key if insertion into index failed or
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399 * when "case_insensitive" is true
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400 *
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401 * Version 1.1: added parameter "case_sensitivity"
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402 */
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403 function text8_set idx:text:insert #1.1 < ascii index_name, * U8 case_sensitivity > ( text8_set key );
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404
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405
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406 /* idx:text:lookup
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407 * perform a lookup in an index
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408 * returns vdb:row_id_range associated with the
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409 *
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410 * Version 1.1: added parameter "case_sensitivity"
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411 */
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412 function vdb:row_id_range idx:text:lookup #1.1 < ascii index_name , ascii query_by_name, * U8 case_sensitivity > ();