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0
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1 /* The MIT License
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2
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3 Copyright (c) 2008 Genome Research Ltd (GRL).
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4
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5 Permission is hereby granted, free of charge, to any person obtaining
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6 a copy of this software and associated documentation files (the
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7 "Software"), to deal in the Software without restriction, including
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8 without limitation the rights to use, copy, modify, merge, publish,
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9 distribute, sublicense, and/or sell copies of the Software, and to
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10 permit persons to whom the Software is furnished to do so, subject to
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11 the following conditions:
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12
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13 The above copyright notice and this permission notice shall be
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14 included in all copies or substantial portions of the Software.
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15
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16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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17 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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18 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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19 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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20 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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21 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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22 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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23 SOFTWARE.
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24 */
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25
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26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
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27
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28 /*
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29 An example:
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30
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31 #include "khash.h"
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32 KHASH_MAP_INIT_INT(32, char)
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33 int main() {
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34 int ret, is_missing;
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35 khiter_t k;
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36 khash_t(32) *h = kh_init(32);
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37 k = kh_put(32, h, 5, &ret);
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38 if (!ret) kh_del(32, h, k);
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39 kh_value(h, k) = 10;
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40 k = kh_get(32, h, 10);
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41 is_missing = (k == kh_end(h));
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42 k = kh_get(32, h, 5);
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43 kh_del(32, h, k);
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44 for (k = kh_begin(h); k != kh_end(h); ++k)
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45 if (kh_exist(h, k)) kh_value(h, k) = 1;
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46 kh_destroy(32, h);
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47 return 0;
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48 }
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49 */
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50
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51 /*
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52 2008-09-19 (0.2.3):
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53
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54 * Corrected the example
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55 * Improved interfaces
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56
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57 2008-09-11 (0.2.2):
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58
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59 * Improved speed a little in kh_put()
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60
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61 2008-09-10 (0.2.1):
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62
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63 * Added kh_clear()
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64 * Fixed a compiling error
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65
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66 2008-09-02 (0.2.0):
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67
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68 * Changed to token concatenation which increases flexibility.
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69
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70 2008-08-31 (0.1.2):
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71
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72 * Fixed a bug in kh_get(), which has not been tested previously.
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73
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74 2008-08-31 (0.1.1):
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75
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76 * Added destructor
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77 */
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78
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79
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80 #ifndef __AC_KHASH_H
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81 #define __AC_KHASH_H
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82
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83 /*!
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84 @header
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85
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86 Generic hash table library.
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87
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88 @copyright Heng Li
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89 */
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90
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91 #define AC_VERSION_KHASH_H "0.2.2"
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92
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93 #include <stdint.h>
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94 #include <stdlib.h>
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95 #include <string.h>
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96
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97 typedef uint32_t khint_t;
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98 typedef khint_t khiter_t;
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99
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100 #define __ac_HASH_PRIME_SIZE 32
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101 static const uint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
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102 {
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103 0ul, 3ul, 11ul, 23ul, 53ul,
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104 97ul, 193ul, 389ul, 769ul, 1543ul,
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105 3079ul, 6151ul, 12289ul, 24593ul, 49157ul,
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106 98317ul, 196613ul, 393241ul, 786433ul, 1572869ul,
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107 3145739ul, 6291469ul, 12582917ul, 25165843ul, 50331653ul,
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108 100663319ul, 201326611ul, 402653189ul, 805306457ul, 1610612741ul,
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109 3221225473ul, 4294967291ul
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110 };
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111
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112 #define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
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113 #define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
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114 #define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
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115 #define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
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116 #define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
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117 #define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
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118 #define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
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119
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120 static const double __ac_HASH_UPPER = 0.77;
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121
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122 #define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
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123 typedef struct { \
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124 khint_t n_buckets, size, n_occupied, upper_bound; \
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125 uint32_t *flags; \
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126 khkey_t *keys; \
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127 khval_t *vals; \
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128 } kh_##name##_t; \
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129 static inline kh_##name##_t *kh_init_##name() { \
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130 return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \
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131 } \
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132 static inline void kh_destroy_##name(kh_##name##_t *h) \
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133 { \
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134 if (h) { \
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135 free(h->keys); free(h->flags); \
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136 free(h->vals); \
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137 free(h); \
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138 } \
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139 } \
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140 static inline void kh_clear_##name(kh_##name##_t *h) \
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141 { \
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142 if (h && h->flags) { \
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143 memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(uint32_t)); \
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144 h->size = h->n_occupied = 0; \
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145 } \
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146 } \
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147 static inline khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
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148 { \
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149 if (h->n_buckets) { \
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150 khint_t inc, k, i, last; \
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151 k = __hash_func(key); i = k % h->n_buckets; \
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152 inc = 1 + k % (h->n_buckets - 1); last = i; \
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153 while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
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154 if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
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155 else i += inc; \
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156 if (i == last) return h->n_buckets; \
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157 } \
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158 return __ac_iseither(h->flags, i)? h->n_buckets : i; \
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159 } else return 0; \
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160 } \
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161 static inline void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
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162 { \
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163 uint32_t *new_flags = 0; \
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164 khint_t j = 1; \
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165 { \
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166 khint_t t = __ac_HASH_PRIME_SIZE - 1; \
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167 while (__ac_prime_list[t] > new_n_buckets) --t; \
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168 new_n_buckets = __ac_prime_list[t+1]; \
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169 if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; \
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170 else { \
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171 new_flags = (uint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(uint32_t)); \
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172 memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(uint32_t)); \
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173 if (h->n_buckets < new_n_buckets) { \
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174 h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
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175 if (kh_is_map) \
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176 h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
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177 } \
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178 } \
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179 } \
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180 if (j) { \
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181 for (j = 0; j != h->n_buckets; ++j) { \
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182 if (__ac_iseither(h->flags, j) == 0) { \
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183 khkey_t key = h->keys[j]; \
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184 khval_t val; \
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185 if (kh_is_map) val = h->vals[j]; \
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186 __ac_set_isdel_true(h->flags, j); \
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187 while (1) { \
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188 khint_t inc, k, i; \
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189 k = __hash_func(key); \
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190 i = k % new_n_buckets; \
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191 inc = 1 + k % (new_n_buckets - 1); \
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192 while (!__ac_isempty(new_flags, i)) { \
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193 if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \
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194 else i += inc; \
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195 } \
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196 __ac_set_isempty_false(new_flags, i); \
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197 if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \
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198 { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
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199 if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
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200 __ac_set_isdel_true(h->flags, i); \
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201 } else { \
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202 h->keys[i] = key; \
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203 if (kh_is_map) h->vals[i] = val; \
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204 break; \
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205 } \
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206 } \
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207 } \
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208 } \
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209 if (h->n_buckets > new_n_buckets) { \
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210 h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
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211 if (kh_is_map) \
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212 h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
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213 } \
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214 free(h->flags); \
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215 h->flags = new_flags; \
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216 h->n_buckets = new_n_buckets; \
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217 h->n_occupied = h->size; \
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218 h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
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219 } \
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220 } \
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221 static inline khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
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222 { \
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223 khint_t x; \
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224 if (h->n_occupied >= h->upper_bound) { \
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225 if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \
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226 else kh_resize_##name(h, h->n_buckets + 1); \
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227 } \
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228 { \
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229 khint_t inc, k, i, site, last; \
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230 x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \
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231 if (__ac_isempty(h->flags, i)) x = i; \
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232 else { \
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233 inc = 1 + k % (h->n_buckets - 1); last = i; \
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234 while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
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235 if (__ac_isdel(h->flags, i)) site = i; \
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236 if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
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237 else i += inc; \
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238 if (i == last) { x = site; break; } \
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239 } \
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240 if (x == h->n_buckets) { \
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241 if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
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242 else x = i; \
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243 } \
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244 } \
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245 } \
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246 if (__ac_isempty(h->flags, x)) { \
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247 h->keys[x] = key; \
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248 __ac_set_isboth_false(h->flags, x); \
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249 ++h->size; ++h->n_occupied; \
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250 *ret = 1; \
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251 } else if (__ac_isdel(h->flags, x)) { \
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252 h->keys[x] = key; \
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253 __ac_set_isboth_false(h->flags, x); \
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254 ++h->size; \
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255 *ret = 2; \
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256 } else *ret = 0; \
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257 return x; \
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258 } \
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259 static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
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260 { \
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261 if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \
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262 __ac_set_isdel_true(h->flags, x); \
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263 --h->size; \
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264 } \
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265 }
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266
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267 /* --- BEGIN OF HASH FUNCTIONS --- */
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268
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269 /*! @function
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270 @abstract Integer hash function
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271 @param key The integer [uint32_t]
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272 @return The hash value [khint_t]
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273 */
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274 #define kh_int_hash_func(key) (uint32_t)(key)
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275 /*! @function
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276 @abstract Integer comparison function
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277 */
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278 #define kh_int_hash_equal(a, b) ((a) == (b))
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279 /*! @function
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280 @abstract 64-bit integer hash function
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281 @param key The integer [uint64_t]
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282 @return The hash value [khint_t]
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283 */
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284 #define kh_int64_hash_func(key) (uint32_t)((key)>>33^(key)^(key)<<11)
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285 /*! @function
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286 @abstract 64-bit integer comparison function
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287 */
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288 #define kh_int64_hash_equal(a, b) ((a) == (b))
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289 /*! @function
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290 @abstract const char* hash function
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291 @param s Pointer to a null terminated string
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292 @return The hash value
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293 */
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294 static inline khint_t __ac_X31_hash_string(const char *s)
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295 {
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296 khint_t h = *s;
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297 if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
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298 return h;
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299 }
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300 /*! @function
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301 @abstract Another interface to const char* hash function
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302 @param key Pointer to a null terminated string [const char*]
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303 @return The hash value [khint_t]
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304 */
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305 #define kh_str_hash_func(key) __ac_X31_hash_string(key)
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306 /*! @function
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307 @abstract Const char* comparison function
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308 */
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309 #define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
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310
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311 /* --- END OF HASH FUNCTIONS --- */
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312
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313 /* Other necessary macros... */
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314
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315 /*!
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316 @abstract Type of the hash table.
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317 @param name Name of the hash table [symbol]
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318 */
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319 #define khash_t(name) kh_##name##_t
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320
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321 /*! @function
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322 @abstract Initiate a hash table.
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323 @param name Name of the hash table [symbol]
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324 @return Pointer to the hash table [khash_t(name)*]
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325 */
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326 #define kh_init(name) kh_init_##name()
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327
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328 /*! @function
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329 @abstract Destroy a hash table.
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330 @param name Name of the hash table [symbol]
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331 @param h Pointer to the hash table [khash_t(name)*]
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332 */
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333 #define kh_destroy(name, h) kh_destroy_##name(h)
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334
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335 /*! @function
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336 @abstract Reset a hash table without deallocating memory.
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337 @param name Name of the hash table [symbol]
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338 @param h Pointer to the hash table [khash_t(name)*]
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339 */
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340 #define kh_clear(name, h) kh_clear_##name(h)
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341
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342 /*! @function
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343 @abstract Resize a hash table.
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344 @param name Name of the hash table [symbol]
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345 @param h Pointer to the hash table [khash_t(name)*]
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346 @param s New size [khint_t]
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347 */
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348 #define kh_resize(name, h, s) kh_resize_##name(h, s)
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349
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350 /*! @function
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351 @abstract Insert a key to the hash table.
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352 @param name Name of the hash table [symbol]
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353 @param h Pointer to the hash table [khash_t(name)*]
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354 @param k Key [type of keys]
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355 @param r Extra return code: 0 if the key is present in the hash table;
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356 1 if the bucket is empty (never used); 2 if the element in
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357 the bucket has been deleted [int*]
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358 @return Iterator to the inserted element [khint_t]
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359 */
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360 #define kh_put(name, h, k, r) kh_put_##name(h, k, r)
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361
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362 /*! @function
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363 @abstract Retrieve a key from the hash table.
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364 @param name Name of the hash table [symbol]
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365 @param h Pointer to the hash table [khash_t(name)*]
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366 @param k Key [type of keys]
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367 @return Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
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368 */
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369 #define kh_get(name, h, k) kh_get_##name(h, k)
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370
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371 /*! @function
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372 @abstract Remove a key from the hash table.
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373 @param name Name of the hash table [symbol]
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374 @param h Pointer to the hash table [khash_t(name)*]
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375 @param k Iterator to the element to be deleted [khint_t]
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376 */
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377 #define kh_del(name, h, k) kh_del_##name(h, k)
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378
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379
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380 /*! @function
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381 @abstract Test whether a bucket contains data.
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382 @param h Pointer to the hash table [khash_t(name)*]
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383 @param x Iterator to the bucket [khint_t]
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384 @return 1 if containing data; 0 otherwise [int]
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385 */
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386 #define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
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387
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388 /*! @function
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389 @abstract Get key given an iterator
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390 @param h Pointer to the hash table [khash_t(name)*]
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391 @param x Iterator to the bucket [khint_t]
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392 @return Key [type of keys]
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393 */
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394 #define kh_key(h, x) ((h)->keys[x])
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395
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396 /*! @function
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397 @abstract Get value given an iterator
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398 @param h Pointer to the hash table [khash_t(name)*]
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399 @param x Iterator to the bucket [khint_t]
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400 @return Value [type of values]
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401 @discussion For hash sets, calling this results in segfault.
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402 */
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403 #define kh_val(h, x) ((h)->vals[x])
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404
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405 /*! @function
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406 @abstract Alias of kh_val()
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407 */
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408 #define kh_value(h, x) ((h)->vals[x])
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409
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410 /*! @function
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411 @abstract Get the start iterator
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412 @param h Pointer to the hash table [khash_t(name)*]
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413 @return The start iterator [khint_t]
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414 */
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415 #define kh_begin(h) (khint_t)(0)
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416
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417 /*! @function
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418 @abstract Get the end iterator
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419 @param h Pointer to the hash table [khash_t(name)*]
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420 @return The end iterator [khint_t]
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421 */
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422 #define kh_end(h) ((h)->n_buckets)
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423
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424 /*! @function
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425 @abstract Get the number of elements in the hash table
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426 @param h Pointer to the hash table [khash_t(name)*]
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427 @return Number of elements in the hash table [khint_t]
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428 */
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429 #define kh_size(h) ((h)->size)
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430
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431 /*! @function
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432 @abstract Get the number of buckets in the hash table
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433 @param h Pointer to the hash table [khash_t(name)*]
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434 @return Number of buckets in the hash table [khint_t]
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435 */
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436 #define kh_n_buckets(h) ((h)->n_buckets)
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437
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438 /* More conenient interfaces */
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439
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440 /*! @function
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441 @abstract Instantiate a hash set containing integer keys
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442 @param name Name of the hash table [symbol]
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443 */
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444 #define KHASH_SET_INIT_INT(name) \
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445 KHASH_INIT(name, uint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
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446
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447 /*! @function
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448 @abstract Instantiate a hash map containing integer keys
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449 @param name Name of the hash table [symbol]
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450 @param khval_t Type of values [type]
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451 */
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452 #define KHASH_MAP_INIT_INT(name, khval_t) \
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453 KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
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454
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455 /*! @function
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456 @abstract Instantiate a hash map containing 64-bit integer keys
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457 @param name Name of the hash table [symbol]
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458 */
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459 #define KHASH_SET_INIT_INT64(name) \
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460 KHASH_INIT(name, uint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
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461
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462 /*! @function
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463 @abstract Instantiate a hash map containing 64-bit integer keys
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464 @param name Name of the hash table [symbol]
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465 @param khval_t Type of values [type]
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466 */
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467 #define KHASH_MAP_INIT_INT64(name, khval_t) \
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468 KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
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469
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470 typedef const char *kh_cstr_t;
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471 /*! @function
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472 @abstract Instantiate a hash map containing const char* keys
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473 @param name Name of the hash table [symbol]
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474 */
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475 #define KHASH_SET_INIT_STR(name) \
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476 KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
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477
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478 /*! @function
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479 @abstract Instantiate a hash map containing const char* keys
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480 @param name Name of the hash table [symbol]
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481 @param khval_t Type of values [type]
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482 */
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483 #define KHASH_MAP_INIT_STR(name, khval_t) \
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484 KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
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485
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486 #endif /* __AC_KHASH_H */
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