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1 /*
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2 * sais.c for sais-lite
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3 * Copyright (c) 2008 Yuta Mori All Rights Reserved.
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4 *
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5 * Permission is hereby granted, free of charge, to any person
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6 * obtaining a copy of this software and associated documentation
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7 * files (the "Software"), to deal in the Software without
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8 * restriction, including without limitation the rights to use,
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9 * copy, modify, merge, publish, distribute, sublicense, and/or sell
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10 * copies of the Software, and to permit persons to whom the
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11 * Software is furnished to do so, subject to the following
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12 * conditions:
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13 *
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14 * The above copyright notice and this permission notice shall be
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15 * included in all copies or substantial portions of the Software.
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16 *
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17 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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18 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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19 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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20 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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21 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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22 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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23 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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24 * OTHER DEALINGS IN THE SOFTWARE.
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25 */
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26
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27 #include <stdlib.h>
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28
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29 typedef unsigned char ubyte_t;
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30 #define chr(i) (cs == sizeof(int) ? ((const int *)T)[i]:((const unsigned char *)T)[i])
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31
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32 /* find the start or end of each bucket */
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33 static void getCounts(const unsigned char *T, int *C, int n, int k, int cs)
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34 {
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35 int i;
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36 for (i = 0; i < k; ++i) C[i] = 0;
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37 for (i = 0; i < n; ++i) ++C[chr(i)];
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38 }
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39 static void getBuckets(const int *C, int *B, int k, int end)
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40 {
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41 int i, sum = 0;
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42 if (end) {
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43 for (i = 0; i < k; ++i) {
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44 sum += C[i];
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45 B[i] = sum;
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46 }
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47 } else {
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48 for (i = 0; i < k; ++i) {
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49 sum += C[i];
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50 B[i] = sum - C[i];
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51 }
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52 }
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53 }
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54
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55 /* compute SA */
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56 static void induceSA(const unsigned char *T, int *SA, int *C, int *B, int n, int k, int cs)
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57 {
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58 int *b, i, j;
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59 int c0, c1;
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60 /* compute SAl */
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61 if (C == B) getCounts(T, C, n, k, cs);
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62 getBuckets(C, B, k, 0); /* find starts of buckets */
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63 j = n - 1;
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64 b = SA + B[c1 = chr(j)];
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65 *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
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66 for (i = 0; i < n; ++i) {
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67 j = SA[i], SA[i] = ~j;
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68 if (0 < j) {
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69 --j;
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70 if ((c0 = chr(j)) != c1) {
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71 B[c1] = b - SA;
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72 b = SA + B[c1 = c0];
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73 }
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74 *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
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75 }
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76 }
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77 /* compute SAs */
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78 if (C == B) getCounts(T, C, n, k, cs);
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79 getBuckets(C, B, k, 1); /* find ends of buckets */
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80 for (i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
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81 if (0 < (j = SA[i])) {
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82 --j;
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83 if ((c0 = chr(j)) != c1) {
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84 B[c1] = b - SA;
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85 b = SA + B[c1 = c0];
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86 }
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87 *--b = ((j == 0) || (chr(j - 1) > c1)) ? ~j : j;
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88 } else SA[i] = ~j;
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89 }
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90 }
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91
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92 /*
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93 * find the suffix array SA of T[0..n-1] in {0..k-1}^n use a working
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94 * space (excluding T and SA) of at most 2n+O(1) for a constant alphabet
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95 */
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96 static int sais_main(const unsigned char *T, int *SA, int fs, int n, int k, int cs)
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97 {
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98 int *C, *B, *RA;
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99 int i, j, c, m, p, q, plen, qlen, name;
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100 int c0, c1;
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101 int diff;
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102
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103 /* stage 1: reduce the problem by at least 1/2 sort all the
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104 * S-substrings */
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105 if (k <= fs) {
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106 C = SA + n;
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107 B = (k <= (fs - k)) ? C + k : C;
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108 } else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
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109 getCounts(T, C, n, k, cs);
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110 getBuckets(C, B, k, 1); /* find ends of buckets */
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111 for (i = 0; i < n; ++i) SA[i] = 0;
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112 for (i = n - 2, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
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113 if ((c0 = chr(i)) < (c1 + c)) c = 1;
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114 else if (c != 0) SA[--B[c1]] = i + 1, c = 0;
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115 }
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116 induceSA(T, SA, C, B, n, k, cs);
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117 if (fs < k) free(C);
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118 /* compact all the sorted substrings into the first m items of SA
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119 * 2*m must be not larger than n (proveable) */
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120 for (i = 0, m = 0; i < n; ++i) {
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121 p = SA[i];
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122 if ((0 < p) && (chr(p - 1) > (c0 = chr(p)))) {
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123 for (j = p + 1; (j < n) && (c0 == (c1 = chr(j))); ++j);
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124 if ((j < n) && (c0 < c1)) SA[m++] = p;
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125 }
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126 }
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127 for (i = m; i < n; ++i) SA[i] = 0; /* init the name array buffer */
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128 /* store the length of all substrings */
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129 for (i = n - 2, j = n, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
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130 if ((c0 = chr(i)) < (c1 + c)) c = 1;
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131 else if (c != 0) {
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132 SA[m + ((i + 1) >> 1)] = j - i - 1;
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133 j = i + 1;
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134 c = 0;
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135 }
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136 }
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137 /* find the lexicographic names of all substrings */
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138 for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
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139 p = SA[i], plen = SA[m + (p >> 1)], diff = 1;
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140 if (plen == qlen) {
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141 for (j = 0; (j < plen) && (chr(p + j) == chr(q + j)); j++);
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142 if (j == plen) diff = 0;
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143 }
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144 if (diff != 0) ++name, q = p, qlen = plen;
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145 SA[m + (p >> 1)] = name;
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146 }
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147
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148 /* stage 2: solve the reduced problem recurse if names are not yet
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149 * unique */
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150 if (name < m) {
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151 RA = SA + n + fs - m;
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152 for (i = n - 1, j = m - 1; m <= i; --i) {
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153 if (SA[i] != 0) RA[j--] = SA[i] - 1;
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154 }
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155 if (sais_main((unsigned char *) RA, SA, fs + n - m * 2, m, name, sizeof(int)) != 0) return -2;
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156 for (i = n - 2, j = m - 1, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
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157 if ((c0 = chr(i)) < (c1 + c)) c = 1;
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158 else if (c != 0) RA[j--] = i + 1, c = 0; /* get p1 */
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159 }
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160 for (i = 0; i < m; ++i) SA[i] = RA[SA[i]]; /* get index */
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161 }
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162 /* stage 3: induce the result for the original problem */
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163 if (k <= fs) {
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164 C = SA + n;
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165 B = (k <= (fs - k)) ? C + k : C;
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166 } else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
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167 /* put all left-most S characters into their buckets */
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168 getCounts(T, C, n, k, cs);
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169 getBuckets(C, B, k, 1); /* find ends of buckets */
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170 for (i = m; i < n; ++i) SA[i] = 0; /* init SA[m..n-1] */
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171 for (i = m - 1; 0 <= i; --i) {
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172 j = SA[i], SA[i] = 0;
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173 SA[--B[chr(j)]] = j;
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174 }
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175 induceSA(T, SA, C, B, n, k, cs);
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176 if (fs < k) free(C);
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177 return 0;
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178 }
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179
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180 /**
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181 * Constructs the suffix array of a given string.
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182 * @param T[0..n-1] The input string.
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183 * @param SA[0..n] The output array of suffixes.
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184 * @param n The length of the given string.
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185 * @return 0 if no error occurred
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186 */
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187 int is_sa(const ubyte_t *T, int *SA, int n)
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188 {
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189 if ((T == NULL) || (SA == NULL) || (n < 0)) return -1;
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190 SA[0] = n;
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191 if (n <= 1) {
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192 if (n == 1) SA[1] = 0;
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193 return 0;
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194 }
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195 return sais_main(T, SA+1, 0, n, 256, 1);
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196 }
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197
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198 /**
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199 * Constructs the burrows-wheeler transformed string of a given string.
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200 * @param T[0..n-1] The input string.
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201 * @param n The length of the given string.
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202 * @return The primary index if no error occurred, -1 or -2 otherwise.
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203 */
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204 int is_bwt(ubyte_t *T, int n)
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205 {
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206 int *SA, i, primary = 0;
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207 SA = (int*)calloc(n+1, sizeof(int));
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208 is_sa(T, SA, n);
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209
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210 for (i = 0; i <= n; ++i) {
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211 if (SA[i] == 0) primary = i;
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212 else SA[i] = T[SA[i] - 1];
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213 }
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214 for (i = 0; i < primary; ++i) T[i] = SA[i];
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215 for (; i < n; ++i) T[i] = SA[i + 1];
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216 free(SA);
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217 return primary;
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218 }
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