void testSSSort () { int a[] = {343425,6,4,3,7,867,22423,678,345435,0}; sssort (a,10); printArray (a,10); }
/* Sorts suffixes of type B*. */ int32_t sort_typeBstar(const uint8_t *T, int32_t *SA, int32_t *bucket_A, int32_t *bucket_B, int32_t n) { int32_t *PAb; int32_t i, j, k, t, m, bufsize; int32_t c0, c1; memset(bucket_A, 0, BUCKET_A_SIZE * sizeof (int32_t)); memset(bucket_B, 0, BUCKET_B_SIZE * sizeof (int32_t)); /* Count the number of occurrences of the first one or two characters of each type A, B and B* suffix. Moreover, store the beginning position of all type B* suffixes into the array SA. */ for (i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) { /* type A suffix. */ do { ++BUCKET_A(c1 = c0); } while ((0 <= --i) && ((c0 = T[i]) >= c1)); if (0 <= i) { /* type B* suffix. */ ++BUCKET_BSTAR(c0, c1); SA[--m] = i; /* type B suffix. */ for (--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { ++BUCKET_B(c0, c1); } } } m = n - m; /* note: A type B* suffix is lexicographically smaller than a type B suffix that begins with the same first two characters. */ /* Calculate the index of start/end point of each bucket. */ for (c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) { t = i + BUCKET_A(c0); BUCKET_A(c0) = i + j; /* start point */ i = t + BUCKET_B(c0, c0); for (c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) { j += BUCKET_BSTAR(c0, c1); BUCKET_BSTAR(c0, c1) = j; /* end point */ i += BUCKET_B(c0, c1); } } if (0 < m) { int32_t *ISAb, *buf; /* Sort the type B* suffixes by their first two characters. */ PAb = SA + n - m; ISAb = SA + m; for (i = m - 2; 0 <= i; --i) { t = PAb[i], c0 = T[t], c1 = T[t + 1]; SA[--BUCKET_BSTAR(c0, c1)] = i; } t = PAb[m - 1], c0 = T[t], c1 = T[t + 1]; SA[--BUCKET_BSTAR(c0, c1)] = m - 1; /* Sort the type B* substrings using sssort. */ buf = SA + m, bufsize = n - (2 * m); for (c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) { for (c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) { i = BUCKET_BSTAR(c0, c1); if (1 < (j - i)) { sssort(T, PAb, SA + i, SA + j, buf, bufsize, 2, n, *(SA + i) == (m - 1)); } } } /* Compute ranks of type B* substrings. */ for (i = m - 1; 0 <= i; --i) { if (0 <= SA[i]) { j = i; do { ISAb[SA[i]] = i; } while ((0 <= --i) && (0 <= SA[i])); SA[i + 1] = i - j; if (i <= 0) { break; } } j = i; do { ISAb[SA[i] = ~SA[i]] = j; } while (SA[--i] < 0); ISAb[SA[i]] = j; } /* Construct the inverse suffix array of type B* suffixes using trsort. */ trsort(ISAb, SA, m, 1); /* Set the sorted order of tyoe B* suffixes. */ for (i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) { for (--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { } if (0 <= i) { t = i; for (--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { } SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t; } } /* Calculate the index of start/end point of each bucket. */ BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */ for (c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) { i = BUCKET_A(c0 + 1) - 1; for (c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) { t = i - BUCKET_B(c0, c1); BUCKET_B(c0, c1) = i; /* end point */ /* Move all type B* suffixes to the correct position. */ for (i = t, j = BUCKET_BSTAR(c0, c1); j <= k; --i, --k) { SA[i] = SA[k]; } } BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */ BUCKET_B(c0, c0) = i; /* end point */ } } return m; }
/* Sorts suffixes of type B*. */ static saidx_t sort_typeBstar(const sauchar_t *T, saidx_t *SA, saidx_t *bucket_A, saidx_t *bucket_B, saidx_t n) { saidx_t *PAb, *ISAb, *buf; #ifdef _OPENMP saidx_t *curbuf; saidx_t l; #endif saidx_t i, j, k, t, m, bufsize; saint_t c0, c1; #ifdef _OPENMP saint_t d0, d1; int tmp; #endif /* Initialize bucket arrays. */ for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; } for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; } /* Count the number of occurrences of the first one or two characters of each type A, B and B* suffix. Moreover, store the beginning position of all type B* suffixes into the array SA. */ for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) { /* type A suffix. */ do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1)); if(0 <= i) { /* type B* suffix. */ ++BUCKET_BSTAR(c0, c1); SA[--m] = i; /* type B suffix. */ for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { ++BUCKET_B(c0, c1); } } } m = n - m; /* note: A type B* suffix is lexicographically smaller than a type B suffix that begins with the same first two characters. */ /* Calculate the index of start/end point of each bucket. */ for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) { t = i + BUCKET_A(c0); BUCKET_A(c0) = i + j; /* start point */ i = t + BUCKET_B(c0, c0); for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) { j += BUCKET_BSTAR(c0, c1); BUCKET_BSTAR(c0, c1) = j; /* end point */ i += BUCKET_B(c0, c1); } } if(0 < m) { /* Sort the type B* suffixes by their first two characters. */ PAb = SA + n - m; ISAb = SA + m; for(i = m - 2; 0 <= i; --i) { t = PAb[i], c0 = T[t], c1 = T[t + 1]; SA[--BUCKET_BSTAR(c0, c1)] = i; } t = PAb[m - 1], c0 = T[t], c1 = T[t + 1]; SA[--BUCKET_BSTAR(c0, c1)] = m - 1; /* Sort the type B* substrings using sssort. */ #ifdef _OPENMP tmp = omp_get_max_threads(); buf = SA + m, bufsize = (n - (2 * m)) / tmp; c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m; #pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp) { tmp = omp_get_thread_num(); curbuf = buf + tmp * bufsize; k = 0; for(;;) { #pragma omp critical(sssort_lock) { if(0 < (l = j)) { d0 = c0, d1 = c1; do { k = BUCKET_BSTAR(d0, d1); if(--d1 <= d0) { d1 = ALPHABET_SIZE - 1; if(--d0 < 0) { break; } } } while(((l - k) <= 1) && (0 < (l = k))); c0 = d0, c1 = d1, j = k; } } if(l == 0) { break; } sssort(T, PAb, SA + k, SA + l, curbuf, bufsize, 2, n, *(SA + k) == (m - 1)); } } #else buf = SA + m, bufsize = n - (2 * m); for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) { for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) { i = BUCKET_BSTAR(c0, c1); if(1 < (j - i)) { sssort(T, PAb, SA + i, SA + j, buf, bufsize, 2, n, *(SA + i) == (m - 1)); } } } #endif /* Compute ranks of type B* substrings. */ for(i = m - 1; 0 <= i; --i) { if(0 <= SA[i]) { j = i; do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i])); SA[i + 1] = i - j; if(i <= 0) { break; } } j = i; do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0); ISAb[SA[i]] = j; } /* Construct the inverse suffix array of type B* suffixes using trsort. */ trsort(ISAb, SA, m, 1); /* Set the sorted order of tyoe B* suffixes. */ for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) { for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { } if(0 <= i) { t = i; for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { } SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t; } } /* Calculate the index of start/end point of each bucket. */ BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */ for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) { i = BUCKET_A(c0 + 1) - 1; for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) { t = i - BUCKET_B(c0, c1); BUCKET_B(c0, c1) = i; /* end point */ /* Move all type B* suffixes to the correct position. */ for(i = t, j = BUCKET_BSTAR(c0, c1); j <= k; --i, --k) { SA[i] = SA[k]; } } BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */ BUCKET_B(c0, c0) = i; /* end point */ } } return m; }