sais.hxx

/*
 * sais.hxx for sais-lite
 * Copyright (c) 2008-2009 Yuta Mori All Rights Reserved.
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

#ifndef _SAIS_HXX
#define _SAIS_HXX 1
#ifdef __cplusplus

#ifdef __INTEL_COMPILER
#pragma warning(disable : 383 981 1418)
// for icc 64-bit
//#define __builtin_vsnprintf(a, b, c, d) __builtin_vsnprintf(a, b, c, (char *)d)
#endif

#include <iterator>
#ifdef _OPENMP
# include <omp.h>
#endif

namespace saisxx_private {

/* find the start or end of each bucket */
template<typename string_type, typename bucket_type, typename index_type>
void
getCounts(const string_type T, bucket_type C, index_type n, index_type k) {
#ifdef _OPENMP
  bucket_type D;
  index_type i, j, p, sum, first, last;
  int thnum, maxthreads = omp_get_max_threads();
#pragma omp parallel default(shared) private(D, i, thnum, first, last)
  {
    thnum = omp_get_thread_num();
    D = C + thnum * k;
    first = n / maxthreads * thnum;
    last = (thnum < (maxthreads - 1)) ? n / maxthreads * (thnum + 1) : n;
    for(i = 0; i < k; ++i) { D[i] = 0; }
    for(i = first; i < last; ++i) { ++D[T[i]]; }
  }
  if(1 < maxthreads) {
#pragma omp parallel for default(shared) private(i, j, p, sum)
    for(i = 0; i < k; ++i) {
      for(j = 1, p = i + k, sum = C[i]; j < maxthreads; ++j, p += k) {
        sum += C[p];
      }
      C[i] = sum;
    }
  }
#else
  index_type i;
  for(i = 0; i < k; ++i) { C[i] = 0; }
  for(i = 0; i < n; ++i) { ++C[T[i]]; }
#endif
}
template<typename bucket_type, typename index_type>
void
getBuckets(const bucket_type C, bucket_type B, index_type k, bool end) {
  index_type i, sum = 0;
  if(end) { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } }
  else { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } }
}

/* compute SA and BWT */
template<typename string_type, typename sarray_type,
         typename bucket_type, typename index_type>
void
induceSA(string_type T, sarray_type SA, bucket_type C, bucket_type B,
         index_type n, index_type k) {
typedef typename std::iterator_traits<string_type>::value_type char_type;
  sarray_type b;
  index_type i, j;
  char_type c0, c1;
  /* compute SAl */
  if(C == B) { getCounts(T, C, n, k); }
  getBuckets(C, B, k, false); /* find starts of buckets */
  b = SA + B[c1 = T[j = n - 1]];
  *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
  for(i = 0; i < n; ++i) {
    j = SA[i], SA[i] = ~j;
    if(0 < j) {
      if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
      *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
    }
  }
  /* compute SAs */
  if(C == B) { getCounts(T, C, n, k); }
  getBuckets(C, B, k, true); /* find ends of buckets */
  for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
    if(0 < (j = SA[i])) {
      if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
      *--b = ((j == 0) || (T[j - 1] > c1)) ? ~j : j;
    } else {
      SA[i] = ~j;
    }
  }
}
template<typename string_type, typename sarray_type,
         typename bucket_type, typename index_type>
int
computeBWT(string_type T, sarray_type SA, bucket_type C, bucket_type B,
           index_type n, index_type k) {
typedef typename std::iterator_traits<string_type>::value_type char_type;
  sarray_type b;
  index_type i, j, pidx = -1;
  char_type c0, c1;
  /* compute SAl */
  if(C == B) { getCounts(T, C, n, k); }
  getBuckets(C, B, k, false); /* find starts of buckets */
  b = SA + B[c1 = T[j = n - 1]];
  *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
  for(i = 0; i < n; ++i) {
    if(0 < (j = SA[i])) {
      SA[i] = ~(c0 = T[--j]);
      if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
      *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
    } else if(j != 0) {
      SA[i] = ~j;
    }
  }
  /* compute SAs */
  if(C == B) { getCounts(T, C, n, k); }
  getBuckets(C, B, k, true); /* find ends of buckets */
  for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
    if(0 < (j = SA[i])) {
      SA[i] = (c0 = T[--j]);
      if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
      *--b = ((0 < j) && (T[j - 1] > c1)) ? ~((index_type)T[j - 1]) : j;
    } else if(j != 0) {
      SA[i] = ~j;
    } else {
      pidx = i;
    }
  }
  return pidx;
}

/* find the suffix array SA of T[0..n-1] in {0..k}^n
   use a working space (excluding s and SA) of at most 2n+O(1) for a constant alphabet */
template<typename string_type, typename sarray_type, typename index_type>
int
suffixsort(string_type T, sarray_type SA,
           index_type fs, index_type n, index_type k,
           bool isbwt) {
typedef typename std::iterator_traits<string_type>::value_type char_type;
  sarray_type RA;
  index_type i, j, m, p, q, plen, qlen, name, pidx = 0;
  bool diff;
  int c;
#ifdef _OPENMP
  int maxthreads = omp_get_max_threads();
#else
# define maxthreads 1
#endif
  char_type c0, c1;

  /* stage 1: reduce the problem by at least 1/2
     sort all the S-substrings */
  if(fs < (maxthreads * k)) {
    index_type *C, *B;
    if((C = new index_type[maxthreads * k]) == 0) { return -2; }
    B = (1 < maxthreads) ? C + k : C;
    getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i)
#endif
    for(i = 0; i < n; ++i) { SA[i] = 0; }
    for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
      if((c0 = T[i]) < (c1 + c)) { c = 1; }
      else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
    }
    induceSA(T, SA, C, B, n, k);
    delete [] C;
  } else {
    sarray_type C, B;
    C = SA + n;
    B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
    getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i)
#endif
    for(i = 0; i < n; ++i) { SA[i] = 0; }
    for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
      if((c0 = T[i]) < (c1 + c)) { c = 1; }
      else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
    }
    induceSA(T, SA, C, B, n, k);
  }

  /* compact all the sorted substrings into the first m items of SA
     2*m must be not larger than n (proveable) */
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i, j, p, c0, c1)
  for(i = 0; i < n; ++i) {
    p = SA[i];
    if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
      for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
      if((j < n) && (c0 < c1)) { SA[i] = ~p; }
    }
  }
  for(i = 0, m = 0; i < n; ++i) { if((p = SA[i]) < 0) { SA[m++] = ~p; } }
#else
  for(i = 0, m = 0; i < n; ++i) {
    p = SA[i];
    if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
      for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
      if((j < n) && (c0 < c1)) { SA[m++] = p; }
    }
  }
#endif
  j = m + (n >> 1);
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i)
#endif
  for(i = m; i < j; ++i) { SA[i] = 0; } /* init the name array buffer */
  /* store the length of all substrings */
  for(i = n - 2, j = n, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
    if((c0 = T[i]) < (c1 + c)) { c = 1; }
    else if(c != 0) { SA[m + ((i + 1) >> 1)] = j - i - 1; j = i + 1; c = 0; }
  }
  /* find the lexicographic names of all substrings */
  for(i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
    p = SA[i], plen = SA[m + (p >> 1)], diff = true;
    if(plen == qlen) {
      for(j = 0; (j < plen) && (T[p + j] == T[q + j]); ++j) { }
      if(j == plen) { diff = false; }
    }
    if(diff != false) { ++name, q = p, qlen = plen; }
    SA[m + (p >> 1)] = name;
  }

  /* stage 2: solve the reduced problem
     recurse if names are not yet unique */
  if(name < m) {
    RA = SA + n + fs - m;
    for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) {
      if(SA[i] != 0) { RA[j--] = SA[i] - 1; }
    }
    if(suffixsort(RA, SA, fs + n - m * 2, m, name, false) != 0) { return -2; }
    for(i = n - 2, j = m - 1, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
      if((c0 = T[i]) < (c1 + c)) { c = 1; }
      else if(c != 0) { RA[j--] = i + 1, c = 0; } /* get p1 */
    }
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i)
#endif
    for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; } /* get index in s */
  }

  /* stage 3: induce the result for the original problem */
  if(fs < (maxthreads * k)) {
    index_type *B, *C;
    if((C = new index_type[maxthreads * k]) == 0) { return -2; }
    B = (1 < maxthreads) ? C + k : C;
    /* put all left-most S characters into their buckets */
    getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i)
#endif
    for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
    for(i = m - 1; 0 <= i; --i) {
      j = SA[i], SA[i] = 0;
      SA[--B[T[j]]] = j;
    }
    if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
    else { pidx = computeBWT(T, SA, C, B, n, k); }
    delete [] C;
  } else {
    sarray_type C, B;
    C = SA + n;
    B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
    /* put all left-most S characters into their buckets */
    getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
#ifdef _OPENMP
#pragma omp parallel for default(shared) private(i)
#endif
    for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
    for(i = m - 1; 0 <= i; --i) {
      j = SA[i], SA[i] = 0;
      SA[--B[T[j]]] = j;
    }
    if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
    else { pidx = computeBWT(T, SA, C, B, n, k); }
  }

  return pidx;
#ifndef _OPENMP
# undef maxthreads
#endif
}

} /* namespace saisxx_private */


/**
 * @brief Constructs the suffix array of a given string in linear time.
 * @param T[0..n-1] The input string. (random access iterator)
 * @param SA[0..n-1] The output array of suffixes. (random access iterator)
 * @param n The length of the given string.
 * @param k The alphabet size.
 * @return 0 if no error occurred, -1 or -2 otherwise.
 */
template<typename string_type, typename sarray_type, typename index_type>
int
saisxx(string_type T, sarray_type SA, index_type n, index_type k = 256) {
  int err;
  if((n < 0) || (k <= 0)) { return -1; }
  if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; }
  try { err = saisxx_private::suffixsort(T, SA, 0, n, k, false); }
  catch(...) { err = -2; }
  return err;
}

/**
 * @brief Constructs the burrows-wheeler transformed string of a given string in linear time.
 * @param T[0..n-1] The input string. (random access iterator)
 * @param U[0..n-1] The output string. (random access iterator)
 * @param A[0..n-1] The temporary array. (random access iterator)
 * @param n The length of the given string.
 * @param k The alphabet size.
 * @return The primary index if no error occurred, -1 or -2 otherwise.
 */
template<typename string_type, typename sarray_type, typename index_type>
index_type
saisxx_bwt(string_type T, string_type U, sarray_type A, index_type n, index_type k = 256) {
typedef typename std::iterator_traits<string_type>::value_type char_type;
  index_type i, pidx;
  if((n < 0) || (k <= 0)) { return -1; }
  if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
  try {
    pidx = saisxx_private::suffixsort(T, A, 0, n, k, true);
    if(0 <= pidx) {
      U[0] = T[n - 1];
      for(i = 0; i < pidx; ++i) { U[i + 1] = (char_type)A[i]; }
      for(i += 1; i < n; ++i) { U[i] = (char_type)A[i]; }
      pidx += 1;
    }
  } catch(...) { pidx = -2; }
  return pidx;
}


#endif /* __cplusplus */
#endif /* _SAIS_HXX */