C++ (Cpp) construct_BWT Examples

Example #1

File: divsufsort.c Project: LuckJC/pro-mk

saidx_t
divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
  saidx_t *B;
  saidx_t *bucket_A, *bucket_B;
  saidx_t m, pidx, i;

  /* Check arguments. */
  if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
  else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }

  if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
  bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
  bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));

  /* Burrows-Wheeler Transform. */
  if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
    m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
    pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);

    /* Copy to output string. */
    U[0] = T[n - 1];
    for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; }
    for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; }
    pidx += 1;
  } else {
    pidx = -2;
  }

  free(bucket_B);
  free(bucket_A);
  if(A == NULL) { free(B); }

  return pidx;
}

Example #2

File: divsufsort.c Project: jkokkala/bwtc

saidx_t
divbwtf(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n,
        unsigned *LFpowers, unsigned nLFpowers, unsigned freqs[256]) {
  saidx_t *B;
  saidx_t *bucket_A, *bucket_B;
  saidx_t m, pidx, i;

  /* Check arguments. */
  if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
  else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }

  if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
  bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
  bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));

  /* Burrows-Wheeler Transform. */
  if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
    m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
    if(nLFpowers > 1) {
      pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m, LFpowers, nLFpowers);
      LFpowers[0] = pidx;
    } else {
      pidx = construct_BWT_orig(T, B, bucket_A, bucket_B, n, m);
      *LFpowers = pidx;
    }

    /* Copy to output string. */
    for(i = 0; i < n; ++i) {
      if(i != pidx) {
        U[i] = (sauchar_t)B[i];
        ++freqs[U[i]];
      }
    }
  } else {
    pidx = -2;
  }

  free(bucket_B);
  free(bucket_A);
  if(A == NULL) { free(B); }

  return pidx;
}

Example #3

File: divsufsort.cpp Project: Hexta/JAA

int32_t
divbwt(const uint8_t *T, uint8_t *U, int32_t *A, int32_t n) {
  int32_t *B;
  int32_t m, pidx, i;

  /* Check arguments. */
  if ((T == NULL) || (U == NULL) || (n < 0)) {
    return -1;
  } else if (n <= 1) {
    if (n == 1) {
      U[0] = T[0];
    }
    return n;
  }

  if ((B = A) == NULL) {
    B = new int32_t [ (n + 1)];
  }

  int32_t bucket_A [BUCKET_A_SIZE];
  int32_t bucket_B [BUCKET_B_SIZE];

  /* Burrows-Wheeler Transform. */
  m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
  pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);

  /* Copy to output string. */
  U[0] = T[n - 1];
  for (i = 0; i < pidx; ++i) {
    U[i + 1] = (uint8_t) B[i];
  }
  for (i += 1; i < n; ++i) {
    U[i] = (uint8_t) B[i];
  }
  pidx += 1;

  if (A == NULL)
    delete[] B;

  return pidx;
}