/*
 * divsufsort.c for libdivsufsort
 * Copyright (c) 2003-2008 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.
 */

#include "divsufsort_private.h"
#ifdef _OPENMP
# include <omp.h>
#endif


/*- Private Functions -*/

/* 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;
}

/* Constructs the suffix array by using the sorted order of type B* suffixes. */
static
void
construct_SA(const sauchar_t* T, saidx_t* SA,
             saidx_t* bucket_A, saidx_t* bucket_B,
             saidx_t n, saidx_t m)
{
    saidx_t* i, *j, *k;
    saidx_t s;
    saint_t c0, c1, c2;

    if (0 < m) {
        /* Construct the sorted order of type B suffixes by using
           the sorted order of type B* suffixes. */
        for (c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
            /* Scan the suffix array from right to left. */
            for (i = SA + BUCKET_BSTAR(c1, c1 + 1),
                 j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
                 i <= j;
                 --j) {
                if (0 < (s = *j)) {
                    assert(T[s] == c1);
                    assert(((s + 1) < n) && (T[s] <= T[s + 1]));
                    assert(T[s - 1] <= T[s]);
                    *j = ~s;
                    c0 = T[--s];
                    if ((0 < s) && (T[s - 1] > c0)) {
                        s = ~s;
                    }
                    if (c0 != c2) {
                        if (0 <= c2) {
                            BUCKET_B(c2, c1) = k - SA;
                        }
                        k = SA + BUCKET_B(c2 = c0, c1);
                    }
                    assert(k < j);
                    *k-- = s;
                } else {
                    assert(((s == 0) && (T[s] == c1)) || (s < 0));
                    *j = ~s;
                }
            }
        }
    }

    /* Construct the suffix array by using
       the sorted order of type B suffixes. */
    k = SA + BUCKET_A(c2 = T[n - 1]);
    *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
    /* Scan the suffix array from left to right. */
    for (i = SA, j = SA + n; i < j; ++i) {
        if (0 < (s = *i)) {
            assert(T[s - 1] >= T[s]);
            c0 = T[--s];
            if ((s == 0) || (T[s - 1] < c0)) {
                s = ~s;
            }
            if (c0 != c2) {
                BUCKET_A(c2) = k - SA;
                k = SA + BUCKET_A(c2 = c0);
            }
            assert(i < k);
            *k++ = s;
        } else {
            assert(s < 0);
            *i = ~s;
        }
    }
}

/* Constructs the burrows-wheeler transformed string directly
   by using the sorted order of type B* suffixes. */
static
saidx_t
construct_BWT(const sauchar_t* T, saidx_t* SA,
              saidx_t* bucket_A, saidx_t* bucket_B,
              saidx_t n, saidx_t m)
{
    saidx_t* i, *j, *k, *orig;
    saidx_t s;
    saint_t c0, c1, c2;

    if (0 < m) {
        /* Construct the sorted order of type B suffixes by using
           the sorted order of type B* suffixes. */
        for (c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
            /* Scan the suffix array from right to left. */
            for (i = SA + BUCKET_BSTAR(c1, c1 + 1),
                 j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
                 i <= j;
                 --j) {
                if (0 < (s = *j)) {
                    assert(T[s] == c1);
                    assert(((s + 1) < n) && (T[s] <= T[s + 1]));
                    assert(T[s - 1] <= T[s]);
                    c0 = T[--s];
                    *j = ~((saidx_t)c0);
                    if ((0 < s) && (T[s - 1] > c0)) {
                        s = ~s;
                    }
                    if (c0 != c2) {
                        if (0 <= c2) {
                            BUCKET_B(c2, c1) = k - SA;
                        }
                        k = SA + BUCKET_B(c2 = c0, c1);
                    }
                    assert(k < j);
                    *k-- = s;
                } else if (s != 0) {
                    *j = ~s;
#ifndef NDEBUG
                } else {
                    assert(T[s] == c1);
#endif
                }
            }
        }
    }

    /* Construct the BWTed string by using
       the sorted order of type B suffixes. */
    k = SA + BUCKET_A(c2 = T[n - 1]);
    *k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1);
    /* Scan the suffix array from left to right. */
    for (i = SA, j = SA + n, orig = SA; i < j; ++i) {
        if (0 < (s = *i)) {
            assert(T[s - 1] >= T[s]);
            c0 = T[--s];
            *i = c0;
            if ((0 < s) && (T[s - 1] < c0)) {
                s = ~((saidx_t)T[s - 1]);
            }
            if (c0 != c2) {
                BUCKET_A(c2) = k - SA;
                k = SA + BUCKET_A(c2 = c0);
            }
            assert(i < k);
            *k++ = s;
        } else if (s != 0) {
            *i = ~s;
        } else {
            orig = i;
        }
    }

    return orig - SA;
}


/*---------------------------------------------------------------------------*/

/*- Function -*/

saint_t
divsufsort(const sauchar_t* T, saidx_t* SA, saidx_t n)
{
    saidx_t* bucket_A, *bucket_B;
    saidx_t m;
    saint_t err = 0;

    /* Check arguments. */
    if ((T == NULL) || (SA == NULL) || (n < 0)) {
        return -1;
    } else if (n == 0) {
        return 0;
    } else if (n == 1) {
        SA[0] = 0;
        return 0;
    } else if (n == 2) {
        m = (T[0] < T[1]);
        SA[m ^ 1] = 0, SA[m] = 1;
        return 0;
    }

    bucket_A = (saidx_t*)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
    bucket_B = (saidx_t*)malloc(BUCKET_B_SIZE * sizeof(saidx_t));

    /* Suffixsort. */
    if ((bucket_A != NULL) && (bucket_B != NULL)) {
        m = sort_typeBstar(T, SA, bucket_A, bucket_B, n);
        construct_SA(T, SA, bucket_A, bucket_B, n, m);
    } else {
        err = -2;
    }

    free(bucket_B);
    free(bucket_A);

    return err;
}

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;
}

const char*
divsufsort_version(void)
{
    return PROJECT_VERSION_FULL;
}
