/*
 * utils.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"


/*- Private Function -*/

/* Binary search for inverse bwt. */
static
saidx_t
binarysearch_lower(const saidx_t* A, saidx_t size, saidx_t value)
{
    saidx_t half, i;
    for (i = 0, half = size >> 1;
         0 < size;
         size = half, half >>= 1) {
        if (A[i + half] < value) {
            i += half + 1;
            half -= (size & 1) ^ 1;
        }
    }
    return i;
}


/*- Functions -*/

/* Burrows-Wheeler transform. */
saint_t
bw_transform(const sauchar_t* T, sauchar_t* U, saidx_t* SA,
             saidx_t n, saidx_t* idx)
{
    saidx_t* A, i, j, p, t;
    saint_t c;

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

    if ((A = SA) == NULL) {
        i = divbwt(T, U, NULL, n);
        if (0 <= i) {
            *idx = i;
            i = 0;
        }
        return (saint_t)i;
    }

    /* BW transform. */
    if (T == U) {
        t = n;
        for (i = 0, j = 0; i < n; ++i) {
            p = t - 1;
            t = A[i];
            if (0 <= p) {
                c = T[j];
                U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
                A[j] = c;
                j++;
            } else {
                *idx = i;
            }
        }
        p = t - 1;
        if (0 <= p) {
            c = T[j];
            U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
            A[j] = c;
        } else {
            *idx = i;
        }
    } else {
        U[0] = T[n - 1];
        for (i = 0; A[i] != 0; ++i) {
            U[i + 1] = T[A[i] - 1];
        }
        *idx = i + 1;
        for (++i; i < n; ++i) {
            U[i] = T[A[i] - 1];
        }
    }

    if (SA == NULL) {
        /* Deallocate memory. */
        free(A);
    }

    return 0;
}

/* Inverse Burrows-Wheeler transform. */
saint_t
inverse_bw_transform(const sauchar_t* T, sauchar_t* U, saidx_t* A,
                     saidx_t n, saidx_t idx)
{
    saidx_t C[ALPHABET_SIZE];
    sauchar_t D[ALPHABET_SIZE];
    saidx_t* B;
    saidx_t i, p;
    saint_t c, d;

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

    if ((B = A) == NULL) {
        /* Allocate n*sizeof(saidx_t) bytes of memory. */
        if ((B = (saidx_t*)malloc((size_t)n * sizeof(saidx_t))) == NULL) {
            return -2;
        }
    }

    /* Inverse BW transform. */
    for (c = 0; c < ALPHABET_SIZE; ++c) {
        C[c] = 0;
    }
    for (i = 0; i < n; ++i) {
        ++C[T[i]];
    }
    for (c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) {
        p = C[c];
        if (0 < p) {
            C[c] = i;
            D[d++] = (sauchar_t)c;
            i += p;
        }
    }
    for (i = 0; i < idx; ++i) {
        B[C[T[i]]++] = i;
    }
    for (; i < n; ++i)       {
        B[C[T[i]]++] = i + 1;
    }
    for (c = 0; c < d; ++c) {
        C[c] = C[D[c]];
    }
    for (i = 0, p = idx; i < n; ++i) {
        U[i] = D[binarysearch_lower(C, d, p)];
        p = B[p - 1];
    }

    if (A == NULL) {
        /* Deallocate memory. */
        free(B);
    }

    return 0;
}

/* Checks the suffix array SA of the string T. */
saint_t
sufcheck(const sauchar_t* T, const saidx_t* SA,
         saidx_t n, saint_t verbose)
{
    saidx_t C[ALPHABET_SIZE];
    saidx_t i, p, q, t;
    saint_t c;

    if (verbose) {
        fprintf(stderr, "sufcheck: ");
    }

    /* Check arguments. */
    if ((T == NULL) || (SA == NULL) || (n < 0)) {
        if (verbose) {
            fprintf(stderr, "Invalid arguments.\n");
        }
        return -1;
    }
    if (n == 0) {
        if (verbose) {
            fprintf(stderr, "Done.\n");
        }
        return 0;
    }

    /* check range: [0..n-1] */
    for (i = 0; i < n; ++i) {
        if ((SA[i] < 0) || (n <= SA[i])) {
            if (verbose) {
                fprintf(stderr, "Out of the range [0,%" PRIdSAIDX_T "].\n"
                        "  SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
                        n - 1, i, SA[i]);
            }
            return -2;
        }
    }

    /* check first characters. */
    for (i = 1; i < n; ++i) {
        if (T[SA[i - 1]] > T[SA[i]]) {
            if (verbose) {
                fprintf(stderr, "Suffixes in wrong order.\n"
                        "  T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d"
                        " > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d\n",
                        i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]);
            }
            return -3;
        }
    }

    /* check suffixes. */
    for (i = 0; i < ALPHABET_SIZE; ++i) {
        C[i] = 0;
    }
    for (i = 0; i < n; ++i) {
        ++C[T[i]];
    }
    for (i = 0, p = 0; i < ALPHABET_SIZE; ++i) {
        t = C[i];
        C[i] = p;
        p += t;
    }

    q = C[T[n - 1]];
    C[T[n - 1]] += 1;
    for (i = 0; i < n; ++i) {
        p = SA[i];
        if (0 < p) {
            c = T[--p];
            t = C[c];
        } else {
            c = T[p = n - 1];
            t = q;
        }
        if ((t < 0) || (p != SA[t])) {
            if (verbose) {
                fprintf(stderr, "Suffix in wrong position.\n"
                        "  SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n"
                        "  SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
                        t, (0 <= t) ? SA[t] : -1, i, SA[i]);
            }
            return -4;
        }
        if (t != q) {
            ++C[c];
            if ((n <= C[c]) || (T[SA[C[c]]] != c)) {
                C[c] = -1;
            }
        }
    }

    if (1 <= verbose) {
        fprintf(stderr, "Done.\n");
    }
    return 0;
}


static
int
_compare(const sauchar_t* T, saidx_t Tsize,
         const sauchar_t* P, saidx_t Psize,
         saidx_t suf, saidx_t* match)
{
    saidx_t i, j;
    saint_t r;
    for (i = suf + *match, j = *match, r = 0;
         (i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { }
    *match = j;
    return (r == 0) ? -(j != Psize) : r;
}

/* Search for the pattern P in the string T. */
saidx_t
sa_search(const sauchar_t* T, saidx_t Tsize,
          const sauchar_t* P, saidx_t Psize,
          const saidx_t* SA, saidx_t SAsize,
          saidx_t* idx)
{
    saidx_t size, lsize, rsize, half;
    saidx_t match, lmatch, rmatch;
    saidx_t llmatch, lrmatch, rlmatch, rrmatch;
    saidx_t i, j, k;
    saint_t r;

    if (idx != NULL) {
        *idx = -1;
    }
    if ((T == NULL) || (P == NULL) || (SA == NULL) ||
        (Tsize < 0) || (Psize < 0) || (SAsize < 0)) {
        return -1;
    }
    if ((Tsize == 0) || (SAsize == 0)) {
        return 0;
    }
    if (Psize == 0) {
        if (idx != NULL) {
            *idx = 0;
        } return SAsize;
    }

    for (i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1;
         0 < size;
         size = half, half >>= 1) {
        match = MIN(lmatch, rmatch);
        r = _compare(T, Tsize, P, Psize, SA[i + half], &match);
        if (r < 0) {
            i += half + 1;
            half -= (size & 1) ^ 1;
            lmatch = match;
        } else if (r > 0) {
            rmatch = match;
        } else {
            lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;

            /* left part */
            for (llmatch = lmatch, lrmatch = match, half = lsize >> 1;
                 0 < lsize;
                 lsize = half, half >>= 1) {
                lmatch = MIN(llmatch, lrmatch);
                r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch);
                if (r < 0) {
                    j += half + 1;
                    half -= (lsize & 1) ^ 1;
                    llmatch = lmatch;
                } else {
                    lrmatch = lmatch;
                }
            }

            /* right part */
            for (rlmatch = match, rrmatch = rmatch, half = rsize >> 1;
                 0 < rsize;
                 rsize = half, half >>= 1) {
                rmatch = MIN(rlmatch, rrmatch);
                r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch);
                if (r <= 0) {
                    k += half + 1;
                    half -= (rsize & 1) ^ 1;
                    rlmatch = rmatch;
                } else {
                    rrmatch = rmatch;
                }
            }

            break;
        }
    }

    if (idx != NULL) {
        *idx = (0 < (k - j)) ? j : i;
    }
    return k - j;
}

/* Search for the character c in the string T. */
saidx_t
sa_simplesearch(const sauchar_t* T, saidx_t Tsize,
                const saidx_t* SA, saidx_t SAsize,
                saint_t c, saidx_t* idx)
{
    saidx_t size, lsize, rsize, half;
    saidx_t i, j, k, p;
    saint_t r;

    if (idx != NULL) {
        *idx = -1;
    }
    if ((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) {
        return -1;
    }
    if ((Tsize == 0) || (SAsize == 0)) {
        return 0;
    }

    for (i = j = k = 0, size = SAsize, half = size >> 1;
         0 < size;
         size = half, half >>= 1) {
        p = SA[i + half];
        r = (p < Tsize) ? T[p] - c : -1;
        if (r < 0) {
            i += half + 1;
            half -= (size & 1) ^ 1;
        } else if (r == 0) {
            lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;

            /* left part */
            for (half = lsize >> 1;
                 0 < lsize;
                 lsize = half, half >>= 1) {
                p = SA[j + half];
                r = (p < Tsize) ? T[p] - c : -1;
                if (r < 0) {
                    j += half + 1;
                    half -= (lsize & 1) ^ 1;
                }
            }

            /* right part */
            for (half = rsize >> 1;
                 0 < rsize;
                 rsize = half, half >>= 1) {
                p = SA[k + half];
                r = (p < Tsize) ? T[p] - c : -1;
                if (r <= 0) {
                    k += half + 1;
                    half -= (rsize & 1) ^ 1;
                }
            }

            break;
        }
    }

    if (idx != NULL) {
        *idx = (0 < (k - j)) ? j : i;
    }
    return k - j;
}
