/**
 * @file
 *
 * @author jeff.daily@pnnl.gov
 *
 * Copyright (c) 2015 Battelle Memorial Institute.
 */
#include "config.h"

#include <stdint.h>
#include <stdlib.h>
#include <string.h>

%(HEADER)s

#include "parasail.h"
#include "parasail/memory.h"
#include "parasail/internal_%(ISA)s.h"

#define NEG_INF %(NEG_INF)s
%(FIXES)s

#ifdef PARASAIL_TABLE
static inline void arr_store_si%(BITS)s(
        int *array,
        %(VTYPE)s vH,
        %(INDEX)s t,
        %(INDEX)s seglen,
        %(INDEX)s d,
        %(INDEX)s dlen,
        %(INDEX)s bias)
{
%(PRINTER_BIAS)s
}
#endif

#ifdef PARASAIL_ROWCOL
static inline void arr_store_col(
        int *col,
        %(VTYPE)s vH,
        %(INDEX)s t,
        %(INDEX)s seglen,
        %(INDEX)s bias)
{
%(PRINTER_BIAS_ROWCOL)s
}
#endif

#ifdef PARASAIL_TABLE
#define FNAME %(NAME_TABLE)s
#define PNAME %(PNAME_TABLE)s
#else
#ifdef PARASAIL_ROWCOL
#define FNAME %(NAME_ROWCOL)s
#define PNAME %(PNAME_ROWCOL)s
#else
#define FNAME %(NAME)s
#define PNAME %(PNAME)s
#endif
#endif

parasail_result_t* FNAME(
        const char * const restrict s1, const int s1Len,
        const char * const restrict s2, const int s2Len,
        const int open, const int gap, const parasail_matrix_t *matrix)
{
    parasail_profile_t *profile = parasail_profile_create_%(ISA)s_%(BITS)s_%(WIDTH)s(s1, s1Len, matrix);
    parasail_result_t *result = PNAME(profile, s2, s2Len, open, gap);
    parasail_profile_free(profile);
    return result;
}

parasail_result_t* PNAME(
        const parasail_profile_t * const restrict profile,
        const char * const restrict s2, const int s2Len,
        const int open, const int gap)
{
    %(INDEX)s i = 0;
    %(INDEX)s j = 0;
    %(INDEX)s k = 0;
    %(INDEX)s end_query = 0;
    %(INDEX)s end_ref = 0;
    const int s1Len = profile->s1Len;
    const parasail_matrix_t *matrix = profile->matrix;
    const %(INDEX)s segWidth = %(LANES)s; /* number of values in vector unit */
    const %(INDEX)s segLen = (s1Len + segWidth - 1) / segWidth;
    %(VTYPE)s* const restrict vProfile = (%(VTYPE)s*)profile->profile%(WIDTH)s.score;
    %(VTYPE)s* restrict pvHStore = parasail_memalign_%(VTYPE)s(%(ALIGNMENT)s, segLen);
    %(VTYPE)s* restrict pvHLoad = parasail_memalign_%(VTYPE)s(%(ALIGNMENT)s, segLen);
    %(VTYPE)s* restrict pvHMax = parasail_memalign_%(VTYPE)s(%(ALIGNMENT)s, segLen);
    %(VTYPE)s* const restrict pvE = parasail_memalign_%(VTYPE)s(%(ALIGNMENT)s, segLen);
    %(VTYPE)s vGapO = %(VSET1)s(open);
    %(VTYPE)s vGapE = %(VSET1)s(gap);
    %(VTYPE)s vZero = %(VSET1)s(0);
    %(INT)s bias = INT%(WIDTH)s_MIN;
    %(INT)s score = bias;
    %(VTYPE)s vBias = %(VSET1)s(bias);
    %(VTYPE)s vMaxH = vBias;
    %(VTYPE)s vMaxHUnit = vBias;
    %(INT)s maxp = INT%(WIDTH)s_MAX - (%(INT)s)(matrix->max+1);
    %(VTYPE)s insert_mask = %(VCMPGT)s(
            %(VSET)s(%(STRIPED_INSERT_MASK)s),
            vZero);
    /*%(INT)s stop = profile->stop == INT32_MAX ?  INT%(WIDTH)s_MAX : (%(INT)s)profile->stop-bias;*/
#ifdef PARASAIL_TABLE
    parasail_result_t *result = parasail_result_new_table1(segLen*segWidth, s2Len);
#else
#ifdef PARASAIL_ROWCOL
    parasail_result_t *result = parasail_result_new_rowcol1(segLen*segWidth, s2Len);
    const %(INDEX)s offset = (s1Len - 1) %% segLen;
    const %(INDEX)s position = (segWidth - 1) - (s1Len - 1) / segLen;
#else
    parasail_result_t *result = parasail_result_new();
#endif
#endif

    /* initialize H and E */
    parasail_memset_%(VTYPE)s(pvHStore, vBias, segLen);
    parasail_memset_%(VTYPE)s(pvE, vBias, segLen);

    /* outer loop over database sequence */
    for (j=0; j<s2Len; ++j) {
        %(VTYPE)s vE;
        %(VTYPE)s vF;
        %(VTYPE)s vH;
        const %(VTYPE)s* vP = NULL;
        %(VTYPE)s* pv = NULL;

        /* Initialize F value to 0.  Any errors to vH values will be
         * corrected in the Lazy_F loop.  */
        vF = vBias;

        /* load final segment of pvHStore and shift left by 2 bytes */
        vH = %(VSHIFT)s(pvHStore[segLen - 1], %(BYTES)s);
        vH = %(VBLEND)s(vH, vBias, insert_mask);

        /* Correct part of the vProfile */
        vP = vProfile + matrix->mapper[(unsigned char)s2[j]] * segLen;

        if (end_ref == j-2) {
            /* Swap in the max buffer. */
            pv = pvHMax;
            pvHMax = pvHLoad;
            pvHLoad = pvHStore;
            pvHStore = pv;
        }
        else {
            /* Swap the 2 H buffers. */
            pv = pvHLoad;
            pvHLoad = pvHStore;
            pvHStore = pv;
        }

        /* inner loop to process the query sequence */
        for (i=0; i<segLen; ++i) {
            vH = %(VADD)s(vH, %(VLOAD)s(vP + i));
            vE = %(VLOAD)s(pvE + i);

            /* Get max from vH, vE and vF. */
            vH = %(VMAX)s(vH, vE);
            vH = %(VMAX)s(vH, vF);
            /* Save vH values. */
            %(VSTORE)s(pvHStore + i, vH);
#ifdef PARASAIL_TABLE
            arr_store_si%(BITS)s(result->score_table, vH, i, segLen, j, s2Len, bias);
#endif
            vMaxH = %(VMAX)s(vH, vMaxH);

            /* Update vE value. */
            vH = %(VSUB)s(vH, vGapO);
            vE = %(VSUB)s(vE, vGapE);
            vE = %(VMAX)s(vE, vH);
            %(VSTORE)s(pvE + i, vE);

            /* Update vF value. */
            vF = %(VSUB)s(vF, vGapE);
            vF = %(VMAX)s(vF, vH);

            /* Load the next vH. */
            vH = %(VLOAD)s(pvHLoad + i);
        }

        /* Lazy_F loop: has been revised to disallow adjecent insertion and
         * then deletion, so don't update E(i, i), learn from SWPS3 */
        for (k=0; k<segWidth; ++k) {
            vF = %(VSHIFT)s(vF, %(BYTES)s);
            vF = %(VBLEND)s(vF, vBias, insert_mask);
            for (i=0; i<segLen; ++i) {
                vH = %(VLOAD)s(pvHStore + i);
                vH = %(VMAX)s(vH,vF);
                %(VSTORE)s(pvHStore + i, vH);
#ifdef PARASAIL_TABLE
                arr_store_si%(BITS)s(result->score_table, vH, i, segLen, j, s2Len, bias);
#endif
                vMaxH = %(VMAX)s(vH, vMaxH);
                vH = %(VSUB)s(vH, vGapO);
                vF = %(VSUB)s(vF, vGapE);
                if (! %(VMOVEMASK)s(%(VCMPGT)s(vF, vH))) goto end;
                /*vF = %(VMAX)s(vF, vH);*/
            }
        }
end:
        {
        }

#ifdef PARASAIL_ROWCOL
        /* extract last value from the column */
        {
            vH = %(VLOAD)s(pvHStore + offset);
            for (k=0; k<position; ++k) {
                vH = %(VSHIFT)s(vH, %(BYTES)s);
            }
            result->score_row[j] = (%(INT)s) %(VEXTRACT)s (vH, %(LAST_POS)s) - bias;
        }
#endif

        {
            %(VTYPE)s vCompare = %(VCMPGT)s(vMaxH, vMaxHUnit);
            if (%(VMOVEMASK)s(vCompare)) {
                score = %(VHMAX)s(vMaxH);
                /* if score has potential to overflow, abort early */
                if (score > maxp) {
                    result->saturated = 1;
                    break;
                }
                vMaxHUnit = %(VSET1)s(score);
                end_ref = j;
            }
        }

        /*if (score == stop) break;*/
    }

#ifdef PARASAIL_ROWCOL
    for (i=0; i<segLen; ++i) {
        %(VTYPE)s vH = %(VLOAD)s(pvHStore+i);
        arr_store_col(result->score_col, vH, i, segLen, bias);
    }
#endif

    if (score == INT%(WIDTH)s_MAX) {
        result->saturated = 1;
    }

    if (result->saturated) {
        score = INT%(WIDTH)s_MAX;
        end_query = 0;
        end_ref = 0;
    }
    else {
        if (end_ref == j-1) {
            /* end_ref was the last store column */
            %(VTYPE)s *pv = pvHMax;
            pvHMax = pvHStore;
            pvHStore = pv;
        }
        else if (end_ref == j-2) {
            /* end_ref was the last load column */
            %(VTYPE)s *pv = pvHMax;
            pvHMax = pvHLoad;
            pvHLoad = pv;
        }
        /* Trace the alignment ending position on read. */
        {
            %(INT)s *t = (%(INT)s*)pvHMax;
            %(INDEX)s column_len = segLen * segWidth;
            end_query = s1Len - 1;
            for (i = 0; i<column_len; ++i, ++t) {
                if (*t == score) {
                    %(INDEX)s temp = i / segWidth + i %% segWidth * segLen;
                    if (temp < end_query) {
                        end_query = temp;
                    }
                }
            }
        }
    }

    result->score = score - bias;
    result->end_query = end_query;
    result->end_ref = end_ref;

    parasail_free(pvE);
    parasail_free(pvHMax);
    parasail_free(pvHLoad);
    parasail_free(pvHStore);

    return result;
}