#include "config.h"
#include <stdlib.h>
#include "parasail.h"
#include "parasail/memory.h"
#include "parasail/internal_altivec.h"
#ifdef PARASAIL_TABLE
static inline void arr_store_si128(
int *array,
vec128i vWH,
int32_t i,
int32_t s1Len,
int32_t j,
int32_t s2Len)
{
if (0 <= i+0 && i+0 < s1Len && 0 <= j-0 && j-0 < s2Len) {
array[1LL*(i+0)*s2Len + (j-0)] = (int32_t)_mm_extract_epi32(vWH, 3);
}
if (0 <= i+1 && i+1 < s1Len && 0 <= j-1 && j-1 < s2Len) {
array[1LL*(i+1)*s2Len + (j-1)] = (int32_t)_mm_extract_epi32(vWH, 2);
}
if (0 <= i+2 && i+2 < s1Len && 0 <= j-2 && j-2 < s2Len) {
array[1LL*(i+2)*s2Len + (j-2)] = (int32_t)_mm_extract_epi32(vWH, 1);
}
if (0 <= i+3 && i+3 < s1Len && 0 <= j-3 && j-3 < s2Len) {
array[1LL*(i+3)*s2Len + (j-3)] = (int32_t)_mm_extract_epi32(vWH, 0);
}
}
#endif
#ifdef PARASAIL_ROWCOL
static inline void arr_store_rowcol(
int *row,
int *col,
vec128i vWH,
int32_t i,
int32_t s1Len,
int32_t j,
int32_t s2Len)
{
if (i+0 == s1Len-1 && 0 <= j-0 && j-0 < s2Len) {
row[j-0] = (int32_t)_mm_extract_epi32(vWH, 3);
}
if (j-0 == s2Len-1 && 0 <= i+0 && i+0 < s1Len) {
col[(i+0)] = (int32_t)_mm_extract_epi32(vWH, 3);
}
if (i+1 == s1Len-1 && 0 <= j-1 && j-1 < s2Len) {
row[j-1] = (int32_t)_mm_extract_epi32(vWH, 2);
}
if (j-1 == s2Len-1 && 0 <= i+1 && i+1 < s1Len) {
col[(i+1)] = (int32_t)_mm_extract_epi32(vWH, 2);
}
if (i+2 == s1Len-1 && 0 <= j-2 && j-2 < s2Len) {
row[j-2] = (int32_t)_mm_extract_epi32(vWH, 1);
}
if (j-2 == s2Len-1 && 0 <= i+2 && i+2 < s1Len) {
col[(i+2)] = (int32_t)_mm_extract_epi32(vWH, 1);
}
if (i+3 == s1Len-1 && 0 <= j-3 && j-3 < s2Len) {
row[j-3] = (int32_t)_mm_extract_epi32(vWH, 0);
}
if (j-3 == s2Len-1 && 0 <= i+3 && i+3 < s1Len) {
col[(i+3)] = (int32_t)_mm_extract_epi32(vWH, 0);
}
}
#endif
#ifdef PARASAIL_TABLE
#define FNAME parasail_nw_stats_table_diag_altivec_128_32
#else
#ifdef PARASAIL_ROWCOL
#define FNAME parasail_nw_stats_rowcol_diag_altivec_128_32
#else
#define FNAME parasail_nw_stats_diag_altivec_128_32
#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)
{
int32_t N = 0;
int32_t PAD = 0;
int32_t PAD2 = 0;
int32_t s1Len = 0;
int32_t s1Len_PAD = 0;
int32_t s2Len_PAD = 0;
int32_t * restrict s1 = NULL;
int32_t * restrict s2B = NULL;
int32_t * restrict _H_pr = NULL;
int32_t * restrict _HM_pr = NULL;
int32_t * restrict _HS_pr = NULL;
int32_t * restrict _HL_pr = NULL;
int32_t * restrict _F_pr = NULL;
int32_t * restrict _FM_pr = NULL;
int32_t * restrict _FS_pr = NULL;
int32_t * restrict _FL_pr = NULL;
int32_t * restrict s2 = NULL;
int32_t * restrict H_pr = NULL;
int32_t * restrict HM_pr = NULL;
int32_t * restrict HS_pr = NULL;
int32_t * restrict HL_pr = NULL;
int32_t * restrict F_pr = NULL;
int32_t * restrict FM_pr = NULL;
int32_t * restrict FS_pr = NULL;
int32_t * restrict FL_pr = NULL;
parasail_result_t *result = NULL;
int32_t i = 0;
int32_t j = 0;
int32_t end_query = 0;
int32_t end_ref = 0;
int32_t NEG_LIMIT = 0;
int32_t POS_LIMIT = 0;
int32_t score = 0;
int32_t matches = 0;
int32_t similar = 0;
int32_t length = 0;
vec128i vNegLimit;
vec128i vPosLimit;
vec128i vSaturationCheckMin;
vec128i vSaturationCheckMax;
vec128i vNegInf;
vec128i vOpen;
vec128i vGap;
vec128i vZero;
vec128i vNegInf0;
vec128i vOne;
vec128i vN;
vec128i vGapN;
vec128i vNegOne;
vec128i vI;
vec128i vJreset;
vec128i vMaxH;
vec128i vMaxM;
vec128i vMaxS;
vec128i vMaxL;
vec128i vILimit;
vec128i vILimit1;
vec128i vJLimit;
vec128i vJLimit1;
vec128i vIBoundary;
PARASAIL_CHECK_NULL(_s2);
PARASAIL_CHECK_GT0(s2Len);
PARASAIL_CHECK_GE0(open);
PARASAIL_CHECK_GE0(gap);
PARASAIL_CHECK_NULL(matrix);
if (matrix->type == PARASAIL_MATRIX_TYPE_PSSM) {
PARASAIL_CHECK_NULL_PSSM_STATS(_s1);
}
else {
PARASAIL_CHECK_NULL(_s1);
PARASAIL_CHECK_GT0(_s1Len);
}
N = 4;
PAD = N-1;
PAD2 = PAD*2;
s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
s1Len_PAD = s1Len+PAD;
s2Len_PAD = s2Len+PAD;
i = 0;
j = 0;
end_query = s1Len-1;
end_ref = s2Len-1;
NEG_LIMIT = (-open < matrix->min ? INT32_MIN + open : INT32_MIN - matrix->min) + 1;
POS_LIMIT = INT32_MAX - matrix->max - 1;
score = NEG_LIMIT;
matches = NEG_LIMIT;
similar = NEG_LIMIT;
length = NEG_LIMIT;
vNegLimit = _mm_set1_epi32(NEG_LIMIT);
vPosLimit = _mm_set1_epi32(POS_LIMIT);
vSaturationCheckMin = vPosLimit;
vSaturationCheckMax = vNegLimit;
vNegInf = _mm_set1_epi32(NEG_LIMIT);
vOpen = _mm_set1_epi32(open);
vGap = _mm_set1_epi32(gap);
vZero = _mm_set1_epi32(0);
vNegInf0 = _mm_insert_epi32(vZero, NEG_LIMIT, 3);
vOne = _mm_set1_epi32(1);
vN = _mm_set1_epi32(N);
vGapN = _mm_set1_epi32(gap*N);
vNegOne = _mm_set1_epi32(-1);
vI = _mm_set_epi32(0,1,2,3);
vJreset = _mm_set_epi32(0,-1,-2,-3);
vMaxH = vNegInf;
vMaxM = vNegInf;
vMaxS = vNegInf;
vMaxL = vNegInf;
vILimit = _mm_set1_epi32(s1Len);
vILimit1 = _mm_sub_epi32(vILimit, vOne);
vJLimit = _mm_set1_epi32(s2Len);
vJLimit1 = _mm_sub_epi32(vJLimit, vOne);
vIBoundary = _mm_set_epi32(
-open-0*gap,
-open-1*gap,
-open-2*gap,
-open-3*gap);
#ifdef PARASAIL_TABLE
result = parasail_result_new_table3(s1Len, s2Len);
#else
#ifdef PARASAIL_ROWCOL
result = parasail_result_new_rowcol3(s1Len, s2Len);
#else
result = parasail_result_new_stats();
#endif
#endif
if (!result) return NULL;
result->flag |= PARASAIL_FLAG_NW | PARASAIL_FLAG_DIAG
| PARASAIL_FLAG_STATS
| PARASAIL_FLAG_BITS_32 | PARASAIL_FLAG_LANES_4;
#ifdef PARASAIL_TABLE
result->flag |= PARASAIL_FLAG_TABLE;
#endif
#ifdef PARASAIL_ROWCOL
result->flag |= PARASAIL_FLAG_ROWCOL;
#endif
s1 = parasail_memalign_int32_t(16, s1Len+PAD);
s2B = parasail_memalign_int32_t(16, s2Len+PAD2);
_H_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
_HM_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
_HS_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
_HL_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
_F_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
_FM_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
_FS_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
_FL_pr = parasail_memalign_int32_t(16, s2Len+PAD2);
s2 = s2B+PAD;
H_pr = _H_pr+PAD;
HM_pr = _HM_pr+PAD;
HS_pr = _HS_pr+PAD;
HL_pr = _HL_pr+PAD;
F_pr = _F_pr+PAD;
FM_pr = _FM_pr+PAD;
FS_pr = _FS_pr+PAD;
FL_pr = _FL_pr+PAD;
if (!s1) return NULL;
if (!s2B) return NULL;
if (!_H_pr) return NULL;
if (!_HM_pr) return NULL;
if (!_HS_pr) return NULL;
if (!_HL_pr) return NULL;
if (!_F_pr) return NULL;
if (!_FM_pr) return NULL;
if (!_FS_pr) return NULL;
if (!_FL_pr) return NULL;
for (i=0; i<s1Len; ++i) {
s1[i] = matrix->mapper[(unsigned char)_s1[i]];
}
for (i=s1Len; i<s1Len_PAD; ++i) {
s1[i] = 0;
}
for (j=0; j<s2Len; ++j) {
s2[j] = matrix->mapper[(unsigned char)_s2[j]];
}
for (j=-PAD; j<0; ++j) {
s2[j] = 0;
}
for (j=s2Len; j<s2Len_PAD; ++j) {
s2[j] = 0;
}
for (j=0; j<s2Len; ++j) {
H_pr[j] = -open - j*gap;
HM_pr[j] = 0;
HS_pr[j] = 0;
HL_pr[j] = 0;
F_pr[j] = NEG_LIMIT;
FM_pr[j] = 0;
FS_pr[j] = 0;
FL_pr[j] = 0;
}
for (j=-PAD; j<0; ++j) {
H_pr[j] = 0;
HM_pr[j] = 0;
HS_pr[j] = 0;
HL_pr[j] = 0;
F_pr[j] = 0;
FM_pr[j] = 0;
FS_pr[j] = 0;
FL_pr[j] = 0;
}
for (j=s2Len; j<s2Len+PAD; ++j) {
H_pr[j] = 0;
HM_pr[j] = 0;
HS_pr[j] = 0;
HL_pr[j] = 0;
F_pr[j] = 0;
FM_pr[j] = 0;
FS_pr[j] = 0;
FL_pr[j] = 0;
}
H_pr[-1] = 0;
for (i=0; i<s1Len; i+=N) {
vec128i case1 = vZero;
vec128i case2 = vZero;
vec128i vNH = vZero;
vec128i vNM = vZero;
vec128i vNS = vZero;
vec128i vNL = vZero;
vec128i vWH = vZero;
vec128i vWM = vZero;
vec128i vWS = vZero;
vec128i vWL = vZero;
vec128i vE = vNegInf0;
vec128i vE_opn = vNegInf;
vec128i vE_ext = vNegInf;
vec128i vEM = vZero;
vec128i vES = vZero;
vec128i vEL = vZero;
vec128i vF = vNegInf0;
vec128i vF_opn = vNegInf;
vec128i vF_ext = vNegInf;
vec128i vFM = vZero;
vec128i vFS = vZero;
vec128i vFL = vZero;
vec128i vJ = vJreset;
vec128i vs1 = _mm_set_epi32(
s1[i+0],
s1[i+1],
s1[i+2],
s1[i+3]);
vec128i vs2 = vNegInf;
const int * const restrict matrow0 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+0] : ((i+0 >= s1Len) ? s1Len-1 : i+0))];
const int * const restrict matrow1 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+1] : ((i+1 >= s1Len) ? s1Len-1 : i+1))];
const int * const restrict matrow2 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+2] : ((i+2 >= s1Len) ? s1Len-1 : i+2))];
const int * const restrict matrow3 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+3] : ((i+3 >= s1Len) ? s1Len-1 : i+3))];
vNH = _mm_insert_epi32(vNH, H_pr[-1], 3);
vWH = _mm_insert_epi32(vWH, -open - i*gap, 3);
H_pr[-1] = -open - (i+N)*gap;
for (j=0; j<s2Len+PAD; ++j) {
vec128i vMat;
vec128i vNWH = vNH;
vec128i vNWM = vNM;
vec128i vNWS = vNS;
vec128i vNWL = vNL;
vNH = _mm_srli_si128(vWH, 4);
vNH = _mm_insert_epi32(vNH, H_pr[j], 3);
vNM = _mm_srli_si128(vWM, 4);
vNM = _mm_insert_epi32(vNM, HM_pr[j], 3);
vNS = _mm_srli_si128(vWS, 4);
vNS = _mm_insert_epi32(vNS, HS_pr[j], 3);
vNL = _mm_srli_si128(vWL, 4);
vNL = _mm_insert_epi32(vNL, HL_pr[j], 3);
vF = _mm_srli_si128(vF, 4);
vF = _mm_insert_epi32(vF, F_pr[j], 3);
vFM = _mm_srli_si128(vFM, 4);
vFM = _mm_insert_epi32(vFM, FM_pr[j], 3);
vFS = _mm_srli_si128(vFS, 4);
vFS = _mm_insert_epi32(vFS, FS_pr[j], 3);
vFL = _mm_srli_si128(vFL, 4);
vFL = _mm_insert_epi32(vFL, FL_pr[j], 3);
vF_opn = _mm_sub_epi32(vNH, vOpen);
vF_ext = _mm_sub_epi32(vF, vGap);
vF = _mm_max_epi32(vF_opn, vF_ext);
case1 = _mm_cmpgt_epi32(vF_opn, vF_ext);
vFM = _mm_blendv_epi8(vFM, vNM, case1);
vFS = _mm_blendv_epi8(vFS, vNS, case1);
vFL = _mm_blendv_epi8(vFL, vNL, case1);
vFL = _mm_add_epi32(vFL, vOne);
vE_opn = _mm_sub_epi32(vWH, vOpen);
vE_ext = _mm_sub_epi32(vE, vGap);
vE = _mm_max_epi32(vE_opn, vE_ext);
case1 = _mm_cmpgt_epi32(vE_opn, vE_ext);
vEM = _mm_blendv_epi8(vEM, vWM, case1);
vES = _mm_blendv_epi8(vES, vWS, case1);
vEL = _mm_blendv_epi8(vEL, vWL, case1);
vEL = _mm_add_epi32(vEL, vOne);
vs2 = _mm_srli_si128(vs2, 4);
vs2 = _mm_insert_epi32(vs2, s2[j], 3);
vMat = _mm_set_epi32(
matrow0[s2[j-0]],
matrow1[s2[j-1]],
matrow2[s2[j-2]],
matrow3[s2[j-3]]
);
vNWH = _mm_add_epi32(vNWH, vMat);
vWH = _mm_max_epi32(vNWH, vE);
vWH = _mm_max_epi32(vWH, vF);
case1 = _mm_cmpeq_epi32(vWH, vNWH);
case2 = _mm_cmpeq_epi32(vWH, vF);
vWM = _mm_blendv_epi8(
_mm_blendv_epi8(vEM, vFM, case2),
_mm_add_epi32(vNWM,
_mm_and_si128(
_mm_cmpeq_epi32(vs1,vs2),
vOne)),
case1);
vWS = _mm_blendv_epi8(
_mm_blendv_epi8(vES, vFS, case2),
_mm_add_epi32(vNWS,
_mm_and_si128(
_mm_cmpgt_epi32(vMat,vZero),
vOne)),
case1);
vWL = _mm_blendv_epi8(
_mm_blendv_epi8(vEL, vFL, case2),
_mm_add_epi32(vNWL, vOne), case1);
{
vec128i cond = _mm_cmpeq_epi32(vJ,vNegOne);
vWH = _mm_blendv_epi8(vWH, vIBoundary, cond);
vWM = _mm_andnot_si128(cond, vWM);
vWS = _mm_andnot_si128(cond, vWS);
vWL = _mm_andnot_si128(cond, vWL);
vE = _mm_blendv_epi8(vE, vNegInf, cond);
vEM = _mm_andnot_si128(cond, vEM);
vES = _mm_andnot_si128(cond, vES);
vEL = _mm_andnot_si128(cond, vEL);
}
if (j > PAD) {
vSaturationCheckMin = _mm_min_epi32(vSaturationCheckMin, vWH);
vSaturationCheckMax = _mm_max_epi32(vSaturationCheckMax, vWH);
vSaturationCheckMax = _mm_max_epi32(vSaturationCheckMax, vWM);
vSaturationCheckMax = _mm_max_epi32(vSaturationCheckMax, vWS);
vSaturationCheckMax = _mm_max_epi32(vSaturationCheckMax, vWL);
vSaturationCheckMax = _mm_max_epi32(vSaturationCheckMax, vWL);
}
#ifdef PARASAIL_TABLE
arr_store_si128(result->stats->tables->score_table, vWH, i, s1Len, j, s2Len);
arr_store_si128(result->stats->tables->matches_table, vWM, i, s1Len, j, s2Len);
arr_store_si128(result->stats->tables->similar_table, vWS, i, s1Len, j, s2Len);
arr_store_si128(result->stats->tables->length_table, vWL, i, s1Len, j, s2Len);
#endif
#ifdef PARASAIL_ROWCOL
arr_store_rowcol(result->stats->rowcols->score_row, result->stats->rowcols->score_col, vWH, i, s1Len, j, s2Len);
arr_store_rowcol(result->stats->rowcols->matches_row, result->stats->rowcols->matches_col, vWM, i, s1Len, j, s2Len);
arr_store_rowcol(result->stats->rowcols->similar_row, result->stats->rowcols->similar_col, vWS, i, s1Len, j, s2Len);
arr_store_rowcol(result->stats->rowcols->length_row, result->stats->rowcols->length_col, vWL, i, s1Len, j, s2Len);
#endif
H_pr[j-3] = (int32_t)_mm_extract_epi32(vWH,0);
HM_pr[j-3] = (int32_t)_mm_extract_epi32(vWM,0);
HS_pr[j-3] = (int32_t)_mm_extract_epi32(vWS,0);
HL_pr[j-3] = (int32_t)_mm_extract_epi32(vWL,0);
F_pr[j-3] = (int32_t)_mm_extract_epi32(vF,0);
FM_pr[j-3] = (int32_t)_mm_extract_epi32(vFM,0);
FS_pr[j-3] = (int32_t)_mm_extract_epi32(vFS,0);
FL_pr[j-3] = (int32_t)_mm_extract_epi32(vFL,0);
{
vec128i cond_valid_I = _mm_cmpeq_epi32(vI, vILimit1);
vec128i cond_valid_J = _mm_cmpeq_epi32(vJ, vJLimit1);
vec128i cond_all = _mm_and_si128(cond_valid_I, cond_valid_J);
vMaxH = _mm_blendv_epi8(vMaxH, vWH, cond_all);
vMaxM = _mm_blendv_epi8(vMaxM, vWM, cond_all);
vMaxS = _mm_blendv_epi8(vMaxS, vWS, cond_all);
vMaxL = _mm_blendv_epi8(vMaxL, vWL, cond_all);
}
vJ = _mm_add_epi32(vJ, vOne);
}
vI = _mm_add_epi32(vI, vN);
vIBoundary = _mm_sub_epi32(vIBoundary, vGapN);
}
for (i=0; i<N; ++i) {
int32_t value;
value = (int32_t) _mm_extract_epi32(vMaxH, 3);
if (value > score) {
score = value;
matches = (int32_t) _mm_extract_epi32(vMaxM, 3);
similar = (int32_t) _mm_extract_epi32(vMaxS, 3);
length= (int32_t) _mm_extract_epi32(vMaxL, 3);
}
vMaxH = _mm_slli_si128(vMaxH, 4);
vMaxM = _mm_slli_si128(vMaxM, 4);
vMaxS = _mm_slli_si128(vMaxS, 4);
vMaxL = _mm_slli_si128(vMaxL, 4);
}
if (_mm_movemask_epi8(_mm_or_si128(
_mm_cmplt_epi32(vSaturationCheckMin, vNegLimit),
_mm_cmpgt_epi32(vSaturationCheckMax, vPosLimit)))) {
result->flag |= PARASAIL_FLAG_SATURATED;
score = 0;
matches = 0;
similar = 0;
length = 0;
end_query = 0;
end_ref = 0;
}
result->score = score;
result->end_query = end_query;
result->end_ref = end_ref;
result->stats->matches = matches;
result->stats->similar = similar;
result->stats->length = length;
parasail_free(_FL_pr);
parasail_free(_FS_pr);
parasail_free(_FM_pr);
parasail_free(_F_pr);
parasail_free(_HL_pr);
parasail_free(_HS_pr);
parasail_free(_HM_pr);
parasail_free(_H_pr);
parasail_free(s2B);
parasail_free(s1);
return result;
}