#include "config.h"
#include <stdlib.h>
#include "parasail.h"
#include "parasail/memory.h"
#include "parasail/internal_altivec.h"
static inline void arr_store_si128(
int8_t *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)] = (int8_t)_mm_extract_epi8(vWH, 15);
}
if (0 <= i+1 && i+1 < s1Len && 0 <= j-1 && j-1 < s2Len) {
array[1LL*(i+1)*s2Len + (j-1)] = (int8_t)_mm_extract_epi8(vWH, 14);
}
if (0 <= i+2 && i+2 < s1Len && 0 <= j-2 && j-2 < s2Len) {
array[1LL*(i+2)*s2Len + (j-2)] = (int8_t)_mm_extract_epi8(vWH, 13);
}
if (0 <= i+3 && i+3 < s1Len && 0 <= j-3 && j-3 < s2Len) {
array[1LL*(i+3)*s2Len + (j-3)] = (int8_t)_mm_extract_epi8(vWH, 12);
}
if (0 <= i+4 && i+4 < s1Len && 0 <= j-4 && j-4 < s2Len) {
array[1LL*(i+4)*s2Len + (j-4)] = (int8_t)_mm_extract_epi8(vWH, 11);
}
if (0 <= i+5 && i+5 < s1Len && 0 <= j-5 && j-5 < s2Len) {
array[1LL*(i+5)*s2Len + (j-5)] = (int8_t)_mm_extract_epi8(vWH, 10);
}
if (0 <= i+6 && i+6 < s1Len && 0 <= j-6 && j-6 < s2Len) {
array[1LL*(i+6)*s2Len + (j-6)] = (int8_t)_mm_extract_epi8(vWH, 9);
}
if (0 <= i+7 && i+7 < s1Len && 0 <= j-7 && j-7 < s2Len) {
array[1LL*(i+7)*s2Len + (j-7)] = (int8_t)_mm_extract_epi8(vWH, 8);
}
if (0 <= i+8 && i+8 < s1Len && 0 <= j-8 && j-8 < s2Len) {
array[1LL*(i+8)*s2Len + (j-8)] = (int8_t)_mm_extract_epi8(vWH, 7);
}
if (0 <= i+9 && i+9 < s1Len && 0 <= j-9 && j-9 < s2Len) {
array[1LL*(i+9)*s2Len + (j-9)] = (int8_t)_mm_extract_epi8(vWH, 6);
}
if (0 <= i+10 && i+10 < s1Len && 0 <= j-10 && j-10 < s2Len) {
array[1LL*(i+10)*s2Len + (j-10)] = (int8_t)_mm_extract_epi8(vWH, 5);
}
if (0 <= i+11 && i+11 < s1Len && 0 <= j-11 && j-11 < s2Len) {
array[1LL*(i+11)*s2Len + (j-11)] = (int8_t)_mm_extract_epi8(vWH, 4);
}
if (0 <= i+12 && i+12 < s1Len && 0 <= j-12 && j-12 < s2Len) {
array[1LL*(i+12)*s2Len + (j-12)] = (int8_t)_mm_extract_epi8(vWH, 3);
}
if (0 <= i+13 && i+13 < s1Len && 0 <= j-13 && j-13 < s2Len) {
array[1LL*(i+13)*s2Len + (j-13)] = (int8_t)_mm_extract_epi8(vWH, 2);
}
if (0 <= i+14 && i+14 < s1Len && 0 <= j-14 && j-14 < s2Len) {
array[1LL*(i+14)*s2Len + (j-14)] = (int8_t)_mm_extract_epi8(vWH, 1);
}
if (0 <= i+15 && i+15 < s1Len && 0 <= j-15 && j-15 < s2Len) {
array[1LL*(i+15)*s2Len + (j-15)] = (int8_t)_mm_extract_epi8(vWH, 0);
}
}
#define FNAME parasail_sw_trace_diag_altivec_128_8
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_PAD = 0;
int32_t s2Len_PAD = 0;
int8_t * restrict s1 = NULL;
int8_t * restrict s2B = NULL;
int8_t * restrict _H_pr = NULL;
int8_t * restrict _F_pr = NULL;
int8_t * restrict s2 = NULL;
int8_t * restrict H_pr = NULL;
int8_t * restrict F_pr = NULL;
parasail_result_t *result = NULL;
int32_t i = 0;
int32_t j = 0;
int32_t s1Len = 0;
int32_t end_query = 0;
int32_t end_ref = 0;
int8_t NEG_LIMIT = 0;
int8_t POS_LIMIT = 0;
int8_t score = 0;
vec128i vNegLimit;
vec128i vPosLimit;
vec128i vSaturationCheckMin;
vec128i vSaturationCheckMax;
vec128i vNegInf;
vec128i vNegInf0;
vec128i vOpen;
vec128i vGap;
vec128i vZero;
vec128i vOne16;
vec128i vNegOne16;
vec128i vN16;
vec128i vILo16;
vec128i vIHi16;
vec128i vJresetLo16;
vec128i vJresetHi16;
vec128i vMaxH;
vec128i vEndILo;
vec128i vEndIHi;
vec128i vEndJLo;
vec128i vEndJHi;
vec128i vILimit16;
vec128i vJLimit16;
vec128i vTDiag;
vec128i vTIns;
vec128i vTDel;
vec128i vTZero;
vec128i vTDiagE;
vec128i vTInsE;
vec128i vTDiagF;
vec128i vTDelF;
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_SQUARE) {
PARASAIL_CHECK_NULL(_s1);
PARASAIL_CHECK_GT0(_s1Len);
}
N = 16;
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 = 0;
end_ref = 0;
NEG_LIMIT = (-open < matrix->min ? INT8_MIN + open : INT8_MIN - matrix->min) + 1;
POS_LIMIT = INT8_MAX - matrix->max - 1;
score = NEG_LIMIT;
vNegLimit = _mm_set1_epi8(NEG_LIMIT);
vPosLimit = _mm_set1_epi8(POS_LIMIT);
vSaturationCheckMin = vPosLimit;
vSaturationCheckMax = vNegLimit;
vNegInf = _mm_set1_epi8(NEG_LIMIT);
vNegInf0 = _mm_srli_si128(vNegInf, 1);
vOpen = _mm_set1_epi8(open);
vGap = _mm_set1_epi8(gap);
vZero = _mm_set1_epi8(0);
vOne16 = _mm_set1_epi16(1);
vNegOne16 = _mm_set1_epi16(-1);
vN16 = _mm_set1_epi16(N);
vILo16 = _mm_set_epi16(8,9,10,11,12,13,14,15);
vIHi16 = _mm_set_epi16(0,1,2,3,4,5,6,7);
vJresetLo16 = _mm_set_epi16(-8,-9,-10,-11,-12,-13,-14,-15);
vJresetHi16 = _mm_set_epi16(0,-1,-2,-3,-4,-5,-6,-7);
vMaxH = vNegInf;
vEndILo = vNegInf;
vEndIHi = vNegInf;
vEndJLo = vNegInf;
vEndJHi = vNegInf;
vILimit16 = _mm_set1_epi16(s1Len);
vJLimit16 = _mm_set1_epi16(s2Len);
vTDiag = _mm_set1_epi8(PARASAIL_DIAG);
vTIns = _mm_set1_epi8(PARASAIL_INS);
vTDel = _mm_set1_epi8(PARASAIL_DEL);
vTZero = _mm_set1_epi8(PARASAIL_ZERO);
vTDiagE = _mm_set1_epi8(PARASAIL_DIAG_E);
vTInsE = _mm_set1_epi8(PARASAIL_INS_E);
vTDiagF = _mm_set1_epi8(PARASAIL_DIAG_F);
vTDelF = _mm_set1_epi8(PARASAIL_DEL_F);
result = parasail_result_new_trace(s1Len, s2Len, 16, sizeof(int8_t));
if (!result) return NULL;
result->flag |= PARASAIL_FLAG_SW | PARASAIL_FLAG_DIAG
| PARASAIL_FLAG_TRACE
| PARASAIL_FLAG_BITS_8 | PARASAIL_FLAG_LANES_16;
s2B= parasail_memalign_int8_t(16, s2Len+PAD2);
_H_pr = parasail_memalign_int8_t(16, s2Len+PAD2);
_F_pr = parasail_memalign_int8_t(16, s2Len+PAD2);
s2 = s2B+PAD;
H_pr = _H_pr+PAD;
F_pr = _F_pr+PAD;
if (!s2B) return NULL;
if (!_H_pr) return NULL;
if (!_F_pr) return NULL;
if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
s1 = parasail_memalign_int8_t(16, s1Len+PAD);
if (!s1) 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] = 0;
F_pr[j] = NEG_LIMIT;
}
for (j=-PAD; j<0; ++j) {
H_pr[j] = NEG_LIMIT;
F_pr[j] = NEG_LIMIT;
}
for (j=s2Len; j<s2Len+PAD; ++j) {
H_pr[j] = NEG_LIMIT;
F_pr[j] = NEG_LIMIT;
}
for (i=0; i<s1Len; i+=N) {
vec128i vNH = vNegInf0;
vec128i vWH = vNegInf0;
vec128i vE = vNegInf;
vec128i vE_opn = vNegInf;
vec128i vE_ext = vNegInf;
vec128i vF = vNegInf;
vec128i vF_opn = vNegInf;
vec128i vF_ext = vNegInf;
vec128i vJLo16 = vJresetLo16;
vec128i vJHi16 = vJresetHi16;
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))];
const int * const restrict matrow4 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+4] : ((i+4 >= s1Len) ? s1Len-1 : i+4))];
const int * const restrict matrow5 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+5] : ((i+5 >= s1Len) ? s1Len-1 : i+5))];
const int * const restrict matrow6 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+6] : ((i+6 >= s1Len) ? s1Len-1 : i+6))];
const int * const restrict matrow7 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+7] : ((i+7 >= s1Len) ? s1Len-1 : i+7))];
const int * const restrict matrow8 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+8] : ((i+8 >= s1Len) ? s1Len-1 : i+8))];
const int * const restrict matrow9 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+9] : ((i+9 >= s1Len) ? s1Len-1 : i+9))];
const int * const restrict matrow10 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+10] : ((i+10 >= s1Len) ? s1Len-1 : i+10))];
const int * const restrict matrow11 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+11] : ((i+11 >= s1Len) ? s1Len-1 : i+11))];
const int * const restrict matrow12 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+12] : ((i+12 >= s1Len) ? s1Len-1 : i+12))];
const int * const restrict matrow13 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+13] : ((i+13 >= s1Len) ? s1Len-1 : i+13))];
const int * const restrict matrow14 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+14] : ((i+14 >= s1Len) ? s1Len-1 : i+14))];
const int * const restrict matrow15 = &matrix->matrix[matrix->size * ((matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) ? s1[i+15] : ((i+15 >= s1Len) ? s1Len-1 : i+15))];
vec128i vIltLimit = _mm_packs_epi16(
_mm_cmplt_epi16(vILo16, vILimit16),
_mm_cmplt_epi16(vIHi16, vILimit16));
for (j=0; j<s2Len+PAD; ++j) {
vec128i vMat;
vec128i vNWH = vNH;
vNH = _mm_srli_si128(vWH, 1);
vNH = _mm_insert_epi8(vNH, H_pr[j], 15);
vF = _mm_srli_si128(vF, 1);
vF = _mm_insert_epi8(vF, F_pr[j], 15);
vF_opn = _mm_subs_epi8(vNH, vOpen);
vF_ext = _mm_subs_epi8(vF, vGap);
vF = _mm_max_epi8(vF_opn, vF_ext);
vE_opn = _mm_subs_epi8(vWH, vOpen);
vE_ext = _mm_subs_epi8(vE, vGap);
vE = _mm_max_epi8(vE_opn, vE_ext);
vMat = _mm_set_epi8(
matrow0[s2[j-0]],
matrow1[s2[j-1]],
matrow2[s2[j-2]],
matrow3[s2[j-3]],
matrow4[s2[j-4]],
matrow5[s2[j-5]],
matrow6[s2[j-6]],
matrow7[s2[j-7]],
matrow8[s2[j-8]],
matrow9[s2[j-9]],
matrow10[s2[j-10]],
matrow11[s2[j-11]],
matrow12[s2[j-12]],
matrow13[s2[j-13]],
matrow14[s2[j-14]],
matrow15[s2[j-15]]
);
vNWH = _mm_adds_epi8(vNWH, vMat);
vNWH = _mm_max_epi8(vNWH, vZero);
vWH = _mm_max_epi8(vNWH, vE);
vWH = _mm_max_epi8(vWH, vF);
{
vec128i cond = _mm_packs_epi16(
_mm_cmpeq_epi16(vJLo16,vNegOne16),
_mm_cmpeq_epi16(vJHi16,vNegOne16));
vWH = _mm_andnot_si128(cond, vWH);
vF = _mm_blendv_epi8(vF, vNegInf, cond);
vE = _mm_blendv_epi8(vE, vNegInf, cond);
}
if (j > PAD) {
vSaturationCheckMin = _mm_min_epi8(vSaturationCheckMin, vWH);
vSaturationCheckMax = _mm_max_epi8(vSaturationCheckMax, vWH);
}
{
vec128i cond_zero = _mm_cmpeq_epi8(vWH, vZero);
vec128i case1 = _mm_cmpeq_epi8(vWH, vNWH);
vec128i case2 = _mm_cmpeq_epi8(vWH, vF);
vec128i vT = _mm_blendv_epi8(
_mm_blendv_epi8(vTIns, vTDel, case2),
_mm_blendv_epi8(vTDiag, vTZero, cond_zero),
case1);
vec128i condE = _mm_cmpgt_epi8(vE_opn, vE_ext);
vec128i condF = _mm_cmpgt_epi8(vF_opn, vF_ext);
vec128i vET = _mm_blendv_epi8(vTInsE, vTDiagE, condE);
vec128i vFT = _mm_blendv_epi8(vTDelF, vTDiagF, condF);
vT = _mm_or_si128(vT, vET);
vT = _mm_or_si128(vT, vFT);
arr_store_si128(result->trace->trace_table, vT, i, s1Len, j, s2Len);
}
H_pr[j-15] = (int8_t)_mm_extract_epi8(vWH,0);
F_pr[j-15] = (int8_t)_mm_extract_epi8(vF,0);
{
vec128i cond_valid_J = _mm_and_si128(
_mm_packs_epi16(
_mm_cmpgt_epi16(vJLo16, vNegOne16),
_mm_cmpgt_epi16(vJHi16, vNegOne16)),
_mm_packs_epi16(
_mm_cmplt_epi16(vJLo16, vJLimit16),
_mm_cmplt_epi16(vJHi16, vJLimit16)));
vec128i cond_valid_IJ = _mm_and_si128(cond_valid_J, vIltLimit);
vec128i cond_eq = _mm_cmpeq_epi8(vWH, vMaxH);
vec128i cond_max = _mm_cmpgt_epi8(vWH, vMaxH);
vec128i cond_all = _mm_and_si128(cond_max, cond_valid_IJ);
vec128i cond_Jlt = _mm_packs_epi16(
_mm_cmplt_epi16(vJLo16, vEndJLo),
_mm_cmplt_epi16(vJHi16, vEndJHi));
vec128i cond_lo = _mm_unpacklo_epi8(cond_all, cond_all);
vec128i cond_hi = _mm_unpackhi_epi8(cond_all, cond_all);
vMaxH = _mm_blendv_epi8(vMaxH, vWH, cond_all);
vEndILo = _mm_blendv_epi8(vEndILo, vILo16, cond_lo);
vEndIHi = _mm_blendv_epi8(vEndIHi, vIHi16, cond_hi);
vEndJLo = _mm_blendv_epi8(vEndJLo, vJLo16, cond_lo);
vEndJHi = _mm_blendv_epi8(vEndJHi, vJHi16, cond_hi);
cond_all = _mm_and_si128(cond_Jlt, cond_eq);
cond_all = _mm_and_si128(cond_all, cond_valid_IJ);
cond_lo = _mm_unpacklo_epi8(cond_all, cond_all);
cond_hi = _mm_unpackhi_epi8(cond_all, cond_all);
vEndILo = _mm_blendv_epi8(vEndILo, vILo16, cond_lo);
vEndIHi = _mm_blendv_epi8(vEndIHi, vIHi16, cond_hi);
vEndJLo = _mm_blendv_epi8(vEndJLo, vJLo16, cond_lo);
vEndJHi = _mm_blendv_epi8(vEndJHi, vJHi16, cond_hi);
}
vJLo16 = _mm_add_epi16(vJLo16, vOne16);
vJHi16 = _mm_add_epi16(vJHi16, vOne16);
}
vILo16 = _mm_add_epi16(vILo16, vN16);
vIHi16 = _mm_add_epi16(vIHi16, vN16);
}
{
int8_t *t = (int8_t*)&vMaxH;
int16_t *ilo = (int16_t*)&vEndILo;
int16_t *jlo = (int16_t*)&vEndJLo;
int16_t *ihi = (int16_t*)&vEndIHi;
int16_t *jhi = (int16_t*)&vEndJHi;
int32_t k;
for (k=0; k<N/2; ++k, ++t, ++ilo, ++jlo) {
if (*t > score) {
score = *t;
end_query = *ilo;
end_ref = *jlo;
}
else if (*t == score) {
if (*jlo < end_ref) {
end_query = *ilo;
end_ref = *jlo;
}
else if (*jlo == end_ref && *ilo < end_query) {
end_query = *ilo;
end_ref = *jlo;
}
}
}
for (k=N/2; k<N; ++k, ++t, ++ihi, ++jhi) {
if (*t > score) {
score = *t;
end_query = *ihi;
end_ref = *jhi;
}
else if (*t == score) {
if (*jhi < end_ref) {
end_query = *ihi;
end_ref = *jhi;
}
else if (*jhi == end_ref && *ihi < end_query) {
end_query = *ihi;
end_ref = *jhi;
}
}
}
}
if (_mm_movemask_epi8(_mm_or_si128(
_mm_cmplt_epi8(vSaturationCheckMin, vNegLimit),
_mm_cmpgt_epi8(vSaturationCheckMax, vPosLimit)))) {
result->flag |= PARASAIL_FLAG_SATURATED;
score = 0;
end_query = 0;
end_ref = 0;
}
result->score = score;
result->end_query = end_query;
result->end_ref = end_ref;
parasail_free(_F_pr);
parasail_free(_H_pr);
parasail_free(s2B);
if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
parasail_free(s1);
}
return result;
}