C++ (Cpp) parasail_memalign_intの例

コード例 #1

ファイル: sw.c プロジェクト: dikaiosune/parasail-sys

parasail_result_t* ENAME(
        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)
{
#ifdef PARASAIL_TABLE
    parasail_result_t *result = parasail_result_new_table1(s1Len, s2Len);
#else
#ifdef PARASAIL_ROWCOL
    parasail_result_t *result = parasail_result_new_rowcol1(s1Len, s2Len);
#else
    parasail_result_t *result = parasail_result_new();
#endif
#endif
    int * const restrict s1 = parasail_memalign_int(16, s1Len);
    int * const restrict s2 = parasail_memalign_int(16, s2Len);
    int * const restrict tbl_pr = parasail_memalign_int(16, s2Len+1);
    int * const restrict del_pr = parasail_memalign_int(16, s2Len+1);
    int i = 0;
    int j = 0;
    int score = NEG_INF_32;
    int end_query = s1Len;
    int end_ref = s2Len;

    for (i=0; i<s1Len; ++i) {
        s1[i] = matrix->mapper[(unsigned char)_s1[i]];
    }
    for (j=0; j<s2Len; ++j) {
        s2[j] = matrix->mapper[(unsigned char)_s2[j]];
    }

コード例 #2

ファイル: sw_stats_scan.c プロジェクト: jeffdaily/parasail

parasail_result_t* ENAME(
        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)
{
#ifdef PARASAIL_TABLE
    parasail_result_t *result = parasail_result_new_table3(s1Len, s2Len);
#else
#ifdef PARASAIL_ROWCOL
    parasail_result_t *result = parasail_result_new_rowcol3(s1Len, s2Len);
#else
    parasail_result_t *result = parasail_result_new_stats();
#endif
#endif
    int * const restrict s1 = parasail_memalign_int(16, s1Len);
    int * const restrict s2 = parasail_memalign_int(16, s2Len);
    int * const restrict HB = parasail_memalign_int(16, s1Len+1);
    int * const restrict H  = HB+1;
    int * const restrict HMB = parasail_memalign_int(16, s1Len+1);
    int * const restrict HM  = HMB+1;
    int * const restrict HSB = parasail_memalign_int(16, s1Len+1);
    int * const restrict HS  = HSB+1;
    int * const restrict HLB = parasail_memalign_int(16, s1Len+1);
    int * const restrict HL  = HLB+1;
    int * const restrict E  = parasail_memalign_int(16, s1Len);
    int * const restrict EM = parasail_memalign_int(16, s1Len);
    int * const restrict ES = parasail_memalign_int(16, s1Len);
    int * const restrict EL = parasail_memalign_int(16, s1Len);
    int * const restrict HtB= parasail_memalign_int(16, s1Len+1);
    int * const restrict Ht = HtB+1;

コード例 #3

ファイル: sg.c プロジェクト: jeffdaily/parasail

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,
        int s1_beg, int s1_end, int s2_beg, int s2_end)
{
#ifdef PARASAIL_TABLE
    parasail_result_t *result = parasail_result_new_table1(s1Len, s2Len);
#else
#ifdef PARASAIL_ROWCOL
    parasail_result_t *result = parasail_result_new_rowcol1(s1Len, s2Len);
#else
    parasail_result_t *result = parasail_result_new();
#endif
#endif
    int * const restrict s1 = parasail_memalign_int(16, s1Len);
    int * const restrict s2 = parasail_memalign_int(16, s2Len);
    int * const restrict H = parasail_memalign_int(16, s2Len+1);
    int * const restrict F = parasail_memalign_int(16, s2Len+1);
    int i = 0;
    int j = 0;
    int score = NEG_INF_32;
    int end_query = s1Len;
    int end_ref = s2Len;

    for (i=0; i<s1Len; ++i) {
        s1[i] = matrix->mapper[(unsigned char)_s1[i]];
    }
    for (j=0; j<s2Len; ++j) {
        s2[j] = matrix->mapper[(unsigned char)_s2[j]];
    }

コード例 #4

ファイル: sg_trace_scan.c プロジェクト: jeffdaily/parasail

#define SG_SUFFIX _scan
#include "sg_helper.h"

#define NEG_INF_32 (INT32_MIN/2)
#define MAX(a,b) ((a)>(b)?(a):(b))

#define FNAME parasail_sg_flags_trace_scan

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,
        int s1_beg, int s1_end, int s2_beg, int s2_end)
{
    parasail_result_t *result = parasail_result_new_trace(s1Len, s2Len, 16, sizeof(int8_t));
    int * const restrict s1 = parasail_memalign_int(16, s1Len);
    int * const restrict s2 = parasail_memalign_int(16, s2Len);
    int * const restrict HB = parasail_memalign_int(16, s1Len+1);
    int * const restrict H  = HB+1;
    int * const restrict E  = parasail_memalign_int(16, s1Len);
    int * const restrict HtB= parasail_memalign_int(16, s1Len+1);
    int * const restrict Ht = HtB+1;
    int8_t * const restrict HT = (int8_t* const restrict)result->trace->trace_table;
    int * const restrict Ex = parasail_memalign_int(16, s1Len);
    int i = 0;
    int j = 0;
    int score = NEG_INF_32;
    int end_query = s1Len;
    int end_ref = s2Len;

    for (i=0; i<s1Len; ++i) {