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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bmsse__util_8h_source.html below:

NCBI C++ ToolKit: include/util/bitset/bmsse_util.h Source File

1 #ifndef BMSSE_UTIL__H__INCLUDED__ 2 #define BMSSE_UTIL__H__INCLUDED__ 35 #pragma GCC diagnostic push 36 #pragma GCC diagnostic ignored "-Wconversion" 91

}

while

(src < src_end);

115

}

while

(src < src_end);

130 __m128i

accA, accB, accC, accD;

171

}

while

(src < src_end);

180 return

macc[0] | macc[1] | macc[2] | macc[3];

263 __m128i

m1A, m2A, m1B, m2B, m1C, m2C, m1D, m2D;

264 __m128i

accA, accB, accC, accD;

298

}

while

(src < src_end);

307 return

macc[0] | macc[1] | macc[2] | macc[3];

316 __m128i

m1A, m2A, m1B, m2B, m1C, m2C, m1D, m2D;

317 __m128i

accA, accB, accC, accD;

351

}

while

(src < src_end);

360 return

macc[0] | macc[1] | macc[2] | macc[3];

375 __m128i

m1A, m2A, m1B, m2B, m1C, m2C, m1D, m2D;

409

}

while

(src < src_end);

416 return

(maskA == 0xFFFFu);

430 __m128i

m1A, m2A, m1B, m2B, m1C, m2C, m1D, m2D;

461

}

while

(src < src_end);

467 return

(maskA == 0xFFFFu);

505

src1 += 4; src2 += 4; dst += 4;

507

}

while

(src1 < src_end1);

513 return

(maskA == 0xFFFFu);

556

src1 += 4; src2 += 4; dst += 4;

558

}

while

(src1 < src_end1);

564 return

(maskA == 0xFFFFu);

620

src1 += 4; src2 += 4;

621

src3 += 4; src4 += 4;

628

}

while

(src1 < src_end1);

634 return

(maskA == 0xFFFFu);

650 __m128i

accA, accB, accC, accD;

675

}

while

(src < src_end);

683 return

macc[0] | macc[1] | macc[2] | macc[3];

698 __m128i

accA, accB, accC, accD;

722

src1 += 4; src2 += 4; dst += 4;

723

}

while

(src1 < src1_end);

731 return

macc[0] | macc[1] | macc[2] | macc[3];

748 __m128i

accA, accB, accC, accD;

788

}

while

(src < src_end);

797 return

macc[0] | macc[1] | macc[2] | macc[3];

828

}

while

(dst < dst_end);

841 __m128i

xmm0, xmm1, xmm2, xmm3;

869

}

while

(src < src_end);

882 __m128i

xmm0, xmm1, xmm2, xmm3;

910

}

while

(src < src_end);

924 __m128i

xmm0, xmm1, xmm2, xmm3;

952

}

while

(src < src_end);

965 __m128i

xmm0, xmm1, xmm2, xmm3;

993

}

while

(src < src_end);

1031

}

while

(dst < (

__m128i

*)dst_end);

1073 unsigned

sse_vect_waves,

1078 for

(

unsigned i

= 0;

< sse_vect_waves; ++

)

1088 unsigned short

* cnt8 = (

unsigned short

*)&xcnt;

1089

*sum += (cnt8[0]) + (cnt8[2]) + (cnt8[4]) + (cnt8[6]);

1110 unsigned

unroll_factor = 8;

1111 unsigned len

= to - from + 1;

1112 unsigned

len_unr =

len

- (

len

% unroll_factor);

1119 __m128i

vect40, vect41, norm_vect40, norm_vect41, cmp_mask_ge;

1122 for

(; k < len_unr; k+=unroll_factor)

1135 return

from + k + (bsf / 4);

1148 return

4 + from + k + (bsf / 4);

1152 for

(; k <

len

; ++k)

1154 if

(arr_base[k] >= target)

1162 #pragma GCC diagnostic pop

ncbi::TMaskedQueryRegions mask

SSE2 reinitialization guard class.

BMFORCEINLINE sse_empty_guard() BMNOEXCEPT

BMFORCEINLINE ~sse_empty_guard() BMNOEXCEPT

static vector< string > arr

void sse2_copy_block(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

SSE2 block copy dst = *src.

unsigned sse2_xor_block_2way(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src1, const __m128i *BMRESTRICT src2) BMNOEXCEPT

3 operand XOR dst = *src1 ^ src2

bool sse2_or_block_5way(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src1, const __m128i *BMRESTRICT src2, const __m128i *BMRESTRICT src3, const __m128i *BMRESTRICT src4) BMNOEXCEPT

OR array elements against another 2 arrays dst |= *src1 | src2 | src3 | src4.

void sse2_stream_block(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

SSE2 block copy dst = *src.

void sse2_stream_block_unalign(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

SSE2 block copy (unaligned src) dst = *src.

unsigned sse2_sub_block(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

AND-NOT (SUB) array elements against another array dst &= ~*src.

void sse2_xor_arr_2_mask(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src, const __m128i *BMRESTRICT src_end, bm::word_t mask) BMNOEXCEPT

XOR array elements to specified mask dst = *src ^ mask.

void sse2_copy_block_unalign(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

SSE2 block copy (unaligned SRC) dst = *src.

unsigned sse2_lower_bound_scan_u32(const unsigned *BMRESTRICT arr, unsigned target, unsigned from, unsigned to) BMNOEXCEPT

lower bound (great or equal) linear scan in ascending order sorted array

unsigned sse2_xor_block(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

XOR block against another dst ^= *src.

bool sse2_or_arr_unal(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src, const __m128i *BMRESTRICT src_end) BMNOEXCEPT

OR array elements against another array (unaligned) dst |= *src.

unsigned sse2_and_block(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

AND blocks2 dst &= *src.

unsigned sse2_and_arr_unal(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src, const __m128i *BMRESTRICT src_end) BMNOEXCEPT

AND array elements against another array (unaligned) dst &= *src.

void sse2_andnot_arr_2_mask(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src, const __m128i *BMRESTRICT src_end, bm::word_t mask) BMNOEXCEPT

Inverts array elements and NOT them to specified mask dst = ~*src & mask.

bool sse2_or_block_3way(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src1, const __m128i *BMRESTRICT src2) BMNOEXCEPT

OR array elements against another 2 arrays dst |= *src1 | src2.

void sse2_set_block(__m128i *BMRESTRICT dst, bm::word_t value) BMNOEXCEPT

SSE2 block memset dst = value.

void sse2_invert_block(__m128i *BMRESTRICT dst) BMNOEXCEPT

Invert bit block dst = ~*dst or dst ^= *dst.

bool sse2_or_block(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src) BMNOEXCEPT

OR array elements against another array dst |= *src.

bool sse2_or_block_2way(__m128i *BMRESTRICT dst, const __m128i *BMRESTRICT src1, const __m128i *BMRESTRICT src2) BMNOEXCEPT

OR 2 blocks anc copy result to the destination dst = *src1 | src2.

BMFORCEINLINE __m128i sse2_or(__m128i a, __m128i b) BMNOEXCEPT

BMFORCEINLINE __m128i sse2_and(__m128i a, __m128i b) BMNOEXCEPT

const unsigned set_block_size

BMFORCEINLINE __m128i sse2_sub(__m128i a, __m128i b) BMNOEXCEPT

unsigned bit_scan_forward32(unsigned w) noexcept

unsigned short gap_word_t

BMFORCEINLINE __m128i sse2_xor(__m128i a, __m128i b) BMNOEXCEPT

const bm::gap_word_t * sse2_gap_sum_arr(const bm::gap_word_t *BMRESTRICT pbuf, unsigned sse_vect_waves, unsigned *sum) BMNOEXCEPT

Gap block population count (array sum) utility.

const GenericPointer< typename T::ValueType > T2 value

static __m128i _mm_setzero_si128()

static __m128i _mm_xor_si128(__m128i a, __m128i b)

static __m128i _mm_sub_epi16(__m128i a, __m128i b)

static void _mm_stream_si128(__m128i *p, __m128i a)

static __m128i _mm_add_epi16(__m128i a, __m128i b)

#define _mm_srli_epi32(a, imm)

static int _mm_movemask_epi8(__m128i a)

static __m128i _mm_cmpgt_epi32(__m128i a, __m128i b)

static __m128i _mm_loadu_si128(const __m128i *p)

static void _mm_store_si128(__m128i *p, __m128i a)

static __m128i _mm_cmpeq_epi8(__m128i a, __m128i b)

static void _mm_prefetch(const void *p, int i)

static __m128i _mm_load_si128(const __m128i *p)

static __m128i _mm_or_si128(__m128i, __m128i)

static __m128i _mm_sub_epi32(__m128i a, __m128i b)

static __m128i _mm_set1_epi32(int)

static __m128i _mm_andnot_si128(__m128i a, __m128i b)

static __m128i _mm_and_si128(__m128i, __m128i)

static __m128i _mm_cmpeq_epi32(__m128i, __m128i)

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