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

1 #ifndef BMALGO__H__INCLUDED__ 2 #define BMALGO__H__INCLUDED__ 25 #ifndef BM__H__INCLUDED__ 28 # error missing include (bm.h or bm64.h) 175 #define BM_SCANNER_OP(x) \ 176 if (0 != (block = blk_blk[j+x])) \ 178 if (BM_IS_GAP(block)) \ 180 ret = bm::for_each_gap_blk(BMGAP_PTR(block), (r+j+x)*bm::bits_in_block,\ 185 ret = bm::for_each_bit_blk(block, (r+j+x)*bm::bits_in_block,bit_functor); \ 187 if (ret < 0) return ret; \ 201 template

class

BV,

class

Func>

205 typedef typename

BV::size_type size_type;

207 const typename

BV::blocks_manager_type& bman = bv.get_blocks_manager();

208 bm::word_t

*** blk_root = bman.top_blocks_root();

213 unsigned

tsize = bman.top_block_size();

214 for

(

unsigned i

= 0;

< tsize; ++

)

237 #elif defined(BM64_SSE4) 265 template

class

BV,

class

Func>

267 typename

BV::size_type left,

268 typename

BV::size_type right,

305 for

(

unsigned i

= 0;

size

; ++

)

340 typedef typename

BV::size_type size_type;

342

func(handle_ptr, callback_ptr);

363 typename

BV::size_type left,

364 typename

BV::size_type right,

368 typedef typename

BV::size_type size_type;

370

func(handle_ptr, callback_ptr);

393 template

typename

BV,

typename

PairVect>

395 typename

BV::size_type rank,

399 typename

BV::size_type

first

last

, pos;

400 bool

found = bv.find_range(

first

last

);

408

target_v.push_back(pv);

415

found = bv.find_rank(rank,

first

, pos);

418

pv.first =

first

; pv.second = pos;

419

target_v.push_back(pv);

430

target_v.push_back(pv);

451 template

typename

BV>

467 void decompress

(BV& bv_target,

const

BV& bv_idx,

const

BV& bv_src);

477 void compress

(BV& bv_target,

const

BV& bv_idx,

const

BV& bv_src);

504 if

(&bv_idx == &bv_src)

512 typedef typename

BV::enumerator enumerator_t;

513

enumerator_t en_s = bv_src.first();

514

enumerator_t en_i = bv_idx.first();

519 for

(; en_i.valid(); )

523 i

= *en_i; s = *en_s;

530

ibuffer[b_size++] = r_idx++;

531 if

(b_size == n_buffer_cap)

544 size_type

r_dist = bv_idx.count_range(

+ 1, s);

551 for

(; s >

; ++r_idx)

577 if

(&bv_idx == &bv_src)

588 typedef typename

BV::enumerator enumerator_t;

589

enumerator_t en_s = bv_src.first();

590

enumerator_t en_i = bv_idx.first();

591 for

(; en_i.valid(); )

599

ibuffer[b_size++] =

;

600 if

(b_size == n_buffer_cap)

605

++en_i; ++en_s; ++r_idx;

615

en_i.skip(s - r_idx);

621

bv_idx.find_rank(rank,

, new_pos);

628

ibuffer[b_size++] = new_pos;

629 if

(b_size == n_buffer_cap)

634

++en_i; ++en_s; ++r_idx;

659

: bv_target_(bv_out),

664 int

add_bits(

size_type

arr_offset,

const unsigned char

* bits,

unsigned

bits_size)

666 for

(

unsigned i

= 0;

< bits_size; ++

)

671 size_type

r_idx = bv_index_.count_to(idx, bc_index_) - 1;

672

bv_target_.set_bit_no_check(r_idx);

683 size_type

r_idx = bv_index_.count_to(idx, bc_index_) - 1;

684

bv_target_.set_bit_no_check(r_idx);

698 if

(&bv_idx == &bv_src)

703

visitor_func func(bv_target, bv_idx, bc_idx);

#define FULL_BLOCK_FAKE_ADDR

#define FULL_SUB_BLOCK_REAL_ADDR

Bit manipulation primitives (internal)

Algorithms for rank compression of bit-vector.

void decompress(BV &bv_target, const BV &bv_idx, const BV &bv_src)

Rank decompression.

void compress_by_source(BV &bv_target, const BV &bv_idx, const rs_index_type &bc_idx, const BV &bv_src)

Source vector priority + index based rank.

void compress(BV &bv_target, const BV &bv_idx, const BV &bv_src)

Rank compression algorithm based on two palallel iterators/enumerators set of source vector gets re-m...

BV::rs_index_type rs_index_type

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

bool avx2_test_all_zero_wave(const void *ptr)

check if wave of pointers is all NULL

bool sse42_test_all_zero_wave(const void *ptr) noexcept

check if wave of pointers is all NULL

int(* bit_visitor_callback_type)(void *handle_ptr, bm::id_t bit_idx)

Callback type to visit (callback style) bits in bit-vector(s)

@ BM_SORTED

input set is sorted (ascending order)

void distance_operation(const BV &bv1, const BV &bv2, distance_metric_descriptor *dmit, distance_metric_descriptor *dmit_end) noexcept

Distance computing template function.

BV::size_type distance_and_operation(const BV &bv1, const BV &bv2) noexcept

Distance AND computing template function.

void distance_operation_any(const BV &bv1, const BV &bv2, distance_metric_descriptor *dmit, distance_metric_descriptor *dmit_end) noexcept

Distance screening template function.

@ COUNT_XOR

(A ^ B).count()

@ COUNT_SUB_AB

(A - B).count()

@ COUNT_AND

(A & B).count()

@ COUNT_OR

(A | B).count()

void rank_range_split(const BV &bv, typename BV::size_type rank, PairVect &target_v)

Algorithm to identify bit-vector ranges (splits) for the rank.

BV::size_type count_and(const BV &bv1, const BV &bv2) noexcept

Computes bitcount of AND operation of two bitsets.

int visit_each_bit(const BV &bv, void *handle_ptr, bit_visitor_callback_type callback_ptr)

bvector visitor scanner to traverse each 1 bit using C callback

int visit_each_bit_range(const BV &bv, typename BV::size_type left, typename BV::size_type right, void *handle_ptr, bit_visitor_callback_type callback_ptr)

bvector visitor scanner to traverse each bits in range (C callback)

bm::distance_metric_descriptor::size_type count_xor(const BV &bv1, const BV &bv2) noexcept

Computes bitcount of XOR operation of two bitsets.

BV::size_type count_sub(const BV &bv1, const BV &bv2) noexcept

Computes bitcount of SUB operation of two bitsets.

BV::size_type any_and(const BV &bv1, const BV &bv2) noexcept

Computes if there is any bit in AND operation of two bitsets.

int for_each_bit_range(const BV &bv, typename BV::size_type left, typename BV::size_type right, Func &bit_functor)

bit-vector range visitor to traverse each 1 bit

int for_each_bit(const BV &bv, Func &bit_functor)

bit-vector visitor scanner to traverse each 1 bit using C++ visitor

BV::size_type any_xor(const BV &bv1, const BV &bv2) noexcept

Computes if there is any bit in XOR operation of two bitsets.

BV::size_type any_or(const BV &bv1, const BV &bv2) noexcept

Computes if there is any bit in OR operation of two bitsets.

BV::size_type count_or(const BV &bv1, const BV &bv2) noexcept

Computes bitcount of OR operation of two bitsets.

BV::size_type any_sub(const BV &bv1, const BV &bv2) noexcept

Computes if there is any bit in SUB operation of two bitsets.

void xor_swap(W &x, W &y) noexcept

XOR swap two variables.

int for_each_bit_range_no_check(const BV &bv, typename BV::size_type left, typename BV::size_type right, Func &bit_functor)

Implementation of for_each_bit_range without boilerplave checks.

const unsigned set_sub_array_size

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

functor-adaptor for C-style callbacks

Functor for bit-copy (for testing)

bit_vistor_copy_functor(BV &bv)

bit_visitor_callback_type func_

int add_bits(size_type offset, const unsigned char *bits, unsigned size)

int add_range(size_type offset, size_type size)

Distance metric descriptor, holds metric code and result.

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