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

{

(lhs); }

(

!= lhs.size_)

<

BVAlloc>

in_buf.byte_buf_ = 0;

this->

= in_buf.size_;

in_buf.size_ = in_buf.capacity_ = 0;

other.byte_buf_ = btmp;

this->

= other.byte_buf_; other.byte_buf_ = 0;

this->

= other.size_;

(

* in_buf,

in_size)

this->

= in_size;

*

(

new_size,

copy_content =

)

this->

= new_size;

tmp_buffer = *

;

this->

(tmp_buffer);

this->

= new_size;

*

(

new_size)

this->

= new_size;

std::logic_error(

);

BM_THROW(BM_ERR_BADALLOC););

this->

= new_size;

tmp_buffer = *

;

this->

(tmp_buffer);

this->

(tmp_buffer);

* p = allocator_type::allocate(words, 0);

<

Val,

BVAlloc,

trivial_type>

*p = this_data + (

* v_size);

*p = this_data + (

* v_size);

*p = this_data + (

* v_size);

constexpr (trivial_type)

constexpr (!trivial_type)

*p = this_data + (

* v_size);

constexpr (!trivial_type)

*p = this_data + (

* v_size);

*p =

.

() + (sz * v_size);

*p =

.

() + (sz * v_size);

*p =

.

() + (sz * v_size);

std::range_error(err_msg);

<

Val,

ROWS,

COLS,

BVAlloc>

(void) rows_in; (void) cols_in; (void) copy_content;

(

set_z=

)

<

Val,

BVAlloc>

(

set_z=

)

(copy_content && this->

())

tmp_matrix(rows_in, cols_in);

tmp_matrix.

(

);

this->

(tmp_matrix);

(size_type j = 0; j < csize; ++j)

[j] = other_row[j];

(

() != dhm.cols())

(

() != dhm.rows())

(dhm, dim_rows, dim_cols);

<

VECT_TYPE>

VECT_TYPE v0 = vect[

];

vect[

] = VECT_TYPE(remap_v);

<

VECT_TYPE>

VECT_TYPE v0 = vect[

];

vect[

] = VECT_TYPE(remap_v);

<

ACC>

<

Value,

BVAlloc,

trivial_type>

#define BM_ASSERT_THROW(x, xerrcode)

Bit manipulation primitives (internal)

unsigned char * byte_buf_

byte buffer pointer to hold data

bool equal(const byte_buffer_ptr &lhs) const noexcept

return true if content and size is the same

bool operator==(const byte_buffer_ptr &lhs) const noexcept

const unsigned char * data() const noexcept

const access to buffer memory

void set_buf(unsigned char *in_buf, size_t in_size) noexcept

Set buffer pointer.

byte_buffer_ptr() noexcept

unsigned char * data() noexcept

Get write access to buffer memory.

size_t size() const noexcept

Get buffer size.

const unsigned char * buf() const noexcept

Get read access to buffer memory.

size_t size_

current buffer size

byte_buffer_ptr(unsigned char *in_buf, size_t in_size) noexcept

construct byte buffer pointer

Byte buffer template, extention of byte_buffer_ptr memory management.

size_t alloc_factor_

number of blocks allocated for buffer

static size_t compute_words(size_t capacity) noexcept

compute number of words for the desired capacity

void swap(byte_buffer &other) noexcept

swap content with another buffer

size_t capacity() const noexcept

Get buffer capacity.

unsigned char * resize(size_t new_size, bool copy_content=true)

adjust current size (buffer content can be preserved)

void optimize()

try to shrink the capacity to more optimal size

byte_buffer(size_t in_capacity)

void reinit(size_t new_capacity)

reserve new capacity (buffer content NOT preserved, size set to 0)

byte_buffer(const byte_buffer &lhs)

byte_buffer & operator=(byte_buffer &&lhs) noexcept

Move assignment operator.

BVAlloc bv_allocator_type

void resize_no_check(size_t new_size) noexcept

adjust current size (no need to reallocate)

size_t capacity_

current capacity

void reallocate(size_t new_capacity)

reserve new capacity (buffer content NOT preserved, size set to 0)

void release()

Free underlying memory.

void move_from(byte_buffer &other) noexcept

take/move content from another buffer

void set_buf(unsigned char *buf, size_t size)

Override from the base class.

void allocate(size_t new_capacity)

void reserve(size_t new_capacity)

reserve new capacity (buffer content preserved)

byte_buffer(byte_buffer &&in_buf) noexcept

Move constructor.

void copy_from(const unsigned char *in_buf, size_t in_size)

copy data from an external buffer

void free_buffer()

Free mmemory.

size_t mem_usage() const noexcept

return memory consumtion

byte_buffer & operator=(const byte_buffer &lhs)

unsigned char * shrink(size_t new_size)

shrink current size without reallocation (buffer content preserved)

bv_allocator_type::block_allocator_type allocator_type

Heap allocated dynamic resizable scalar-type matrix.

bool equal_overlap(const dynamic_heap_matrix< Val, BVAlloc > &dhm) const noexcept

Approximate equals on the rows-columns overlap area.

void set(size_type row_idx, size_type col_idx, value_type v) noexcept

const value_type * row(size_type row_idx) const noexcept

buffer_type & get_buffer() noexcept

Get low-level buffer access.

const value_type & get(size_type row_idx, size_type col_idx) const noexcept

void swap(dynamic_heap_matrix &other) noexcept

bool equal(const dynamic_heap_matrix< Val, BVAlloc > &dhm) const noexcept

Check if two matrix objects matches on the content.

value_type get(size_type row_idx, size_type col_idx) noexcept

void move_from(dynamic_heap_matrix &other) noexcept

void free() noexcept

Free memory.

size_type rows() const noexcept

const buffer_type & get_buffer() const noexcept

Get low-level buffer access.

size_type cols() const noexcept

void remapz(VECT_TYPE *vect) const noexcept

void remap(VECT_TYPE *vect, size_type size) const noexcept

value_type * row(size_type row_idx) noexcept

BVAlloc bv_allocator_type

void set_zero() noexcept

memset all buffer to all zeroes

void replicate_triange() noexcept

copy values of the left triangle elements to the right triangle (operation specific to matrices with ...

static size_type size_in_bytes(size_type rows, size_type cols) noexcept

void init_resize(size_type rows_in, size_type cols_in)

bool is_init() const noexcept

void resize(size_type rows_in, size_type cols_in, bool copy_content=true)

dynamic_heap_matrix(size_type rows_in=0, size_type cols_in=0) noexcept

By default object is constructed but NOT allocated.

void copy_from(const dynamic_heap_matrix< value_type, bv_allocator_type > &other) noexcept

bm::byte_buffer< bv_allocator_type > buffer_type

size_type size_in_bytes() const noexcept

size_type row_size_in_bytes() const noexcept

void sum(ACC &acc, size_type row_idx) const noexcept

Sum of row elements.

bool equal_sz(const dynamic_heap_matrix< Val, BVAlloc > &dhm, size_type dim_rows, size_type dim_cols) const noexcept

void init(bool set_z=false)

Post construction allocation, initialization.

Heap allocated scalar-type matrix.

BVAlloc bv_allocator_type

buffer_type & get_buffer() noexcept

Get low-level buffer access.

void resize(size_type rows_in, size_type cols_in, bool copy_content=true)

value_type * row(size_type row_idx) noexcept

const buffer_type & get_buffer() const noexcept

Get low-level buffer access.

heap_matrix(bool init_buf)

bm::byte_buffer< bv_allocator_type > buffer_type

value_type get(size_type row_idx, size_type col_idx) const noexcept

heap_matrix() noexcept

By default object is constructed NOT allocated.

bool is_init() const noexcept

const value_type * row(size_type row_idx) const noexcept

void swap(heap_matrix &other) noexcept

void set_zero() noexcept

memset all buffer to all zeroes

void init(bool set_z=false)

Post construction allocation, initialization.

static size_t cols() noexcept

void move_from(heap_matrix &other) noexcept

static size_t rows() noexcept

Simple heap allocated vector based on bvector allocator.

value_type * data() const noexcept

void resize(size_type new_size)

vector resize

void resize_no_check(size_type new_size)

resize without content preservation or capacity verification

heap_vector(const heap_vector< Val, BVAlloc, trivial_type > &hv)

value_type & at(size_type pos)

size_type capacity() const noexcept

value_type & add()

Add element to the end of the vector, return reference.

size_type size() const noexcept

const value_type * begin() const noexcept

bm::byte_buffer< bv_allocator_type > buffer_type

void reset() noexcept

Quick resize to zero.

void push_back_no_check(const value_type &v) noexcept

Push back value without capacity check.

void push_back(const value_type &v)

push new element to the back of the vector

static size_type value_size() noexcept

void swap(heap_vector< Val, BVAlloc, trivial_type > &other) noexcept

const value_type & at(size_type pos) const

BVAlloc bv_allocator_type

bool empty() const noexcept

void reserve(size_type new_size)

heap_vector & operator=(const heap_vector< Val, BVAlloc, trivial_type > &hv)

value_type * resize_no_copy(size_type new_size)

resize without content preservation

const value_type & operator[](size_type pos) const noexcept

value_type & operator[](size_type pos) noexcept

buffer_type::size_type size_type

void throw_range_error(const char *err_msg) const

void resize_internal(size_type new_size)

Simple queue based on memory controlled dynamic vector.

heap_vector_type::size_type size_type

void reserve(size_type capacity)

Capacity reservation.

bool empty() const noexcept

Return true if queue has no elements.

bm::heap_vector< Value, bv_allocator_type, trivial_type > heap_vector_type

simple_queue & operator=(const simple_queue &)=delete

size_type size() const noexcept

bool try_pop(value_type &front_value) noexcept

Try to extract the front element from the queue.

const value_type & front() const noexcept

Return front element.

heap_vector_type queue_vector_

bool try_push(const value_type &v) noexcept

Try push into the queue if capacity allows.

BVAlloc bv_allocator_type

void push(const value_type &v)

Push value into the queue (with re-allocation)

void pop() noexcept

Pop the front element.

simple_queue(const simple_queue &)=delete

size_type front_idx_

index of the front element

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

XOR swap two variables.

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

GenericValue< UTF8<> > Value

GenericValue with UTF8 encoding.

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

static const sljit_gpr r1

static const sljit_gpr r2

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