BitMagic-C++
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Bitvector Bit-vector container with runtime compression of bits. More...
#include <bm.h>
Data Structures | |
struct | allocation_policy |
memory allocation policy More... | |
class | bulk_insert_iterator |
Output iterator iterator designed to set "ON" bits based on input sequence of integers. More... | |
class | counted_enumerator |
Constant iterator designed to enumerate "ON" bits counted_enumerator keeps bitcount, ie number of ON bits starting from the position 0 in the bit string up to the currently enumerated bit. More... | |
class | enumerator |
Constant iterator designed to enumerate "ON" bits. More... | |
class | insert_iterator |
Output iterator iterator designed to set "ON" bits based on input sequence of integers (bit indeces). More... | |
class | iterator_base |
Base class for all iterators. More... | |
class | mem_pool_guard |
class | reference |
Class reference implements an object for bit assignment. More... | |
struct | statistics |
Statistical information about bitset's memory allocation details. More... | |
Public Types | |
enum | optmode { opt_none = 0, opt_free_0 = 1, opt_free_01 = 2, opt_compress = 3 } |
Optimization mode Every next level means additional checks (better compression vs time) More... | |
typedef Alloc | allocator_type |
typedef allocator_type::allocator_pool_type | allocator_pool_type |
typedef blocks_manager< Alloc > | blocks_manager_type |
typedef blocks_manager_type::block_idx_type | block_idx_type |
typedef bm::id_t | size_type |
typedef bool | const_reference |
typedef rs_index< allocator_type > | blocks_count |
typedef rs_index< allocator_type > | rs_index_type |
Public Member Functions | |
Construction, initialization, assignment | |
bvector (strategy strat=BM_BIT, const gap_word_t *glevel_len=bm::gap_len_table< true >::_len, size_type bv_size=bm::id_max, const Alloc &alloc=Alloc()) | |
Constructs bvector class. More... | |
bvector (size_type bv_size, strategy strat=BM_BIT, const gap_word_t *glevel_len=bm::gap_len_table< true >::_len, const Alloc &alloc=Alloc()) | |
Constructs bvector class. More... | |
bvector (const bvector< Alloc > &bvect) | |
Copy constructor. More... | |
bvector (const bvector< Alloc > &bvect, size_type left, size_type right) | |
Copy constructor for range copy [left..right]. More... | |
~bvector () BMNOEXCEPT | |
void | init () |
Explicit post-construction initialization. More... | |
bvector & | operator= (const bvector< Alloc > &bvect) |
Copy assignment operator. More... | |
bvector (bvector< Alloc > &&bvect) BMNOEXCEPT | |
Move constructor. More... | |
bvector (std::initializer_list< size_type > il) | |
Brace constructor. More... | |
bvector & | operator= (bvector< Alloc > &&bvect) BMNOEXCEPT |
Move assignment operator. More... | |
void | move_from (bvector< Alloc > &bvect) BMNOEXCEPT |
Move bvector content from another bvector. More... | |
void | swap (bvector< Alloc > &bvect) BMNOEXCEPT |
Exchanges content of bv and this bvector. More... | |
void | merge (bm::bvector< Alloc > &bvect) |
Merge/move content from another vector. More... | |
reference | operator[] (size_type n) |
bool | operator[] (size_type n) const BMNOEXCEPT |
void | operator&= (const bvector< Alloc > &bv) |
void | operator^= (const bvector< Alloc > &bv) |
void | operator|= (const bvector< Alloc > &bv) |
void | operator-= (const bvector< Alloc > &bv) |
bool | operator< (const bvector< Alloc > &bv) const |
bool | operator<= (const bvector< Alloc > &bv) const |
bool | operator> (const bvector< Alloc > &bv) const |
bool | operator>= (const bvector< Alloc > &bv) const |
bool | operator== (const bvector< Alloc > &bv) const BMNOEXCEPT |
bool | operator!= (const bvector< Alloc > &bv) const BMNOEXCEPT |
bvector< Alloc > | operator~ () const |
Alloc | get_allocator () const |
void | set_allocator_pool (allocator_pool_type *pool_ptr) BMNOEXCEPT |
Set allocator pool for local (non-th readed) memory cyclic(lots of alloc-free ops) opertations. More... | |
allocator_pool_type * | get_allocator_pool () BMNOEXCEPT |
Get curent allocator pool (if set) More... | |
Bit access/modification methods | |
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bool | set_bit (size_type n, bool val=true) |
Sets bit n. More... | |
bool | set_bit_and (size_type n, bool val=true) |
Sets bit n using bit AND with the provided value. More... | |
bool | inc (size_type n) |
Increment the specified element. More... | |
bool | set_bit_conditional (size_type n, bool val, bool condition) |
Sets bit n only if current value equals the condition. More... | |
bvector< Alloc > & | set (size_type n, bool val=true) |
Sets bit n if val is true, clears bit n if val is false. More... | |
bvector< Alloc > & | set () |
Sets every bit in this bitset to 1. More... | |
void | set (const size_type *ids, size_type ids_size, bm::sort_order so=bm::BM_UNKNOWN) |
Set list of bits in this bitset to 1. More... | |
void | keep (const size_type *ids, size_type ids_size, bm::sort_order so=bm::BM_UNKNOWN) |
Keep list of bits in this bitset, others are cleared. More... | |
void | clear (const size_type *ids, size_type ids_size, bm::sort_order so=bm::BM_UNKNOWN) |
clear list of bits in this bitset More... | |
void | set_bit_no_check (size_type n) |
Set bit without checking preconditions (size, etc) More... | |
bool | set_bit_no_check (size_type n, bool val) |
Set specified bit without checking preconditions (size, etc) More... | |
bvector< Alloc > & | set_range (size_type left, size_type right, bool value=true) |
Sets all bits in the specified closed interval [left,right] Interval must be inside the bvector's size. This method DOES NOT resize vector. More... | |
void | clear_range (size_type left, size_type right) |
Sets all bits to zero in the specified closed interval [left,right] Interval must be inside the bvector's size. This method DOES NOT resize vector. More... | |
void | keep_range (size_type left, size_type right) |
Sets all bits to zero outside of the closed interval [left,right] Expected result: 00000...0[left, right]0....0000. More... | |
void | copy_range (const bvector< Alloc > &bvect, size_type left, size_type right) |
Copy all bits in the specified closed interval [left,right]. More... | |
bool | clear_bit (size_type n) |
Clears bit n. More... | |
void | clear_bit_no_check (size_type n) |
Clears bit n without precondiion checks. More... | |
void | clear (bool free_mem=false) |
Clears every bit in the bitvector. More... | |
bvector< Alloc > & | reset () |
Clears every bit in the bitvector. More... | |
bvector< Alloc > & | flip (size_type n) |
Flips bit n. More... | |
bvector< Alloc > & | flip () |
Flips all bits. More... | |
insert_iterator | inserter () |
Size and capacity | |
By default bvector is dynamically sized, manual control methods available | |
size_type | size () const BMNOEXCEPT |
Returns bvector's capacity (number of bits it can store) More... | |
void | resize (size_type new_size) |
Change size of the bvector. More... | |
Population counting, ranks, ranges and intervals | |
size_type | count () const BMNOEXCEPT |
population cout (count of ON bits) More... | |
block_idx_type | count_blocks (unsigned *arr) const BMNOEXCEPT |
Computes bitcount values for all bvector blocks. More... | |
size_type | count_range (size_type left, size_type right, const rs_index_type &rs_idx) const BMNOEXCEPT |
Returns count of 1 bits in the given range [left..right] Uses rank-select index to accelerate the search. More... | |
size_type | count_range (size_type left, size_type right) const BMNOEXCEPT |
Returns count of 1 bits in the given range [left..right]. More... | |
bool | is_all_one_range (size_type left, size_type right) const BMNOEXCEPT |
Returns true if all bits in the range are 1s (saturated interval) Function uses closed interval [left, right]. More... | |
bool | any_range (size_type left, size_type right) const BMNOEXCEPT |
Returns true if any bits in the range are 1s (non-empty interval) Function uses closed interval [left, right]. More... | |
void | build_rs_index (rs_index_type *rs_idx, bvector< Alloc > *bv_blocks=0) const |
compute running total of all blocks in bit vector (rank-select index) More... | |
size_type | count_to (size_type n, const rs_index_type &rs_idx) const BMNOEXCEPT |
Returns count of 1 bits (population) in [0..right] range. More... | |
size_type | rank (size_type n, const rs_index_type &rs_idx) const BMNOEXCEPT |
Returns rank of specified bit position (same as count_to()) More... | |
size_type | rank_corrected (size_type n, const rs_index_type &rs_idx) const BMNOEXCEPT |
Returns rank corrceted by the requested border value (as -1) More... | |
size_type | count_to_test (size_type n, const rs_index_type &rs_idx) const BMNOEXCEPT |
popcount in [0..right] range if test(right) == true More... | |
size_type | recalc_count () BMNOEXCEPT |
void | forget_count () BMNOEXCEPT |
Bit access (read-only) | |
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bool | get_bit (size_type n) const BMNOEXCEPT |
returns true if bit n is set and false is bit n is 0. More... | |
bool | test (size_type n) const BMNOEXCEPT |
returns true if bit n is set and false is bit n is 0. More... | |
bit-shift and insert operations | |
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bool | shift_right () |
Shift right by 1 bit, fill with zero return carry out. More... | |
bool | shift_left () |
Shift left by 1 bit, fill with zero return carry out. More... | |
bool | insert (size_type n, bool value) |
Insert bit into specified position All the vector content after insert position is shifted right. More... | |
void | erase (size_type n) |
Erase bit in the specified position All the vector content after erase position is shifted left. More... | |
Check for empty-ness of container | |
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bool | any () const BMNOEXCEPT |
Returns true if any bits in this bitset are set, and otherwise returns false. More... | |
bool | none () const BMNOEXCEPT |
Returns true if no bits are set, otherwise returns false. More... | |
Scan and find bits and indexes | |
bool | find (size_type &pos) const BMNOEXCEPT |
Finds index of first 1 bit. More... | |
bool | find (size_type from, size_type &pos) const BMNOEXCEPT |
Find index of 1 bit starting from position. More... | |
size_type | get_first () const BMNOEXCEPT |
find first 1 bit in vector. Function may return 0 and this requires an extra check if bit 0 is actually set or bit-vector is empty More... | |
size_type | get_next (size_type prev) const BMNOEXCEPT |
Finds the number of the next bit ON. More... | |
size_type | extract_next (size_type prev) |
Finds the number of the next bit ON and sets it to 0. More... | |
bool | find_reverse (size_type &pos) const BMNOEXCEPT |
Finds last index of 1 bit. More... | |
bool | find_range (size_type &first, size_type &last) const BMNOEXCEPT |
Finds dynamic range of bit-vector [first, last]. More... | |
bool | find_rank (size_type rank, size_type from, size_type &pos) const BMNOEXCEPT |
Find bit-vector position for the specified rank(bitcount) More... | |
bool | find_rank (size_type rank, size_type from, size_type &pos, const rs_index_type &rs_idx) const BMNOEXCEPT |
Find bit-vector position for the specified rank(bitcount) More... | |
bool | select (size_type rank, size_type &pos, const rs_index_type &rs_idx) const BMNOEXCEPT |
select bit-vector position for the specified rank(bitcount) More... | |
Algebra of Sets operations | |
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bm::bvector< Alloc > & | bit_or (const bm::bvector< Alloc > &bv1, const bm::bvector< Alloc > &bv2, typename bm::bvector< Alloc >::optmode opt_mode) |
3-operand OR : this := bv1 OR bv2 More... | |
bm::bvector< Alloc > & | bit_xor (const bm::bvector< Alloc > &bv1, const bm::bvector< Alloc > &bv2, typename bm::bvector< Alloc >::optmode opt_mode) |
3-operand XOR : this := bv1 XOR bv2 More... | |
bm::bvector< Alloc > & | bit_and (const bm::bvector< Alloc > &bv1, const bm::bvector< Alloc > &bv2, typename bm::bvector< Alloc >::optmode opt_mode) |
3-operand AND : this := bv1 AND bv2 More... | |
bm::bvector< Alloc > & | bit_sub (const bm::bvector< Alloc > &bv1, const bm::bvector< Alloc > &bv2, typename bm::bvector< Alloc >::optmode opt_mode) |
3-operand SUB : this := bv1 MINUS bv2 SUBtraction is also known as AND NOT More... | |
bm::bvector< Alloc > & | bit_or (const bm::bvector< Alloc > &bv) |
2 operand logical OR More... | |
bm::bvector< Alloc > & | bit_and (const bm::bvector< Alloc > &bv, optmode opt_mode=opt_none) |
2 operand logical AND More... | |
bm::bvector< Alloc > & | bit_xor (const bm::bvector< Alloc > &bv) |
2 operand logical XOR More... | |
bm::bvector< Alloc > & | bit_sub (const bm::bvector< Alloc > &bv) |
2 operand logical SUB(AND NOT). Also known as MINUS. More... | |
bvector< Alloc > & | invert () |
Invert/NEG all bits It should be noted, invert is affected by size() if size is set - it only inverts [0..size-1] bits. More... | |
void | combine_operation (const bm::bvector< Alloc > &bvect, bm::operation opcode) |
perform a set-algebra operation by operation code More... | |
void | combine_operation_or (const bm::bvector< Alloc > &bvect) |
perform a set-algebra operation OR More... | |
void | combine_operation_and (const bm::bvector< Alloc > &bvect, optmode opt_mode) |
perform a set-algebra operation AND More... | |
void | combine_operation_sub (const bm::bvector< Alloc > &bvect) |
perform a set-algebra operation MINUS (AND NOT) More... | |
void | combine_operation_xor (const bm::bvector< Alloc > &bvect) |
perform a set-algebra operation XOR More... | |
Iterator-traversal methods | |
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enumerator | first () const |
Returns enumerator pointing on the first non-zero bit. More... | |
enumerator | end () const |
Returns enumerator pointing on the next bit after the last. More... | |
enumerator | get_enumerator (size_type pos) const |
Returns enumerator pointing on specified or the next available bit. More... | |
Memory management and compression | |
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void | calc_stat (struct bm::bvector< Alloc >::statistics *st) const BMNOEXCEPT |
Calculates bitvector statistics. More... | |
void | set_new_blocks_strat (strategy strat) |
Sets new blocks allocation strategy. More... | |
strategy | get_new_blocks_strat () const BMNOEXCEPT |
Returns blocks allocation strategy. More... | |
void | optimize (bm::word_t *temp_block=0, optmode opt_mode=opt_compress, statistics *stat=0) |
Optimize memory bitvector's memory allocation. More... | |
void | optimize_gap_size () |
Optimize sizes of GAP blocks. More... | |
void | set_gap_levels (const gap_word_t *glevel_len) |
Sets new GAP lengths table. All GAP blocks will be reallocated to match the new scheme. More... | |
bool | is_init () const BMNOEXCEPT |
Return true if bvector is initialized at all. More... | |
Comparison | |
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int | compare (const bvector< Alloc > &bvect) const BMNOEXCEPT |
Lexicographical comparison with a bitvector. More... | |
bool | equal (const bvector< Alloc > &bvect) const BMNOEXCEPT |
Equal comparison with an agr bit-vector. More... | |
bool | find_first_mismatch (const bvector< Alloc > &bvect, size_type &pos, size_type search_to=bm::id_max) const BMNOEXCEPT |
Find index of first bit different between this and the agr vector. More... | |
Friends | |
class | iterator_base |
class | enumerator |
template<class BV > | |
class | aggregator |
template<class BV > | |
class | operation_deserializer |
Open internals | |
void | combine_operation_with_block (block_idx_type nb, const bm::word_t *arg_blk, bool arg_gap, bm::operation opcode) |
const blocks_manager_type & | get_blocks_manager () const BMNOEXCEPT |
get access to memory manager (internal) Use only if you are BitMagic library More... | |
blocks_manager_type & | get_blocks_manager () BMNOEXCEPT |
get access to memory manager (internal) Use only if you are BitMagic library More... | |
static void | throw_bad_alloc () |
void | sync_size () |
Syncronize size if it got extended due to bulk import. More... | |
void | import (const size_type *ids, size_type ids_size, bm::sort_order sorted_idx) |
Import integers (set bits). More... | |
void | import_block (const size_type *ids, block_idx_type nblock, size_type start, size_type stop) |
Bitvector Bit-vector container with runtime compression of bits.
typedef allocator_type::allocator_pool_type bm::bvector< Alloc >::allocator_pool_type |
typedef Alloc bm::bvector< Alloc >::allocator_type |
typedef blocks_manager_type::block_idx_type bm::bvector< Alloc >::block_idx_type |
typedef rs_index<allocator_type> bm::bvector< Alloc >::blocks_count |
typedef blocks_manager<Alloc> bm::bvector< Alloc >::blocks_manager_type |
typedef bool bm::bvector< Alloc >::const_reference |
typedef rs_index<allocator_type> bm::bvector< Alloc >::rs_index_type |
typedef bm::id_t bm::bvector< Alloc >::size_type |
enum bm::bvector::optmode |
Optimization mode Every next level means additional checks (better compression vs time)
Enumerator | |
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opt_none | no optimization |
opt_free_0 | Free unused 0 blocks. |
opt_free_01 | Free unused 0 and 1 blocks. |
opt_compress | compress blocks when possible (GAP/prefix sum) |
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Constructs bvector class.
strat | - operation mode strategy, BM_BIT - default strategy, bvector use plain bitset blocks, (performance oriented strategy). BM_GAP - memory effitent strategy, bvector allocates blocks as array of intervals(gaps) and convert blocks into plain bitsets only when enthropy grows. |
glevel_len |
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bv_size |
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alloc | - alllocator for this instance |
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Copy constructor for range copy [left..right].
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bool bm::bvector< Alloc >::any | ( | ) | const |
Returns true if any bits in this bitset are set, and otherwise returns false.
Definition at line 2244 of file bm.h.
Referenced by DNA_FingerprintScanner::Find(), and bm::bvector<>::none().
bool bm::bvector< Alloc >::any_range | ( | size_type | left, |
size_type | right | ||
) | const |
Returns true if any bits in the range are 1s (non-empty interval) Function uses closed interval [left, right].
left | - index of first bit start checking |
right | - index of last bit |
Definition at line 2865 of file bm.h.
Referenced by add_object(), and main().
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bm::bvector< Alloc > & bm::bvector< Alloc >::bit_and | ( | const bm::bvector< Alloc > & | bv1, |
const bm::bvector< Alloc > & | bv2, | ||
typename bm::bvector< Alloc >::optmode | opt_mode | ||
) |
3-operand AND : this := bv1 AND bv2
bv1 | - Argument vector 1 |
bv2 | - Argument vector 2 |
opt_mode | - optimization compression (when it is performed on the fly it is faster than a separate call to optimize() |
Definition at line 5017 of file bm.h.
Referenced by bm::bvector<>::bit_and(), DemoAND(), bm::sparse_vector< unsigned, bm::bvector<> >::filter(), bm::bvector<>::keep(), bm::operator&(), and bm::bvector<>::operator&=().
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bm::bvector< Alloc > & bm::bvector< Alloc >::bit_or | ( | const bm::bvector< Alloc > & | bv1, |
const bm::bvector< Alloc > & | bv2, | ||
typename bm::bvector< Alloc >::optmode | opt_mode | ||
) |
3-operand OR : this := bv1 OR bv2
bv1 | - Argument vector 1 |
bv2 | - Argument vector 2 |
opt_mode | - optimization compression (when it is performed on the fly it is faster than a separate call to optimize() |
Definition at line 4809 of file bm.h.
Referenced by bm::bvector<>::bit_and(), bm::bvector<>::bit_or(), bm::bvector<>::bit_sub(), DemoOR(), bm::dynamic_range_clip_high(), bm::dynamic_range_clip_low(), main(), bm::operator|(), bm::bvector<>::operator|=(), and bm::sparse_vector_find_mismatch().
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bm::bvector< Alloc > & bm::bvector< Alloc >::bit_sub | ( | const bm::bvector< Alloc > & | bv1, |
const bm::bvector< Alloc > & | bv2, | ||
typename bm::bvector< Alloc >::optmode | opt_mode | ||
) |
3-operand SUB : this := bv1 MINUS bv2 SUBtraction is also known as AND NOT
bv1 | - Argument vector 1 |
bv2 | - Argument vector 2 |
opt_mode | - optimization compression (when it is performed on the fly it is faster than a separate call to optimize() |
Definition at line 5111 of file bm.h.
Referenced by bm::bvector<>::bit_sub(), bm::bvector<>::clear(), DemoSUB(), bm::operator-(), and bm::bvector<>::operator-=().
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bm::bvector< Alloc > & bm::bvector< Alloc >::bit_xor | ( | const bm::bvector< Alloc > & | bv1, |
const bm::bvector< Alloc > & | bv2, | ||
typename bm::bvector< Alloc >::optmode | opt_mode | ||
) |
3-operand XOR : this := bv1 XOR bv2
bv1 | - Argument vector 1 |
bv2 | - Argument vector 2 |
opt_mode | - optimization compression (when it is performed on the fly it is faster than a separate call to optimize() |
Definition at line 4906 of file bm.h.
Referenced by bm::bvector<>::bit_xor(), DemoXOR(), bm::operator^(), bm::bvector<>::operator^=(), and bm::sparse_vector_find_mismatch().
void bm::bvector< Alloc >::build_rs_index | ( | rs_index_type * | rs_idx, |
bvector< Alloc > * | bv_blocks = 0 |
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compute running total of all blocks in bit vector (rank-select index)
rs_idx | - [out] pointer to index / count structure |
bv_blocks | - [out] list of block ids in the vector (internal, optional) Function will fill full array of running totals |
Definition at line 2290 of file bm.h.
Referenced by bv_count_range_acc(), bv_count_to_acc(), and bv_count_to_range_acc().
void bm::bvector< Alloc >::calc_stat | ( | struct bm::bvector< Alloc >::statistics * | st | ) | const |
Calculates bitvector statistics.
st | - pointer on statistics structure to be filled in. |
Function fills statistics structure containing information about how this vector uses memory and estimation of max. amount of memory bvector needs to serialize itself.
Definition at line 3393 of file bm.h.
Referenced by calc_memory_footprint(), convert_bv2bvs(), generate_bvector(), bm::bvector<>::optimize(), bm::bvector<>::optimize_gap_size(), and print_statistics().
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void bm::bvector< Alloc >::clear | ( | const size_type * | ids, |
size_type | ids_size, | ||
bm::sort_order | so = bm::BM_UNKNOWN |
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clear list of bits in this bitset
This is equivalent of AND NOT (Set Substract), argument set as an array.
ids | - pointer on array of indexes to set |
ids_size | - size of the input (ids) |
so | - sort order (use BM_SORTED for faster load) |
Definition at line 3546 of file bm.h.
Referenced by bm::bvector<>::build_rs_index(), bv_count_and(), bm::bvector<>::combine_operation_and(), bm::bvector<>::copy_range(), DemoSUB(), bm::bvector<>::keep(), main(), bm::bvector<>::reset(), speed_test_bv_index(), speed_test_bvs_index(), speed_test_sv_index(), and speed_test_vect_index().
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Clears bit n without precondiion checks.
n | - bit's index to be cleaned. |
Definition at line 1211 of file bm.h.
Referenced by bm::basic_bmatrix< bm::bvector<> >::set_octet(), and bm::sparse_vector< unsigned, bm::bvector<> >::set_value_no_null().
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void bm::bvector< Alloc >::combine_operation | ( | const bm::bvector< Alloc > & | bvect, |
bm::operation | opcode | ||
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void bm::bvector< Alloc >::combine_operation_and | ( | const bm::bvector< Alloc > & | bvect, |
optmode | opt_mode | ||
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perform a set-algebra operation AND
Definition at line 5377 of file bm.h.
Referenced by bm::bvector<>::bit_and().
void bm::bvector< Alloc >::combine_operation_or | ( | const bm::bvector< Alloc > & | bvect | ) |
perform a set-algebra operation OR
Definition at line 5206 of file bm.h.
Referenced by bm::bvector<>::bit_or().
void bm::bvector< Alloc >::combine_operation_sub | ( | const bm::bvector< Alloc > & | bvect | ) |
perform a set-algebra operation MINUS (AND NOT)
Definition at line 5465 of file bm.h.
Referenced by bm::bvector<>::bit_sub().
void bm::bvector< Alloc >::combine_operation_with_block | ( | block_idx_type | nb, |
const bm::word_t * | arg_blk, | ||
bool | arg_gap, | ||
bm::operation | opcode | ||
) |
Definition at line 4792 of file bm.h.
Referenced by bm::bvector<>::combine_operation(), and bm::bvector<>::combine_operation_with_block().
void bm::bvector< Alloc >::combine_operation_xor | ( | const bm::bvector< Alloc > & | bvect | ) |
perform a set-algebra operation XOR
Definition at line 5278 of file bm.h.
Referenced by bm::bvector<>::bit_xor().
int bm::bvector< Alloc >::compare | ( | const bvector< Alloc > & | bvect | ) | const |
Lexicographical comparison with a bitvector.
Function compares current bitvector with the provided argument bit by bit and returns -1 if this bitvector less than the argument, 1 - greater, 0 - equal
Definition at line 3159 of file bm.h.
Referenced by convert_bv2bvs(), fingerprint_compare(), main(), bm::bvector<>::operator<(), bm::bvector<>::operator<=(), bm::bvector<>::operator>(), bm::bvector<>::operator>=(), and run_benchmark().
void bm::bvector< Alloc >::copy_range | ( | const bvector< Alloc > & | bvect, |
size_type | left, | ||
size_type | right | ||
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bvector< Alloc >::size_type bm::bvector< Alloc >::count | ( | ) | const |
population cout (count of ON bits)
Definition at line 2194 of file bm.h.
Referenced by bv_count_test(), convert_bv2vect(), main(), pre_heat(), print_bvector(), print_statistics(), bm::bvector<>::recalc_count(), run_benchmark(), and serialize_bvector().
bvector< Alloc >::block_idx_type bm::bvector< Alloc >::count_blocks | ( | unsigned * | arr | ) | const |
bvector< Alloc >::size_type bm::bvector< Alloc >::count_range | ( | size_type | left, |
size_type | right | ||
) | const |
bvector< Alloc >::size_type bm::bvector< Alloc >::count_range | ( | size_type | left, |
size_type | right, | ||
const rs_index_type & | rs_idx | ||
) | const |
Returns count of 1 bits in the given range [left..right] Uses rank-select index to accelerate the search.
left | - index of first bit start counting from |
right | - index of last bit |
rs_idx | - block count structure to accelerate search |
Definition at line 2959 of file bm.h.
Referenced by bv_count_range(), and bv_count_range_acc().
bvector< Alloc >::size_type bm::bvector< Alloc >::count_to | ( | size_type | n, |
const rs_index_type & | rs_idx | ||
) | const |
Returns count of 1 bits (population) in [0..right] range.
This operation is also known as rank of bit N.
n | - index of bit to rank |
rs_idx | - rank-select to accelerate search should be prepared using build_rs_index |
Definition at line 2533 of file bm.h.
Referenced by bv_count_to_acc(), bv_count_to_range_acc(), bm::bvector<>::count_range(), and bm::bvector<>::rank().
bvector< Alloc >::size_type bm::bvector< Alloc >::count_to_test | ( | size_type | n, |
const rs_index_type & | rs_idx | ||
) | const |
popcount in [0..right] range if test(right) == true
This is conditional rank operation, which is faster than test() plus count_to()
n | - index of bit to test and rank |
rs_idx | - rank-select index (block count structure to accelerate search) should be prepared using build_rs_index() |
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Returns enumerator pointing on the next bit after the last.
Definition at line 1776 of file bm.h.
Referenced by combine_or_test(), main(), speed_test_sv_index(), and speed_test_vect_index().
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Equal comparison with an agr bit-vector.
Definition at line 1883 of file bm.h.
Referenced by main(), bm::bvector<>::operator!=(), and bm::bvector<>::operator==().
void bm::bvector< Alloc >::erase | ( | size_type | n | ) |
Erase bit in the specified position All the vector content after erase position is shifted left.
n | - index of the bit to insert |
Definition at line 4555 of file bm.h.
Referenced by bm::bvector<>::shift_left().
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Finds the number of the next bit ON and sets it to 0.
prev | - Index of the previously found bit. |
bool bm::bvector< Alloc >::find | ( | size_type & | pos | ) | const |
Finds index of first 1 bit.
pos | - [out] index of the found 1 bit |
Definition at line 4035 of file bm.h.
Referenced by bm::bvector<>::find(), bm::bvector<>::find_first_mismatch(), bm::bvector<>::find_range(), and main().
bool bm::bvector< Alloc >::find | ( | size_type | from, |
size_type & | pos | ||
) | const |
Find index of 1 bit starting from position.
from | - position to start search from |
pos | - [out] index of the found 1 bit |
bool bm::bvector< Alloc >::find_first_mismatch | ( | const bvector< Alloc > & | bvect, |
size_type & | pos, | ||
size_type | search_to = bm::id_max |
||
) | const |
Find index of first bit different between this and the agr vector.
bvect | - argumnet vector to compare with |
pos | - [out] position of the first difference |
search_to | - search limiter [0..to] to avoid overscan (default: unlimited to the vectors end) |
Definition at line 3277 of file bm.h.
Referenced by bm::bvector<>::equal(), and main().
bool bm::bvector< Alloc >::find_range | ( | size_type & | first, |
size_type & | last | ||
) | const |
Finds dynamic range of bit-vector [first, last].
first | - index of the first found 1 bit |
last | - index of the last found 1 bit |
Definition at line 4081 of file bm.h.
Referenced by main().
bool bm::bvector< Alloc >::find_rank | ( | size_type | rank, |
size_type | from, | ||
size_type & | pos | ||
) | const |
Find bit-vector position for the specified rank(bitcount)
Rank based search, counts number of 1s from specified position until finds the ranked position relative to start from position. In other words: range population count between from and pos == rank.
rank | - rank to find (bitcount) |
from | - start positioon for rank search |
pos | - position with speciefied rank (relative to from position) |
bool bm::bvector< Alloc >::find_rank | ( | size_type | rank, |
size_type | from, | ||
size_type & | pos, | ||
const rs_index_type & | rs_idx | ||
) | const |
Find bit-vector position for the specified rank(bitcount)
Rank based search, counts number of 1s from specified position until finds the ranked position relative to start from position. In other words: range population count between from and pos == rank.
rank | - rank to find (bitcount) |
from | - start positioon for rank search |
pos | - position with speciefied rank (relative to from position) |
rs_idx | - rank-select index to accelarate search (should be prepared using build_rs_index) |
bool bm::bvector< Alloc >::find_reverse | ( | size_type & | pos | ) | const |
Finds last index of 1 bit.
pos | - index of the last found 1 bit |
Definition at line 3978 of file bm.h.
Referenced by bm::bvector<>::build_rs_index(), bm::bvector<>::clear(), bm::bvector<>::find_range(), bm::bvector<>::keep(), main(), and bm::bvector<>::sync_size().
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Returns enumerator pointing on the first non-zero bit.
Definition at line 1770 of file bm.h.
Referenced by bv2delta(), bv_counted_enumerator(), convert_bv2sv(), convert_bv2vect(), generate_random_subset(), main(), print_bvector(), print_sorted(), speed_test_bv_index(), speed_test_bvs_index(), speed_test_sv_index(), speed_test_vect_index(), and DNA_FingerprintScanner::TranslateResults().
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bool bm::bvector< Alloc >::get_bit | ( | size_type | n | ) | const |
returns true if bit n is set and false is bit n is 0.
n | - Index of the bit to check. |
Definition at line 3037 of file bm.h.
Referenced by bm::bvector<>::operator[](), and bm::bvector<>::test().
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get access to memory manager (internal) Use only if you are BitMagic library
Definition at line 1924 of file bm.h.
Referenced by bm::bvector<>::bit_and(), bm::bvector<>::bit_or(), bm::bvector<>::bit_sub(), bm::bvector<>::bit_xor(), and bm::basic_bmatrix< bm::bvector<> >::optimize_block().
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Returns enumerator pointing on specified or the next available bit.
Definition at line 1782 of file bm.h.
Referenced by bm::bvector<>::first().
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find first 1 bit in vector. Function may return 0 and this requires an extra check if bit 0 is actually set or bit-vector is empty
Definition at line 1531 of file bm.h.
Referenced by bm::bvector_mini< A >::compare(), and print_bvector().
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Returns blocks allocation strategy.
Definition at line 1818 of file bm.h.
Referenced by bm::bvector<>::inc(), and bm::bvector<>::set_bit_no_check().
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Finds the number of the next bit ON.
prev | - Index of the previously found bit. |
Definition at line 1540 of file bm.h.
Referenced by bm::bvector_mini< A >::compare(), and print_bvector().
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Import integers (set bits).
(Fast, no checks).
Definition at line 3634 of file bm.h.
Referenced by bm::bvector<>::clear(), bm::bvector< Alloc >::bulk_insert_iterator::flush(), bm::bvector<>::keep(), and bm::bvector< Alloc >::bulk_insert_iterator::operator=().
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Definition at line 3685 of file bm.h.
Referenced by bm::bvector<>::import().
bool bm::bvector< Alloc >::inc | ( | size_type | n | ) |
Increment the specified element.
Bit increment rules: 0 + 1 = 1 (no carry over) 1 + 1 = 0 (with carry over returned)
n | - index of the bit to be set |
Definition at line 3800 of file bm.h.
Referenced by bm::bvector<>::flip(), and bm::sparse_vector< unsigned, bm::bvector<> >::inc().
void bm::bvector< Alloc >::init | ( | ) |
Explicit post-construction initialization.
Definition at line 2123 of file bm.h.
Referenced by bm::bvector<>::build_rs_index(), bm::bvector< Alloc >::bulk_insert_iterator::bulk_insert_iterator(), bv_set_bit_no_check_test(), bm::bvector<>::bvector(), bm::bvector< Alloc >::insert_iterator::insert_iterator(), bm::basic_bmatrix< bm::bvector<> >::insert_octet(), load_snp_report(), main(), run_benchmark(), bm::basic_bmatrix< bm::bvector<> >::set_octet(), and vector_search().
bool bm::bvector< Alloc >::insert | ( | size_type | n, |
bool | value | ||
) |
Insert bit into specified position All the vector content after insert position is shifted right.
n | - index of the bit to insert |
value | - insert value |
Definition at line 4378 of file bm.h.
Referenced by bm::basic_bmatrix< bm::bvector<> >::insert_octet(), bm::sparse_vector< unsigned, bm::bvector<> >::insert_value_no_null(), and bm::bvector<>::shift_right().
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bvector< Alloc > & bm::bvector< Alloc >::invert | ( | ) |
Invert/NEG all bits It should be noted, invert is affected by size() if size is set - it only inverts [0..size-1] bits.
Definition at line 2987 of file bm.h.
Referenced by DemoINV(), bm::bvector<>::flip(), bm::bvector<>::operator~(), and bm::sparse_vector_find_mismatch().
bool bm::bvector< Alloc >::is_all_one_range | ( | size_type | left, |
size_type | right | ||
) | const |
Returns true if all bits in the range are 1s (saturated interval) Function uses closed interval [left, right].
left | - index of first bit start checking |
right | - index of last bit |
Definition at line 2781 of file bm.h.
Referenced by main().
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void bm::bvector< Alloc >::keep | ( | const size_type * | ids, |
size_type | ids_size, | ||
bm::sort_order | so = bm::BM_UNKNOWN |
||
) |
Keep list of bits in this bitset, others are cleared.
This is equivalent of AND (Set Intersect), argument set as an array.
ids | - pointer on array of indexes to set |
ids_size | - size of the input (ids) |
so | - sort order (use BM_SORTED for faster load) |
Definition at line 3518 of file bm.h.
Referenced by DemoAND().
void bm::bvector< Alloc >::keep_range | ( | size_type | left, |
size_type | right | ||
) |
void bm::bvector< Alloc >::merge | ( | bm::bvector< Alloc > & | bvect | ) |
Merge/move content from another vector.
Merge performs a logical OR operation, but the source vector is not immutable. Source content gets destroyed (memory moved) to create a union of two vectors. Merge operation can be more efficient than OR if argument is a temporary vector.
bvect | - [in, out] - source vector (NOT immutable) |
Definition at line 4724 of file bm.h.
Referenced by DemoOR(), and bm::sparse_vector< unsigned, bm::bvector<> >::merge().
void bm::bvector< Alloc >::move_from | ( | bvector< Alloc > & | bvect | ) |
Move bvector content from another bvector.
Definition at line 2132 of file bm.h.
Referenced by bm::bvector<>::merge(), and bm::bvector<>::operator=().
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void bm::bvector< Alloc >::optimize | ( | bm::word_t * | temp_block = 0 , |
optmode | opt_mode = opt_compress , |
||
statistics * | stat = 0 |
||
) |
Optimize memory bitvector's memory allocation.
Function analyze all blocks in the bitvector, compresses blocks with a regular structure, frees some memory. This function is recommended after a bulk modification of the bitvector using set_bit, clear_bit or logical operations.
Optionally function can calculate vector post optimization statistics
Definition at line 3071 of file bm.h.
Referenced by generate_bvector(), main(), make_BLOB(), bm::basic_bmatrix< bm::bvector<> >::optimize(), serialize_bvector(), speed_test_bv_index(), speed_test_bvs_index(), speed_test_sv_index(), and speed_test_vect_index().
void bm::bvector< Alloc >::optimize_gap_size | ( | ) |
Optimize sizes of GAP blocks.
This method runs an analysis to find optimal GAP levels for the specific vector. Current GAP compression algorithm uses several fixed GAP sizes. By default bvector uses some reasonable preset.
Definition at line 3117 of file bm.h.
Referenced by bm::sparse_vector< unsigned, bm::bvector<> >::optimize_gap_size().
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Returns rank of specified bit position (same as count_to())
n | - index of bit to rank |
rs_idx | - rank-select index |
Definition at line 1371 of file bm.h.
Referenced by bm::bvector< Alloc >::enumerator::skip(), and bm::bvector< Alloc >::enumerator::skip_to_rank().
bvector< Alloc >::size_type bm::bvector< Alloc >::rank_corrected | ( | size_type | n, |
const rs_index_type & | rs_idx | ||
) | const |
Returns rank corrceted by the requested border value (as -1)
This is rank function (bit-count) minus value of bit 'n' if bit-n is true function returns rank()-1 if false returns rank() faster than rank() + test().
n | - index of bit to rank |
rs_idx | - rank-select index |
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Clears every bit in the bitvector.
Definition at line 1225 of file bm.h.
Referenced by bv_set_bit_test(), and generate_test_set().
void bm::bvector< Alloc >::resize | ( | size_type | new_size | ) |
Change size of the bvector.
new_size | - new size in bits |
Definition at line 2256 of file bm.h.
Referenced by bm::bvector<>::clear(), convert_bv2sv(), DemoAND(), DemoINV(), DemoOR(), DemoSUB(), DemoXOR(), bm::bvector<>::keep(), bm::bvector< Alloc >::insert_iterator::operator=(), bm::bvector<>::operator=(), bm::bvector<>::operator[](), pick_benchmark_set(), bm::bvector<>::set_bit(), bm::bvector<>::set_bit_conditional(), bm::bvector<>::set_range(), bm::sparse_vector_find_first_mismatch(), bm::sparse_vector_find_mismatch(), and bm::bvector<>::sync_size().
bool bm::bvector< Alloc >::select | ( | size_type | rank, |
size_type & | pos, | ||
const rs_index_type & | rs_idx | ||
) | const |
select bit-vector position for the specified rank(bitcount)
Rank based search, counts number of 1s from specified position until finds the ranked position relative to start from position. Uses In other words: range population count between from and pos == rank.
rank | - rank to find (bitcount) |
pos | - position with speciefied rank (relative to from position) [out] |
rs_idx | - block count structure to accelerate rank search |
Definition at line 4225 of file bm.h.
Referenced by main().
bvector< Alloc > & bm::bvector< Alloc >::set | ( | ) |
Sets every bit in this bitset to 1.
Definition at line 3572 of file bm.h.
Referenced by bm::bvector<>::insert().
void bm::bvector< Alloc >::set | ( | const size_type * | ids, |
size_type | ids_size, | ||
bm::sort_order | so = bm::BM_UNKNOWN |
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) |
Set list of bits in this bitset to 1.
Method implements optimized bulk setting of multiple bits at once. The best results are achieved when the imput comes sorted. This is equivalent of OR (Set Union), argument set as an array.
ids | - pointer on array of indexes to set |
ids_size | - size of the input (ids) |
so | - sort order (use BM_SORTED for faster load) |
bvector< Alloc > & bm::bvector< Alloc >::set | ( | size_type | n, |
bool | val = true |
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) |
Sets bit n if val is true, clears bit n if val is false.
n | - index of the bit to be set |
val | - new bit value |
Definition at line 3581 of file bm.h.
Referenced by bm::bvector<>::build_rs_index(), bvector_bulk_set_test(), bm::sparse_vector< unsigned, bm::bvector<> >::clear(), DemoOR(), fill_bvector(), generate_bvector(), bm::sparse_vector< unsigned, bm::bvector<> >::import(), main(), pick_benchmark_set(), and run_benchmark().
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bool bm::bvector< Alloc >::set_bit | ( | size_type | n, |
bool | val = true |
||
) |
Sets bit n.
n | - index of the bit to be set. |
val | - new bit value |
Definition at line 3617 of file bm.h.
Referenced by bv_set_bit_test(), bm::bvector<>::clear_bit(), fill_bvector(), generate_random_vector(), and bm::bvector<>::set().
bool bm::bvector< Alloc >::set_bit_and | ( | size_type | n, |
bool | val = true |
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bool bm::bvector< Alloc >::set_bit_conditional | ( | size_type | n, |
bool | val, | ||
bool | condition | ||
) |
void bm::bvector< Alloc >::set_bit_no_check | ( | size_type | n | ) |
Set bit without checking preconditions (size, etc)
Fast set bit method, without safety net. Make sure you call bvector<>::init() before setting bits with this function.
n | - bit number |
Definition at line 3468 of file bm.h.
Referenced by bv_set_bit_no_check_test(), bm::bvector<>::bvector(), bm::bvector<>::clear_bit_no_check(), bm::bvector<>::erase(), bm::bvector<>::import(), bm::sparse_vector< unsigned, bm::bvector<> >::inc(), bm::bvector<>::insert(), bm::basic_bmatrix< bm::bvector<> >::insert_octet(), bm::bvector<>::invert(), load_snp_report(), main(), bm::bvector< Alloc >::insert_iterator::operator=(), run_benchmark(), bm::bvector<>::set_bit(), bm::basic_bmatrix< bm::bvector<> >::set_octet(), bm::sparse_vector< unsigned, bm::bvector<> >::set_value(), bm::sparse_vector< unsigned, bm::bvector<> >::set_value_no_null(), and vector_search().
bool bm::bvector< Alloc >::set_bit_no_check | ( | size_type | n, |
bool | val | ||
) |
void bm::bvector< Alloc >::set_gap_levels | ( | const gap_word_t * | glevel_len | ) |
Sets new GAP lengths table. All GAP blocks will be reallocated to match the new scheme.
glevel_len | - pointer on C-style array keeping GAP block sizes. |
Definition at line 3143 of file bm.h.
Referenced by bm::bvector<>::optimize_gap_size().
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bvector< Alloc > & bm::bvector< Alloc >::set_range | ( | size_type | left, |
size_type | right, | ||
bool | value = true |
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Sets all bits in the specified closed interval [left,right] Interval must be inside the bvector's size. This method DOES NOT resize vector.
left | - interval start |
right | - interval end (closed interval) |
value | - value to set interval in |
Definition at line 2158 of file bm.h.
Referenced by add_object(), bv_count_and(), bm::bvector<>::clear_range(), bm::bvector<>::combine_operation(), generate_bvector(), bm::sparse_vector< unsigned, bm::bvector<> >::import(), bm::sparse_vector< unsigned, bm::bvector<> >::join(), main(), bm::sparse_vector< unsigned, bm::bvector<> >::merge(), bm::bvector<>::resize(), bm::bvector<>::set(), and bm::bvector<>::set_range().
bool bm::bvector< Alloc >::shift_left | ( | ) |
bool bm::bvector< Alloc >::shift_right | ( | ) |
Shift right by 1 bit, fill with zero return carry out.
Definition at line 4360 of file bm.h.
Referenced by DNA_FingerprintScanner::Find().
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Returns bvector's capacity (number of bits it can store)
return current size of the vector (bits)
Definition at line 1258 of file bm.h.
Referenced by bm::bvector< Alloc >::insert_iterator::operator=(), bm::bvector<>::operator=(), print_bvector(), run_benchmark(), and bm::sparse_vector_find_mismatch().
void bm::bvector< Alloc >::swap | ( | bvector< Alloc > & | bvect | ) |
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Syncronize size if it got extended due to bulk import.
Definition at line 2277 of file bm.h.
Referenced by bm::bvector< Alloc >::bulk_insert_iterator::flush(), and bm::bvector<>::set().
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returns true if bit n is set and false is bit n is 0.
n | - Index of the bit to check. |
Definition at line 1440 of file bm.h.
Referenced by bm::bvector<>::any_range(), bm::bvector<>::count_range(), bm::bvector<>::erase(), bm::bvector<>::is_all_one_range(), load_snp_report(), main(), pick_benchmark_set(), and bm::bvector<>::shift_left().
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Definition at line 809 of file bm.h.
Referenced by bm::bvector<>::end(), and bm::bvector<>::get_enumerator().
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