BitMagic-C++
Modules | Data Structures | Functions
bvector<> algorithms

Set algebra algorithms using bit-vectors, arrays. Binary metrics and distances. Random sub-sets. More...

Collaboration diagram for bvector<> algorithms:

Modules

 Binary-distance metrics
 Distance metrics and algorithms to compute binary distances.
 

Data Structures

class  bm::rank_compressor< BV >
 Algorithms for rank compression of bit-vector. More...
 
class  bm::aggregator< BV >
 Algorithms for fast aggregation of a group of bit-vectors. More...
 
class  bm::random_subset< BV >
 
class  bm::sparse_vector_scanner< SV >
 algorithms for sparse_vector scan/search More...
 
class  bm::set2set_11_transform< SV >
 Integer set to set transformation (functional image in groups theory) https://en.wikipedia.org/wiki/Image_(mathematics) More...
 

Functions

template<class BV >
BV::size_type bm::count_and (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes bitcount of AND operation of two bitsets. More...
 
template<class BV >
BV::size_type bm::any_and (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes if there is any bit in AND operation of two bitsets. More...
 
template<class BV >
bm::distance_metric_descriptor::size_type bm::count_xor (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes bitcount of XOR operation of two bitsets. More...
 
template<class BV >
BV::size_type bm::any_xor (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes if there is any bit in XOR operation of two bitsets. More...
 
template<class BV >
BV::size_type bm::count_sub (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes bitcount of SUB operation of two bitsets. More...
 
template<class BV >
BV::size_type bm::any_sub (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes if there is any bit in SUB operation of two bitsets. More...
 
template<class BV >
BV::size_type bm::count_or (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes bitcount of OR operation of two bitsets. More...
 
template<class BV >
BV::size_type bm::any_or (const BV &bv1, const BV &bv2) BMNOEXCEPT
 Computes if there is any bit in OR operation of two bitsets. More...
 
template<class BV , class Func >
void bm::for_each_bit (const BV &bv, Func &bit_functor)
 bit-vector visitor scanner to traverse each 1 bit using C++ visitor More...
 
template<class BV , class Func >
void bm::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 More...
 
template<class BV >
void bm::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 More...
 
template<class BV >
void bm::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) More...
 
template<typename BV , typename PairVect >
void bm::rank_range_split (const BV &bv, typename BV::size_type rank, PairVect &target_v)
 Algorithm to identify bit-vector ranges (splits) for the rank. More...
 
template<class BV , class It >
void bm::combine_or (BV &bv, It first, It last)
 OR Combine bitvector and the iterable sequence. More...
 
template<class BV , class It >
void bm::combine_xor (BV &bv, It first, It last)
 XOR Combine bitvector and the iterable sequence. More...
 
template<class BV , class It >
void bm::combine_sub (BV &bv, It first, It last)
 SUB Combine bitvector and the iterable sequence. More...
 
template<class BV , class It >
void bm::combine_and_sorted (BV &bv, It first, It last)
 AND Combine bitvector and the iterable sequence. More...
 
template<class BV , class It >
void bm::combine_and (BV &bv, It first, It last)
 AND Combine bitvector and the iterable sequence. More...
 
template<class BV >
BV::size_type bm::count_intervals (const BV &bv)
 Compute number of bit intervals (GAPs) in the bitvector. More...
 
template<typename BV , class It >
void bm::export_array (BV &bv, It first, It last)
 Export bitset from an array of binary data representing the bit vector. More...
 
template<typename Agg , typename It >
void bm::aggregator_pipeline_execute (It first, It last)
 Experimental method ro run multiple aggregators in sync. More...
 

Detailed Description

Set algebra algorithms using bit-vectors, arrays. Binary metrics and distances. Random sub-sets.

Function Documentation

◆ aggregator_pipeline_execute()

template<typename Agg , typename It >
void bm::aggregator_pipeline_execute ( It  first,
It  last 
)

Experimental method ro run multiple aggregators in sync.

Pipeleine algorithm walts the sequence of iterators (pointers on aggregators) and run them all via aggregator<>::run_step() method

Parameters
first- iterator (pointer on aggregator)
last- iterator (pointer on aggregator)
Examples
xsample04.cpp.

Definition at line 491 of file bmaggregator.h.

References bm::set_sub_array_size.

Referenced by DNA_FingerprintScanner::FindCollection().

◆ any_and()

template<class BV >
BV::size_type bm::any_and ( const BV &  bv1,
const BV &  bv2 
)

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

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
non zero value if there is any bit

Definition at line 62 of file bmalgo.h.

References bm::COUNT_AND, bm::distance_operation_any(), and bm::distance_metric_descriptor::result.

◆ any_or()

template<class BV >
BV::size_type bm::any_or ( const BV &  bv1,
const BV &  bv2 
)

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

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
non zero value if there is any bit

Definition at line 165 of file bmalgo.h.

References bm::COUNT_OR, bm::distance_operation_any(), and bm::distance_metric_descriptor::result.

◆ any_sub()

template<class BV >
BV::size_type bm::any_sub ( const BV &  bv1,
const BV &  bv2 
)

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

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
non zero value if there is any bit

Definition at line 132 of file bmalgo.h.

References bm::COUNT_SUB_AB, bm::distance_operation_any(), and bm::distance_metric_descriptor::result.

◆ any_xor()

template<class BV >
BV::size_type bm::any_xor ( const BV &  bv1,
const BV &  bv2 
)

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

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
non zero value if there is any bit

Definition at line 97 of file bmalgo.h.

References bm::COUNT_XOR, bm::distance_operation_any(), and bm::distance_metric_descriptor::result.

◆ combine_and()

template<class BV , class It >
void bm::combine_and ( BV &  bv,
It  first,
It  last 
)

AND Combine bitvector and the iterable sequence.

Algorithm combines bvector with sequence of integers (represents another set). When the agrument set is sorted this method can give serious increase in performance.

Parameters
bv- destination bitvector
first- first element of the iterated sequence
last- last element of the iterated sequence
See also
combine_and_sorted
Examples
bvsetalgebra.cpp, and sample7.cpp.

Definition at line 1301 of file bmalgo_impl.h.

References bm::combine_or().

Referenced by bm::aggregator< bvector_type >::combine_and(), DemoAND(), and main().

◆ combine_and_sorted()

template<class BV , class It >
void bm::combine_and_sorted ( BV &  bv,
It  first,
It  last 
)

AND Combine bitvector and the iterable sequence.

Algorithm combines bvector with sorted sequence of integers (represents another set).

Parameters
bv- destination bitvector
first- first element of the iterated sequence
last- last element of the iterated sequence
Examples
sample7.cpp.

Definition at line 1269 of file bmalgo_impl.h.

References BM_ASSERT.

Referenced by main().

◆ combine_or()

template<class BV , class It >
void bm::combine_or ( BV &  bv,
It  first,
It  last 
)

OR Combine bitvector and the iterable sequence.

Algorithm combines bvector with sequence of integers (represents another set). When the agrument set is sorted this method can give serious increase in performance.

Parameters
bv- destination bitvector
first- first element of the iterated sequence
last- last element of the iterated sequence
Examples
bvsetalgebra.cpp, sample12.cpp, sample7.cpp, svsample06.cpp, and xsample01.cpp.

Definition at line 1016 of file bmalgo_impl.h.

References bm::block_range_scan(), BM_ASSERT, BMGAP_PTR, bm::gap_limit(), bm::gap_set_value(), bm::id_max, bm::set_block_mask, bm::set_block_shift, bm::set_word_mask, and bm::set_word_shift.

Referenced by bm::combine_and(), bm::aggregator< bvector_type >::combine_or(), combine_or_test(), DemoOR(), main(), speed_test_sv_index(), and speed_test_vect_index().

◆ combine_sub()

template<class BV , class It >
void bm::combine_sub ( BV &  bv,
It  first,
It  last 
)

SUB Combine bitvector and the iterable sequence.

Algorithm combines bvector with sequence of integers (represents another set). When the agrument set is sorted this method can give serious increase in performance.

Parameters
bv- destination bitvector
first- first element of the iterated sequence
last- last element of the iterated sequence
Examples
bvsetalgebra.cpp, and sample7.cpp.

Definition at line 1184 of file bmalgo_impl.h.

References bm::block_range_scan(), BM_ASSERT, BMGAP_PTR, bm::gap_limit(), bm::gap_set_value(), bm::gap_test_unr(), bm::id_max, bm::set_block_mask, bm::set_block_shift, bm::set_word_mask, and bm::set_word_shift.

Referenced by DemoSUB(), and main().

◆ combine_xor()

template<class BV , class It >
void bm::combine_xor ( BV &  bv,
It  first,
It  last 
)

XOR Combine bitvector and the iterable sequence.

Algorithm combines bvector with sequence of integers (represents another set). When the agrument set is sorted this method can give serious increase in performance.

Parameters
bv- destination bitvector
first- first element of the iterated sequence
last- last element of the iterated sequence
Examples
bvsetalgebra.cpp.

Definition at line 1097 of file bmalgo_impl.h.

References bm::block_range_scan(), BM_ASSERT, BMGAP_PTR, bm::gap_limit(), bm::gap_set_value(), bm::gap_test_unr(), bm::id_max, bm::set_block_mask, bm::set_block_shift, bm::set_word_mask, and bm::set_word_shift.

Referenced by DemoXOR().

◆ count_and()

template<class BV >
BV::size_type bm::count_and ( const BV &  bv1,
const BV &  bv2 
)

Computes bitcount of AND operation of two bitsets.

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
bitcount of the result
Examples
sample11.cpp, sample9.cpp, and xsample07a.cpp.

Definition at line 49 of file bmalgo.h.

References bm::distance_and_operation().

Referenced by assign_to_best_cluster(), bv_count_and(), compute_and_sim_row(), CSeqGroup::count_and_union_sync(), and main().

◆ count_intervals()

template<class BV >
BV::size_type bm::count_intervals ( const BV &  bv)

Compute number of bit intervals (GAPs) in the bitvector.

Algorithm traverses bit vector and count number of uninterrupted intervals of 1s and 0s.

For example: 
  empty vector   - 1 interval
  00001111100000 - gives us 3 intervals
  10001111100000 - 4 intervals
  00000000000000 - 1 interval
  11111111111111 - 1 interval
Returns
Number of intervals

Definition at line 1325 of file bmalgo_impl.h.

References bm::for_each_block(), and bm::id_max.

◆ count_or()

template<class BV >
BV::size_type bm::count_or ( const BV &  bv1,
const BV &  bv2 
)

Computes bitcount of OR operation of two bitsets.

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
bitcount of the result

Definition at line 149 of file bmalgo.h.

References bm::COUNT_OR, bm::distance_operation(), and bm::distance_metric_descriptor::result.

◆ count_sub()

template<class BV >
BV::size_type bm::count_sub ( const BV &  bv1,
const BV &  bv2 
)

Computes bitcount of SUB operation of two bitsets.

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
bitcount of the result

Definition at line 115 of file bmalgo.h.

References bm::COUNT_SUB_AB, bm::distance_operation(), and bm::distance_metric_descriptor::result.

◆ count_xor()

template<class BV >
bm::distance_metric_descriptor::size_type bm::count_xor ( const BV &  bv1,
const BV &  bv2 
)

Computes bitcount of XOR operation of two bitsets.

Parameters
bv1- Argument bit-vector.
bv2- Argument bit-vector.
Returns
bitcount of the result
Examples
sample9.cpp.

Definition at line 81 of file bmalgo.h.

References bm::COUNT_XOR, bm::distance_operation(), and bm::distance_metric_descriptor::result.

Referenced by main().

◆ export_array()

template<typename BV , class It >
void bm::export_array ( BV &  bv,
It  first,
It  last 
)

Export bitset from an array of binary data representing the bit vector.

Input array can be array of ints, chars or other native C types. Method works with iterators, which makes it compatible with STL containers and C arrays

Parameters
bv- destination bitvector
first- first element of the iterated sequence
last- last element of the iterated sequence

Definition at line 1359 of file bmalgo_impl.h.

References BM_ASSERT, bm::BM_BIT, bm::set_block_size, and bm::set_total_blocks.

◆ for_each_bit()

template<class BV , class Func >
void bm::for_each_bit ( const BV &  bv,
Func &  bit_functor 
)

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

Parameters
bv- bit vector to scan
bit_functor- visitor: should support add_bits(), add_range()
See also
for_each_bit_range visit_each_bit

Definition at line 200 of file bmalgo.h.

References BM_SCANNER_OP, FULL_BLOCK_FAKE_ADDR, FULL_SUB_BLOCK_REAL_ADDR, bm::set_sub_array_size, and bm::sse42_test_all_zero_wave().

Referenced by bm::rank_compressor< bvector_type >::compress_by_source(), and bm::visit_each_bit().

◆ for_each_bit_range()

template<class BV , class Func >
void bm::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

Parameters
bv- bit vector to scan
right- start of closed interval [from..to]
left- end of close interval [from..to]
bit_functor- visitor: should support add_bits(), add_range()
See also
for_each_bit

Definition at line 264 of file bmalgo.h.

References BM_ASSERT, bm::for_each_bit_range_no_check(), bm::id_max, and bm::xor_swap().

Referenced by bm::visit_each_bit_range().

◆ rank_range_split()

template<typename BV , typename PairVect >
void bm::rank_range_split ( const BV &  bv,
typename BV::size_type  rank,
PairVect &  target_v 
)

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

Rank range split algorithm walks the bit-vector to create list of non-overlapping ranges [s1..e1],[s2..e2]...[sN...eN] with requested (rank) number of 1 bits. All ranges should be the same popcount weight, except the last one, which may have less. Scan is progressing from left to right so result ranges will be naturally sorted.

Parameters
bv- bit vector to perform the range split scan
rank- requested number of bits in each range if 0 it will create single range [first..last] to cover the whole bv
target_v- [out] STL(or STL-like) vector of pairs to keep pairs results
Examples
sample24.cpp, xsample07.cpp, and xsample07a.cpp.

Definition at line 411 of file bmalgo.h.

Referenced by compute_jaccard_clusters(), count_kmers_parallel(), and main().

◆ visit_each_bit()

template<class BV >
void bm::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

Parameters
bv- bit vector to scan
handle_ptr- handle to private memory used by callback
callback_ptr- callback function
See also
bit_visitor_callback_type

Definition at line 356 of file bmalgo.h.

References bm::for_each_bit().

◆ visit_each_bit_range()

template<class BV >
void bm::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)

Parameters
bv- bit vector to scan
left- from [left..right]
right- to [left..right]
handle_ptr- handle to private memory used by callback
callback_ptr- callback function
See also
bit_visitor_callback_type for_each_bit

Definition at line 380 of file bmalgo.h.

References bm::for_each_bit_range().