Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 123]

Cbm::_copyright< T >	Internal structure
Cbm::agg_run_options< OBvects, OCounts, OSearchMasks >	Aggregation options to control execution Default settings are to support only result bit-vector filters
Cbm::aggregator< BV >	Algorithms for fast aggregation of a group of bit-vectors
Cbm::all_set< T >	Structure carries pointer on bit block with all bits 1
Cbm::all_set< T >::all_set_block
Cbm::alloc_pool< BA, PA >	Allocation pool object
Cbm::bvector< Alloc >::allocation_policy	Memory allocation policy
Cbm::and_func	And functor
Cbm::aggregator< BV >::arena	Temporary operations vectors
Cbm::aggregator< BV >::arg_groups	Aggregator arg groups
Cbm::rsc_sparse_vector< Val, SV >::back_insert_iterator	Back insert iterator implements buffered insert, faster than generic access assignment
Cbm::sparse_vector< Val, BV >::back_insert_iterator	Back insert iterator implements buffered insert, faster than generic access assignment
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::back_insert_iterator	Back insert iterator implements buffered insert, faster than generic access assignment
Cbm::base_sparse_vector< Val, BV, MAX_SIZE >	Base class for bit-transposed(bit-sliced) sparse vector construction
Cbm::sparse_vector< unsigned, bm::bvector<> >
Cbm::sparse_vector< unsigned char, bm::bvector<> >
Cbm::sparse_vector< unsigned, bvector_type >
Cbm::sparse_vector< int, bm::bvector<> >
Cbm::sparse_vector< bm::id_t, bm::bvector<> >
Cbm::sparse_vector< unsigned short, bvector_type >
Cbm::str_sparse_vector< char, bm::bvector<>, 64 >
Cbm::str_sparse_vector< char, bvector_type, 32 >
Cbm::str_sparse_vector< char, bvector_type, 3 >
Cbm::str_sparse_vector< char, bvector_type, 5 >
Cbm::str_sparse_vector< char, bvector_type, 8 >
Cbm::str_sparse_vector< char, bvector_type, 16 >
Cbm::base_sparse_vector< CharType, BV, STR_SIZE >
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >	Succinct sparse vector for strings with compression using bit-slicing ( transposition) method
Cbm::base_sparse_vector< Val, BV, 1 >
Cbm::sparse_vector< Val, BV >	Succinct sparse vector with runtime compression using bit-slicing / transposition method
Cbm::basic_bmatrix< BV >	Basic dense bit-matrix class
Cbm::bit_AND< W >	Bit AND functor
Cbm::bit_ASSIGN< W >	Bit ASSIGN functor
Cbm::bit_block_t	Bit-block array wrapped into union for correct interpretation of 32-bit vs 64-bit access vs SIMD
Cbm::bit_COUNT< W >	Bit COUNT functor
Cbm::bit_COUNT_A< W >	Bit COUNT A functor
Cbm::bit_COUNT_AND< W >	Bit COUNT AND functor
Cbm::bit_COUNT_B< W >	Bit COUNT B functor
Cbm::bit_COUNT_OR< W >	Bit COUNT OR functor
Cbm::bit_COUNT_SUB_AB< W >	Bit COUNT SUB AB functor
Cbm::bit_COUNT_SUB_BA< W >	Bit SUB BA functor
Cbm::bit_count_table< T >	Structure to aid in counting bits table contains count of bits in 0-255 diapason of numbers
Cbm::bit_COUNT_XOR< W >	Bit COUNT XOR functor
Cbm::bit_decode_cache	Bit-decode cache structure
Cbm::bit_grabber< T, BPC >
Cbm::bit_grabber< unsigned char, 8 >
Cbm::bit_grabber< unsigned short, 16 >
Cbm::bit_grabber< unsigned, 32 >
Cbm::bit_in< TDecoder >	Byte based reader for un-aligned bit streaming
Cbm::bit_OR< W >	Bit OR functor
Cbm::bit_out< TEncoder >	Byte based writer for un-aligned bit streaming
Cbm::bit_SUB< W >	Bit SUB functor
Cbm::bit_trans_grabber< T, BPC, BPS >
Cbm::bit_visitor_back_inserter_adaptor< BII, size_type >	Functor-adaptor for back-inserter
Cbm::bit_visitor_callback_adaptor< VCBT, size_type >	Functor-adaptor for C-style callbacks
Cbit_visitor_functor	Visitor calss for bm::for_each_bit() algorithm It is NOT a classic functor (with function call operator() overload) For efficiency it needs to support two methods: add_bits and add_range which corresponds to different internal methods of representation of sets in the bm::bvector<> (bit-stream and D-GAP/RLE representation)
Cbm::bit_vistor_copy_functor< BV >	Functor for bit-copy (for testing)
Cbm::bit_XOR< W >	Bit XOR functor
Cbm::bvector< Alloc >::iterator_base::bitblock_descr	Bit-block descriptor
Cbm::bitblock_get_adapter	Bit-block get adapter, takes bitblock and represents it as a get_32() accessor function
Cbm::bitblock_store_adapter	Bit-block store adapter, takes bitblock and saves results into it
Cbm::bitblock_sum_adapter	Bit-block sum adapter, takes values and sums it /internal
Cbm::block_allocator	Default malloc based bitblock allocator class
Cbm::bvector< Alloc >::iterator_base::block_descr
Cbm::block_match_chain< BLOCK_IDX >	XOR match chain
Cbm::block_set_table< T >	Structure keeps all-left/right ON bits masks
Cbm::block_waves_xor_descr	Structure to compute XOR gap-count profile by sub-block waves
Cbm::block_xor_match_descr	Capture the XOR filter results (xor block against ref.block)
Cbm::globals< T >::bo
Cbm::serializer< BV >::bookmark_state	Bookmark state structure
Cbm::bvector< Alloc >::bulk_insert_iterator	Output iterator iterator designed to set "ON" bits based on input sequence of integers
Cbm::bit_block_t::bunion_t
Cbm::bv_arena_statistics	Structure with statistical information about memory allocation for arena based vectors
Cbv_index
Cbm::bv_ref_vector< BV >	List of reference bit-vectors with their true index associations
Cbm::bv_statistics	Structure with statistical information about memory allocation footprint, serialization projection, number of vectors
Cbm::bvector< Alloc >::statistics	Statistical information about bitset's memory allocation details
Cbm::rsc_sparse_vector< Val, SV >::statistics
Cbm::sparse_vector< Val, BV >::statistics
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::statistics
Cbm::bvector< Alloc >	Bitvector Bit-vector container with runtime compression of bits
Cbm::bvector_mini< A >	Bitvector class with very limited functionality
Cbm::bvmini< N >	Mini bit-vector for auxiliary purposes
Cbm::bvps_addr_resolver< BV >	Bit-bector prefix sum address resolver using bit-vector prefix sum as a space compactor
Cbvs_index
Cbm::chrono_taker< TOut >	Utility class to collect performance measurements and statistics
CCKMerAcc	Utility class to accumulate cahnges to cluster before commiting it (mutex syncronous operation)
Cbm::compressed_collection< Value, BV >	Compressed (sparse collection of objects)
Cbm::compressed_collection< serializer< BV >::buffer, BV >
Cbm::compressed_buffer_collection< BV >	Compressed (sparse collection of objects)
Cbm::compressed_collection_deserializer< CBC >	Deseriaizer for compressed collections
Cbm::compressed_collection_serializer< CBC >	Seriaizer for compressed collections
Cbm::compute_sim_matrix_plan_builder< BV >	Parallel plan builder for the XOR filter scanner
Cbm::conditional< b >	Ad-hoc conditional expressions
Cbm::conditional< false >
Cbm::rsc_sparse_vector< Val, SV >::const_iterator	Const iterator to traverse the rsc sparse vector
Cbm::sparse_vector< Val, BV >::const_iterator	Const iterator to traverse the sparse vector
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::const_iterator	Const iterator to do quick traverse of the sparse vector
Cbm::copy_to_array_functor< B >	Adaptor to copy 1 bits to array
CCounting_JobFunctor< DNA_Scan >	K-mer counting job functor class using bm::aggregator<>
CCSeqClusters
CCSeqGroup	Group (clustrer) of sequences
CCSequenceColl	Collection of sequences and k-mer fingerprint vectors
Cbm::d_copy_func< T >	D-Gap copy functor
Cdata_model	Data frame object, sued to buid succinct data model
Cdbg_block_allocator
Cdbg_ptr_allocator
Cbm::DeBruijn_bit_position< T >	DeBruijn majic table
Cbm::decoder_base	Base class for all decoding functionality
Cbm::decoder	Class for decoding data from memory buffer
Cbm::decoder_little_endian	Class for decoding data from memory buffer
Cbm::decoder_range_adapter< DEC >	Adapter to get words from a range stream (see range serialized bit-block)
Cbm::deseriaizer_base< DEC, BLOCK_IDX >	Base deserialization class
Cbm::deserializer< BV, bm::decoder_little_endian >
Cbm::deserializer< BV, bm::decoder_big_endian >
Cbm::serial_stream_iterator< bm::decoder, block_idx_type >
Cbm::serial_stream_iterator< bm::decoder_big_endian, block_idx_type >
Cbm::serial_stream_iterator< bm::decoder_little_endian, block_idx_type >
Cbm::serial_stream_iterator< DEC, BLOCK_IDX >	Serialization stream iterator
Cbm::deseriaizer_base< bm::decoder, BV::block_idx_type >
Cbm::deserializer< BV, bm::decoder >
Cbm::deseriaizer_base< bm::decoder, bvector_type::block_idx_type >
Cbm::deserializer< bvector_type, bm::decoder >
Cbm::deseriaizer_base< bm::decoder_big_endian, bvector_type::block_idx_type >
Cbm::deserializer< bvector_type, bm::decoder_big_endian >
Cbm::deseriaizer_base< bm::decoder_little_endian, bvector_type::block_idx_type >
Cbm::deserializer< bvector_type, bm::decoder_little_endian >
Cbm::deseriaizer_base< DEC, BV::block_idx_type >
Cbm::deserializer< BV, DEC >	Deserializer for bit-vector
Cbm::bvector< Alloc >::iterator_base::dgap_descr	Information about current DGAP block
Cbm::distance_metric_descriptor	Distance metric descriptor, holds metric code and result
CDNA_FingerprintScanner	Utility for keeping all DNA finger print vectors and search using various techniques
Cbm::encoder	Memory encoding
Cbm::first_bit_table< T >	Structure keeps index of first right 1 bit for every byte
Cbm::gamma_decoder< T, TBitIO >	Elias Gamma decoder
Cbm::gamma_encoder< T, TBitIO >	Functor for Elias Gamma encoding
Cbm::gap_len_table< T >	Default GAP lengths table
Cbm::gap_len_table_min< T >	Alternative GAP lengths table. Good for for memory saver mode and very sparse bitsets
Cbm::gap_len_table_nl< T >	Non-linear size growth GAP lengths table
Cgap_len_table_sparse< T >
Cbm::gap_transpose_engine< GT, BT, BLOCK_SIZE >	Bit-plane splicing of a GAP block
Cbm::set2set_11_transform< SV >::gather_buffer< BSIZE >
Cbm::globals< T >	Internal structure
Cbm::bvector< Alloc >::insert_iterator	Output iterator iterator designed to set "ON" bits based on input sequence of integers (bit indeces)
Cbm::interval_enumerator< BV >	Forward iterator class to traverse bit-vector as ranges
Cbm::rsc_sparse_vector< Val, SV >::is_dynamic_splices
Cbm::sparse_vector< Val, BV >::is_dynamic_splices
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::is_dynamic_splices
Cbm::is_lock_noexcept< T >	"noexcept" traits detection for T::lock()
Cbm::rsc_sparse_vector< Val, SV >::is_remap_support
Cbm::sparse_vector< Val, BV >::is_remap_support
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::is_remap_support
Cbm::rsc_sparse_vector< Val, SV >::is_rsc_support
Cbm::sparse_vector< Val, BV >::is_rsc_support
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::is_rsc_support
Cbm::bvector< Alloc >::iterator_base	Base class for all iterators
Cbm::bvector< Alloc >::enumerator	Constant iterator designed to enumerate "ON" bits
Cbm::bvector< Alloc >::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
Cbm::iterator_deserializer< BV, SerialIterator >	Iterator to walk forward the serialized stream
Cbm::lock_guard< Lock >	Simple scoped lock guard
Cbm::lzcnt_table< T >	Structure for LZCNT constants (4-bit)
Cbm::match_pair	XOR match pair
Cbm::mem_alloc< BA, PA, APool >	BM style allocator adapter
Cbm::miniset< A, N >	Template class implements memory saving set functionality
Cbm::operation_deserializer< BV >	Deserializer, performs logical operations between bit-vector and serialized bit-vector
Cbm::operation_functions< T >
Cbm::optimize_plan_builder< SVect, Lock >	Builder class to prepare a batch of tasks for parallel optimization of a sparse vector
Cbm::or_func	Or functor
Cbm::pad0_struct	Empty padding
Cbm::pad60_struct	Pad 60 bytes so that the final ocupiles 64 bytes (1 cache line)
Cbm::pair< First, Second >	Pair type
Cbm::aggregator< BV >::pipeline< Opt >	Pipeline vector for running a group of aggregation operations on a family of vectors
Cbm::sparse_vector_scanner< SV, S_FACTOR >::pipeline< Opt >	Pipeline to run multiple searches against a particular SV faster using cache optimizations
Cbm::aggregator< BV >::pipeline_bcache	Block cache for pipeline execution
Cbm::pointer_pool_array	Pool of pointers to buffer cyclic allocations
Cbm::ptr_allocator	Default malloc based bitblock allocator class
Cbm::ptr_guard< T >	Mini auto-pointer for internal memory management
Cbm::ptr_payload_t	Helper union to interpret pointer as integers
Cbm::queue_sync< Value, Lock >	Thread-sync queue with MT access protecion
Cbm::random_subset< BV >
Cbm::rank_compressor< BV >	Algorithms for rank compression of bit-vector
Cbm::bvector< Alloc >::reference	Class reference implements an object for bit assignment
Cbm::rsc_sparse_vector< Val, SV >::reference	Reference class to access elements via common [] operator
Cbm::sparse_vector< Val, BV >::reference	Reference class to access elements via common [] operator
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::reference_base
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::const_reference	Reference class to access elements via common [] operator
Cbm::str_sparse_vector< CharType, BV, STR_SIZE >::reference	Reference class to access elements via common [] operator
Cbm::rsc_sparse_vector< Val, SV >	Rank-Select compressed sparse vector
Cbm::tmatrix< T, ROWS, COLS >::rstat	Row characteristics for transposed matrix
Cbm::aggregator< BV >::run_options	Aggregation options for runtime control
Csample_data_frame	Sample data-frame structure with multiple bm vectors
Cbm::sv_serialization_plan_builder< SV >::serialization_params
Cbm::serializer< BV >	Bit-vector serialization class
Cbm::set2set_11_transform< SV >	Integer set to set transformation (functional image in groups theory) https://en.wikipedia.org/wiki/Image_(mathematics)
Cbm::similarity_batch< SDESCR >
Cbm::similarity_descriptor< SO, DMD_SZ, IDX_VALUE, SValue, SFunc >
CSortCounting_JobFunctor< BV >	Functor to process job batch (task)
Csparse_vect_index
Cbm::sparse_vector_deserializer< SV >	Sparse vector de-serializer
Cbm::sparse_vector_scanner< SV, S_FACTOR >	Algorithms for sparse_vector scan/search
Cbm::sparse_vector_serial_layout< SV >	Layout class for serialization buffer structure
Cbm::sparse_vector_serializer< SV >
Cbm::spin_lock< Pad >	Spin-lock with two-phase acquire (read + cas) padding parameter optionally adds a buffer to avoid CPU cache line contention
Cbm::sse_empty_guard	SSE2 reinitialization guard class
Cbm::chrono_taker< TOut >::statistics	Collected statistics
Cbm::compressed_buffer_collection< BV >::statistics	Collection statistics
Cbm::sub_func	Sub functor
Cbm::sv_addr_resolver< SV >	Sparse vector based address resolver (no space compactor, just bit-plane compressors provided by sparse_vector)
Cbm::sv_sample_index< SV >	Index for SV sorted vectors for approximate range queries
Cbm::sv_serialization_plan_builder< SV >	Parallel plan builder for succinct sparse vector serialization
Cbm::task_batch_base	Interface definition (base class) for a group of tasks (batch)
Cbm::task_batch< allocator_type >
Cbm::compute_sim_matrix_plan_builder< BV >::task_batch
Cbm::optimize_plan_builder< SVect, Lock >::task_batch
Cbm::sv_serialization_plan_builder< SV >::task_batch
Cbm::task_batch< BVAlloc >	Basic implementation for collection of tasks for parallel execution
Cbm::task_descr	BitMagic task with a captured function
Cbm::thread_pool< QValue, Lock >	Thread pool with custom (thread safe) queue
Cbm::thread_pool_executor< TPool >	Utility class to submit task batch to the running thread pool and optionally wait for it getting done
Cbm::tmatrix< T, ROWS, COLS >	Mini-matrix for bit transposition purposes
Cbm::tzcnt_table< T >	Structure for TZCNT constants
Csparse_vect_index::vect_addr
Cvect_index
Cbm::xor_func	Xor functor
Cbm::xor_scanner< BV >	XOR scanner to search for complement-similarities in collections of bit-vectors
Cbm::xor_sim_model< BV >	XOR similarity model
Cbm::xor_sim_params	Parameters for XOR similarity search