Data Structures

Here are the data structures with brief descriptions:

[detail level 1234]

Nbm
Cbvector	Bitvector Bit-vector container with runtime compression of bits
Cstatistics	Statistical information about bitset's memory allocation details
Creference	Class reference implements an object for bit assignment
Citerator_base	Base class for all iterators
Cbitblock_descr	Bit-block descriptor
Cdgap_descr	Information about current DGAP block
Cblock_descr
Cinsert_iterator	Output iterator iterator designed to set "ON" bits based on input sequence of integers (bit indeces)
Cbulk_insert_iterator	Output iterator iterator designed to set "ON" bits based on input sequence of integers
Cenumerator	Constant iterator designed to enumerate "ON" bits
Ccounted_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
Callocation_policy	Memory allocation policy
Cbv_statistics	Structure with statistical information about memory allocation footprint, serialization projection, number of vectors
Cbv_arena_statistics	Structure with statistical information about memory allocation for arena based vectors
Cpair	Pair type
Cbit_decode_cache	Bit-decode cache structure
Ccopy_to_array_functor	Adaptor to copy 1 bits to array
Call_set	Structure carries pointer on bit block with all bits 1
Call_set_block
Cd_copy_func	D-Gap copy functor
Cbitblock_get_adapter	Bit-block get adapter, takes bitblock and represents it as a get_32() accessor function
Cbitblock_store_adapter	Bit-block store adapter, takes bitblock and saves results into it
Cbitblock_sum_adapter	Bit-block sum adapter, takes values and sums it /internal
Cdecoder_range_adapter	Adapter to get words from a range stream (see range serialized bit-block)
Cbit_AND	Bit AND functor
Cbit_OR	Bit OR functor
Cbit_SUB	Bit SUB functor
Cbit_XOR	Bit XOR functor
Cbit_ASSIGN	Bit ASSIGN functor
Cbit_COUNT	Bit COUNT functor
Cbit_COUNT_AND	Bit COUNT AND functor
Cbit_COUNT_XOR	Bit COUNT XOR functor
Cbit_COUNT_OR	Bit COUNT OR functor
Cbit_COUNT_SUB_AB	Bit COUNT SUB AB functor
Cbit_COUNT_SUB_BA	Bit SUB BA functor
Cbit_COUNT_A	Bit COUNT A functor
Cbit_COUNT_B	Bit COUNT B functor
Coperation_functions
Cptr_payload_t	Helper union to interpret pointer as integers
Cxor_sim_params	Parameters for XOR similarity search
Cblock_waves_xor_descr	Structure to compute XOR gap-count profile by sub-block waves
Cblock_xor_match_descr	Capture the XOR filter results (xor block against ref.block)
Cmatch_pair	XOR match pair
Cblock_match_chain	XOR match chain
Cbv_ref_vector	List of reference bit-vectors with their true index associations
Cxor_sim_model	XOR similarity model
Cxor_scanner	XOR scanner to search for complement-similarities in collections of bit-vectors
Cminiset	Template class implements memory saving set functionality
Cbvmini	Mini bit-vector for auxiliary purposes
Cbvector_mini	Bitvector class with very limited functionality
Cencoder	Memory encoding
Cdecoder_base	Base class for all decoding functionality
Cdecoder	Class for decoding data from memory buffer
Cdecoder_little_endian	Class for decoding data from memory buffer
Cbit_out	Byte based writer for un-aligned bit streaming
Cbit_in	Byte based reader for un-aligned bit streaming
Cgamma_encoder	Functor for Elias Gamma encoding
Cgamma_decoder	Elias Gamma decoder
Cbasic_bmatrix	Basic dense bit-matrix class
Cbase_sparse_vector	Base class for bit-transposed(bit-sliced) sparse vector construction
C_copyright	Internal structure
CDeBruijn_bit_position	DeBruijn majic table
Cfirst_bit_table	Structure keeps index of first right 1 bit for every byte
Cbit_count_table	Structure to aid in counting bits table contains count of bits in 0-255 diapason of numbers
Clzcnt_table	Structure for LZCNT constants (4-bit)
Ctzcnt_table	Structure for TZCNT constants
Cblock_set_table	Structure keeps all-left/right ON bits masks
Cgap_len_table	Default GAP lengths table
Cgap_len_table_min	Alternative GAP lengths table. Good for for memory saver mode and very sparse bitsets
Cgap_len_table_nl	Non-linear size growth GAP lengths table
Cglobals	Internal structure
Cbo
Csse_empty_guard	SSE2 reinitialization guard class
Cbit_vistor_copy_functor	Functor for bit-copy (for testing)
Crank_compressor	Algorithms for rank compression of bit-vector
Cdistance_metric_descriptor	Distance metric descriptor, holds metric code and result
Cbit_visitor_callback_adaptor	Functor-adaptor for C-style callbacks
Cbit_visitor_back_inserter_adaptor	Functor-adaptor for back-inserter
Csimilarity_descriptor
Csimilarity_batch
Cinterval_enumerator	Forward iterator class to traverse bit-vector as ranges
Ctask_descr	BitMagic task with a captured function
Ctask_batch_base	Interface definition (base class) for a group of tasks (batch)
Ctask_batch	Basic implementation for collection of tasks for parallel execution
Cis_lock_noexcept	"noexcept" traits detection for T::lock()
Clock_guard	Simple scoped lock guard
Cpad60_struct	Pad 60 bytes so that the final ocupiles 64 bytes (1 cache line)
Cpad0_struct	Empty padding
Cspin_lock	Spin-lock with two-phase acquire (read + cas) padding parameter optionally adds a buffer to avoid CPU cache line contention
Cthread_pool	Thread pool with custom (thread safe) queue
Cqueue_sync	Thread-sync queue with MT access protecion
Cthread_pool_executor	Utility class to submit task batch to the running thread pool and optionally wait for it getting done
Coptimize_plan_builder	Builder class to prepare a batch of tasks for parallel optimization of a sparse vector
Ctask_batch
Ccompute_sim_matrix_plan_builder	Parallel plan builder for the XOR filter scanner
Ctask_batch
Csv_serialization_plan_builder	Parallel plan builder for succinct sparse vector serialization
Cserialization_params
Ctask_batch
Ctmatrix	Mini-matrix for bit transposition purposes
Crstat	Row characteristics for transposed matrix
Cbit_grabber
Cbit_grabber< unsigned, 32 >
Cbit_grabber< unsigned short, 16 >
Cbit_grabber< unsigned char, 8 >
Cbit_trans_grabber
Cgap_transpose_engine	Bit-plane splicing of a GAP block
Cbit_block_t	Bit-block array wrapped into union for correct interpretation of 32-bit vs 64-bit access vs SIMD
Cbunion_t
Cconditional	Ad-hoc conditional expressions
Cconditional< false >
Cptr_guard	Mini auto-pointer for internal memory management
Cand_func	And functor
Cxor_func	Xor functor
Cor_func	Or functor
Csub_func	Sub functor
Cagg_run_options	Aggregation options to control execution Default settings are to support only result bit-vector filters
Caggregator	Algorithms for fast aggregation of a group of bit-vectors
Carg_groups	Aggregator arg groups
Cpipeline_bcache	Block cache for pipeline execution
Crun_options	Aggregation options for runtime control
Cpipeline	Pipeline vector for running a group of aggregation operations on a family of vectors
Carena	Temporary operations vectors
Cserializer	Bit-vector serialization class
Cbookmark_state	Bookmark state structure
Cdeseriaizer_base	Base deserialization class
Cdeserializer	Deserializer for bit-vector
Citerator_deserializer	Iterator to walk forward the serialized stream
Cserial_stream_iterator	Serialization stream iterator
Coperation_deserializer	Deserializer, performs logical operations between bit-vector and serialized bit-vector
Cblock_allocator	Default malloc based bitblock allocator class
Cptr_allocator	Default malloc based bitblock allocator class
Cpointer_pool_array	Pool of pointers to buffer cyclic allocations
Calloc_pool	Allocation pool object
Cmem_alloc	BM style allocator adapter
Crandom_subset
Csparse_vector	Succinct sparse vector with runtime compression using bit-slicing / transposition method
Cstatistics
Cis_remap_support
Cis_rsc_support
Cis_dynamic_splices
Creference	Reference class to access elements via common [] operator
Cconst_iterator	Const iterator to traverse the sparse vector
Cback_insert_iterator	Back insert iterator implements buffered insert, faster than generic access assignment
Csv_sample_index	Index for SV sorted vectors for approximate range queries
Csparse_vector_scanner	Algorithms for sparse_vector scan/search
Cpipeline	Pipeline to run multiple searches against a particular SV faster using cache optimizations
Cset2set_11_transform	Integer set to set transformation (functional image in groups theory) https://en.wikipedia.org/wiki/Image_(mathematics)
Cgather_buffer
Csparse_vector_serial_layout	Layout class for serialization buffer structure
Csparse_vector_serializer
Csparse_vector_deserializer	Sparse vector de-serializer
Ccompressed_collection_serializer	Seriaizer for compressed collections
Ccompressed_collection_deserializer	Deseriaizer for compressed collections
Crsc_sparse_vector	Rank-Select compressed sparse vector
Cis_remap_support
Cis_rsc_support
Cis_dynamic_splices
Cstatistics
Creference	Reference class to access elements via common [] operator
Cconst_iterator	Const iterator to traverse the rsc sparse vector
Cback_insert_iterator	Back insert iterator implements buffered insert, faster than generic access assignment
Cstr_sparse_vector	Succinct sparse vector for strings with compression using bit-slicing ( transposition) method
Cstatistics
Cis_remap_support
Cis_rsc_support
Cis_dynamic_splices
Creference_base
Cconst_reference	Reference class to access elements via common [] operator
Creference	Reference class to access elements via common [] operator
Cconst_iterator	Const iterator to do quick traverse of the sparse vector
Cback_insert_iterator	Back insert iterator implements buffered insert, faster than generic access assignment
Cbvps_addr_resolver	Bit-bector prefix sum address resolver using bit-vector prefix sum as a space compactor
Csv_addr_resolver	Sparse vector based address resolver (no space compactor, just bit-plane compressors provided by sparse_vector)
Ccompressed_collection	Compressed (sparse collection of objects)
Ccompressed_buffer_collection	Compressed (sparse collection of objects)
Cstatistics	Collection statistics
Cchrono_taker	Utility class to collect performance measurements and statistics
Cstatistics	Collected statistics
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)
Cbv_index
Cbvs_index
CCKMerAcc	Utility class to accumulate cahnges to cluster before commiting it (mutex syncronous operation)
CCounting_JobFunctor	K-mer counting job functor class using bm::aggregator<>
CCSeqClusters
CCSeqGroup	Group (clustrer) of sequences
CCSequenceColl	Collection of sequences and k-mer fingerprint vectors
Cdata_model	Data frame object, sued to buid succinct data model
Cdbg_block_allocator
Cdbg_ptr_allocator
CDNA_FingerprintScanner	Utility for keeping all DNA finger print vectors and search using various techniques
Cgap_len_table_sparse
Csample_data_frame	Sample data-frame structure with multiple bm vectors
CSortCounting_JobFunctor	Functor to process job batch (task)
Csparse_vect_index
Cvect_addr
Cvect_index