Class Hierarchy

Go to the graphical class hierarchy

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

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