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NCBI C++ ToolKit: bm::base_sparse_vector< Val, BV, MAX_SIZE

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Base class for bit-transposed(bit-sliced) sparse vector construction. More...

#include <util/bitset/bmbmatrix.h>

  base_sparse_vector ()     base_sparse_vector (bm::null_support null_able, bool is_dynamic, allocation_policy_type ap=allocation_policy_type(), size_type bv_max_size=bm::id_max, const allocator_type &alloc=allocator_type())     base_sparse_vector (const base_sparse_vector< Val, BV, MAX_SIZE > &bsv)     base_sparse_vector (base_sparse_vector< Val, BV, MAX_SIZE > &&bsv) noexcept   void  swap (base_sparse_vector< Val, BV, MAX_SIZE > &bsv) noexcept   size_type  size () const noexcept   void  resize (size_type new_size, bool set_null)   void  clear_range (size_type left, size_type right, bool set_null)   void  keep_range_no_check (size_type left, size_type right, bm::null_support slice_null)   void  clear_all (bool free_mem=true) noexcept   resize to zero, free memory More...
  bool  empty () const noexcept   void  swap_elements (size_type idx1, size_type idx2)   swap two vector elements More...
  void  optimize (bm::word_t *temp_block=0, typename bvector_type::optmode opt_mode=bvector_type::opt_compress, typename bvector_type::statistics *stat=0)   run memory optimization for all bit-vector rows More...
  void  calc_stat (typename bvector_type::statistics *st) const noexcept   Calculates memory statistics. More...
  bool  equal (const base_sparse_vector< Val, BV, MAX_SIZE > &sv, bm::null_support null_able=bm::use_null) const noexcept   check if another sparse vector has the same content and size More...
  void  copy_from (const base_sparse_vector< Val, BV, MAX_SIZE > &bsv)   void  merge_matr (bmatrix_type &bmatr)   Merge plane bvectors from an outside base matrix Note: outside base matrix gets destroyed. More...
  void  freeze_matr ()   Turn on RO mode. More...
  void  clear_value_planes_from (unsigned plane_idx, size_type idx)   void  insert_clear_value_planes_from (unsigned plane_idx, size_type idx)   void  erase_column (size_type idx, bool erase_null)   void  insert_null (size_type idx, bool not_null)   void  bit_sub_rows (const bvector_type &bv, bool use_null)   Set SUB (MINUS) operation on all existing bit-slices. More...
  void  bit_and_rows (const bvector_type &bv)   Set AND (intersect) operation on all existing bit-slices. More...
  void  optimize_block (block_idx_type nb, typename BV::optmode opt_mode)   plane index for the "NOT NULL" flags plane More...
  void  sync_ro () noexcept   Sybc read-only state. More...
  void  copy_range_slices (const base_sparse_vector< Val, BV, MAX_SIZE > &bsv, typename base_sparse_vector< Val, BV, MAX_SIZE >::size_type left, typename base_sparse_vector< Val, BV, MAX_SIZE >::size_type right, bm::null_support slice_null)   Perform copy_range() on a set of planes. More...
  void  set_ro_flag (bool b) noexcept   Force RO flag without running freeze ops on content. More...
  template<typename Val, typename BV, unsigned MAX_SIZE>
class bm::base_sparse_vector< Val, BV, MAX_SIZE >

Base class for bit-transposed(bit-sliced) sparse vector construction.

Keeps the basic housekeeping lements like matrix of sparse elements

Definition at line 485 of file bmbmatrix.h.

◆ allocation_policy_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 506 of file bmbmatrix.h.

◆ allocator_pool_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 508 of file bmbmatrix.h.

◆ allocator_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 505 of file bmbmatrix.h.

◆ block_idx_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 809 of file bmbmatrix.h.

◆ bmatrix_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 509 of file bmbmatrix.h.

◆ bvector_enumerator_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 507 of file bmbmatrix.h.

◆ bvector_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 500 of file bmbmatrix.h.

◆ bvector_type_const_ptr

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 503 of file bmbmatrix.h.

◆ bvector_type_ptr

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 502 of file bmbmatrix.h.

◆ const_reference

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 504 of file bmbmatrix.h.

◆ size_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 501 of file bmbmatrix.h.

◆ unsigned_value_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 510 of file bmbmatrix.h.

◆ value_type

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 499 of file bmbmatrix.h.

◆ bit_planes

template<typename Val , typename BV , unsigned MAX_SIZE>

Enumerator sv_slices  sv_value_slices 

Definition at line 488 of file bmbmatrix.h.

◆ vector_capacity

template<typename Val , typename BV , unsigned MAX_SIZE>

Enumerator max_vector_size 

Definition at line 494 of file bmbmatrix.h.

◆ base_sparse_vector() [1/4]

template<class Val , class BV , unsigned MAX_SIZE>

Definition at line 1833 of file bmbmatrix.h.

◆ base_sparse_vector() [2/4]

template<class Val , class BV , unsigned MAX_SIZE>

◆ base_sparse_vector() [3/4]

template<class Val , class BV , unsigned MAX_SIZE>

Definition at line 1860 of file bmbmatrix.h.

◆ base_sparse_vector() [4/4]

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ bit_and_rows()

template<typename Val , typename BV , unsigned MAX_SIZE>

Set AND (intersect) operation on all existing bit-slices.

Parameters
bv - argument vector row[i] -= bv

Definition at line 806 of file bmbmatrix.h.

◆ bit_sub_rows()

template<typename Val , typename BV , unsigned MAX_SIZE>

Set SUB (MINUS) operation on all existing bit-slices.

Parameters
bv - argument vector row[i] -= bv

Definition at line 799 of file bmbmatrix.h.

◆ calc_stat()

template<class Val , class BV , unsigned MAX_SIZE>

Calculates memory statistics.

Function fills statistics structure containing information about how this vector uses memory and estimation of max. amount of memory bvector needs to serialize itself.

Parameters
st - pointer on statistics structure to be filled in.
See also
statistics

Definition at line 2126 of file bmbmatrix.h.

References BM_ASSERT, and st().

◆ clear_all()

template<class Val , class BV , unsigned MAX_SIZE>

resize to zero, free memory

Parameters
free_mem - fully destroys the plane vectors if true

Definition at line 1967 of file bmbmatrix.h.

References i.

◆ clear_range()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ clear_value_planes_from()

template<class Val , class BV , unsigned MAX_SIZE>

clear column in all value planes

Parameters
plane_idx - row (plane index to start from) idx - bit (column) to clear

Definition at line 2142 of file bmbmatrix.h.

◆ copy_from()

template<class Val , class BV , unsigned MAX_SIZE>

Definition at line 1871 of file bmbmatrix.h.

References bm::base_sparse_vector< Val, BV, MAX_SIZE >::bmatr_, bm::base_sparse_vector< Val, BV, MAX_SIZE >::effective_slices_, bm::base_sparse_vector< Val, BV, MAX_SIZE >::get_bmatrix(), bm::basic_bmatrix< BV >::get_null_idx(), i, pythonpp::resize(), bm::basic_bmatrix< BV >::row(), bm::basic_bmatrix< BV >::rows(), and bm::base_sparse_vector< Val, BV, MAX_SIZE >::size().

◆ copy_range_slices()

template<class Val , class BV , unsigned MAX_SIZE>

void bm::base_sparse_vector< Val, BV, MAX_SIZE >::copy_range_slices ( const base_sparse_vector< Val, BV, MAX_SIZE > &  bsv, typename base_sparse_vector< Val, BV, MAX_SIZE >::size_type  left, typename base_sparse_vector< Val, BV, MAX_SIZE >::size_type  right, bm::null_support  slice_null  ) protected ◆ effective_slices()

template<typename Val , typename BV , unsigned MAX_SIZE>

Number of effective bit-planes in the value type.

Definition at line 648 of file bmbmatrix.h.

◆ empty()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ equal()

template<class Val , class BV , unsigned MAX_SIZE>

check if another sparse vector has the same content and size

Parameters
sv - sparse vector for comparison null_able - flag to consider NULL vector in comparison (default) or compare only value content planes
Returns
true, if it is the same

Definition at line 2169 of file bmbmatrix.h.

References BM_ASSERT, eq(), and bm::use_null.

◆ erase_column()

template<class Val , class BV , unsigned MAX_SIZE>

erase bit (column) from all planes

Parameters
idx - bit (column) to erase erase_null - erase the NULL vector

Definition at line 2160 of file bmbmatrix.h.

◆ free_slice()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ freeze_matr()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ get_allocator_pool()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ get_bmatrix() [1/2]

template<typename Val , typename BV , unsigned MAX_SIZE>

get read-only access to inetrnal bit-matrix

Definition at line 687 of file bmbmatrix.h.

Referenced by bm::base_sparse_vector< Val, BV, MAX_SIZE >::copy_from(), bm::sparse_vector< Val, BV >::join(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::remap_from_impl(), TestSparseVector(), TestSparseVector_XOR_Scanner(), TestSparseVectorSerialization2(), and TestStrSparseVector().

◆ get_bmatrix() [2/2]

template<typename Val , typename BV , unsigned MAX_SIZE>

access to internal bit-matrix

Definition at line 693 of file bmbmatrix.h.

◆ get_create_slice()

template<class Val , class BV , unsigned MAX_SIZE>

get access to bit-plain, function checks and creates a plane

Returns
bit-vector for the bit plain

Definition at line 2059 of file bmbmatrix.h.

References i.

◆ get_null_bvect()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ get_null_bvector()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ get_null_support()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ get_slice()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ get_slice_mask()

template<class Val , class BV , unsigned MAX_SIZE>

return mask of allocated bit-planes 1 in the mask - means bit-plane N is present returns 64-bit unsigned mask for sub 64-bit types (like int) unallocated mask bits will be zero extended

Returns
64-bit mask

Definition at line 2078 of file bmbmatrix.h.

References i, and mask.

◆ insert_clear_value_planes_from()

template<class Val , class BV , unsigned MAX_SIZE>

insert false (clear) column in all value planes

Parameters
plane_idx - row (plane index to start from) idx - bit (column) to clear insert

Definition at line 2151 of file bmbmatrix.h.

◆ insert_null()

template<class Val , class BV , unsigned MAX_SIZE>

◆ is_null()

template<class Val , class BV , unsigned MAX_SIZE>

◆ is_nullable()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ is_signed()

template<typename Val , typename BV , unsigned MAX_SIZE>

inlinestaticconstexprnoexcept ◆ keep_range_no_check()

template<class Val , class BV , unsigned MAX_SIZE>

◆ mark_null_idx()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ merge_matr()

template<class Val , class BV , unsigned MAX_SIZE>

◆ optimize()

template<class Val , class BV , unsigned MAX_SIZE>

void bm::base_sparse_vector< Val, BV, MAX_SIZE >::optimize ( bm::word_t *  temp_block = 0, typename bvector_type::optmode  opt_mode = bvector_type::opt_compress, typename bvector_type::statistics *  stat = 0  )

run memory optimization for all bit-vector rows

Parameters
temp_block - pre-allocated memory block to avoid unnecessary re-allocs opt_mode - requested compression depth stat - memory allocation statistics after optimization

Definition at line 2096 of file bmbmatrix.h.

References st().

◆ optimize_block()

template<typename Val , typename BV , unsigned MAX_SIZE>

plane index for the "NOT NULL" flags plane

optimize block in all matrix planes

Definition at line 819 of file bmbmatrix.h.

◆ resize()

template<class Val , class BV , unsigned MAX_SIZE>

◆ s2u()

template<class Val , class BV , unsigned MAX_SIZE>

◆ set_allocator_pool()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ set_ro_flag()

template<typename Val , typename BV , unsigned MAX_SIZE>

Force RO flag without running freeze ops on content.

Definition at line 835 of file bmbmatrix.h.

◆ size()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ slice() [1/2]

template<typename Val , typename BV , unsigned MAX_SIZE>

Definition at line 656 of file bmbmatrix.h.

◆ slice() [2/2]

template<typename Val , typename BV , unsigned MAX_SIZE>

get access to bit-plane as is (can return NULL)

Definition at line 655 of file bmbmatrix.h.

◆ slices()

template<typename Val , typename BV , unsigned MAX_SIZE>

get total number of bit-planes in the vector

Definition at line 637 of file bmbmatrix.h.

◆ stored_slices()

template<typename Val , typename BV , unsigned MAX_SIZE>

Number of stored bit-planes (value planes + extra.

Definition at line 642 of file bmbmatrix.h.

◆ swap()

template<class Val , class BV , unsigned MAX_SIZE>

◆ swap_elements()

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ sync_ro()

template<class Val , class BV , unsigned MAX_SIZE>

◆ u2s()

template<class Val , class BV , unsigned MAX_SIZE>

◆ value_bits()

template<typename Val , typename BV , unsigned MAX_SIZE>

inlinestaticconstexprprotectednoexcept ◆ bmatr_

template<typename Val , typename BV , unsigned MAX_SIZE>

bit-transposed matrix

Definition at line 838 of file bmbmatrix.h.

Referenced by bm::base_sparse_vector< Val, BV, 1 >::base_sparse_vector(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::base_sparse_vector(), bm::base_sparse_vector< Val, BV, 1 >::bit_and_rows(), bm::base_sparse_vector< Val, BV, 1 >::bit_sub_rows(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::copy_from(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::copy_range_slices(), bm::base_sparse_vector< Val, BV, 1 >::free_slice(), bm::base_sparse_vector< Val, BV, 1 >::freeze_matr(), bm::base_sparse_vector< Val, BV, 1 >::get_allocator_pool(), bm::base_sparse_vector< Val, BV, 1 >::get_bmatrix(), bm::base_sparse_vector< Val, BV, 1 >::get_null_bvect(), bm::base_sparse_vector< Val, BV, 1 >::get_null_bvector(), bm::base_sparse_vector< Val, BV, 1 >::get_slice(), bm::base_sparse_vector< Val, BV, 1 >::is_nullable(), bm::sparse_vector< Val, BV >::join(), bm::sparse_vector< Val, BV >::join_null_slice(), bm::base_sparse_vector< Val, BV, 1 >::mark_null_idx(), bm::sparse_vector< Val, BV >::merge(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::merge(), bm::base_sparse_vector< Val, BV, 1 >::optimize_block(), bm::base_sparse_vector< Val, BV, 1 >::set_allocator_pool(), bm::base_sparse_vector< Val, BV, 1 >::set_ro_flag(), bm::base_sparse_vector< Val, BV, 1 >::slice(), and bm::base_sparse_vector< Val, BV, 1 >::swap_elements().

◆ effective_slices_

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ size_

template<typename Val , typename BV , unsigned MAX_SIZE>

◆ slice_mask_

template<typename Val , typename BV , unsigned MAX_SIZE>

The documentation for this class was generated from the following file:

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