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GAP functions
[BitMagic C++ Library]

Collaboration diagram for GAP functions:


Data Structures

struct  bm::gap_len_table< T >
 Default GAP lengths table. More...
struct  bm::gap_len_table_min< T >
 Alternative GAP lengths table. Good for for memory saver mode and very sparse bitsets. More...

Functions

template<typename T>
unsigned bm::gap_test (const T *buf, unsigned pos)
 Tests if bit = pos is true.
template<typename T>
unsigned bm::gap_bit_count (const T *buf)
 Calculates number of bits ON in GAP buffer.
template<typename T>
int bm::gapcmp (const T *buf1, const T *buf2)
 Lexicographical comparison of GAP buffers.
template<typename T, class F>
void bm::gap_buff_op (T *BMRESTRICT dest, const T *BMRESTRICT vect1, unsigned vect1_mask, const T *BMRESTRICT vect2, unsigned vect2_mask, F f)
 Abstract operation for GAP buffers. Receives functor F as a template argument.
template<typename T, class F>
unsigned bm::gap_buff_any_op (const T *BMRESTRICT vect1, unsigned vect1_mask, const T *BMRESTRICT vect2, unsigned vect2_mask, F f)
 Abstract distance test operation for GAP buffers. Receives functor F as a template argument.
template<typename T>
unsigned bm::gap_set_value (unsigned val, T *BMRESTRICT buf, unsigned pos, unsigned *BMRESTRICT is_set)
 Abstract distance(similarity) operation for GAP buffers. Receives functor F as a template argument Sets or clears bit in the GAP buffer.
template<typename T>
int bm::gap_find_in_block (const T *buf, unsigned nbit, bm::id_t *prev)
 Searches for the next 1 bit in the GAP block.
template<typename T>
void bm::gap_sub_to_bitset (unsigned *dest, const T *buf)
 SUB (AND NOT) GAP block to bitblock.
template<typename T>
void bm::gap_xor_to_bitset (unsigned *dest, const T *buf)
 XOR GAP block to bitblock.
template<typename T>
void bm::gap_add_to_bitset (unsigned *dest, const T *buf)
 Adds(OR) GAP block to bitblock.
template<typename T>
void bm::gap_and_to_bitset (unsigned *dest, const T *buf)
 ANDs GAP block to bitblock.
template<typename T>
void bm::gap_convert_to_bitset (unsigned *dest, const T *buf)
 GAP block to bitblock conversion.
template<typename T>
void bm::gap_convert_to_bitset (unsigned *dest, const T *buf, unsigned dest_len)
 GAP block to bitblock conversion.
template<typename T>
unsigned * bm::gap_convert_to_bitset_smart (unsigned *dest, const T *buf, id_t set_max)
 Smart GAP block to bitblock conversion.
template<typename T>
unsigned bm::gap_control_sum (const T *buf)
 Calculates sum of all words in GAP block. (For debugging purposes).
template<class T>
void bm::gap_set_all (T *buf, unsigned set_max, unsigned value)
 Sets all bits to 0 or 1 (GAP).
template<class T>
void bm::gap_init_range_block (T *buf, unsigned from, unsigned to, unsigned value, unsigned set_max)
 Init gap block so it has block in it (can be whole block).
template<typename T>
void bm::gap_invert (T *buf)
 Inverts all bits in the GAP buffer.
template<typename T>
bool bm::gap_is_all_zero (const T *buf, unsigned set_max)
 Temporary inverts all bits in the GAP buffer. Checks if GAP block is all-zero.
template<typename T>
bool bm::gap_is_all_one (const T *buf, unsigned set_max)
 Checks if GAP block is all-one.
template<typename T>
unsigned bm::gap_length (const T *buf)
 Returs GAP block length.
template<typename T>
unsigned bm::gap_capacity (const T *buf, const T *glevel_len)
 Returs GAP block capacity.
template<typename T>
unsigned bm::gap_limit (const T *buf, const T *glevel_len)
 Returs GAP block capacity limit.
template<typename T>
unsigned bm::gap_level (const T *buf)
 Returs GAP blocks capacity level.
template<typename T>
void bm::set_gap_level (T *buf, unsigned level)
 Sets GAP block capacity level.
template<typename T>
int bm::gap_calc_level (int len, const T *glevel_len)
 Calculates GAP block capacity level.
template<typename T>
unsigned bm::gap_free_elements (const T *buf, const T *glevel_len)
 Returns number of free elements in GAP block array. Difference between GAP block capacity on this level and actual GAP length.
template<typename T>
unsigned bm::bit_convert_to_gap (T *BMRESTRICT dest, const unsigned *BMRESTRICT src, bm::id_t bits, unsigned dest_len)
 Converts bit block to GAP.
template<typename D, typename T>
bm::gap_convert_to_arr (D *BMRESTRICT dest, const T *BMRESTRICT buf, unsigned dest_len)
 Convert gap block into array of ints corresponding to 1 bits.
gap_word_tbm::gap_operation_and (const gap_word_t *BMRESTRICT vect1, const gap_word_t *BMRESTRICT vect2, gap_word_t *BMRESTRICT tmp_buf)
 GAP AND operation.
unsigned bm::gap_operation_any_and (const gap_word_t *BMRESTRICT vect1, const gap_word_t *BMRESTRICT vect2)
 GAP AND operation test.
gap_word_tbm::gap_operation_xor (const gap_word_t *BMRESTRICT vect1, const gap_word_t *BMRESTRICT vect2, gap_word_t *BMRESTRICT tmp_buf)
 GAP XOR operation.
unsigned bm::gap_operation_any_xor (const gap_word_t *BMRESTRICT vect1, const gap_word_t *BMRESTRICT vect2)
 GAP XOR operation test.
gap_word_tbm::gap_operation_or (const gap_word_t *BMRESTRICT vect1, const gap_word_t *BMRESTRICT vect2, gap_word_t *BMRESTRICT tmp_buf)
 GAP OR operation.
gap_word_tbm::gap_operation_sub (const gap_word_t *BMRESTRICT vect1, const gap_word_t *BMRESTRICT vect2, gap_word_t *BMRESTRICT tmp_buf)
 GAP SUB (AND NOT) operation.
unsigned bm::gap_operation_any_sub (const gap_word_t *BMRESTRICT vect1, const gap_word_t *BMRESTRICT vect2)
 GAP SUB operation test.
template<typename T>
unsigned bm::gap_overhead (const T *length, const T *length_end, const T *glevel_len)
 Calculates memory overhead for number of gap blocks sharing the same memory allocation table (level lengths table).
template<typename T>
bool bm::improve_gap_levels (const T *length, const T *length_end, T *glevel_len)
 Finds optimal gap blocks lengths.

Detailed Description

GAP functions implement different opereations on GAP compressed blocks and serve as a minimal building blocks.

Function Documentation

template<typename T>
unsigned bit_convert_to_gap T *BMRESTRICT  dest,
const unsigned *BMRESTRICT  src,
bm::id_t  bits,
unsigned  dest_len
 

Converts bit block to GAP.

Parameters:
dest - Destinatio GAP buffer.
src - Source bitblock buffer.
bits - Number of bits to convert.
dest_len - length of the dest. buffer.
Returns:
New ength of GAP block or 0 if conversion failed (insufficicent space).

Definition at line 2172 of file bmfunc.h.

References BM_ASSERT, and BMRESTRICT.

template<typename T>
void gap_add_to_bitset unsigned *  dest,
const T *  buf
 

Adds(OR) GAP block to bitblock.

Parameters:
dest - bitblock buffer pointer.
buf - GAP buffer pointer.

Definition at line 1399 of file bmfunc.h.

References BM_ASSERT, and bm::or_bit_block().

Referenced by bm::gap_convert_to_bitset().

template<typename T>
void gap_and_to_bitset unsigned *  dest,
const T *  buf
 

ANDs GAP block to bitblock.

Parameters:
dest - bitblock buffer pointer.
buf - GAP buffer pointer.

Definition at line 1431 of file bmfunc.h.

References BM_ASSERT, and bm::sub_bit_block().

template<typename T>
unsigned gap_bit_count const T *  buf  ) 
 

Calculates number of bits ON in GAP buffer.

Parameters:
buf - GAP buffer pointer.
Returns:
Number of non-zero bits.

Definition at line 659 of file bmfunc.h.

Referenced by bm::bvector< Alloc, MS >::stat().

template<typename T, class F>
unsigned gap_buff_any_op const T *BMRESTRICT  vect1,
unsigned  vect1_mask,
const T *BMRESTRICT  vect2,
unsigned  vect2_mask,
f
 

Abstract distance test operation for GAP buffers. Receives functor F as a template argument.

Parameters:
vect1 - operand 1 GAP encoded buffer.
vect1_mask - XOR mask for starting bitflag for vector1 can be 0 or 1 (1 inverts the vector)
vect2 - operand 2 GAP encoded buffer.
vect2_mask - same as vect1_mask
f - operation functor.
Note:
Internal function.
Returns:
non zero value if operation result returns any 1 bit

Definition at line 884 of file bmfunc.h.

Referenced by bm::gap_operation_any_and(), bm::gap_operation_any_sub(), and bm::gap_operation_any_xor().

template<typename T, class F>
void gap_buff_op T *BMRESTRICT  dest,
const T *BMRESTRICT  vect1,
unsigned  vect1_mask,
const T *BMRESTRICT  vect2,
unsigned  vect2_mask,
f
 

Abstract operation for GAP buffers. Receives functor F as a template argument.

Parameters:
dest - destination memory buffer.
vect1 - operand 1 GAP encoded buffer.
vect1_mask - XOR mask for starting bitflag for vector1 can be 0 or 1 (1 inverts the vector)
vect2 - operand 2 GAP encoded buffer.
vect2_mask - same as vect1_mask
f - operation functor.
Note:
Internal function.

Definition at line 803 of file bmfunc.h.

Referenced by bm::gap_operation_and(), bm::gap_operation_or(), bm::gap_operation_sub(), and bm::gap_operation_xor().

template<typename T>
int gap_calc_level int  len,
const T *  glevel_len
[inline]
 

Calculates GAP block capacity level.

Parameters:
len - GAP buffer length.
glevel_len - GAP lengths table
Returns:
GAP block capacity level. -1 if block does not fit any level.

Definition at line 2099 of file bmfunc.h.

References BM_ASSERT.

Referenced by bm::gap_overhead().

template<typename T>
unsigned gap_capacity const T *  buf,
const T *  glevel_len
 

Returs GAP block capacity.

Parameters:
buf - GAP buffer pointer.
Returns:
GAP block capacity.

Definition at line 2041 of file bmfunc.h.

Referenced by bm::gap_free_elements().

template<typename T>
unsigned gap_control_sum const T *  buf  ) 
 

Calculates sum of all words in GAP block. (For debugging purposes).

Note:
For debugging and testing ONLY.
Parameters:
buf - GAP buffer pointer.
Returns:
Sum of all words.

Definition at line 1867 of file bmfunc.h.

References BM_ASSERT.

Referenced by bm::bvector< Alloc, MS >::stat().

template<typename D, typename T>
D gap_convert_to_arr D *BMRESTRICT  dest,
const T *BMRESTRICT  buf,
unsigned  dest_len
 

Convert gap block into array of ints corresponding to 1 bits.

Definition at line 2261 of file bmfunc.h.

References BMRESTRICT.

template<typename T>
void gap_convert_to_bitset unsigned *  dest,
const T *  buf,
unsigned  dest_len
 

GAP block to bitblock conversion.

Parameters:
dest - bitblock buffer pointer.
buf - GAP buffer pointer.
dest_size - length of the destination buffer.

Definition at line 1824 of file bmfunc.h.

References bm::gap_add_to_bitset().

template<typename T>
void gap_convert_to_bitset unsigned *  dest,
const T *  buf
 

GAP block to bitblock conversion.

Parameters:
dest - bitblock buffer pointer.
buf - GAP buffer pointer.

Definition at line 1808 of file bmfunc.h.

References bm::bit_block_set(), and bm::gap_add_to_bitset().

Referenced by bm::bvector< Alloc, MS >::compare(), and bm::gap_convert_to_bitset_smart().

template<typename T>
unsigned* gap_convert_to_bitset_smart unsigned *  dest,
const T *  buf,
id_t  set_max
 

Smart GAP block to bitblock conversion.

Checks if GAP block is ALL-ZERO or ALL-ON. In those cases returns pointer on special static bitblocks.

Parameters:
dest - bitblock buffer pointer.
buf - GAP buffer pointer.
set_max - max possible bitset length

Definition at line 1845 of file bmfunc.h.

References FULL_BLOCK_ADDR, and bm::gap_convert_to_bitset().

template<typename T>
int gap_find_in_block const T *  buf,
unsigned  nbit,
bm::id_t prev
 

Searches for the next 1 bit in the GAP block.

Parameters:
buf - GAP buffer
nbit - bit index to start checking from.
prev - returns previously checked value

Definition at line 1119 of file bmfunc.h.

References BM_ASSERT, and bm::gap_bfind().

template<typename T>
unsigned gap_free_elements const T *  buf,
const T *  glevel_len
[inline]
 

Returns number of free elements in GAP block array. Difference between GAP block capacity on this level and actual GAP length.

Parameters:
buf - GAP buffer pointer glevel_len - GAP lengths table
Returns:
Number of free GAP elements

Definition at line 2120 of file bmfunc.h.

References bm::gap_capacity(), and bm::gap_length().

template<class T>
void gap_init_range_block T *  buf,
unsigned  from,
unsigned  to,
unsigned  value,
unsigned  set_max
 

Init gap block so it has block in it (can be whole block).

Parameters:
buf - GAP buffer pointer.
from - one block start
to - one block end
value - (block value)1 or 0
set_max - max possible bitset length

Definition at line 1919 of file bmfunc.h.

References BM_ASSERT, and bm::gap_set_all().

template<typename T>
void gap_invert T *  buf  ) 
 

Inverts all bits in the GAP buffer.

Parameters:
buf - GAP buffer pointer.

Definition at line 1969 of file bmfunc.h.

Referenced by bm::gap_operation_or().

template<typename T>
bool gap_is_all_one const T *  buf,
unsigned  set_max
 

Checks if GAP block is all-one.

Parameters:
buf - GAP buffer pointer.
set_max - max possible bitset length
Returns:
true if all-one.

Definition at line 2015 of file bmfunc.h.

template<typename T>
bool gap_is_all_zero const T *  buf,
unsigned  set_max
 

Temporary inverts all bits in the GAP buffer. Checks if GAP block is all-zero.

Parameters:
buf - GAP buffer pointer.
set_max - max possible bitset length
Returns:
true if all-zero.

Definition at line 2001 of file bmfunc.h.

Referenced by bm::bvector< Alloc, MS >::compare().

template<typename T>
unsigned gap_length const T *  buf  ) 
 

Returs GAP block length.

Parameters:
buf - GAP buffer pointer.
Returns:
GAP block length.

Definition at line 2027 of file bmfunc.h.

Referenced by bm::gap_free_elements(), and bm::bvector< Alloc, MS >::stat().

template<typename T>
unsigned gap_level const T *  buf  ) 
 

Returs GAP blocks capacity level.

Parameters:
buf - GAP buffer pointer.
Returns:
GAP block capacity level.

Definition at line 2069 of file bmfunc.h.

Referenced by bm::bvector< Alloc, MS >::stat().

template<typename T>
unsigned gap_limit const T *  buf,
const T *  glevel_len
 

Returs GAP block capacity limit.

Parameters:
buf - GAP buffer pointer.
glevel_len - GAP lengths table (gap_len_table)
Returns:
GAP block limit.

Definition at line 2056 of file bmfunc.h.

gap_word_t* gap_operation_and const gap_word_t *BMRESTRICT  vect1,
const gap_word_t *BMRESTRICT  vect2,
gap_word_t *BMRESTRICT  tmp_buf
[inline]
 

GAP AND operation.

Function performs AND logical oparation on gap vectors. If possible function put the result into vect1 and returns this pointer. Otherwise result is put into tmp_buf, which should be twice of the vector size.

Parameters:
vect1 - operand 1
vect2 - operand 2
tmp_buf - pointer on temporary buffer
Returns:
Result pointer (tmp_buf OR vect1)

Definition at line 2777 of file bmfunc.h.

References bm::gap_buff_op().

unsigned gap_operation_any_and const gap_word_t *BMRESTRICT  vect1,
const gap_word_t *BMRESTRICT  vect2
[inline]
 

GAP AND operation test.

Function performs AND logical oparation on gap vectors. If possible function put the result into vect1 and returns this pointer. Otherwise result is put into tmp_buf, which should be twice of the vector size.

Parameters:
vect1 - operand 1
vect2 - operand 2
Returns:
non zero value if operation returns any 1 bit

Definition at line 2800 of file bmfunc.h.

References bm::gap_buff_any_op().

unsigned gap_operation_any_sub const gap_word_t *BMRESTRICT  vect1,
const gap_word_t *BMRESTRICT  vect2
[inline]
 

GAP SUB operation test.

Function performs AND logical oparation on gap vectors. If possible function put the result into vect1 and returns this pointer. Otherwise result is put into tmp_buf, which should be twice of the vector size.

Parameters:
vect1 - operand 1
vect2 - operand 2
Returns:
non zero value if operation returns any 1 bit

Definition at line 2919 of file bmfunc.h.

References bm::gap_buff_any_op().

unsigned gap_operation_any_xor const gap_word_t *BMRESTRICT  vect1,
const gap_word_t *BMRESTRICT  vect2
[inline]
 

GAP XOR operation test.

Function performs AND logical oparation on gap vectors. If possible function put the result into vect1 and returns this pointer. Otherwise result is put into tmp_buf, which should be twice of the vector size.

Parameters:
vect1 - operand 1
vect2 - operand 2
Returns:
non zero value if operation returns any 1 bit

Definition at line 2846 of file bmfunc.h.

References bm::gap_buff_any_op().

gap_word_t* gap_operation_or const gap_word_t *BMRESTRICT  vect1,
const gap_word_t *BMRESTRICT  vect2,
gap_word_t *BMRESTRICT  tmp_buf
[inline]
 

GAP OR operation.

Function performs OR logical oparation on gap vectors. If possible function put the result into vect1 and returns this pointer. Otherwise result is put into tmp_buf, which should be twice of the vector size.

Parameters:
vect1 - operand 1
vect2 - operand 2
tmp_buf - pointer on temporary buffer
Returns:
Result pointer (tmp_buf)

Definition at line 2869 of file bmfunc.h.

References bm::gap_buff_op(), and bm::gap_invert().

gap_word_t* gap_operation_sub const gap_word_t *BMRESTRICT  vect1,
const gap_word_t *BMRESTRICT  vect2,
gap_word_t *BMRESTRICT  tmp_buf
[inline]
 

GAP SUB (AND NOT) operation.

Function performs SUB logical oparation on gap vectors. If possible function put the result into vect1 and returns this pointer. Otherwise result is put into tmp_buf, which should be twice of the vector size.

Parameters:
vect1 - operand 1
vect2 - operand 2
tmp_buf - pointer on temporary buffer
Returns:
Result pointer (tmp_buf)

Definition at line 2896 of file bmfunc.h.

References bm::gap_buff_op().

gap_word_t* gap_operation_xor const gap_word_t *BMRESTRICT  vect1,
const gap_word_t *BMRESTRICT  vect2,
gap_word_t *BMRESTRICT  tmp_buf
[inline]
 

GAP XOR operation.

Function performs XOR logical oparation on gap vectors. If possible function put the result into vect1 and returns this pointer. Otherwise result is put into tmp_buf, which should be twice of the vector size.

Parameters:
vect1 - operand 1
vect2 - operand 2
tmp_buf - pointer on temporary buffer
Returns:
Result pointer (tmp_buf)

Definition at line 2823 of file bmfunc.h.

References bm::gap_buff_op().

template<typename T>
unsigned gap_overhead const T *  length,
const T *  length_end,
const T *  glevel_len
 

Calculates memory overhead for number of gap blocks sharing the same memory allocation table (level lengths table).

Definition at line 3949 of file bmfunc.h.

References BM_ASSERT, and bm::gap_calc_level().

Referenced by bm::improve_gap_levels().

template<class T>
void gap_set_all T *  buf,
unsigned  set_max,
unsigned  value
 

Sets all bits to 0 or 1 (GAP).

Parameters:
buf - GAP buffer pointer.
set_max - max possible bitset length

Definition at line 1898 of file bmfunc.h.

References BM_ASSERT.

Referenced by bm::gap_init_range_block().

template<typename T>
unsigned gap_set_value unsigned  val,
T *BMRESTRICT  buf,
unsigned  pos,
unsigned *BMRESTRICT  is_set
 

Abstract distance(similarity) operation for GAP buffers. Receives functor F as a template argument Sets or clears bit in the GAP buffer.

Parameters:
val - new bit value
buf - GAP buffer.
pos - Index of bit to set.
is_set - (OUT) flag if bit was actually set.
Returns:
New GAP buffer length.

Definition at line 1027 of file bmfunc.h.

References BM_ASSERT, and bm::gap_bfind().

Referenced by bm::miniset< A, N >::set().

template<typename T>
void gap_sub_to_bitset unsigned *  dest,
const T *  buf
 

SUB (AND NOT) GAP block to bitblock.

Parameters:
dest - bitblock buffer pointer.
buf - GAP buffer pointer.

Definition at line 1335 of file bmfunc.h.

References BM_ASSERT, and bm::sub_bit_block().

template<typename T>
unsigned gap_test const T *  buf,
unsigned  pos
 

Tests if bit = pos is true.

Parameters:
buf - GAP buffer pointer.
pos - index of the element.
Returns:
true if position is in "1" gap

Definition at line 497 of file bmfunc.h.

References BM_ASSERT.

Referenced by bm::bvector< Alloc, MS >::get_bit(), and bm::miniset< A, N >::test().

template<typename T>
void gap_xor_to_bitset unsigned *  dest,
const T *  buf
 

XOR GAP block to bitblock.

Parameters:
dest - bitblock buffer pointer.
buf - GAP buffer pointer.

Definition at line 1367 of file bmfunc.h.

References BM_ASSERT, and bm::xor_bit_block().

template<typename T>
int gapcmp const T *  buf1,
const T *  buf2
 

Lexicographical comparison of GAP buffers.

Parameters:
buf1 - First GAP buffer pointer.
buf2 - Second GAP buffer pointer.
Returns:
<0 - less, =0 - equal, >0 - greater.

Definition at line 739 of file bmfunc.h.

Referenced by bm::bvector< Alloc, MS >::compare().

template<typename T>
bool improve_gap_levels const T *  length,
const T *  length_end,
T *  glevel_len
 

Finds optimal gap blocks lengths.

Parameters:
length - first element of GAP lengths array
length_end - end of the GAP lengths array
glevel_len - destination GAP lengths array

Definition at line 3977 of file bmfunc.h.

References BM_ASSERT, and bm::gap_overhead().

Referenced by bm::bvector< Alloc, MS >::optimize_gap_size().

template<typename T>
void set_gap_level T *  buf,
unsigned  level
 

Sets GAP block capacity level.

Parameters:
buf - GAP buffer pointer.
level new GAP block capacity level.

Definition at line 2082 of file bmfunc.h.

References BM_ASSERT.


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