/*
* constructor. the code in of the constructor is imported from Simon Gog's SDSL library
*/
libmaus::util::NearestNeighbourDictionary::NearestNeighbourDictionary(::libmaus::bitio::BitVector const & v)
{
assert ( nndblocksize );
uint64_t max_distance_between_two_ones = 0;
uint64_t ones = 0; // counter for the ones in v
// get maximal distance between to ones in the bit vector
// speed this up by broadword computing
for (uint64_t i=0, last_one_pos_plus_1=0; i < v.size(); ++i)
{
if ( (v)[i])
{
if (i+1-last_one_pos_plus_1 > max_distance_between_two_ones)
max_distance_between_two_ones = i+1-last_one_pos_plus_1;
last_one_pos_plus_1 = i+1;
++ones;
}
}
m_ones = ones;
m_size = v.size();
// initialize absolute samples m_abs_samples[0]=0
::libmaus::bitio::CompactArray::unique_ptr_type tm_abs_samples(new ::libmaus::bitio::CompactArray( m_ones/nndblocksize + 1, ::libmaus::math::numbits(v.size()-1) ));
m_abs_samples = UNIQUE_PTR_MOVE(tm_abs_samples);
// initialize different values
::libmaus::bitio::CompactArray::unique_ptr_type tm_differences(new ::libmaus::bitio::CompactArray( m_ones - m_ones/nndblocksize, ::libmaus::math::numbits(max_distance_between_two_ones) ));
m_differences = UNIQUE_PTR_MOVE(tm_differences);
// initialize m_contains_abs_sample
::libmaus::bitio::IndexedBitVector::unique_ptr_type tm_contains_abs_sample(new ::libmaus::bitio::IndexedBitVector( (v.size()+nndblocksize-1)/nndblocksize ));
m_contains_abs_sample = UNIQUE_PTR_MOVE(tm_contains_abs_sample);
ones = 0;
for (uint64_t i=0, last_one_pos=0; i < v.size(); ++i)
{
if ( (v)[i])
{
++ones;
if ((ones % nndblocksize) == 0)
{
// insert absolute samples
assert ( ones/nndblocksize < m_abs_samples->size() );
(*m_abs_samples)[ones/nndblocksize] = i;
assert ( i/nndblocksize < m_contains_abs_sample->size() );
(*m_contains_abs_sample)[i/nndblocksize] = 1;
}
else
{
assert ( ones - ones/nndblocksize - 1 < m_differences->size() );
(*m_differences)[ones - ones/nndblocksize - 1] = i - last_one_pos;
}
last_one_pos = i;
}
}
m_contains_abs_sample->setupIndex();
}
/*! \param bp The balanced parentheses sequence for that the pioneers should be calculated.
* \param block_size Size of the blocks for which the pioneers should be calculated.
* \param pioneer_bitmap Reference to the resulting bit_vector.
* \par Time complexity
* \f$ \Order{n} \f$, where \f$ n=\f$bp.size()
* \par Space complexity
* \f$ \Order{2n + n} \f$ bits: \f$n\f$ bits for input, \f$n\f$ bits for output, and \f$n\f$ bits for a succinct stack.
* \pre The parentheses sequence represented by bp has to be balanced.
*/
static ::libmaus::bitio::IndexedBitVector::unique_ptr_type calculatePioneerBitVector(::libmaus::bitio::BitVector const & bp, uint64_t const block_size)
{
::libmaus::bitio::IndexedBitVector::unique_ptr_type Ppioneer_bitmap(new ::libmaus::bitio::IndexedBitVector(bp.size()));
::libmaus::bitio::IndexedBitVector & pioneer_bitmap = *Ppioneer_bitmap;
IncreasingStack opening_parenthesis(bp.size());
uint64_t cur_pioneer_block = 0;
uint64_t last_start = 0;
uint64_t last_j = 0;
uint64_t cur_block=0;
uint64_t first_index_in_block=0;
// calculate positions of findclose and findopen pioneers
for(uint64_t j=0, new_block=block_size; j < bp.size(); ++j, --new_block)
{
if( !(new_block) )
{
cur_pioneer_block = j/block_size;
++cur_block;
first_index_in_block = j;
new_block = block_size;
}
// opening parenthesis
if( bp[j] )
{
/*j < bp.size() is not neccecssary as the last parenthesis is always a closing one*/
/* if closing par immediately follows opening, skip both and carry on */
if( new_block>1 and !bp[j+1] )
{
++j;
--new_block;
}
/* otherwise push opening par */
else
{
opening_parenthesis.push(j);
}
}
else
{
uint64_t const start = opening_parenthesis.top();
opening_parenthesis.pop();
// if start is not in this block (i.e. far parenthesis)
if( start < first_index_in_block )
{
// same block as previous pioneer
if( (start/block_size)==cur_pioneer_block )
{
// erase previous pioneer
pioneer_bitmap[last_start] = false;
pioneer_bitmap[last_j] = false;
}
// set this pioneer
pioneer_bitmap[start] = true;
pioneer_bitmap[j] = true;
cur_pioneer_block = start/block_size;
last_start = start;
last_j = j;
}
}
}
pioneer_bitmap.setupIndex();
return UNIQUE_PTR_MOVE(Ppioneer_bitmap);
}