/usr/include/sdsl/select_support_mcl.hpp is in libsdsl-dev 2.0.3-4.
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Copyright (C) 2008 Simon Gog
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/ .
*/
/*! \file select_support_mcl.hpp
\brief select_support_mcl.hpp contains classes that support a sdsl::bit_vector with constant time select information.
\author Simon Gog
*/
#ifndef INCLUDED_SDSL_SELECT_SUPPORT_MCL
#define INCLUDED_SDSL_SELECT_SUPPORT_MCL
#include "int_vector.hpp"
#include "util.hpp"
#include "select_support.hpp"
//! Namespace for the succinct data structure library.
namespace sdsl
{
//! A class supporting constant time select queries.
/*!
* \par Space usage
* The space usage of the data structure depends on the number of \f$ m \f$ of ones in the
* original bitvector $b$. We store the position of every $4096$th set bit
* (called L1-sampled bits) of $b$.
* This takes in the worst case \f$\frac{m}{4096} \log{n} \leq \frac{64}{n}\f$ bits.
* Next,
* (1) if the distance of two adjacent L1-sampled bits $b[i]$ and $b[j]$
* is greater or equal than $\log^4 n$, then
* we store each of the 4096 positions of the set $b$ in [i..j-1] with
* $\log{n}$ bits. This results in at most
* \$ \frac{4096\cdot \log n}{\log^4 n}=\frac{4096}{\log^3 n}\$ bits per bit.
* For a bitvector of 1GB, i.e. \f$ \log n = 35 \f$ we get about 0.01 bits per bit.
* If the $j-i+1 < \log^4 n$ then
* (2) we store the relative position of every $64$th set bit (called L2-sampled bits)
* in b[i..j-1] in at most $4\log\log n$ bits per L2-sampled bits.
* An pessimistic upper bound for the space would be
* \f$ \frac{4\log\log n}{64} \leq \frac{24}{64} = 0.375\f$ bit per
* bit (since $\log\log n\leq 6$. It is very pessimistic, since we store
* the relative position in $\log\log(j-i+1)\leq \log\log n$ bits.
*
* \tparam t_b Bit pattern `0`,`1`,`10`,`01` which should be ranked.
* \tparam t_pat_len Length of the bit pattern.
*
* The implementation is a practical variant of the following reference:
*
* \par Reference
* David Clark:
* PhD Thesis: Compact Pat Trees
* University of Waterloo, 1996 (Section 2.2.2).
* http://www.nlc-bnc.ca/obj/s4/f2/dsk3/ftp04/nq21335.pdf
*
* @ingroup select_support_group
*/
template<uint8_t t_b=1, uint8_t t_pat_len=1>
class select_support_mcl : public select_support
{
private:
static_assert(t_b == 1u or t_b == 0u or t_b == 10u , "select_support_mcl: bit pattern must be `0`,`1`,`10` or `01`");
static_assert(t_pat_len == 1u or t_pat_len == 2u , "select_support_mcl: bit pattern length must be 1 or 2");
public:
typedef bit_vector bit_vector_type;
enum { bit_pat = t_b };
private:
uint32_t m_logn = 0, // \f$ log(size) \f$
m_logn2 = 0, // \f$ log^2(size) \f$
m_logn4 = 0; // \f$ log^4(size) \f$
// entry i of m_superblock equals the answer to select_1(B,i*4096)
int_vector<0> m_superblock;
int_vector<0>* m_longsuperblock = nullptr;
int_vector<0>* m_miniblock = nullptr;
size_type m_arg_cnt = 0;
void copy(const select_support_mcl<t_b, t_pat_len>& ss);
void initData();
void init_fast(const bit_vector* v=nullptr);
public:
explicit select_support_mcl(const bit_vector* v=nullptr);
select_support_mcl(const select_support_mcl<t_b,t_pat_len>& ss);
select_support_mcl(select_support_mcl<t_b,t_pat_len>&& ss);
~select_support_mcl();
void init_slow(const bit_vector* v=nullptr);
//! Select function
inline size_type select(size_type i) const;
//! Alias for select(i).
inline size_type operator()(size_type i)const;
size_type serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const;
void load(std::istream& in, const bit_vector* v=nullptr);
void set_vector(const bit_vector* v=nullptr);
select_support_mcl<t_b, t_pat_len>& operator=(const select_support_mcl& ss);
select_support_mcl<t_b, t_pat_len>& operator=(select_support_mcl&&);
void swap(select_support_mcl<t_b, t_pat_len>& ss);
};
template<uint8_t t_b, uint8_t t_pat_len>
select_support_mcl<t_b,t_pat_len>::select_support_mcl(const bit_vector* f_v):select_support(f_v)
{
if (t_pat_len>1 or(v!=nullptr and v->size() < 100000))
init_slow(v);
else
init_fast(v);
return;
}
template<uint8_t t_b, uint8_t t_pat_len>
select_support_mcl<t_b,t_pat_len>::select_support_mcl(const select_support_mcl& ss):select_support(ss.m_v)
{
copy(ss);
}
template<uint8_t t_b, uint8_t t_pat_len>
select_support_mcl<t_b,t_pat_len>::select_support_mcl(select_support_mcl&& ss) : select_support(ss.m_v)
{
*this = std::move(ss);
}
template<uint8_t t_b, uint8_t t_pat_len>
select_support_mcl<t_b, t_pat_len>& select_support_mcl<t_b,t_pat_len>::operator=(const select_support_mcl& ss)
{
if (this != &ss) {
copy(ss);
}
return *this;
}
template<uint8_t t_b, uint8_t t_pat_len>
select_support_mcl<t_b, t_pat_len>& select_support_mcl<t_b,t_pat_len>::operator=(select_support_mcl&& ss)
{
if (this != &ss) {
m_logn = ss.m_logn; // copy log n
m_logn2 = ss.m_logn2; // copy (logn)^2
m_logn4 = ss.m_logn4; // copy (logn)^4
m_superblock = std::move(ss.m_superblock); // move long superblock
m_arg_cnt = ss.m_arg_cnt; // copy count of 1-bits
m_v = ss.m_v; // copy pointer to the supported bit vector
if (m_longsuperblock!=nullptr)
delete [] m_longsuperblock;
m_longsuperblock = ss.m_longsuperblock;
ss.m_longsuperblock = nullptr;
if (m_miniblock!=nullptr)
delete [] m_miniblock;
m_miniblock = ss.m_miniblock;
ss.m_miniblock = nullptr;
}
return *this;
}
template<uint8_t t_b, uint8_t t_pat_len>
void select_support_mcl<t_b,t_pat_len>::swap(select_support_mcl& ss)
{
std::swap(m_logn, ss.m_logn);
std::swap(m_logn2, ss.m_logn2);
std::swap(m_logn4, ss.m_logn4);
m_superblock.swap(ss.m_superblock);
std::swap(m_longsuperblock, ss.m_longsuperblock);
std::swap(m_miniblock, ss.m_miniblock);
std::swap(m_arg_cnt, ss.m_arg_cnt);
}
template<uint8_t t_b, uint8_t t_pat_len>
void select_support_mcl<t_b,t_pat_len>::copy(const select_support_mcl<t_b, t_pat_len>& ss)
{
m_logn = ss.m_logn; // copy log n
m_logn2 = ss.m_logn2; // copy (logn)^2
m_logn4 = ss.m_logn4; // copy (logn)^4
m_superblock = ss.m_superblock; // copy long superblock
m_arg_cnt = ss.m_arg_cnt; // copy count of 1-bits
m_v = ss.m_v; // copy pointer to the supported bit vector
size_type sb = (m_arg_cnt+4095)>>12;
if (m_longsuperblock!=nullptr)
delete [] m_longsuperblock;
m_longsuperblock = nullptr;
if (ss.m_longsuperblock!=nullptr) {
m_longsuperblock = new int_vector<0>[sb]; //copy longsuperblocks
for (size_type i=0; i<sb; ++i) {
m_longsuperblock[i] = ss.m_longsuperblock[i];
}
}
if (m_miniblock!=nullptr)
delete [] m_miniblock;
m_miniblock = nullptr;
if (ss.m_miniblock!=nullptr) {
m_miniblock = new int_vector<0>[sb]; // copy miniblocks
for (size_type i=0; i<sb; ++i) {
m_miniblock[i] = ss.m_miniblock[i];
}
}
}
template<uint8_t t_b, uint8_t t_pat_len>
select_support_mcl<t_b,t_pat_len>::~select_support_mcl()
{
if (m_longsuperblock!=nullptr)
delete[] m_longsuperblock;
if (m_miniblock!=nullptr)
delete[] m_miniblock;
}
template<uint8_t t_b, uint8_t t_pat_len>
void select_support_mcl<t_b,t_pat_len>::init_slow(const bit_vector* v)
{
set_vector(v);
initData();
if (m_v==nullptr)
return;
// Count the number of arguments in the bit vector
m_arg_cnt = select_support_trait<t_b,t_pat_len>::arg_cnt(*v);
const size_type SUPER_BLOCK_SIZE = 4096;
if (m_arg_cnt==0) // if there are no arguments in the vector we are done...
return;
size_type sb = (m_arg_cnt+SUPER_BLOCK_SIZE-1)/SUPER_BLOCK_SIZE; // number of superblocks
if (m_miniblock != nullptr) delete [] m_miniblock;
m_miniblock = new int_vector<0>[sb];
m_superblock = int_vector<0>(sb, 0, m_logn);
size_type arg_position[SUPER_BLOCK_SIZE], arg_cnt=0;
size_type sb_cnt=0;
for (size_type i=0; i < v->size(); ++i) {
if (select_support_trait<t_b,t_pat_len>::found_arg(i, *v)) {
arg_position[ arg_cnt%SUPER_BLOCK_SIZE ] = i;
assert(arg_position[arg_cnt%SUPER_BLOCK_SIZE] == i);
++arg_cnt;
if (arg_cnt % SUPER_BLOCK_SIZE == 0 or arg_cnt == m_arg_cnt) { //
assert(sb_cnt < sb);
m_superblock[sb_cnt] = arg_position[0];
size_type pos_diff = arg_position[(arg_cnt-1)%SUPER_BLOCK_SIZE]-arg_position[0];
if (pos_diff > m_logn4) { // longblock
if (m_longsuperblock == nullptr) m_longsuperblock = new int_vector<0>[sb]; // create longsuperblock
m_longsuperblock[sb_cnt] = int_vector<0>(SUPER_BLOCK_SIZE, 0, bits::hi(arg_position[(arg_cnt-1)%SUPER_BLOCK_SIZE]) + 1);
for (size_type j=0; j <= (arg_cnt-1)%SUPER_BLOCK_SIZE ; ++j) m_longsuperblock[sb_cnt][j] = arg_position[j]; // copy argument positions to longsuperblock
} else { // short block
m_miniblock[sb_cnt] = int_vector<0>(64, 0, bits::hi(pos_diff)+1);
for (size_type j=0; j <= (arg_cnt-1)%SUPER_BLOCK_SIZE; j+=64) {
m_miniblock[sb_cnt][j/64] = arg_position[j]-arg_position[0];
}
}
++sb_cnt;
}
}
}
}
// TODO: find bug, detected by valgrind
template<uint8_t t_b, uint8_t t_pat_len>
void select_support_mcl<t_b,t_pat_len>::init_fast(const bit_vector* v)
{
set_vector(v);
initData();
if (m_v==nullptr)
return;
// Count the number of arguments in the bit vector
m_arg_cnt = select_support_trait<t_b,t_pat_len>::arg_cnt(*v);
const size_type SUPER_BLOCK_SIZE = 64*64;
if (m_arg_cnt==0) // if there are no arguments in the vector we are done...
return;
// size_type sb = (m_arg_cnt+63+SUPER_BLOCK_SIZE-1)/SUPER_BLOCK_SIZE; // number of superblocks, add 63 as the last block could contain 63 uninitialized bits
size_type sb = (m_arg_cnt+SUPER_BLOCK_SIZE-1)/SUPER_BLOCK_SIZE; // number of superblocks
if (m_miniblock != nullptr) delete [] m_miniblock;
m_miniblock = new int_vector<0>[sb];
m_superblock = int_vector<0>(sb, 0, m_logn);// TODO: hier koennte man logn noch optimieren...s
bit_vector::size_type arg_position[SUPER_BLOCK_SIZE];
const uint64_t* data = v->data();
uint64_t carry_new=0;
size_type last_k64 = 1, sb_cnt=0;
for (size_type i=0, cnt_old=0, cnt_new=0, last_k64_sum=1; i < v->capacity(); i+=64, ++data) {
cnt_new += select_support_trait<t_b, t_pat_len>::args_in_the_word(*data, carry_new);
if (cnt_new >= last_k64_sum) {
arg_position[last_k64-1] = i + select_support_trait<t_b, t_pat_len>::ith_arg_pos_in_the_word(*data, last_k64_sum - cnt_old, carry_new);
last_k64 += 64;
last_k64_sum += 64;
if (last_k64 == SUPER_BLOCK_SIZE+1) {
m_superblock[sb_cnt] = arg_position[0];
size_type pos_of_last_arg_in_the_block = arg_position[last_k64-65];
for (size_type i=arg_position[last_k64-65]+1, j=last_k64-65; i < v->size() and j < SUPER_BLOCK_SIZE; ++i)
if (select_support_trait<t_b,t_pat_len>::found_arg(i, *v)) {
pos_of_last_arg_in_the_block = i;
++j;
}
size_type pos_diff = pos_of_last_arg_in_the_block - arg_position[0];
if (pos_diff > m_logn4) { // long block
if (m_longsuperblock == nullptr) m_longsuperblock = new int_vector<0>[sb+1]; // create longsuperblock
// GEANDERT am 2010-07-17 +1 nach pos_of_last_arg..
m_longsuperblock[sb_cnt] = int_vector<0>(SUPER_BLOCK_SIZE, 0, bits::hi(pos_of_last_arg_in_the_block) + 1);
for (size_type j=arg_position[0], k=0; k < SUPER_BLOCK_SIZE and j <= pos_of_last_arg_in_the_block; ++j)
if (select_support_trait<t_b, t_pat_len>::found_arg(j, *v)) {
if (k>=SUPER_BLOCK_SIZE) {
for (size_type ii=0; ii < SUPER_BLOCK_SIZE; ++ii) {
std::cout<<"("<<ii<<","<<m_longsuperblock[sb_cnt][ii]<<") ";
}
std::cout << std::endl;
std::cout<<"k="<<k<<" SUPER_BLOCK_SIZE="<<SUPER_BLOCK_SIZE<<std::endl;
std::cout<<"pos_of_last_arg_in_the_block"<< pos_of_last_arg_in_the_block<<std::endl;
std::cout.flush();
}
m_longsuperblock[sb_cnt][k++] = j;
}
} else {
m_miniblock[sb_cnt] = int_vector<0>(64, 0, bits::hi(pos_diff)+1);
for (size_type j=0; j < SUPER_BLOCK_SIZE; j+=64) {
m_miniblock[sb_cnt][j/64] = arg_position[j]-arg_position[0];
}
}
++sb_cnt;
last_k64 = 1;
}
}
cnt_old = cnt_new;
}
// handle last block: append long superblock
if (last_k64 > 1) {
if (m_longsuperblock == nullptr) m_longsuperblock = new int_vector<0>[sb+1]; // create longsuperblock
m_longsuperblock[sb_cnt] = int_vector<0>(SUPER_BLOCK_SIZE, 0, bits::hi(v->size()-1) + 1);
for (size_type i=arg_position[0],k=0; i < v->size(); ++i) {
if (select_support_trait<t_b, t_pat_len>::found_arg(i, *v)) {
m_longsuperblock[sb_cnt][k++] = i;
}
}
++sb_cnt;
}
}
template<uint8_t t_b, uint8_t t_pat_len>
inline auto select_support_mcl<t_b,t_pat_len>::select(size_type i)const -> size_type
{
assert(i > 0 and i <= m_arg_cnt);
i = i-1;
size_type sb_idx = i>>12; // i/4096
size_type offset = i&0xFFF; // i%4096
if (m_longsuperblock!=nullptr and !m_longsuperblock[sb_idx].empty()) {
return m_longsuperblock[sb_idx][offset];
} else {
if ((offset&0x3F)==0) {
assert(sb_idx < m_superblock.size());
assert((offset>>6) < m_miniblock[sb_idx].size());
return m_superblock[sb_idx] + m_miniblock[sb_idx][offset>>6/*/64*/];
} else {
i = i-(sb_idx<<12)-((offset>>6)<<6);
// now i > 0 and i <= 64
assert(i > 0);
size_type pos = m_superblock[sb_idx] + m_miniblock[sb_idx][offset>>6] + 1;
// now pos is the position from where we search for the ith argument
size_type word_pos = pos>>6;
size_type word_off = pos&0x3F;
const uint64_t* data = m_v->data() + word_pos;
uint64_t carry = select_support_trait<t_b,t_pat_len>::init_carry(data, word_pos);
size_type args = select_support_trait<t_b,t_pat_len>::args_in_the_first_word(*data, word_off, carry);
if (args >= i) {
return (word_pos<<6)+select_support_trait<t_b,t_pat_len>::ith_arg_pos_in_the_first_word(*data, i, word_off, carry);
}
word_pos+=1;
size_type sum_args = args;
carry = select_support_trait<t_b,t_pat_len>::get_carry(*data);
uint64_t old_carry = carry;
args = select_support_trait<t_b,t_pat_len>::args_in_the_word(*(++data), carry);
while (sum_args + args < i) {
sum_args += args;
assert(data+1 < m_v->data() + (m_v->capacity()>>6));
old_carry = carry;
args = select_support_trait<t_b,t_pat_len>::args_in_the_word(*(++data), carry);
word_pos+=1;
}
return (word_pos<<6) +
select_support_trait<t_b,t_pat_len>::ith_arg_pos_in_the_word(*data, i-sum_args, old_carry);
}
}
}
template<uint8_t t_b, uint8_t t_pat_len>
inline auto select_support_mcl<t_b,t_pat_len>::operator()(size_type i)const -> size_type
{
return select(i);
}
template<uint8_t t_b, uint8_t t_pat_len>
void select_support_mcl<t_b,t_pat_len>::initData()
{
m_arg_cnt = 0;
if (nullptr == m_v) {
m_logn = m_logn2 = m_logn4 = 0;
} else {
m_logn = bits::hi(m_v->capacity())+1; // TODO maybe it's better here to take a max(...,12)
m_logn2 = m_logn*m_logn;
m_logn4 = m_logn2*m_logn2;
}
if (nullptr != m_longsuperblock)
delete[] m_longsuperblock;
m_longsuperblock = nullptr;
if (nullptr != m_miniblock)
delete[] m_miniblock;
m_miniblock = nullptr;
}
template<uint8_t t_b, uint8_t t_pat_len>
void select_support_mcl<t_b,t_pat_len>::set_vector(const bit_vector* v)
{
m_v = v;
}
template<uint8_t t_b, uint8_t t_pat_len>
auto select_support_mcl<t_b,t_pat_len>::serialize(std::ostream& out, structure_tree_node* v, std::string name)const -> size_type
{
structure_tree_node* child = structure_tree::add_child(v, name, util::class_name(*this));
size_type written_bytes = 0;
// write the number of 1-bits in the supported bit_vector
out.write((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
written_bytes = sizeof(size_type)/sizeof(char);
// number of superblocks in the data structure
size_type sb = (m_arg_cnt+4095)>>12;
if (m_arg_cnt) { // if there exists 1-bits to be supported
written_bytes += m_superblock.serialize(out, child, "superblock"); // serialize superblocks
bit_vector mini_or_long;// Helper vector: mini or long block?
if (m_longsuperblock!=nullptr) {
mini_or_long.resize(sb); // resize indicator bit_vector to the number of superblocks
for (size_type i=0; i< sb; ++i)
mini_or_long[i] = !m_miniblock[i].empty();
}
written_bytes += mini_or_long.serialize(out, child, "mini_or_long");
size_type written_bytes_long = 0;
size_type written_bytes_mini = 0;
for (size_type i=0; i < sb; ++i)
if (!mini_or_long.empty() and !mini_or_long[i]) {
written_bytes_long += m_longsuperblock[i].serialize(out);
} else {
written_bytes_mini += m_miniblock[i].serialize(out);
}
written_bytes += written_bytes_long;
written_bytes += written_bytes_mini;
structure_tree_node* child_long = structure_tree::add_child(child, "longsuperblock", util::class_name(m_longsuperblock));
structure_tree::add_size(child_long, written_bytes_long);
structure_tree_node* child_mini = structure_tree::add_child(child, "minisuperblock", util::class_name(m_miniblock));
structure_tree::add_size(child_mini, written_bytes_mini);
}
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
template<uint8_t t_b, uint8_t t_pat_len>
void select_support_mcl<t_b,t_pat_len>::load(std::istream& in, const bit_vector* v)
{
set_vector(v);
initData();
// read the number of 1-bits in the supported bit_vector
in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
size_type sb = (m_arg_cnt+4095)>>12;
if (m_arg_cnt) { // if there exists 1-bits to be supported
m_superblock.load(in); // load superblocks
if (m_miniblock!=nullptr) {
delete[] m_miniblock;
m_miniblock = nullptr;
}
if (m_longsuperblock!=nullptr) {
delete[] m_longsuperblock;
m_longsuperblock = nullptr;
}
bit_vector mini_or_long;// Helper vector: mini or long block?
mini_or_long.load(in); // Load the helper vector
m_miniblock = new int_vector<0>[sb]; // Create miniblock int_vector<0>
if (!mini_or_long.empty())
m_longsuperblock = new int_vector<0>[sb]; // Create longsuperblock int_vector<0>
for (size_type i=0; i < sb; ++i)
if (!mini_or_long.empty() and not mini_or_long[i]) {
m_longsuperblock[i].load(in);
} else {
m_miniblock[i].load(in);
}
}
}
}
#endif
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