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/* sdsl - succinct data structures library
Copyright (C) 2012 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 csa_sampling_strategy.hpp
\brief csa_sampling_strategy.hpp includes different strategy classes for suffix array sampling in the CSAs.
\author Simon Gog
*/
#ifndef INCLUDED_CSA_SAMPLING_STRATEGY
#define INCLUDED_CSA_SAMPLING_STRATEGY
/*
* Text = ABCDEFABCDEF$
* 0123456789012
* sa_sample_dens = 2
* *1 SA *2
* * 12 * $
* 06 * ABCDEF$
* * 00 * ABCDEFABCDEF$
* 07 BCDEF$
* * 01 BCDEFABCDEF$
* 08 * CDEF$
* * 02 * CDEFABCDEF$
* 09 DEF$
* * 03 DEFABCDEF$
* 10 * EF$
* * 04 * EFABCDEF$
* 11 F$
* * 05 FABCDEF$
*
* The first sampling (*1) is called suffix order sampling. It has the advantage, that
* we don't need to store a bitvector, which marks the sampled suffixes, since a suffix
* at index \(i\) in the suffix array is marked if \( 0 \equiv i \mod sa_sample_dens \).
*
* The second sampling (*2) is called text order sampling. It is also called regular in [1].
*
* [1] P.Ferragina, J. Siren, R. Venturini: Distribution-Aware Compressed Full-Text Indexes, ESA 2011
*/
#include "int_vector.hpp"
#include "csa_alphabet_strategy.hpp" // for key_trait
#include "inv_perm_support.hpp"
#include "wavelet_trees.hpp"
#include <set>
#include <tuple>
namespace sdsl
{
template<class t_csa, uint8_t t_width=0>
class _sa_order_sampling : public int_vector<t_width>
{
public:
typedef int_vector<t_width> base_type;
typedef typename base_type::size_type size_type; // make typedefs of base_type visible
typedef typename base_type::value_type value_type; //
enum { sample_dens = t_csa::sa_sample_dens };
enum { text_order = false };
typedef sa_sampling_tag sampling_category;
//! Default constructor
_sa_order_sampling() {}
//! Constructor
/*
* \param cconfig Cache configuration (SA is expected to be cached.).
* \param csa Pointer to the corresponding CSA. Not used in this class.
* \par Time complexity
* Linear in the size of the suffix array.
*/
_sa_order_sampling(const cache_config& cconfig, SDSL_UNUSED const t_csa* csa=nullptr)
{
int_vector_buffer<> sa_buf(cache_file_name(conf::KEY_SA, cconfig));
size_type n = sa_buf.size();
this->width(bits::hi(n)+1);
this->resize((n+sample_dens-1)/sample_dens);
for (size_type i=0, cnt_mod=sample_dens, cnt_sum=0; i < n; ++i, ++cnt_mod) {
size_type sa = sa_buf[i];
if (sample_dens == cnt_mod) {
cnt_mod = 0;
base_type::operator[](cnt_sum++) = sa;
}
}
}
//! Determine if index i is sampled or not
inline bool is_sampled(size_type i) const
{
return 0 == (i % sample_dens);
}
//! Return the suffix array value for the sampled index i
inline value_type operator[](size_type i) const
{
return base_type::operator[](i/sample_dens);
}
};
template<uint8_t t_width=0>
struct sa_order_sa_sampling {
template<class t_csa>
using type = _sa_order_sampling<t_csa, t_width>;
using sampling_category = sa_sampling_tag;
};
template<class t_csa,
class t_bv=bit_vector,
class t_rank=typename t_bv::rank_1_type,
uint8_t t_width=0
>
class _text_order_sampling : public int_vector<t_width>
{
private:
t_bv m_marked;
t_rank m_rank_marked;
public:
typedef int_vector<t_width> base_type;
typedef typename base_type::size_type size_type; // make typedefs of base_type visible
typedef typename base_type::value_type value_type; //
typedef t_bv bv_type;
enum { sample_dens = t_csa::sa_sample_dens };
enum { text_order = true };
typedef sa_sampling_tag sampling_category;
const bv_type& marked = m_marked;
const t_rank& rank_marked = m_rank_marked;
//! Default constructor
_text_order_sampling() {}
//! Constructor
/*
* \param cconfig Cache configuration (SA is expected to be cached.).
* \param csa Pointer to the corresponding CSA. Not used in this class.
* \par Time complexity
* Linear in the size of the suffix array.
*/
_text_order_sampling(const cache_config& cconfig, SDSL_UNUSED const t_csa* csa=nullptr)
{
int_vector_buffer<> sa_buf(cache_file_name(conf::KEY_SA, cconfig));
size_type n = sa_buf.size();
bit_vector marked(n, 0); // temporary bitvector for the marked text positions
this->width(bits::hi(n/sample_dens)+1);
this->resize((n+sample_dens-1)/sample_dens);
for (size_type i=0, sa_cnt=0; i < n; ++i) {
size_type sa = sa_buf[i];
if (0 == (sa % sample_dens)) {
marked[i] = 1;
base_type::operator[](sa_cnt++) = sa / sample_dens;
}
}
m_marked = std::move(t_bv(marked));
util::init_support(m_rank_marked, &m_marked);
}
//! Copy constructor
_text_order_sampling(const _text_order_sampling& st) : base_type(st)
{
m_marked = st.m_marked;
m_rank_marked = st.m_rank_marked;
m_rank_marked.set_vector(&m_marked);
}
//! Determine if index i is sampled or not
inline bool is_sampled(size_type i) const
{
return m_marked[i];
}
//! Return the suffix array value for the sampled index i
inline value_type operator[](size_type i) const
{
return base_type::operator[](m_rank_marked(i)) * sample_dens;
}
value_type condensed_sa(size_type i) const
{
return base_type::operator[](i);
}
//! Assignment operation
_text_order_sampling& operator=(const _text_order_sampling& st)
{
if (this != &st) {
base_type::operator=(st);
m_marked = st.m_marked;
m_rank_marked = st.m_rank_marked;
m_rank_marked.set_vector(&m_marked);
}
return *this;
}
//! Swap operation
void swap(_text_order_sampling& st)
{
base_type::swap(st);
m_marked.swap(st.m_marked);
util::swap_support(m_rank_marked, st.m_rank_marked, &m_marked, &(st.m_marked));
}
size_type serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const
{
structure_tree_node* child = structure_tree::add_child(v, name, util::class_name(*this));
size_type written_bytes = 0;
written_bytes += base_type::serialize(out, child, "samples");
written_bytes += m_marked.serialize(out, child, "marked");
written_bytes += m_rank_marked.serialize(out, child, "rank_marked");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
void load(std::istream& in)
{
base_type::load(in);
m_marked.load(in);
m_rank_marked.load(in);
m_rank_marked.set_vector(&m_marked);
}
};
template<class t_bit_vec=sd_vector<>,
class t_rank_sup=typename t_bit_vec::rank_1_type,
uint8_t t_width=0>
struct text_order_sa_sampling {
template<class t_csa>
using type = _text_order_sampling<t_csa, t_bit_vec, t_rank_sup, t_width>;
using sampling_category = sa_sampling_tag;
};
template<class t_csa,
class t_bv_sa=sd_vector<>,
class t_bv_isa=sd_vector<>,
class t_rank_sa=typename t_bv_sa::rank_1_type,
class t_select_isa=typename t_bv_isa::select_1_type
>
class _fuzzy_sa_sampling
{
private:
t_bv_sa m_marked_sa;
t_rank_sa m_rank_marked_sa;
t_bv_isa m_marked_isa;
t_select_isa m_select_marked_isa;
wt_int<rrr_vector<63>> m_inv_perm;
public:
typedef typename bit_vector::size_type size_type; // make typedefs of base_type visible
typedef typename bit_vector::value_type value_type; //
typedef t_bv_sa bv_sa_type;
enum { sample_dens = t_csa::sa_sample_dens };
enum { text_order = true };
typedef sa_sampling_tag sampling_category;
const t_bv_sa& marked_sa = m_marked_sa;
const t_rank_sa& rank_marked_sa = m_rank_marked_sa;
const t_bv_isa& marked_isa = m_marked_isa;
const t_select_isa& select_marked_isa = m_select_marked_isa;
//! Default constructor
_fuzzy_sa_sampling() {}
//! Constructor
/*
* \param cconfig Cache configuration (SA is expected to be cached.).
* \param csa Pointer to the corresponding CSA. Not used in this class.
* \par Time complexity
* Linear in the size of the suffix array.
*/
_fuzzy_sa_sampling(cache_config& cconfig, SDSL_UNUSED const t_csa* csa=nullptr)
{
{
// (2) check, if the suffix array is cached
if (!cache_file_exists(conf::KEY_ISA, cconfig)) {
auto event = memory_monitor::event("ISA");
construct_isa(cconfig);
}
register_cache_file(conf::KEY_SA, cconfig);
}
{
int_vector_buffer<> isa_buf(cache_file_name(conf::KEY_ISA, cconfig));
size_type n = isa_buf.size();
bit_vector marked_isa(n, 0); // temporary bitvector for marked ISA positions
bit_vector marked_sa(n, 0); // temporary bitvector for marked SA positions
int_vector<> inv_perm((n+sample_dens-1)/sample_dens, 0, bits::hi(n)+1);
size_type cnt = 0;
size_type runs = 1;
uint64_t min_prev_val = 0;
for (size_type i=0; i < n; i += sample_dens) {
size_type pos_min = i;
size_type pos_cnd = isa_buf[i] >= min_prev_val ? i : n;
for (size_type j=i+1; j < i+sample_dens and j < n; ++j) {
if (isa_buf[j] < isa_buf[pos_min]) pos_min = j;
if (isa_buf[j] >= min_prev_val) {
if (pos_cnd == n) {
pos_cnd = j;
} else if (isa_buf[j] < isa_buf[pos_cnd]) {
pos_cnd = j;
}
}
}
if (pos_cnd == n) { // increasing sequence can not be extended
pos_cnd = pos_min;
++runs;
}
min_prev_val = isa_buf[pos_cnd];
marked_isa[pos_cnd] = 1;
inv_perm[cnt++] = min_prev_val;
marked_sa[min_prev_val] = 1;
}
m_marked_isa = std::move(t_bv_isa(marked_isa));
util::init_support(m_select_marked_isa, &m_marked_isa);
{
rank_support_v<> rank_marked_sa(&marked_sa);
for (size_type i=0; i<inv_perm.size(); ++i) {
inv_perm[i] = rank_marked_sa(inv_perm[i]);
}
}
util::bit_compress(inv_perm);
m_marked_sa = std::move(t_bv_sa(marked_sa));
util::init_support(m_rank_marked_sa, &m_marked_sa);
std::string tmp_key = "fuzzy_isa_samples_"+util::to_string(util::pid())+"_"+util::to_string(util::id());
std::string tmp_file_name = cache_file_name(tmp_key, cconfig);
store_to_file(inv_perm, tmp_file_name);
construct(m_inv_perm, tmp_file_name, 0);
sdsl::remove(tmp_file_name);
}
}
//! Copy constructor
_fuzzy_sa_sampling(const _fuzzy_sa_sampling& st)
{
m_marked_sa = st.m_marked_sa;
m_rank_marked_sa = st.m_rank_marked_sa;
m_rank_marked_sa.set_vector(&m_marked_sa);
m_marked_isa = st.m_marked_isa;
m_select_marked_isa = st.m_select_marked_isa;
m_select_marked_isa.set_vector(&m_marked_isa);
m_inv_perm = st.m_inv_perm;
}
//! Determine if index i is sampled or not
inline bool is_sampled(size_type i) const
{
return m_marked_sa[i];
}
//! Return the suffix array value for the sampled index i
inline value_type operator[](size_type i) const
{
return m_select_marked_isa(m_inv_perm.select(1, m_rank_marked_sa(i))+1);
}
//! Return the inv permutation at position i (already condensed!!!)
inline value_type inv(size_type i) const
{
return m_inv_perm[i];
}
size_type size() const
{
return m_inv_perm.size();
}
//! Assignment operation
_fuzzy_sa_sampling& operator=(const _fuzzy_sa_sampling& st)
{
if (this != &st) {
m_marked_sa = st.m_marked_sa;
m_rank_marked_sa = st.m_rank_marked_sa;
m_rank_marked_sa.set_vector(&m_marked_sa);
m_marked_isa = st.m_marked_isa;
m_select_marked_isa = st.m_select_marked_isa;
m_select_marked_isa.set_vector(&m_marked_isa);
m_inv_perm = st.m_inv_perm;
}
return *this;
}
//! Swap operation
void swap(_fuzzy_sa_sampling& st)
{
m_marked_sa.swap(st.m_marked_sa);
util::swap_support(m_rank_marked_sa, st.m_rank_marked_sa, &m_marked_sa, &(st.m_marked_sa));
m_marked_isa.swap(st.m_marked_isa);
util::swap_support(m_select_marked_isa, st.m_select_marked_isa, &m_marked_isa, &(st.m_marked_isa));
m_inv_perm.swap(st.m_inv_perm);
}
size_type serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const
{
structure_tree_node* child = structure_tree::add_child(v, name, util::class_name(*this));
size_type written_bytes = 0;
written_bytes += m_marked_sa.serialize(out, child, "marked_sa");
written_bytes += m_rank_marked_sa.serialize(out, child, "rank_marked_sa");
written_bytes += m_marked_isa.serialize(out, child, "marked_isa");
written_bytes += m_select_marked_isa.serialize(out, child, "select_marked_isa");
written_bytes += m_inv_perm.serialize(out, child, "inv_perm");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
void load(std::istream& in)
{
m_marked_sa.load(in);
m_rank_marked_sa.load(in);
m_rank_marked_sa.set_vector(&m_marked_sa);
m_marked_isa.load(in);
m_select_marked_isa.load(in);
m_select_marked_isa.set_vector(&m_marked_isa);
m_inv_perm.load(in);
}
};
template<class t_bv_sa=sd_vector<>,
class t_bv_isa=sd_vector<>,
class t_rank_sa=typename t_bv_sa::rank_1_type,
class t_select_isa=typename t_bv_isa::select_1_type
>
struct fuzzy_sa_sampling {
template<class t_csa>
using type = _fuzzy_sa_sampling<t_csa, t_bv_sa, t_bv_isa,
t_rank_sa, t_select_isa>;
using sampling_category = sa_sampling_tag;
};
/*
* Text = ABCDEFABCDEF$
* 0123456789012
* sa_sample_dens = 4
* sa_sample_chars = {B,E}
* SA BWT (1)
* 12 F * $
* 06 F ABCDEF$
* 00 $ * ABCDEFABCDEF$
* 07 A BCDEF$
* 01 A BCDEFABCDEF$
* 08 B * CDEF$
* 02 B * CDEFABCDEF$
* 09 C DEF$
* 03 C DEFABCDEF$
* 10 D EF$
* 04 D * EFABCDEF$
* 11 E * F$
* 05 E * FABCDEF$
*
* In this sampling a suffix x=SA[i] is marked if x \( 0 \equiv x \mod sa_sample_dens \) or
* BWT[i] is contained in sa_sample_chars.
*/
template<class t_csa,
class t_bv=bit_vector,
class t_rank=typename t_bv::rank_1_type,
uint8_t t_width=0
>
class _bwt_sampling : public int_vector<t_width>
{
private:
t_bv m_marked;
t_rank m_rank_marked;
public:
typedef int_vector<t_width> base_type;
typedef typename base_type::size_type size_type; // make typedefs of base_type visible
typedef typename base_type::value_type value_type; //
enum { sample_dens = t_csa::sa_sample_dens };
enum { text_order = false };
typedef sa_sampling_tag sampling_category;
//! Default constructor
_bwt_sampling() {}
//! Constructor
/*
* \param cconfig Cache configuration (BWT,SA, and SAMPLE_CHARS are expected to be cached.).
* \param csa Pointer to the corresponding CSA. Not used in this class.
* \par Time complexity
* Linear in the size of the suffix array.
*/
_bwt_sampling(const cache_config& cconfig, SDSL_UNUSED const t_csa* csa=nullptr)
{
int_vector_buffer<> sa_buf(cache_file_name(conf::KEY_SA, cconfig));
int_vector_buffer<t_csa::alphabet_type::int_width>
bwt_buf(cache_file_name(key_trait<t_csa::alphabet_type::int_width>::KEY_BWT,cconfig));
size_type n = sa_buf.size();
bit_vector marked(n, 0); // temporary bitvector for the marked text positions
this->width(bits::hi(n)+1);
int_vector<> sample_char;
typedef typename t_csa::char_type char_type;
std::set<char_type> char_map;
if (load_from_cache(sample_char, conf::KEY_SAMPLE_CHAR,cconfig)) {
for (uint64_t i=0; i<sample_char.size(); ++i) {
char_map.insert((char_type)sample_char[i]);
}
}
size_type sa_cnt = 0;
for (size_type i=0; i < n; ++i) {
size_type sa = sa_buf[i];
char_type bwt = bwt_buf[i];
if (0 == (sa % sample_dens)) {
marked[i] = 1;
++sa_cnt;
} else if (char_map.find(bwt) != char_map.end()) {
marked[i] = 1;
++sa_cnt;
}
}
this->resize(sa_cnt);
sa_cnt = 0;
for (size_type i=0; i < n; ++i) {
size_type sa = sa_buf[i];
if (marked[i]) {
base_type::operator[](sa_cnt++) = sa;
}
}
util::assign(m_marked, marked);
util::init_support(m_rank_marked, &m_marked);
}
//! Copy constructor
_bwt_sampling(const _bwt_sampling& st) : base_type(st)
{
m_marked = st.m_marked;
m_rank_marked = st.m_rank_marked;
m_rank_marked.set_vector(&m_marked);
}
//! Determine if index i is sampled or not
inline bool is_sampled(size_type i) const
{
return m_marked[i];
}
//! Return the suffix array value for the sampled index i
inline value_type operator[](size_type i) const
{
return base_type::operator[](m_rank_marked(i)) * sample_dens;
}
//! Assignment operation
_bwt_sampling& operator=(const _bwt_sampling& st)
{
if (this != &st) {
base_type::operator=(st);
m_marked = st.m_marked;
m_rank_marked = st.m_rank_marked;
m_rank_marked.set_vector(&m_marked);
}
return *this;
}
//! Swap operation
void swap(_bwt_sampling& st)
{
base_type::swap(st);
m_marked.swap(st.m_marked);
util::swap_support(m_rank_marked, st.m_rank_marked, &m_marked, &(st.m_marked));
}
size_type serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const
{
structure_tree_node* child = structure_tree::add_child(v, name, util::class_name(*this));
size_type written_bytes = 0;
written_bytes += base_type::serialize(out, child, "samples");
written_bytes += m_marked.serialize(out, child, "marked");
written_bytes += m_rank_marked.serialize(out, child, "rank_marked");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
void load(std::istream& in)
{
base_type::load(in);
m_marked.load(in);
m_rank_marked.load(in);
m_rank_marked.set_vector(&m_marked);
}
};
template<class t_bit_vec=bit_vector,
class t_rank_sup=typename t_bit_vec::rank_1_type,
uint8_t t_width=0>
struct sa_bwt_sampling {
template<class t_csa>
using type = _bwt_sampling<t_csa, t_bit_vec, t_rank_sup, t_width>;
using sampling_category = sa_sampling_tag;
};
template<class t_csa, uint8_t t_width=0>
class _isa_sampling : public int_vector<t_width>
{
public:
typedef int_vector<t_width> base_type;
typedef typename base_type::size_type size_type; // make typedefs of base_type visible
typedef typename base_type::value_type value_type; //
typedef typename t_csa::sa_sample_type sa_type; // sa sample type
enum { sample_dens = t_csa::isa_sample_dens };
typedef isa_sampling_tag sampling_category;
//! Default constructor
_isa_sampling() {}
//! Constructor
/*
* \param cconfig Cache configuration (SA is expected to be cached.).
* \param sa_sample Pointer to the corresponding SA sampling. Not used in this class.
* \par Time complexity
* Linear in the size of the suffix array.
*/
_isa_sampling(const cache_config& cconfig, SDSL_UNUSED const sa_type* sa_sample=nullptr)
{
int_vector_buffer<> sa_buf(cache_file_name(conf::KEY_SA, cconfig));
size_type n = sa_buf.size();
if (n >= 1) { // so n+t_csa::isa_sample_dens >= 2
this->width(bits::hi(n)+1);
this->resize((n-1)/sample_dens+1);
}
for (size_type i=0; i < this->size(); ++i) base_type::operator[](i) = 0;
for (size_type i=0; i < n; ++i) {
size_type sa = sa_buf[i];
if ((sa % sample_dens) == 0) {
base_type::operator[](sa/sample_dens) = i;
}
}
}
//! Returns the ISA value at position j, where
inline value_type operator[](size_type i) const
{
return base_type::operator[](i/sample_dens);
}
//! Returns the rightmost ISA sample <= i and its position
inline std::tuple<value_type, size_type>
sample_leq(size_type i) const
{
size_type ci = i/sample_dens;
return std::make_tuple(base_type::operator[](ci), ci*sample_dens);
}
//! Returns the leftmost ISA sample >= i and its position
inline std::tuple<value_type, size_type>
sample_qeq(size_type i) const
{
size_type ci = (i/sample_dens + 1) % this->size();
return std::make_tuple(base_type::operator[](ci), ci*sample_dens);
}
//! Load sampling from disk
void load(std::istream& in, SDSL_UNUSED const sa_type* sa_sample=nullptr)
{
base_type::load(in);
}
void set_vector(SDSL_UNUSED const sa_type*) {}
};
template<uint8_t t_width=0>
struct isa_sampling {
template<class t_csa>
using type = _isa_sampling<t_csa, t_width>;
using sampling_category = isa_sampling_tag;
};
template<class t_csa, class t_inv_perm, class t_sel>
class _text_order_isa_sampling_support
{
static_assert(t_csa::sa_sample_dens == t_csa::isa_sample_dens,
"ISA sampling requires: sa_sample_dens == isa_sample_dens");
public:
typedef typename bit_vector::size_type size_type;
typedef typename bit_vector::value_type value_type;
typedef typename t_csa::sa_sample_type sa_type; // sa sample type
typedef typename sa_type::bv_type bv_type; // bitvector type used to mark SA samples
enum { sample_dens = t_csa::isa_sample_dens };
typedef isa_sampling_tag sampling_category;
private:
t_sel m_select_marked;
t_inv_perm m_inv_perm;
public:
const t_sel& select_marked = m_select_marked;
//! Default constructor
_text_order_isa_sampling_support() {}
//! Constructor
/*
* \param cconfig Cache configuration. (Not used in this class)
* \param sa_sample Pointer to the corresponding SA sampling..
* \par Time complexity
* Linear in the size of the suffix array.
*/
_text_order_isa_sampling_support(SDSL_UNUSED const cache_config& cconfig,
const typename std::enable_if<sa_type::text_order, sa_type*>::type sa_sample)
{
// and initialize the select support on bitvector marked
m_select_marked = t_sel(&(sa_sample->marked));
const int_vector<>* perm = (const int_vector<>*)sa_sample;
m_inv_perm = t_inv_perm(perm);
m_inv_perm.set_vector(perm);
}
//! Copy constructor
_text_order_isa_sampling_support(const _text_order_isa_sampling_support& st)
{
m_inv_perm = st.m_inv_perm;
m_select_marked = st.m_select_marked;
}
//! Return the inverse suffix array value for the sampled index i
inline value_type operator[](size_type i) const
{
return m_select_marked(m_inv_perm[i/sample_dens]+1);
}
//! Returns the rightmost ISA sample <= i and its position
inline std::tuple<value_type, size_type>
sample_leq(size_type i) const
{
size_type ci = i/sample_dens;
return std::make_tuple(m_select_marked(m_inv_perm[ci]+1), ci*sample_dens);
}
//! Returns the leftmost ISA sample >= i and its position
inline std::tuple<value_type, size_type>
sample_qeq(size_type i) const
{
size_type ci = (i/sample_dens + 1) % m_inv_perm.size();
return std::make_tuple(m_select_marked(m_inv_perm[ci]+1), ci*sample_dens);
}
//! Assignment operation
_text_order_isa_sampling_support& operator=(const _text_order_isa_sampling_support& st)
{
if (this != &st) {
m_inv_perm = st.m_inv_perm;
m_select_marked = st.m_select_marked;
}
return *this;
}
//! Swap operation
void swap(_text_order_isa_sampling_support& st)
{
if (this != &st) {
m_inv_perm.swap(st.m_inv_perm);
m_select_marked.swap(st.m_select_marked);
}
}
size_type serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const
{
structure_tree_node* child = structure_tree::add_child(v, name, util::class_name(*this));
size_type written_bytes = 0;
written_bytes += m_inv_perm.serialize(out, child, "inv_perm");
written_bytes += m_select_marked.serialize(out, child, "select_marked");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
//! Load sampling from disk
void load(std::istream& in, const sa_type* sa_sample=nullptr)
{
m_inv_perm.load(in);
m_select_marked.load(in);
set_vector(sa_sample);
}
void set_vector(const sa_type* sa_sample=nullptr)
{
if (sa_sample == nullptr) {
m_select_marked.set_vector(nullptr);
m_inv_perm.set_vector(nullptr);
} else {
m_select_marked.set_vector(&(sa_sample->marked));
m_inv_perm.set_vector((const int_vector<>*)sa_sample);
}
}
};
template<class t_inv_perm=inv_perm_support<8>, class t_sel=void>
struct text_order_isa_sampling_support {
template<class t_csa>
using type = _text_order_isa_sampling_support<
t_csa,
t_inv_perm,
typename std::conditional<std::is_void<t_sel>::value,
typename t_csa::sa_sample_type::bv_type::select_1_type,
t_sel>::type>;
using sampling_category = isa_sampling_tag;
};
template<class t_csa, class t_select_sa>
class _fuzzy_isa_sampling_support
{
static_assert(t_csa::sa_sample_dens == t_csa::isa_sample_dens,
"ISA sampling requires: sa_sample_dens==isa_sample_dens");
public:
typedef typename bit_vector::size_type size_type;
typedef typename bit_vector::value_type value_type;
typedef typename t_csa::sa_sample_type sa_type; // sa sample type
enum { sample_dens = t_csa::isa_sample_dens };
typedef isa_sampling_tag sampling_category;
private:
const sa_type* m_sa_p = nullptr; // pointer to sa_sample_strategy
t_select_sa m_select_marked_sa;
public:
//! Default constructor
_fuzzy_isa_sampling_support() {}
//! Constructor
/*
* \param cconfig Cache configuration. (Not used in this class)
* \param sa_sample Pointer to the corresponding SA sampling..
* \par Time complexity
* Linear in the size of the suffix array.
*/
_fuzzy_isa_sampling_support(SDSL_UNUSED const cache_config& cconfig,
const sa_type* sa_sample) :
m_sa_p(sa_sample)
{
util::init_support(m_select_marked_sa, &(sa_sample->marked_sa));
}
//! Copy constructor
_fuzzy_isa_sampling_support(const _fuzzy_isa_sampling_support& st) :
m_select_marked_sa(st.m_select_marked_sa)
{
set_vector(st.m_sa_p);
}
//! Return the inverse suffix array value for the sampled index i
inline value_type operator[](size_type i) const
{
return m_sa_p->inv(i);
}
//! Returns the rightmost ISA sample <= i and its position
inline std::tuple<value_type, size_type>
sample_leq(size_type i) const
{
size_type ci = i/sample_dens;
size_type j = m_sa_p->select_marked_isa(ci+1);
if (j > i) {
if (ci > 0) {
ci = ci - 1;
} else {
ci = m_sa_p->size()-1;
}
j = m_sa_p->select_marked_isa(ci+1);
}
return std::make_tuple(m_select_marked_sa(m_sa_p->inv(ci)+1),
j);
}
//! Returns the leftmost ISA sample >= i and its position
inline std::tuple<value_type, size_type>
sample_qeq(size_type i) const
{
size_type ci = i/sample_dens;
size_type j = m_sa_p->select_marked_isa(ci+1);
if (j < i) {
if (ci < m_sa_p->size()-1) {
ci = ci + 1;
} else {
ci = 0;
}
j = m_sa_p->select_marked_isa(ci+1);
}
return std::make_tuple(m_select_marked_sa(m_sa_p->inv(ci)+1),
j);
}
//! Assignment operation
_fuzzy_isa_sampling_support&
operator=(const _fuzzy_isa_sampling_support& st)
{
if (this != &st) {
m_select_marked_sa = st.m_select_marked_sa;
set_vector(st.m_sa_p);
}
return *this;
}
//! Swap operation
void swap(_fuzzy_isa_sampling_support& st)
{
m_select_marked_sa.swap(st.m_select_marked_sa);
}
size_type
serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const
{
structure_tree_node* child = structure_tree::add_child(v, name, util::class_name(*this));
size_type written_bytes = 0;
written_bytes += m_select_marked_sa.serialize(out, v, "select_marked_sa");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
//! Load sampling from disk
void load(std::istream& in, const sa_type* sa_sample=nullptr)
{
m_select_marked_sa.load(in);
set_vector(sa_sample);
}
void set_vector(const sa_type* sa_sample=nullptr)
{
m_sa_p = sa_sample;
if (nullptr != m_sa_p) {
m_select_marked_sa.set_vector(&(sa_sample->marked_sa));
}
}
};
template<class t_select_sa=void>
struct fuzzy_isa_sampling_support {
template<class t_csa>
using type = _fuzzy_isa_sampling_support<t_csa,
typename std::conditional<std::is_void<t_select_sa>::value,
typename t_csa::sa_sample_type::bv_sa_type::select_1_type,
t_select_sa>::type>;
using sampling_category = isa_sampling_tag;
};
} // end namespace
#endif
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