/usr/include/sdsl/csa_wt.hpp is in libsdsl-dev 2.0.3-4.
This file is owned by root:root, with mode 0o644.
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Copyright (C) 2009-2013 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_wt.hpp
\brief csa_wt.hpp contains an implementation of the compressed suffix array based on a wavelet tree.
\author Simon Gog
*/
#ifndef INCLUDED_SDSL_CSA_WT
#define INCLUDED_SDSL_CSA_WT
#include "wavelet_trees.hpp"
#include "suffix_array_helper.hpp"
#include "iterators.hpp"
#include "util.hpp"
#include "fast_cache.hpp"
#include "csa_sampling_strategy.hpp"
#include "csa_alphabet_strategy.hpp"
#include <iostream>
#include <algorithm> // for std::swap
#include <cassert>
#include <cstring> // for strlen
#include <iomanip>
#include <iterator>
namespace sdsl
{
template<class t_csa>
class psi_of_csa_wt; // forward declaration of PSI-array class
template<class t_csa>
class bwt_of_csa_wt; // forward declaration of BWT-array class
//! A class for the Compressed Suffix Array (CSA) based on a Wavelet Tree (WT) of the Burrow Wheeler Transform of the original text.
/*!
* \tparam t_wt Wavelet tree
* \tparam t_dens Sampling density of SA values
* \tparam t_int_dens Sampling density of ISA values
* \tparam t_sa_sample_strat Policy of SA sampling. E.g. sample in SA-order or text-order.
* \tparam t_isa Vector type for ISA sample values.
* \tparam t_alphabet_strat Policy for alphabet representation.
*
* \sa sdsl::csa_sada, sdsl::csa_bitcompressed
* @ingroup csa
*/
template<class t_wt = wt_huff<>, // Wavelet tree type
uint32_t t_dens = 32, // Sample density for suffix array (SA) values
uint32_t t_inv_dens = 64, // Sample density for inverse suffix array (ISA) values
class t_sa_sample_strat = sa_order_sa_sampling<>, // Policy class for the SA sampling. Alternative text_order_sa_sampling.
class t_isa = int_vector<>, // Container for the ISA samples.
class t_alphabet_strat = // Policy class for the representation of the alphabet.
typename alphabet_trait<typename t_wt::alphabet_category>::type
>
class csa_wt
{
friend class bwt_of_csa_wt<csa_wt>;
public:
enum { sa_sample_dens = t_dens,
isa_sample_dens = t_inv_dens
};
typedef uint64_t value_type;
typedef random_access_const_iterator<csa_wt> const_iterator;
typedef const_iterator iterator;
typedef const value_type const_reference;
typedef const_reference reference;
typedef const_reference* pointer;
typedef const pointer const_pointer;
typedef int_vector<>::size_type size_type;
typedef size_type csa_size_type;
typedef ptrdiff_t difference_type;
typedef traverse_csa_wt<csa_wt,true> psi_type;
typedef traverse_csa_wt<csa_wt,false> lf_type;
typedef bwt_of_csa_wt<csa_wt> bwt_type;
typedef isa_of_csa_wt<csa_wt> isa_type;
typedef first_row_of_csa<csa_wt> first_row_type;
typedef text_of_csa<csa_wt> text_type;
typedef t_wt wavelet_tree_type;
typedef typename t_sa_sample_strat::template type<csa_wt>::sample_type sa_sample_type;
typedef t_isa isa_sample_type;
typedef t_alphabet_strat alphabet_type;
typedef typename alphabet_type::char_type char_type; // Note: This is the char type of the CSA not the WT!
typedef typename alphabet_type::comp_char_type comp_char_type;
typedef typename alphabet_type::string_type string_type;
typedef csa_wt csa_type;
typedef csa_tag index_category;
typedef lf_tag extract_category;
typedef typename alphabet_type::alphabet_category alphabet_category;
private:
t_wt m_wavelet_tree; // the wavelet tree
sa_sample_type m_sa_sample; // suffix array samples
isa_sample_type m_isa_sample; // inverse suffix array samples
alphabet_type m_alphabet;
//#define USE_CSA_CACHE
#ifdef USE_CSA_CACHE
mutable fast_cache csa_cache;
#endif
void copy(const csa_wt& csa) {
m_wavelet_tree = csa.m_wavelet_tree;
m_sa_sample = csa.m_sa_sample;
m_isa_sample = csa.m_isa_sample;
m_alphabet = csa.m_alphabet;
}
public:
const typename alphabet_type::char2comp_type& char2comp = m_alphabet.char2comp;
const typename alphabet_type::comp2char_type& comp2char = m_alphabet.comp2char;
const typename alphabet_type::C_type& C = m_alphabet.C;
const typename alphabet_type::sigma_type& sigma = m_alphabet.sigma;
const psi_type psi = psi_type(*this);
const lf_type lf = lf_type(*this);
const bwt_type bwt = bwt_type(*this);
const text_type text = text_type(*this);
const first_row_type F = first_row_type(*this);
const bwt_type L = bwt_type(*this);
const isa_type isa = isa_type(*this);
const sa_sample_type& sa_sample = m_sa_sample;
const isa_sample_type& isa_sample = m_isa_sample;
const wavelet_tree_type& wavelet_tree = m_wavelet_tree;
//! Default constructor
csa_wt() {}
//! Copy constructor
csa_wt(const csa_wt& csa) {
copy(csa);
}
//! Move constructor
csa_wt(csa_wt&& csa) {
*this = std::move(csa);
}
//! Constructor taking a cache_config
csa_wt(cache_config& config);
//! Number of elements in the \f$\CSA\f$.
/*! Required for the Container Concept of the STL.
* \sa max_size, empty
* \par Time complexity
* \f$ \Order{1} \f$
*/
size_type size()const {
return m_wavelet_tree.size();
}
//! Returns the largest size that csa_wt can ever have.
/*! Required for the Container Concept of the STL.
* \sa size
*/
static size_type max_size() {
return bit_vector::max_size();
}
//! Returns if the data strucutre is empty.
/*! Required for the Container Concept of the STL.
* \sa size
*/
bool empty()const {
return m_wavelet_tree.empty();
}
//! Swap method for csa_wt
/*! The swap method can be defined in terms of assignment.
This requires three assignments, each of which, for a container type, is linear
in the container's size. In a sense, then, a.swap(b) is redundant.
This implementation guaranties a run-time complexity that is constant rather than linear.
\param csa csa_wt to swap.
Required for the Assignable Conecpt of the STL.
*/
void swap(csa_wt& csa);
//! Returns a const_iterator to the first element.
/*! Required for the STL Container Concept.
* \sa end
*/
const_iterator begin()const {
return const_iterator(this, 0);
}
//! Returns a const_iterator to the element after the last element.
/*! Required for the STL Container Concept.
* \sa begin.
*/
const_iterator end()const {
return const_iterator(this, size());
}
//! []-operator
/*! \param i Index of the value. \f$ i \in [0..size()-1]\f$.
* Required for the STL Random Access Container Concept.
* \par Time complexity
* \f$ \Order{s_{SA}\cdot t_{\Psi}} \f$, where every \f$s_{SA}\f$th suffix array entry is sampled and \f$t_{\Psi}\f$
* is the access time for an element in the \f$\Psi\f$-function.
*/
inline value_type operator[](size_type i)const;
//! Assignment Operator.
/*!
* Required for the Assignable Concept of the STL.
*/
csa_wt& operator=(const csa_wt& csa);
//! Assignment Move Operator.
/*!
* Required for the Assignable Concept of the STL.
*/
csa_wt& operator=(csa_wt&& csa);
//! Serialize to a stream.
/*! \param out Output stream to write the data structure.
* \return The number of written bytes.
*/
size_type serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const;
//! Load from a stream.
/*! \param in Input stream to load the data structure from.
*/
void load(std::istream& in);
private:
// Calculates how many symbols c are in the prefix [0..i-1] of the BWT of the original text.
/*
* \param i The exclusive index of the prefix range [0..i-1], so \f$i\in [0..size()]\f$.
* \param c The symbol to count the occurrences in the prefix.
* \returns The number of occurrences of symbol c in the prefix [0..i-1] of the BWT.
* \par Time complexity
* \f$ \Order{\log |\Sigma|} \f$
*/
size_type rank_bwt(size_type i, const char_type c)const {
return m_wavelet_tree.rank(i, c);
}
// Calculates the position of the i-th c in the BWT of the original text.
/*
* \param i The i-th occurrence. \f$i\in [1..rank(size(),c)]\f$.
* \param c Symbol c.
* \returns The position of the i-th c in the BWT or size() if c does occur less then i times.
* \par Time complexity
* \f$ \Order{t_{\Psi}} \f$
*/
size_type select_bwt(size_type i, const char_type c)const {
assert(i > 0);
char_type cc = char2comp[c];
if (cc==0 and c!=0) // character is not in the text => return size()
return size();
assert(cc != 255);
if (C[cc]+i-1 < C[cc+1]) {
return m_wavelet_tree.select(i, c);
} else
return size();
}
};
// == template functions ==
template<class t_wt, uint32_t t_dens, uint32_t t_inv_dens, class t_sa_sample_strat, class t_isa, class t_alphabet_strat>
csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::csa_wt(cache_config& config)
{
if (!cache_file_exists(key_trait<alphabet_type::int_width>::KEY_BWT, config)) {
return;
}
{
auto event = memory_monitor::event("construct csa-alpbabet");
int_vector_buffer<alphabet_type::int_width> bwt_buf(cache_file_name(key_trait<alphabet_type::int_width>::KEY_BWT,config));
size_type n = bwt_buf.size();
alphabet_type tmp_alphabet(bwt_buf, n);
m_alphabet.swap(tmp_alphabet);
}
{
auto event = memory_monitor::event("construct wavelet tree");
int_vector_buffer<alphabet_type::int_width> bwt_buf(cache_file_name(key_trait<alphabet_type::int_width>::KEY_BWT,config));
size_type n = bwt_buf.size();
wavelet_tree_type tmp_wt(bwt_buf, n);
m_wavelet_tree.swap(tmp_wt);
}
{
auto event = memory_monitor::event("sample SA");
sa_sample_type tmp_sa_sample(config);
m_sa_sample.swap(tmp_sa_sample);
}
{
auto event = memory_monitor::event("sample ISA");
int_vector_buffer<> sa_buf(cache_file_name(conf::KEY_SA, config));
set_isa_samples<csa_wt>(sa_buf, m_isa_sample);
}
}
template<class t_wt, uint32_t t_dens, uint32_t t_inv_dens, class t_sa_sample_strat, class t_isa, class t_alphabet_strat>
inline auto csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::operator[](size_type i)const -> value_type
{
size_type off = 0;
while (!m_sa_sample.is_sampled(i)) {
i = lf[i];
++off;
}
value_type result = m_sa_sample.sa_value(i);
if (result + off < size()) {
return result + off;
} else {
return result + off - size();
}
}
template<class t_wt, uint32_t t_dens, uint32_t t_inv_dens, class t_sa_sample_strat, class t_isa, class t_alphabet_strat>
auto csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::operator=(const csa_wt<t_wt,t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>& csa) -> csa_wt& {
if (this != &csa) {
copy(csa);
}
return *this;
}
template<class t_wt, uint32_t t_dens, uint32_t t_inv_dens, class t_sa_sample_strat, class t_isa, class t_alphabet_strat>
auto csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::operator=(csa_wt<t_wt,t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>&& csa) -> csa_wt& {
if (this != &csa) {
m_wavelet_tree = std::move(csa.m_wavelet_tree);
m_sa_sample = std::move(csa.m_sa_sample);
m_isa_sample = std::move(csa.m_isa_sample);
m_alphabet = std::move(csa.m_alphabet);
}
return *this;
}
template<class t_wt, uint32_t t_dens, uint32_t t_inv_dens, class t_sa_sample_strat, class t_isa, class t_alphabet_strat>
auto csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::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;
written_bytes += m_wavelet_tree.serialize(out, child, "wavelet_tree");
written_bytes += m_sa_sample.serialize(out, child, "sa_samples");
written_bytes += m_isa_sample.serialize(out, child, "isa_samples");
written_bytes += m_alphabet.serialize(out, child, "alphabet");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
template<class t_wt, uint32_t t_dens, uint32_t t_inv_dens, class t_sa_sample_strat, class t_isa, class t_alphabet_strat>
void csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::load(std::istream& in)
{
m_wavelet_tree.load(in);
m_sa_sample.load(in);
m_isa_sample.load(in);
m_alphabet.load(in);
}
template<class t_wt, uint32_t t_dens, uint32_t t_inv_dens, class t_sa_sample_strat, class t_isa, class t_alphabet_strat>
void csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::swap(csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>& csa)
{
if (this != &csa) {
m_wavelet_tree.swap(csa.m_wavelet_tree);
m_sa_sample.swap(csa.m_sa_sample);
m_isa_sample.swap(csa.m_isa_sample);
m_alphabet.swap(csa.m_alphabet);
}
}
} // end namespace sdsl
#endif
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