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// Copyright (c) 2016, the SDSL Project Authors. All rights reserved.
// Please see the AUTHORS file for details. Use of this source code is governed
// by a BSD license that can be found in the LICENSE file.
/*! \file construct_sa.hpp
\brief construct_sa.hpp contains an interface to access suffix array construction algorithms
\author Simon Gog
*/
#ifndef INCLUDED_SDSL_CONSTRUCT_SA
#define INCLUDED_SDSL_CONSTRUCT_SA
#include "config.hpp"
#include "int_vector.hpp"
#include "divsufsort.hpp"
#include "qsufsort.hpp"
#include "construct_sa_se.hpp"
#include "construct_config.hpp"
namespace sdsl {
//! Constructs the Suffix Array (SA) from text over byte-alphabet.
/*! The algorithm constructs the SA and stores it to disk.
* \param config Reference to cache configuration
* \par Space complexity
* Usually less than \f$1.5n \f$ bytes of main memory and
* \f$10n \f$ bytes of secondary memory
* \pre Text exist in the cache. Keys:
* * conf::KEY_TEXT
* \post SA exist in the cache. Key
* * conf::KEY_SA
*
* This construction method uses less main memory, since data-structures
* are only kept in main memory, when random access to them is needed.
* Otherwise they are stored on disk. The disk-usage peak of this algorithm
* is about 10 times the input.
*
* \par References
* [1] T. Beller, M. Zwerger, S. Gog and E. Ohlebusch:
* ,,Space-Efficient Construction of the Burrows-Wheeler Transform'',
* Proceedings of SPIRE 2013.
*
*/
inline void construct_sa_se(cache_config& config)
{
int_vector<8> text;
load_from_file(text, cache_file_name(conf::KEY_TEXT, config));
if (text.size() <= 2) {
// If text is c$ or $ write suffix array [1, 0] or [0]
int_vector_buffer<> sa(cache_file_name(conf::KEY_SA, config), std::ios::out, 8, 2);
if (text.size() == 2) {
sa.push_back(1);
}
sa.push_back(0);
} else {
_construct_sa_se<int_vector<8>>(text, cache_file_name(conf::KEY_SA, config), 256, 0);
}
register_cache_file(conf::KEY_SA, config);
}
namespace algorithm {
//
// Forward declarations
//----------------------------------------------------------
//! Calculates the Suffix Array for a text.
/*!
* \param c Text (c-string) to calculate the suffix array. The lex. order is given by the ascii-codes of the characters.
* \param len Length of the text. *(c+len)=0 and for i<len *(c+len)!=0
* \param sa Reference to a RandomAccessContainer which will contain the result of the calculation.
* \pre sa.size() has to be equal to len.
*/
template <typename t_int_vec>
void calculate_sa(const unsigned char* c, typename t_int_vec::size_type len, t_int_vec& sa)
{
typedef typename t_int_vec::size_type size_type;
constexpr uint8_t t_width = t_int_vec::fixed_int_width;
if (len <= 1) { // handle special case
sa.width(1);
sa.resize(len);
if (len > 0) sa[0] = 0;
return;
}
bool small_file = (sizeof(len) <= 4 or len < 0x7FFFFFFFULL);
if (small_file) {
uint8_t sa_width = sa.width();
if (32 == t_width or (0 == t_width and 32 >= sa_width)) {
sa.width(32);
sa.resize(len);
divsufsort(c, (int32_t*)sa.data(), (int32_t)len);
// copy integers back to the right positions
if (sa_width != 32) {
for (size_type i = 0, p = 0; i < len; ++i, p += sa_width) {
sa.set_int(p, sa.get_int(i << 5, 32), sa_width);
}
sa.width(sa_width);
sa.resize(len);
}
} else {
if (sa.width() < bits::hi(len) + 1) {
throw std::logic_error("width of int_vector is to small for the text!!!");
}
int_vector<> sufarray(len, 0, 32);
divsufsort(c, (int32_t*)sufarray.data(), (int32_t)len);
sa.resize(len);
for (size_type i = 0; i < len; ++i) {
sa[i] = sufarray[i];
}
}
} else {
uint8_t sa_width = sa.width();
sa.width(64);
sa.resize(len);
divsufsort64(c, (int64_t*)sa.data(), len);
// copy integers back to the right positions
if (sa_width != 64) {
for (size_type i = 0, p = 0; i < len; ++i, p += sa_width) {
sa.set_int(p, sa.get_int(i << 6, 64), sa_width);
}
sa.width(sa_width);
sa.resize(len);
}
}
}
} // end namespace algorithm
//! Constructs the Suffix Array (SA) from text over byte- or integer-alphabet.
/*! The algorithm constructs the SA and stores it to disk.
* \tparam t_width Width of the text. 0==integer alphabet, 8=byte alphabet.
* \param config Reference to cache configuration
* \par Space complexity
* \f$ 5n \f$ byte for t_width=8 and input < 2GB
* \f$ 9n \f$ byte for t_width=8 and input > 2GB
* \f$ n \log \sigma \f$ bits for t_width=0
* \pre Text exist in the cache. Keys:
* * conf::KEY_TEXT for t_width=8 or conf::KEY_TEXT_INT for t_width=0
* \post SA exist in the cache. Key
* * conf::KEY_SA
* \par Reference
* For t_width=8: DivSufSort (http://code.google.com/p/libdivsufsort/)
* For t_width=0: qsufsort (http://www.larsson.dogma.net/qsufsort.c)
*/
template <uint8_t t_width>
void construct_sa(cache_config& config)
{
static_assert(t_width == 0 or t_width == 8,
"construct_sa: width must be `0` for integer alphabet and `8` for byte alphabet");
const char* KEY_TEXT = key_text_trait<t_width>::KEY_TEXT;
if (t_width == 8) {
if (construct_config().byte_algo_sa == LIBDIVSUFSORT) {
read_only_mapper<t_width> text(KEY_TEXT, config);
auto sa = write_out_mapper<0>::create(
cache_file_name(conf::KEY_SA, config), 0, bits::hi(text.size()) + 1);
// call divsufsort
algorithm::calculate_sa((const unsigned char*)text.data(), text.size(), sa);
} else if (construct_config().byte_algo_sa == SE_SAIS) {
construct_sa_se(config);
}
} else if (t_width == 0) {
// call qsufsort
int_vector<> sa;
sdsl::qsufsort::construct_sa(sa, cache_file_name(KEY_TEXT, config).c_str(), 0);
store_to_cache(sa, conf::KEY_SA, config);
} else {
std::cerr << "Unknown alphabet type" << std::endl;
}
}
} // end namespace sdsl
#endif
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