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/* sdsl - succinct data structures library
Copyright (C) 2010 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 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.h"
#include "divsufsort64.h"
#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.
*
*/
void construct_sa_se(cache_config& 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<uint8_t fixedIntWidth>
void calculate_sa(const unsigned char* c, typename int_vector<fixedIntWidth>::size_type len, int_vector<fixedIntWidth>& sa)
{
typedef typename int_vector<fixedIntWidth>::size_type size_type;
if (len <= 1) { // handle special case
sa = int_vector<fixedIntWidth>(len,0);
return;
}
bool small_file = (sizeof(len) <= 4 or len < 0x7FFFFFFFULL);
if (small_file) {
uint8_t oldIntWidth = sa.width();
if (32 == fixedIntWidth or(0==fixedIntWidth and 32 >= oldIntWidth)) {
sa.width(32);
sa.resize(len);
divsufsort(c, (int32_t*)sa.data(), len);
// copy integers back to the right positions
if (oldIntWidth!=32) {
for (size_type i=0; i<len; ++i) {
sa.set_int(i*oldIntWidth, sa.get_int(i<<5, 32), oldIntWidth);
}
sa.width(oldIntWidth);
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(), len);
for (size_type i=0; i<len; ++i) {
sa[i] = sufarray[i];
}
}
} else {
uint8_t oldIntWidth = sa.width();
sa.width(64);
sa.resize(len);
divsufsort64(c, (int64_t*)sa.data(), len);
// copy integers back to the right positions
if (oldIntWidth!=64) {
for (size_type i=0; i<len; ++i) {
sa.set_int(i*oldIntWidth, sa.get_int(i<<6, 64), oldIntWidth);
}
sa.width(oldIntWidth);
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) {
typedef int_vector<t_width> text_type;
text_type text;
load_from_cache(text, KEY_TEXT, config);
// call divsufsort
int_vector<> sa(text.size(), 0, bits::hi(text.size())+1);
algorithm::calculate_sa((const unsigned char*)text.data(), text.size(), sa);
store_to_cache(sa, conf::KEY_SA, config);
} 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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