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libsais64.h
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/*--
This file is a part of libsais, a library for linear time suffix array,
longest common prefix array and burrows wheeler transform construction.
Copyright (c) 2021-2024 Ilya Grebnov <[email protected]>
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Please see the file LICENSE for full copyright information.
--*/
#ifndef LIBSAIS64_H
#define LIBSAIS64_H 1
#define LIBSAIS64_VERSION_MAJOR 2
#define LIBSAIS64_VERSION_MINOR 8
#define LIBSAIS64_VERSION_PATCH 6
#define LIBSAIS64_VERSION_STRING "2.8.6"
#ifdef _WIN32
#ifdef LIBSAIS_SHARED
#ifdef LIBSAIS_EXPORTS
#define LIBSAIS64_API __declspec(dllexport)
#else
#define LIBSAIS64_API __declspec(dllimport)
#endif
#else
#define LIBSAIS64_API
#endif
#else
#define LIBSAIS64_API
#endif
#ifdef __cplusplus
extern "C" {
#endif
#include <stdint.h>
/**
* Constructs the suffix array of a given string.
* @param T [0..n-1] The input string.
* @param SA [0..n-1+fs] The output array of suffixes.
* @param n The length of the given string.
* @param fs The extra space available at the end of SA array (0 should be enough for most cases).
* @param freq [0..255] The output symbol frequency table (can be NULL).
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64(const uint8_t * T, int64_t * SA, int64_t n, int64_t fs, int64_t * freq);
/**
* Constructs the suffix array of a given integer array.
* Note, during construction input array will be modified, but restored at the end if no errors occurred.
* @param T [0..n-1] The input integer array.
* @param SA [0..n-1+fs] The output array of suffixes.
* @param n The length of the integer array.
* @param k The alphabet size of the input integer array.
* @param fs Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_long(int64_t * T, int64_t * SA, int64_t n, int64_t k, int64_t fs);
#if defined(LIBSAIS_OPENMP)
/**
* Constructs the suffix array of a given string in parallel using OpenMP.
* @param T [0..n-1] The input string.
* @param SA [0..n-1+fs] The output array of suffixes.
* @param n The length of the given string.
* @param fs The extra space available at the end of SA array (0 should be enough for most cases).
* @param freq [0..255] The output symbol frequency table (can be NULL).
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_omp(const uint8_t * T, int64_t * SA, int64_t n, int64_t fs, int64_t * freq, int64_t threads);
/**
* Constructs the suffix array of a given integer array in parallel using OpenMP.
* Note, during construction input array will be modified, but restored at the end if no errors occurred.
* @param T [0..n-1] The input integer array.
* @param SA [0..n-1+fs] The output array of suffixes.
* @param n The length of the integer array.
* @param k The alphabet size of the input integer array.
* @param fs Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_long_omp(int64_t * T, int64_t * SA, int64_t n, int64_t k, int64_t fs, int64_t threads);
#endif
/**
* Constructs the burrows-wheeler transformed string (BWT) of a given string.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n-1+fs] The temporary array.
* @param n The length of the given string.
* @param fs The extra space available at the end of A array (0 should be enough for most cases).
* @param freq [0..255] The output symbol frequency table (can be NULL).
* @return The primary index if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_bwt(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, int64_t fs, int64_t * freq);
/**
* Constructs the burrows-wheeler transformed string (BWT) of a given string with auxiliary indexes.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n-1+fs] The temporary array.
* @param n The length of the given string.
* @param fs The extra space available at the end of A array (0 should be enough for most cases).
* @param freq [0..255] The output symbol frequency table (can be NULL).
* @param r The sampling rate for auxiliary indexes (must be power of 2).
* @param I [0..(n-1)/r] The output auxiliary indexes.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_bwt_aux(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, int64_t fs, int64_t * freq, int64_t r, int64_t * I);
#if defined(LIBSAIS_OPENMP)
/**
* Constructs the burrows-wheeler transformed string (BWT) of a given string in parallel using OpenMP.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n-1+fs] The temporary array.
* @param n The length of the given string.
* @param fs The extra space available at the end of A array (0 should be enough for most cases).
* @param freq [0..255] The output symbol frequency table (can be NULL).
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return The primary index if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_bwt_omp(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, int64_t fs, int64_t * freq, int64_t threads);
/**
* Constructs the burrows-wheeler transformed string (BWT) of a given string with auxiliary indexes in parallel using OpenMP.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n-1+fs] The temporary array.
* @param n The length of the given string.
* @param fs The extra space available at the end of A array (0 should be enough for most cases).
* @param freq [0..255] The output symbol frequency table (can be NULL).
* @param r The sampling rate for auxiliary indexes (must be power of 2).
* @param I [0..(n-1)/r] The output auxiliary indexes.
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_bwt_aux_omp(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, int64_t fs, int64_t * freq, int64_t r, int64_t * I, int64_t threads);
#endif
/**
* Constructs the original string from a given burrows-wheeler transformed string (BWT) with primary index.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
* @param n The length of the given string.
* @param freq [0..255] The input symbol frequency table (can be NULL).
* @param i The primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_unbwt(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, const int64_t * freq, int64_t i);
/**
* Constructs the original string from a given burrows-wheeler transformed string (BWT) with auxiliary indexes.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
* @param n The length of the given string.
* @param freq [0..255] The input symbol frequency table (can be NULL).
* @param r The sampling rate for auxiliary indexes (must be power of 2).
* @param I [0..(n-1)/r] The input auxiliary indexes.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_unbwt_aux(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, const int64_t * freq, int64_t r, const int64_t * I);
#if defined(LIBSAIS_OPENMP)
/**
* Constructs the original string from a given burrows-wheeler transformed string (BWT) with primary index in parallel using OpenMP.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
* @param n The length of the given string.
* @param freq [0..255] The input symbol frequency table (can be NULL).
* @param i The primary index.
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_unbwt_omp(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, const int64_t * freq, int64_t i, int64_t threads);
/**
* Constructs the original string from a given burrows-wheeler transformed string (BWT) with auxiliary indexes in parallel using OpenMP.
* @param T [0..n-1] The input string.
* @param U [0..n-1] The output string (can be T).
* @param A [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
* @param n The length of the given string.
* @param freq [0..255] The input symbol frequency table (can be NULL).
* @param r The sampling rate for auxiliary indexes (must be power of 2).
* @param I [0..(n-1)/r] The input auxiliary indexes.
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
LIBSAIS64_API int64_t libsais64_unbwt_aux_omp(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, const int64_t * freq, int64_t r, const int64_t * I, int64_t threads);
#endif
/**
* Constructs the permuted longest common prefix array (PLCP) of a given string and a suffix array.
* @param T [0..n-1] The input string.
* @param SA [0..n-1] The input suffix array.
* @param PLCP [0..n-1] The output permuted longest common prefix array.
* @param n The length of the string and the suffix array.
* @return 0 if no error occurred, -1 otherwise.
*/
LIBSAIS64_API int64_t libsais64_plcp(const uint8_t * T, const int64_t * SA, int64_t * PLCP, int64_t n);
/**
* Constructs the longest common prefix array (LCP) of a given permuted longest common prefix array (PLCP) and a suffix array.
* @param PLCP [0..n-1] The input permuted longest common prefix array.
* @param SA [0..n-1] The input suffix array.
* @param LCP [0..n-1] The output longest common prefix array (can be SA).
* @param n The length of the permuted longest common prefix array and the suffix array.
* @return 0 if no error occurred, -1 otherwise.
*/
LIBSAIS64_API int64_t libsais64_lcp(const int64_t * PLCP, const int64_t * SA, int64_t * LCP, int64_t n);
#if defined(LIBSAIS_OPENMP)
/**
* Constructs the permuted longest common prefix array (PLCP) of a given string and a suffix array in parallel using OpenMP.
* @param T [0..n-1] The input string.
* @param SA [0..n-1] The input suffix array.
* @param PLCP [0..n-1] The output permuted longest common prefix array.
* @param n The length of the string and the suffix array.
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return 0 if no error occurred, -1 otherwise.
*/
LIBSAIS64_API int64_t libsais64_plcp_omp(const uint8_t * T, const int64_t * SA, int64_t * PLCP, int64_t n, int64_t threads);
/**
* Constructs the longest common prefix array (LCP) of a given permuted longest common prefix array (PLCP) and a suffix array in parallel using OpenMP.
* @param PLCP [0..n-1] The input permuted longest common prefix array.
* @param SA [0..n-1] The input suffix array.
* @param LCP [0..n-1] The output longest common prefix array (can be SA).
* @param n The length of the permuted longest common prefix array and the suffix array.
* @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
* @return 0 if no error occurred, -1 otherwise.
*/
LIBSAIS64_API int64_t libsais64_lcp_omp(const int64_t * PLCP, const int64_t * SA, int64_t * LCP, int64_t n, int64_t threads);
#endif
#ifdef __cplusplus
}
#endif
#endif