#include /* * divsufsort.h for libdivsufsort-lite * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: * * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR * OTHER DEALINGS IN THE SOFTWARE. */ #ifndef _DIVSUFSORT_H #define _DIVSUFSORT_H 1 #ifdef __cplusplus extern "C" { #endif /* __cplusplus */ /*- Prototypes -*/ /** * Constructs the suffix array of a given string. * @param T[0..n-1] The input string. * @param SA[0..n-1] The output array of suffixes. * @param n The length of the given string. * @param openMP enables OpenMP optimization. * @return 0 if no error occurred, -1 or -2 otherwise. */ int divsufsort(const unsigned char *T, int *SA, int n, int openMP); /** * Constructs the burrows-wheeler transformed string 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] The temporary array. (can be NULL) * @param n The length of the given string. * @param num_indexes The length of secondary indexes array. (can be NULL) * @param indexes The secondary indexes array. (can be NULL) * @param openMP enables OpenMP optimization. * @return The primary index if no error occurred, -1 or -2 otherwise. */ int divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP); #ifdef __cplusplus } /* extern "C" */ #endif /* __cplusplus */ #endif /* _DIVSUFSORT_H */