68 lines
2.4 KiB
C
68 lines
2.4 KiB
C
/*
|
|
* 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 */
|