1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
|
#include <contrib/libs/zstd06/renames.h>
/*
* 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 */
|
