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     1 /*
    2  * divsufsort.h for libdivsufsort-lite
    3  * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
    4  *
    5  * Permission is hereby granted, free of charge, to any person
    6  * obtaining a copy of this software and associated documentation
    7  * files (the "Software"), to deal in the Software without
    8  * restriction, including without limitation the rights to use,
    9  * copy, modify, merge, publish, distribute, sublicense, and/or sell
   10  * copies of the Software, and to permit persons to whom the
   11  * Software is furnished to do so, subject to the following
   12  * conditions:
   13  *
   14  * The above copyright notice and this permission notice shall be
   15  * included in all copies or substantial portions of the Software.
   16  *
   17  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   18  * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
   19  * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   20  * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
   21  * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
   22  * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
   23  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
   24  * OTHER DEALINGS IN THE SOFTWARE.
   25  */
   26 
   27 #ifndef _DIVSUFSORT_H
   28 #define _DIVSUFSORT_H 1
   29 
   30 #ifdef __cplusplus
   31 extern "C" {
   32 #endif /* __cplusplus */
   33 
   34 
   35 /*- Prototypes -*/
   36 
   37 /**
   38  * Constructs the suffix array of a given string.
   39  * @param T [0..n-1] The input string.
   40  * @param SA [0..n-1] The output array of suffixes.
   41  * @param n The length of the given string.
   42  * @param openMP enables OpenMP optimization.
   43  * @return 0 if no error occurred, -1 or -2 otherwise.
   44  */
   45 int
   46 divsufsort(const unsigned char *T, int *SA, int n, int openMP);
   47 
   48 /**
   49  * Constructs the burrows-wheeler transformed string of a given string.
   50  * @param T [0..n-1] The input string.
   51  * @param U [0..n-1] The output string. (can be T)
   52  * @param A [0..n-1] The temporary array. (can be NULL)
   53  * @param n The length of the given string.
   54  * @param num_indexes The length of secondary indexes array. (can be NULL)
   55  * @param indexes The secondary indexes array. (can be NULL)
   56  * @param openMP enables OpenMP optimization.
   57  * @return The primary index if no error occurred, -1 or -2 otherwise.
   58  */
   59 int
   60 divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP);
   61 
   62 
   63 #ifdef __cplusplus
   64 } /* extern "C" */
   65 #endif /* __cplusplus */
   66 
   67 #endif /* _DIVSUFSORT_H */
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