Revision 480a94cbe722741cd3f1c2d35549a5af06c3e774 authored by fenderglass on 18 July 2014, 18:59:24 UTC, committed by fenderglass on 18 July 2014, 18:59:24 UTC
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suffix_array.h
/*
* sais.h for sais-lite
* Copyright (c) 2008-2010 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 _SAIS_H
#define _SAIS_H 1

#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */

  /* find the suffix array SA of T[0..n-1]
  use a working space (excluding T and SA) of at most 2n+O(lg n) */
  int
    sais(const unsigned char *T, long long *SA, long long n);

  /* find the suffix array SA of T[0..n-1] in {0..k-1}^n
  use a working space (excluding T and SA) of at most MAX(4k,2n) */
  int
    sais_int(const int *T, int *SA, long long n, int k);

  /* burrows-wheeler transform */
  int
    sais_bwt(const unsigned char *T, unsigned char *U, int *A, long long n);
  int
    sais_int_bwt(const int *T, int *U, int *A, long long n, int k);


#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */

#endif /* _SAIS_H */
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