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1 /*
2  * divsufsort64.h for libdivsufsort64
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 _DIVSUFSORT64_H
28 #define _DIVSUFSORT64_H 1
29 
30 #ifdef __cplusplus
31 extern "C" {
32 #endif /* __cplusplus */
33 
34 #include <inttypes.h>
35 
36 #ifndef DIVSUFSORT_API
37 # ifdef DIVSUFSORT_BUILD_DLL
38 #  define DIVSUFSORT_API
39 # else
40 #  define DIVSUFSORT_API
41 # endif
42 #endif
43 
44 /*- Datatypes -*/
45 #ifndef SAUCHAR_T
46 #define SAUCHAR_T
47 typedef uint8_t sauchar_t;
48 #endif /* SAUCHAR_T */
49 #ifndef SAINT_T
50 #define SAINT_T
51 typedef int32_t saint_t;
52 #endif /* SAINT_T */
53 #ifndef SAIDX64_T
54 #define SAIDX64_T
55 typedef int64_t saidx64_t;
56 #endif /* SAIDX64_T */
57 #ifndef PRIdSAINT_T
58 #define PRIdSAINT_T PRId32
59 #endif /* PRIdSAINT_T */
60 #ifndef PRIdSAIDX64_T
61 #define PRIdSAIDX64_T PRId64
62 #endif /* PRIdSAIDX64_T */
63 
64 
65 /*- Prototypes -*/
66 
67 /**
68  * Constructs the suffix array of a given string.
69  * @param T[0..n-1] The input string.
70  * @param SA[0..n-1] The output array of suffixes.
71  * @param n The length of the given string.
72  * @return 0 if no error occurred, -1 or -2 otherwise.
73  */
74 DIVSUFSORT_API
75 saint_t
76 divsufsort64(const sauchar_t *T, saidx64_t *SA, saidx64_t n);
77 
78 /**
79  * Constructs the burrows-wheeler transformed string of a given string.
80  * @param T[0..n-1] The input string.
81  * @param U[0..n-1] The output string. (can be T)
82  * @param A[0..n-1] The temporary array. (can be NULL)
83  * @param n The length of the given string.
84  * @return The primary index if no error occurred, -1 or -2 otherwise.
85  */
86 DIVSUFSORT_API
87 saidx64_t
88 divbwt64(const sauchar_t *T, sauchar_t *U, saidx64_t *A, saidx64_t n);
89 
90 /**
91  * Returns the version of the divsufsort library.
92  * @return The version number string.
93  */
94 DIVSUFSORT_API
95 const char *
96 divsufsort64_version(void);
97 
98 
99 /**
100  * Constructs the burrows-wheeler transformed string of a given string and suffix array.
101  * @param T[0..n-1] The input string.
102  * @param U[0..n-1] The output string. (can be T)
103  * @param SA[0..n-1] The suffix array. (can be NULL)
104  * @param n The length of the given string.
105  * @param idx The output primary index.
106  * @return 0 if no error occurred, -1 or -2 otherwise.
107  */
108 DIVSUFSORT_API
109 saint_t
110 bw_transform64(const sauchar_t *T, sauchar_t *U,
111              saidx64_t *SA /* can NULL */,
112              saidx64_t n, saidx64_t *idx);
113 
114 /**
115  * Inverse BW-transforms a given BWTed string.
116  * @param T[0..n-1] The input string.
117  * @param U[0..n-1] The output string. (can be T)
118  * @param A[0..n-1] The temporary array. (can be NULL)
119  * @param n The length of the given string.
120  * @param idx The primary index.
121  * @return 0 if no error occurred, -1 or -2 otherwise.
122  */
123 DIVSUFSORT_API
124 saint_t
125 inverse_bw_transform64(const sauchar_t *T, sauchar_t *U,
126                      saidx64_t *A /* can NULL */,
127                      saidx64_t n, saidx64_t idx);
128 
129 /**
130  * Checks the correctness of a given suffix array.
131  * @param T[0..n-1] The input string.
132  * @param SA[0..n-1] The input suffix array.
133  * @param n The length of the given string.
134  * @param verbose The verbose mode.
135  * @return 0 if no error occurred.
136  */
137 DIVSUFSORT_API
138 saint_t
139 sufcheck64(const sauchar_t *T, const saidx64_t *SA, saidx64_t n, saint_t verbose);
140 
141 /**
142  * Search for the pattern P in the string T.
143  * @param T[0..Tsize-1] The input string.
144  * @param Tsize The length of the given string.
145  * @param P[0..Psize-1] The input pattern string.
146  * @param Psize The length of the given pattern string.
147  * @param SA[0..SAsize-1] The input suffix array.
148  * @param SAsize The length of the given suffix array.
149  * @param idx The output index.
150  * @return The count of matches if no error occurred, -1 otherwise.
151  */
152 DIVSUFSORT_API
153 saidx64_t
154 sa_search64(const sauchar_t *T, saidx64_t Tsize,
155           const sauchar_t *P, saidx64_t Psize,
156           const saidx64_t *SA, saidx64_t SAsize,
157           saidx64_t *left);
158 
159 /**
160  * Search for the character c in the string T.
161  * @param T[0..Tsize-1] The input string.
162  * @param Tsize The length of the given string.
163  * @param SA[0..SAsize-1] The input suffix array.
164  * @param SAsize The length of the given suffix array.
165  * @param c The input character.
166  * @param idx The output index.
167  * @return The count of matches if no error occurred, -1 otherwise.
168  */
169 DIVSUFSORT_API
170 saidx64_t
171 sa_simplesearch64(const sauchar_t *T, saidx64_t Tsize,
172                 const saidx64_t *SA, saidx64_t SAsize,
173                 saint_t c, saidx64_t *left);
174 
175 
176 #ifdef __cplusplus
177 } /* extern "C" */
178 #endif /* __cplusplus */
179 
180 #endif /* _DIVSUFSORT64_H */
181