libsais_sys/
libsais64.rs

1/* automatically generated by rust-bindgen 0.72.0 and slightly edited */
2
3pub const LIBSAIS64_VERSION_MAJOR: u32 = 2;
4pub const LIBSAIS64_VERSION_MINOR: u32 = 10;
5pub const LIBSAIS64_VERSION_PATCH: u32 = 3;
6pub const LIBSAIS64_VERSION_STRING: &str = "2.10.3";
7
8unsafe extern "C" {
9    /// Constructs the suffix array of a given string.
10    ///
11    /// # Arguments
12    ///
13    /// * `T` - [0..n-1] The input string.
14    /// * `SA` - [0..n-1+fs] The output array of suffixes.
15    /// * `n` - The length of the given string.
16    /// * `fs` - The extra space available at the end of SA array (0 should be enough for most cases).
17    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
18    ///
19    /// # Returns
20    ///
21    /// 0 if no error occurred, -1 or -2 otherwise.
22    pub fn libsais64(T: *const u8, SA: *mut i64, n: i64, fs: i64, freq: *mut i64) -> i64;
23
24    /// Constructs the generalized suffix array (GSA) of given string set.
25    ///
26    /// # Arguments
27    ///
28    /// * `T` - [0..n-1] The input string set using 0 as separators (T[n-1] must be 0).
29    /// * `SA` - [0..n-1+fs] The output array of suffixes.
30    /// * `n` - The length of the given string set.
31    /// * `fs` - The extra space available at the end of SA array (0 should be enough for most cases).
32    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
33    ///
34    /// # Returns
35    ///
36    /// 0 if no error occurred, -1 or -2 otherwise.
37    pub fn libsais64_gsa(T: *const u8, SA: *mut i64, n: i64, fs: i64, freq: *mut i64) -> i64;
38
39    /// Constructs the suffix array of a given integer array.Note, during construction input array will be modified, but restored at the end if no errors occurred.
40    ///
41    /// # Arguments
42    ///
43    /// * `T` - [0..n-1] The input integer array.
44    /// * `SA` - [0..n-1+fs] The output array of suffixes.
45    /// * `n` - The length of the integer array.
46    /// * `k` - The alphabet size of the input integer array.
47    /// * `fs` - Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
48    ///
49    /// # Returns
50    ///
51    /// 0 if no error occurred, -1 or -2 otherwise.
52    pub fn libsais64_long(T: *mut i64, SA: *mut i64, n: i64, k: i64, fs: i64) -> i64;
53
54    /// Constructs the suffix array of a given string in parallel using OpenMP.
55    ///
56    /// # Arguments
57    ///
58    /// * `T` - [0..n-1] The input string.
59    /// * `SA` - [0..n-1+fs] The output array of suffixes.
60    /// * `n` - The length of the given string.
61    /// * `fs` - The extra space available at the end of SA array (0 should be enough for most cases).
62    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
63    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
64    ///
65    /// # Returns
66    ///
67    /// 0 if no error occurred, -1 or -2 otherwise.
68    #[cfg(feature = "openmp")]
69    pub fn libsais64_omp(
70        T: *const u8,
71        SA: *mut i64,
72        n: i64,
73        fs: i64,
74        freq: *mut i64,
75        threads: i64,
76    ) -> i64;
77
78    /// Constructs the generalized suffix array (GSA) of given string set in parallel using OpenMP.
79    ///
80    /// # Arguments
81    ///
82    /// * `T` - [0..n-1] The input string set using 0 as separators (T[n-1] must be 0).
83    /// * `SA` - [0..n-1+fs] The output array of suffixes.
84    /// * `n` - The length of the given string set.
85    /// * `fs` - The extra space available at the end of SA array (0 should be enough for most cases).
86    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
87    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
88    ///
89    /// # Returns
90    ///
91    /// 0 if no error occurred, -1 or -2 otherwise.
92    #[cfg(feature = "openmp")]
93    pub fn libsais64_gsa_omp(
94        T: *const u8,
95        SA: *mut i64,
96        n: i64,
97        fs: i64,
98        freq: *mut i64,
99        threads: i64,
100    ) -> i64;
101
102    /// Constructs the suffix array of a given integer array in parallel using OpenMP.Note, during construction input array will be modified, but restored at the end if no errors occurred.
103    ///
104    /// # Arguments
105    ///
106    /// * `T` - [0..n-1] The input integer array.
107    /// * `SA` - [0..n-1+fs] The output array of suffixes.
108    /// * `n` - The length of the integer array.
109    /// * `k` - The alphabet size of the input integer array.
110    /// * `fs` - Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
111    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
112    ///
113    /// # Returns
114    ///
115    /// 0 if no error occurred, -1 or -2 otherwise.
116    #[cfg(feature = "openmp")]
117    pub fn libsais64_long_omp(
118        T: *mut i64,
119        SA: *mut i64,
120        n: i64,
121        k: i64,
122        fs: i64,
123        threads: i64,
124    ) -> i64;
125
126    /// Constructs the burrows-wheeler transformed string (BWT) of a given string.
127    ///
128    /// # Arguments
129    ///
130    /// * `T` - [0..n-1] The input string.
131    /// * `U` - [0..n-1] The output string (can be T).
132    /// * `A` - [0..n-1+fs] The temporary array.
133    /// * `n` - The length of the given string.
134    /// * `fs` - The extra space available at the end of A array (0 should be enough for most cases).
135    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
136    ///
137    /// # Returns
138    ///
139    /// The primary index if no error occurred, -1 or -2 otherwise.
140    pub fn libsais64_bwt(
141        T: *const u8,
142        U: *mut u8,
143        A: *mut i64,
144        n: i64,
145        fs: i64,
146        freq: *mut i64,
147    ) -> i64;
148
149    /// Constructs the burrows-wheeler transformed string (BWT) of a given string with auxiliary indexes.
150    ///
151    /// # Arguments
152    ///
153    /// * `T` - [0..n-1] The input string.
154    /// * `U` - [0..n-1] The output string (can be T).
155    /// * `A` - [0..n-1+fs] The temporary array.
156    /// * `n` - The length of the given string.
157    /// * `fs` - The extra space available at the end of A array (0 should be enough for most cases).
158    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
159    /// * `r` - The sampling rate for auxiliary indexes (must be power of 2).
160    /// * `I` - [0..(n-1)/r] The output auxiliary indexes.
161    ///
162    /// # Returns
163    ///
164    /// 0 if no error occurred, -1 or -2 otherwise.
165    pub fn libsais64_bwt_aux(
166        T: *const u8,
167        U: *mut u8,
168        A: *mut i64,
169        n: i64,
170        fs: i64,
171        freq: *mut i64,
172        r: i64,
173        I: *mut i64,
174    ) -> i64;
175
176    /// Constructs the burrows-wheeler transformed string (BWT) of a given string in parallel using OpenMP.
177    ///
178    /// # Arguments
179    ///
180    /// * `T` - [0..n-1] The input string.
181    /// * `U` - [0..n-1] The output string (can be T).
182    /// * `A` - [0..n-1+fs] The temporary array.
183    /// * `n` - The length of the given string.
184    /// * `fs` - The extra space available at the end of A array (0 should be enough for most cases).
185    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
186    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
187    ///
188    /// # Returns
189    ///
190    /// The primary index if no error occurred, -1 or -2 otherwise.
191    #[cfg(feature = "openmp")]
192    pub fn libsais64_bwt_omp(
193        T: *const u8,
194        U: *mut u8,
195        A: *mut i64,
196        n: i64,
197        fs: i64,
198        freq: *mut i64,
199        threads: i64,
200    ) -> i64;
201
202    /// Constructs the burrows-wheeler transformed string (BWT) of a given string with auxiliary indexes in parallel using OpenMP.
203    ///
204    /// # Arguments
205    ///
206    /// * `T` - [0..n-1] The input string.
207    /// * `U` - [0..n-1] The output string (can be T).
208    /// * `A` - [0..n-1+fs] The temporary array.
209    /// * `n` - The length of the given string.
210    /// * `fs` - The extra space available at the end of A array (0 should be enough for most cases).
211    /// * `freq` - [0..255] The output symbol frequency table (can be NULL).
212    /// * `r` - The sampling rate for auxiliary indexes (must be power of 2).
213    /// * `I` - [0..(n-1)/r] The output auxiliary indexes.
214    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
215    ///
216    /// # Returns
217    ///
218    /// 0 if no error occurred, -1 or -2 otherwise.
219    #[cfg(feature = "openmp")]
220    pub fn libsais64_bwt_aux_omp(
221        T: *const u8,
222        U: *mut u8,
223        A: *mut i64,
224        n: i64,
225        fs: i64,
226        freq: *mut i64,
227        r: i64,
228        I: *mut i64,
229        threads: i64,
230    ) -> i64;
231
232    /// Constructs the original string from a given burrows-wheeler transformed string (BWT) with primary index.
233    ///
234    /// # Arguments
235    ///
236    /// * `T` - [0..n-1] The input string.
237    /// * `U` - [0..n-1] The output string (can be T).
238    /// * `A` - [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
239    /// * `n` - The length of the given string.
240    /// * `freq` - [0..255] The input symbol frequency table (can be NULL).
241    /// * `i` - The primary index.
242    ///
243    /// # Returns
244    ///
245    /// 0 if no error occurred, -1 or -2 otherwise.
246    pub fn libsais64_unbwt(
247        T: *const u8,
248        U: *mut u8,
249        A: *mut i64,
250        n: i64,
251        freq: *const i64,
252        i: i64,
253    ) -> i64;
254
255    /// Constructs the original string from a given burrows-wheeler transformed string (BWT) with auxiliary indexes.
256    ///
257    /// # Arguments
258    ///
259    /// * `T` - [0..n-1] The input string.
260    /// * `U` - [0..n-1] The output string (can be T).
261    /// * `A` - [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
262    /// * `n` - The length of the given string.
263    /// * `freq` - [0..255] The input symbol frequency table (can be NULL).
264    /// * `r` - The sampling rate for auxiliary indexes (must be power of 2).
265    /// * `I` - [0..(n-1)/r] The input auxiliary indexes.
266    ///
267    /// # Returns
268    ///
269    /// 0 if no error occurred, -1 or -2 otherwise.
270    pub fn libsais64_unbwt_aux(
271        T: *const u8,
272        U: *mut u8,
273        A: *mut i64,
274        n: i64,
275        freq: *const i64,
276        r: i64,
277        I: *const i64,
278    ) -> i64;
279
280    /// Constructs the original string from a given burrows-wheeler transformed string (BWT) with primary index in parallel using OpenMP.
281    ///
282    /// # Arguments
283    ///
284    /// * `T` - [0..n-1] The input string.
285    /// * `U` - [0..n-1] The output string (can be T).
286    /// * `A` - [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
287    /// * `n` - The length of the given string.
288    /// * `freq` - [0..255] The input symbol frequency table (can be NULL).
289    /// * `i` - The primary index.
290    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
291    ///
292    /// # Returns
293    ///
294    /// 0 if no error occurred, -1 or -2 otherwise.
295    #[cfg(feature = "openmp")]
296    pub fn libsais64_unbwt_omp(
297        T: *const u8,
298        U: *mut u8,
299        A: *mut i64,
300        n: i64,
301        freq: *const i64,
302        i: i64,
303        threads: i64,
304    ) -> i64;
305
306    /// Constructs the original string from a given burrows-wheeler transformed string (BWT) with auxiliary indexes in parallel using OpenMP.
307    ///
308    /// # Arguments
309    ///
310    /// * `T` - [0..n-1] The input string.
311    /// * `U` - [0..n-1] The output string (can be T).
312    /// * `A` - [0..n] The temporary array (NOTE, temporary array must be n + 1 size).
313    /// * `n` - The length of the given string.
314    /// * `freq` - [0..255] The input symbol frequency table (can be NULL).
315    /// * `r` - The sampling rate for auxiliary indexes (must be power of 2).
316    /// * `I` - [0..(n-1)/r] The input auxiliary indexes.
317    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
318    ///
319    /// # Returns
320    ///
321    /// 0 if no error occurred, -1 or -2 otherwise.
322    #[cfg(feature = "openmp")]
323    pub fn libsais64_unbwt_aux_omp(
324        T: *const u8,
325        U: *mut u8,
326        A: *mut i64,
327        n: i64,
328        freq: *const i64,
329        r: i64,
330        I: *const i64,
331        threads: i64,
332    ) -> i64;
333
334    /// Constructs the permuted longest common prefix array (PLCP) of a given string and a suffix array.
335    ///
336    /// # Arguments
337    ///
338    /// * `T` - [0..n-1] The input string.
339    /// * `SA` - [0..n-1] The input suffix array.
340    /// * `PLCP` - [0..n-1] The output permuted longest common prefix array.
341    /// * `n` - The length of the string and the suffix array.
342    ///
343    /// # Returns
344    ///
345    /// 0 if no error occurred, -1 otherwise.
346    pub fn libsais64_plcp(T: *const u8, SA: *const i64, PLCP: *mut i64, n: i64) -> i64;
347
348    /// Constructs the permuted longest common prefix array (PLCP) of a given string set and a generalized suffix array (GSA).
349    ///
350    /// # Arguments
351    ///
352    /// * `T` - [0..n-1] The input string set using 0 as separators (T[n-1] must be 0).
353    /// * `SA` - [0..n-1] The input generalized suffix array.
354    /// * `PLCP` - [0..n-1] The output permuted longest common prefix array.
355    /// * `n` - The length of the string set and the generalized suffix array.
356    ///
357    /// # Returns
358    ///
359    /// 0 if no error occurred, -1 otherwise.
360    pub fn libsais64_plcp_gsa(T: *const u8, SA: *const i64, PLCP: *mut i64, n: i64) -> i64;
361
362    /// Constructs the longest common prefix array (LCP) of a given permuted longest common prefix array (PLCP) and a suffix array.
363    ///
364    /// # Arguments
365    ///
366    /// * `PLCP` - [0..n-1] The input permuted longest common prefix array.
367    /// * `SA` - [0..n-1] The input suffix array or generalized suffix array (GSA).
368    /// * `LCP` - [0..n-1] The output longest common prefix array (can be SA).
369    /// * `n` - The length of the permuted longest common prefix array and the suffix array.
370    ///
371    /// # Returns
372    ///
373    /// 0 if no error occurred, -1 otherwise.
374    pub fn libsais64_lcp(PLCP: *const i64, SA: *const i64, LCP: *mut i64, n: i64) -> i64;
375
376    /// Constructs the permuted longest common prefix array (PLCP) of a given string and a suffix array in parallel using OpenMP.
377    ///
378    /// # Arguments
379    ///
380    /// * `T` - [0..n-1] The input string.
381    /// * `SA` - [0..n-1] The input suffix array.
382    /// * `PLCP` - [0..n-1] The output permuted longest common prefix array.
383    /// * `n` - The length of the string and the suffix array.
384    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
385    ///
386    /// # Returns
387    ///
388    /// 0 if no error occurred, -1 otherwise.
389    #[cfg(feature = "openmp")]
390    pub fn libsais64_plcp_omp(
391        T: *const u8,
392        SA: *const i64,
393        PLCP: *mut i64,
394        n: i64,
395        threads: i64,
396    ) -> i64;
397
398    /// Constructs the permuted longest common prefix array (PLCP) of a given string set and a generalized suffix array (GSA) in parallel using OpenMP.
399    ///
400    /// # Arguments
401    ///
402    /// * `T` - [0..n-1] The input string set using 0 as separators (T[n-1] must be 0).
403    /// * `SA` - [0..n-1] The input generalized suffix array.
404    /// * `PLCP` - [0..n-1] The output permuted longest common prefix array.
405    /// * `n` - The length of the string set and the generalized suffix array.
406    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
407    ///
408    /// # Returns
409    ///
410    /// 0 if no error occurred, -1 otherwise.
411    #[cfg(feature = "openmp")]
412    pub fn libsais64_plcp_gsa_omp(
413        T: *const u8,
414        SA: *const i64,
415        PLCP: *mut i64,
416        n: i64,
417        threads: i64,
418    ) -> i64;
419
420    /// Constructs the longest common prefix array (LCP) of a given permuted longest common prefix array (PLCP) and a suffix array in parallel using OpenMP.
421    ///
422    /// # Arguments
423    ///
424    /// * `PLCP` - [0..n-1] The input permuted longest common prefix array.
425    /// * `SA` - [0..n-1] The input suffix array or generalized suffix array (GSA).
426    /// * `LCP` - [0..n-1] The output longest common prefix array (can be SA).
427    /// * `n` - The length of the permuted longest common prefix array and the suffix array.
428    /// * `threads` - The number of OpenMP threads to use (can be 0 for OpenMP default).
429    ///
430    /// # Returns
431    ///
432    /// 0 if no error occurred, -1 otherwise.
433    #[cfg(feature = "openmp")]
434    pub fn libsais64_lcp_omp(
435        PLCP: *const i64,
436        SA: *const i64,
437        LCP: *mut i64,
438        n: i64,
439        threads: i64,
440    ) -> i64;
441}
libsais_sys/libsais64.rs

libsais_sys/
libsais64.rs
