minibwa 0.0.0

data/ext/minibwa/minibwa/libsais.h

@@ -0,0 +1,106 @@
+/*--
+
+This file is a part of libsais, a library for linear time suffix array,
+longest common prefix array and burrows wheeler transform construction.
+
+   Copyright (c) 2021-2025 Ilya Grebnov <ilya.grebnov@gmail.com>
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+Please see the file LICENSE for full copyright information.
+
+--*/
+
+#ifndef LIBSAIS_H
+#define LIBSAIS_H 1
+
+#define LIBSAIS_VERSION_MAJOR   2
+#define LIBSAIS_VERSION_MINOR   10
+#define LIBSAIS_VERSION_PATCH   4
+#define LIBSAIS_VERSION_STRING  "2.10.4"
+
+#ifdef _WIN32
+    #ifdef LIBSAIS_SHARED
+        #ifdef LIBSAIS_EXPORTS
+            #define LIBSAIS_API __declspec(dllexport)
+        #else
+            #define LIBSAIS_API __declspec(dllimport)
+        #endif
+    #else
+        #define LIBSAIS_API
+    #endif
+#else
+    #define LIBSAIS_API
+#endif
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+    #include <stdint.h>
+
+    /**
+    * Constructs the suffix array of a given string.
+    * @param T [0..n-1] The input string.
+    * @param SA [0..n-1+fs] The output array of suffixes.
+    * @param n The length of the given string.
+    * @param fs The extra space available at the end of SA array (0 should be enough for most cases).
+    * @param freq [0..255] The output symbol frequency table (can be NULL).
+    * @return 0 if no error occurred, -1 or -2 otherwise.
+    */
+    LIBSAIS_API int32_t libsais(const uint8_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq);
+
+    /**
+    * 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.
+    * @param T [0..n-1] The input integer array.
+    * @param SA [0..n-1+fs] The output array of suffixes.
+    * @param n The length of the integer array.
+    * @param k The alphabet size of the input integer array.
+    * @param fs Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
+    * @return 0 if no error occurred, -1 or -2 otherwise.
+    */
+    LIBSAIS_API int32_t libsais_int(int32_t * T, int32_t * SA, int32_t n, int32_t k, int32_t fs);
+
+#if defined(LIBSAIS_OPENMP)
+    /**
+    * Constructs the suffix array of a given string in parallel using OpenMP.
+    * @param T [0..n-1] The input string.
+    * @param SA [0..n-1+fs] The output array of suffixes.
+    * @param n The length of the given string.
+    * @param fs The extra space available at the end of SA array (0 should be enough for most cases).
+    * @param freq [0..255] The output symbol frequency table (can be NULL).
+    * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
+    * @return 0 if no error occurred, -1 or -2 otherwise.
+    */
+    LIBSAIS_API int32_t libsais_omp(const uint8_t * T, int32_t * SA, int32_t n, int32_t fs, int32_t * freq, int32_t threads);
+
+    /**
+    * 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.
+    * @param T [0..n-1] The input integer array.
+    * @param SA [0..n-1+fs] The output array of suffixes.
+    * @param n The length of the integer array.
+    * @param k The alphabet size of the input integer array.
+    * @param fs Extra space available at the end of SA array (can be 0, but 4k or better 6k is recommended for optimal performance).
+    * @param threads The number of OpenMP threads to use (can be 0 for OpenMP default).
+    * @return 0 if no error occurred, -1 or -2 otherwise.
+    */
+    LIBSAIS_API int32_t libsais_int_omp(int32_t * T, int32_t * SA, int32_t n, int32_t k, int32_t fs, int32_t threads);
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif