Implemented suffix array construction of a long integer array (libsai…

…s64).

CHANGES

@@ -1,3 +1,6 @@
+Changes in 2.8.2 (May 27, 2024)
+- Implemented suffix array construction of a long integer array (libsais64).
+
 Changes in 2.8.1 (April 5, 2024)
 - Fixed out-of-bound memory access issue for large inputs (libsais64).
 

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.10)
 
-project(libsais VERSION 2.8.1 LANGUAGES C DESCRIPTION "libsais is a library for linear time suffix array, longest common prefix array and burrows wheeler transform construction based on induced sorting algorithm.")
+project(libsais VERSION 2.8.2 LANGUAGES C DESCRIPTION "libsais is a library for linear time suffix array, longest common prefix array and burrows wheeler transform construction based on induced sorting algorithm.")
 
 set(CMAKE_C_STANDARD 99)
 set(CMAKE_C_STANDARD_REQUIRED ON)

README.md

@@ -23,6 +23,8 @@ The libsais provides simple C99 API to construct suffix array and Burrows-Wheele
 The libsais is released under the [Apache License Version 2.0](LICENSE "Apache license")
 
 ## Changes
+* May 27, 2024 (2.8.2)
+  * Implemented suffix array construction of a long integer array (libsais64).
 * April 5, 2024 (2.8.1)
   * Fixed out-of-bound memory access issue for large inputs (libsais64).
 * March 3, 2024 (2.8.0)

VERSION

@@ -1 +1 @@
-2.8.1
+2.8.2

include/libsais.h

@@ -26,8 +26,8 @@ Please see the file LICENSE for full copyright information.
 
 #define LIBSAIS_VERSION_MAJOR   2
 #define LIBSAIS_VERSION_MINOR   8
-#define LIBSAIS_VERSION_PATCH   1
-#define LIBSAIS_VERSION_STRING  "2.8.1"
+#define LIBSAIS_VERSION_PATCH   2
+#define LIBSAIS_VERSION_STRING  "2.8.2"
 
 #ifdef _WIN32
     #ifdef LIBSAIS_SHARED

include/libsais16.h

@@ -26,8 +26,8 @@ Please see the file LICENSE for full copyright information.
 
 #define LIBSAIS16_VERSION_MAJOR   2
 #define LIBSAIS16_VERSION_MINOR   8
-#define LIBSAIS16_VERSION_PATCH   1
-#define LIBSAIS16_VERSION_STRING  "2.8.1"
+#define LIBSAIS16_VERSION_PATCH   2
+#define LIBSAIS16_VERSION_STRING  "2.8.2"
 
 #ifdef _WIN32
     #ifdef LIBSAIS_SHARED

include/libsais64.h

@@ -26,8 +26,8 @@ Please see the file LICENSE for full copyright information.
 
 #define LIBSAIS64_VERSION_MAJOR   2
 #define LIBSAIS64_VERSION_MINOR   8
-#define LIBSAIS64_VERSION_PATCH   1
-#define LIBSAIS64_VERSION_STRING  "2.8.1"
+#define LIBSAIS64_VERSION_PATCH   2
+#define LIBSAIS64_VERSION_STRING  "2.8.2"
 
 #ifdef _WIN32
     #ifdef LIBSAIS_SHARED
@@ -60,6 +60,18 @@ extern "C" {
     */
     LIBSAIS64_API int64_t libsais64(const uint8_t * T, int64_t * SA, int64_t n, int64_t fs, int64_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.
+    */
+    LIBSAIS64_API int64_t libsais64_long(int64_t * T, int64_t * SA, int64_t n, int64_t k, int64_t fs);
+
 #if defined(LIBSAIS_OPENMP)
     /**
     * Constructs the suffix array of a given string in parallel using OpenMP.
@@ -72,6 +84,19 @@ extern "C" {
     * @return 0 if no error occurred, -1 or -2 otherwise.
     */
     LIBSAIS64_API int64_t libsais64_omp(const uint8_t * T, int64_t * SA, int64_t n, int64_t fs, int64_t * freq, int64_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.
+    */
+    LIBSAIS64_API int64_t libsais64_long_omp(int64_t * T, int64_t * SA, int64_t n, int64_t k, int64_t fs, int64_t threads);
 #endif
 
     /**

src/libsais.c

@@ -6528,7 +6528,7 @@ static sa_sint_t libsais_main(const uint8_t * T, sa_sint_t * SA, sa_sint_t n, sa
     return index;
 }
 
-static int32_t libsais_main_int(sa_sint_t * T, sa_sint_t * SA, sa_sint_t n, sa_sint_t k, sa_sint_t fs, sa_sint_t threads)
+static sa_sint_t libsais_main_int(sa_sint_t * T, sa_sint_t * SA, sa_sint_t n, sa_sint_t k, sa_sint_t fs, sa_sint_t threads)
 {
     LIBSAIS_THREAD_STATE * RESTRICT thread_state = threads > 1 ? libsais_alloc_thread_state(threads) : NULL;
 

src/libsais64.c

@@ -6584,6 +6584,19 @@ static sa_sint_t libsais64_main(const uint8_t * T, sa_sint_t * SA, sa_sint_t n,
     return index;
 }
 
+static sa_sint_t libsais64_main_long(sa_sint_t * T, sa_sint_t * SA, sa_sint_t n, sa_sint_t k, sa_sint_t fs, sa_sint_t threads)
+{
+    LIBSAIS_THREAD_STATE * RESTRICT thread_state = threads > 1 ? libsais64_alloc_thread_state(threads) : NULL;
+
+    sa_sint_t index = thread_state != NULL || threads == 1
+        ? libsais64_main_32s_entry(T, SA, n, k, fs, threads, thread_state)
+        : -2;
+
+    libsais64_free_thread_state(thread_state);
+
+    return index;
+}
+
 static void libsais64_bwt_copy_8u(uint8_t * RESTRICT U, sa_sint_t * RESTRICT A, sa_sint_t n)
 {
     const fast_sint_t prefetch_distance = 32;
@@ -6666,6 +6679,21 @@ int64_t libsais64(const uint8_t * T, int64_t * SA, int64_t n, int64_t fs, int64_
     return libsais64_main(T, SA, n, 0, 0, NULL, fs, freq, 1);
 }
 
+int64_t libsais64_long(int64_t * T, int64_t * SA, int64_t n, int64_t k, int64_t fs)
+{
+    if ((T == NULL) || (SA == NULL) || (n < 0) || (fs < 0))
+    {
+        return -1;
+    }
+    else if (n < 2)
+    {
+        if (n == 1) { SA[0] = 0; }
+        return 0;
+    }
+
+    return libsais64_main_long(T, SA, n, k, fs, 1);
+}
+
 int64_t libsais64_bwt(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, int64_t fs, int64_t * freq)
 {
     if ((T == NULL) || (U == NULL) || (A == NULL) || (n < 0) || (fs < 0))
@@ -6779,6 +6807,23 @@ int64_t libsais64_omp(const uint8_t * T, int64_t * SA, int64_t n, int64_t fs, in
     return libsais64_main(T, SA, n, 0, 0, NULL, fs, freq, threads);
 }
 
+int64_t libsais64_long_omp(int64_t * T, int64_t * SA, int64_t n, int64_t k, int64_t fs, int64_t threads)
+{
+    if ((T == NULL) || (SA == NULL) || (n < 0) || (fs < 0) || (threads < 0))
+    {
+        return -1;
+    }
+    else if (n < 2)
+    {
+        if (n == 1) { SA[0] = 0; }
+        return 0;
+    }
+
+    threads = threads > 0 ? threads : omp_get_max_threads();
+
+    return libsais64_main_long(T, SA, n, k, fs, threads);
+}
+
 int64_t libsais64_bwt_omp(const uint8_t * T, uint8_t * U, int64_t * A, int64_t n, int64_t fs, int64_t * freq, int64_t threads)
 {
     if ((T == NULL) || (U == NULL) || (A == NULL) || (n < 0) || (fs < 0) || (threads < 0))