Initial import of the open source release

7 files changed, 882 insertions, 0 deletions

diff --git a/tools/apultra_src/src/libdivsufsort/include/CMakeLists.txt b/tools/apultra_src/src/libdivsufsort/include/CMakeLists.txt
new file mode 100644
index 0000000..37781cc
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/include/CMakeLists.txt
@@ -0,0 +1,162 @@
+include(CheckIncludeFiles)
+include(CheckIncludeFile)
+include(CheckSymbolExists)
+include(CheckTypeSize)
+include(CheckFunctionKeywords)
+include(CheckLFS)
+
+## Checks for header files ##
+check_include_file("inttypes.h" HAVE_INTTYPES_H)
+check_include_file("memory.h" HAVE_MEMORY_H)
+check_include_file("stddef.h" HAVE_STDDEF_H)
+check_include_file("stdint.h" HAVE_STDINT_H)
+check_include_file("stdlib.h" HAVE_STDLIB_H)
+check_include_file("string.h" HAVE_STRING_H)
+check_include_file("strings.h" HAVE_STRINGS_H)
+check_include_file("sys/types.h" HAVE_SYS_TYPES_H)
+if(HAVE_INTTYPES_H)
+  set(INCFILE "#include <inttypes.h>")
+elseif(HAVE_STDINT_H)
+  set(INCFILE "#include <stdint.h>")
+else(HAVE_INTTYPES_H)
+  set(INCFILE "")
+endif(HAVE_INTTYPES_H)
+
+## create configuration files from .cmake file ##
+if(BUILD_EXAMPLES)
+  ## Checks for WinIO ##
+  if(WIN32)
+    check_include_file("io.h" HAVE_IO_H)
+    check_include_file("fcntl.h" HAVE_FCNTL_H)
+    check_symbol_exists("_setmode" "io.h;fcntl.h" HAVE__SETMODE)
+    if(NOT HAVE__SETMODE)
+      check_symbol_exists("setmode" "io.h;fcntl.h" HAVE_SETMODE)
+    endif(NOT HAVE__SETMODE)
+    check_symbol_exists("_fileno" "stdio.h" HAVE__FILENO)
+    check_symbol_exists("fopen_s" "stdio.h" HAVE_FOPEN_S)
+    check_symbol_exists("_O_BINARY" "fcntl.h" HAVE__O_BINARY)
+  endif(WIN32)
+
+  ## Checks for large file support ##
+  check_lfs(WITH_LFS)
+  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lfs.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/lfs.h" @ONLY)
+endif(BUILD_EXAMPLES)
+
+## generate config.h ##
+check_function_keywords("inline;__inline;__inline__;__declspec(dllexport);__declspec(dllimport)")
+if(HAVE_INLINE)
+  set(INLINE "inline")
+elseif(HAVE___INLINE)
+  set(INLINE "__inline")
+elseif(HAVE___INLINE__)
+  set(INLINE "__inline__")
+else(HAVE_INLINE)
+  set(INLINE "")
+endif(HAVE_INLINE)
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/config.h")
+
+## Checks for types ##
+# sauchar_t (8bit)
+check_type_size("uint8_t" UINT8_T)
+if(HAVE_UINT8_T)
+  set(SAUCHAR_TYPE "uint8_t")
+else(HAVE_UINT8_T)
+  check_type_size("unsigned char" SIZEOF_UNSIGNED_CHAR)
+  if("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1")
+    set(SAUCHAR_TYPE "unsigned char")
+  else("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1")
+    message(FATAL_ERROR "Cannot find unsigned 8-bit integer type")
+  endif("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1")
+endif(HAVE_UINT8_T)
+# saint_t (32bit)
+check_type_size("int32_t" INT32_T)
+if(HAVE_INT32_T)
+  set(SAINT32_TYPE "int32_t")
+  check_symbol_exists("PRId32" "inttypes.h" HAVE_PRID32)
+  if(HAVE_PRID32)
+    set(SAINT32_PRId "PRId32")
+  else(HAVE_PRID32)
+    set(SAINT32_PRId "\"d\"")
+  endif(HAVE_PRID32)
+else(HAVE_INT32_T)
+  check_type_size("int" SIZEOF_INT)
+  check_type_size("long" SIZEOF_LONG)
+  check_type_size("short" SIZEOF_SHORT)
+  check_type_size("__int32" SIZEOF___INT32)
+  if("${SIZEOF_INT}" STREQUAL "4")
+    set(SAINT32_TYPE "int")
+    set(SAINT32_PRId "\"d\"")
+  elseif("${SIZEOF_LONG}" STREQUAL "4")
+    set(SAINT32_TYPE "long")
+    set(SAINT32_PRId "\"ld\"")
+  elseif("${SIZEOF_SHORT}" STREQUAL "4")
+    set(SAINT32_TYPE "short")
+    set(SAINT32_PRId "\"d\"")
+  elseif("${SIZEOF___INT32}" STREQUAL "4")
+    set(SAINT32_TYPE "__int32")
+    set(SAINT32_PRId "\"d\"")
+  else("${SIZEOF_INT}" STREQUAL "4")
+    message(FATAL_ERROR "Cannot find 32-bit integer type")
+  endif("${SIZEOF_INT}" STREQUAL "4")
+endif(HAVE_INT32_T)
+# saint64_t (64bit)
+if(BUILD_DIVSUFSORT64)
+  check_type_size("int64_t" INT64_T)
+  if(HAVE_INT64_T)
+    set(SAINT64_TYPE "int64_t")
+    check_symbol_exists("PRId64" "inttypes.h" HAVE_PRID64)
+    if(HAVE_PRID64)
+      set(SAINT64_PRId "PRId64")
+    else(HAVE_PRID64)
+      set(SAINT64_PRId "\"lld\"")
+    endif(HAVE_PRID64)
+  else(HAVE_INT64_T)
+    check_type_size("int" SIZEOF_INT)
+    check_type_size("long" SIZEOF_LONG)
+    check_type_size("long long" SIZEOF_LONG_LONG)
+    check_type_size("__int64" SIZEOF___INT64)
+    if("${SIZEOF_INT}" STREQUAL "8")
+      set(SAINT64_TYPE "int")
+      set(SAINT64_PRId "\"d\"")
+    elseif("${SIZEOF_LONG}" STREQUAL "8")
+      set(SAINT64_TYPE "long")
+      set(SAINT64_PRId "\"ld\"")
+    elseif("${SIZEOF_LONG_LONG}" STREQUAL "8")
+      set(SAINT64_TYPE "long long")
+      set(SAINT64_PRId "\"lld\"")
+    elseif("${SIZEOF___INT64}" STREQUAL "8")
+      set(SAINT64_TYPE "__int64")
+      set(SAINT64_PRId "\"I64d\"")
+    else("${SIZEOF_INT}" STREQUAL "8")
+      message(SEND_ERROR "Cannot find 64-bit integer type")
+      set(BUILD_DIVSUFSORT64 OFF)
+    endif("${SIZEOF_INT}" STREQUAL "8")
+  endif(HAVE_INT64_T)
+endif(BUILD_DIVSUFSORT64)
+
+## generate divsufsort.h ##
+set(DIVSUFSORT_IMPORT "")
+set(DIVSUFSORT_EXPORT "")
+if(BUILD_SHARED_LIBS)
+  if(HAVE___DECLSPEC_DLLIMPORT_)
+    set(DIVSUFSORT_IMPORT "__declspec(dllimport)")
+  endif(HAVE___DECLSPEC_DLLIMPORT_)
+  if(HAVE___DECLSPEC_DLLEXPORT_)
+    set(DIVSUFSORT_EXPORT "__declspec(dllexport)")
+  endif(HAVE___DECLSPEC_DLLEXPORT_)
+endif(BUILD_SHARED_LIBS)
+set(W64BIT "")
+set(SAINDEX_TYPE "${SAINT32_TYPE}")
+set(SAINDEX_PRId "${SAINT32_PRId}")
+set(SAINT_PRId "${SAINT32_PRId}")
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake"
+               "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" @ONLY)
+install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+if(BUILD_DIVSUFSORT64)
+  set(W64BIT "64")
+  set(SAINDEX_TYPE "${SAINT64_TYPE}")
+  set(SAINDEX_PRId "${SAINT64_PRId}")
+  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake"
+                 "${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" @ONLY)
+  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+endif(BUILD_DIVSUFSORT64)
diff --git a/tools/apultra_src/src/libdivsufsort/include/config.h.cmake b/tools/apultra_src/src/libdivsufsort/include/config.h.cmake
new file mode 100644
index 0000000..6a1cf47
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/include/config.h.cmake
@@ -0,0 +1,81 @@
+/*
+ * config.h for libdivsufsort
+ * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#ifndef _CONFIG_H
+#define _CONFIG_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/** Define to the version of this package. **/
+#cmakedefine PROJECT_VERSION_FULL "${PROJECT_VERSION_FULL}"
+
+/** Define to 1 if you have the header files. **/
+#cmakedefine HAVE_INTTYPES_H 1
+#cmakedefine HAVE_STDDEF_H 1
+#cmakedefine HAVE_STDINT_H 1
+#cmakedefine HAVE_STDLIB_H 1
+#cmakedefine HAVE_STRING_H 1
+#cmakedefine HAVE_STRINGS_H 1
+#cmakedefine HAVE_MEMORY_H 1
+#cmakedefine HAVE_SYS_TYPES_H 1
+
+/** for WinIO **/
+#cmakedefine HAVE_IO_H 1
+#cmakedefine HAVE_FCNTL_H 1
+#cmakedefine HAVE__SETMODE 1
+#cmakedefine HAVE_SETMODE 1
+#cmakedefine HAVE__FILENO 1
+#cmakedefine HAVE_FOPEN_S 1
+#cmakedefine HAVE__O_BINARY 1
+#ifndef HAVE__SETMODE
+# if HAVE_SETMODE
+#  define _setmode setmode
+#  define HAVE__SETMODE 1
+# endif
+# if HAVE__SETMODE && !HAVE__O_BINARY
+#  define _O_BINARY 0
+#  define HAVE__O_BINARY 1
+# endif
+#endif
+
+/** for inline **/
+#ifndef INLINE
+# define INLINE @INLINE@
+#endif
+
+/** for VC++ warning **/
+#ifdef _MSC_VER
+#pragma warning(disable: 4127)
+#endif
+
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _CONFIG_H */
diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort.h b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h
new file mode 100644
index 0000000..7ebb412
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h
@@ -0,0 +1,189 @@
+/*
+ * divsufsort.h for libdivsufsort
+ * Copyright (c) 2003-2008 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 _DIVSUFSORT_H
+#define _DIVSUFSORT_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#define DIVSUFSORT_API
+
+/*- Datatypes -*/
+#ifndef SAUCHAR_T
+#define SAUCHAR_T
+typedef unsigned char sauchar_t;
+#endif /* SAUCHAR_T */
+#ifndef SAINT_T
+#define SAINT_T
+typedef int saint_t;
+#endif /* SAINT_T */
+#ifndef SAIDX_T
+#define SAIDX_T
+typedef int saidx_t;
+#endif /* SAIDX_T */
+#ifndef PRIdSAIDX_T
+#define PRIdSAIDX_T "d"
+#endif
+
+/*- divsufsort context */
+typedef struct _divsufsort_ctx_t {
+   saidx_t *bucket_A;
+   saidx_t *bucket_B;
+} divsufsort_ctx_t;
+
+/*- Prototypes -*/
+
+/**
+ * Initialize suffix array context
+ *
+ * @return 0 for success, or non-zero in case of an error
+ */
+int divsufsort_init(divsufsort_ctx_t *ctx);
+
+/**
+ * Destroy suffix array context
+ *
+ * @param ctx suffix array context to destroy
+ */
+void divsufsort_destroy(divsufsort_ctx_t *ctx);
+
+/**
+ * Constructs the suffix array of a given string.
+ * @param ctx suffix array context
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n-1] The output array of suffixes.
+ * @param n The length of the given string.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t divsufsort_build_array(divsufsort_ctx_t *ctx, const sauchar_t *T, saidx_t *SA, saidx_t n);
+
+#if 0
+/**
+ * Constructs the burrows-wheeler transformed string of a given string.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param A[0..n-1] The temporary array. (can be NULL)
+ * @param n The length of the given string.
+ * @return The primary index if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saidx_t
+divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n);
+
+/**
+ * Returns the version of the divsufsort library.
+ * @return The version number string.
+ */
+DIVSUFSORT_API
+const char *
+divsufsort_version(void);
+
+
+/**
+ * Constructs the burrows-wheeler transformed string of a given string and suffix array.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param SA[0..n-1] The suffix array. (can be NULL)
+ * @param n The length of the given string.
+ * @param idx The output primary index.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+bw_transform(const sauchar_t *T, sauchar_t *U,
+             saidx_t *SA /* can NULL */,
+             saidx_t n, saidx_t *idx);
+
+/**
+ * Inverse BW-transforms a given BWTed string.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param A[0..n-1] The temporary array. (can be NULL)
+ * @param n The length of the given string.
+ * @param idx The primary index.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+inverse_bw_transform(const sauchar_t *T, sauchar_t *U,
+                     saidx_t *A /* can NULL */,
+                     saidx_t n, saidx_t idx);
+
+/**
+ * Checks the correctness of a given suffix array.
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n-1] The input suffix array.
+ * @param n The length of the given string.
+ * @param verbose The verbose mode.
+ * @return 0 if no error occurred.
+ */
+DIVSUFSORT_API
+saint_t
+sufcheck(const sauchar_t *T, const saidx_t *SA, saidx_t n, saint_t verbose);
+
+/**
+ * Search for the pattern P in the string T.
+ * @param T[0..Tsize-1] The input string.
+ * @param Tsize The length of the given string.
+ * @param P[0..Psize-1] The input pattern string.
+ * @param Psize The length of the given pattern string.
+ * @param SA[0..SAsize-1] The input suffix array.
+ * @param SAsize The length of the given suffix array.
+ * @param idx The output index.
+ * @return The count of matches if no error occurred, -1 otherwise.
+ */
+DIVSUFSORT_API
+saidx_t
+sa_search(const sauchar_t *T, saidx_t Tsize,
+          const sauchar_t *P, saidx_t Psize,
+          const saidx_t *SA, saidx_t SAsize,
+          saidx_t *left);
+
+/**
+ * Search for the character c in the string T.
+ * @param T[0..Tsize-1] The input string.
+ * @param Tsize The length of the given string.
+ * @param SA[0..SAsize-1] The input suffix array.
+ * @param SAsize The length of the given suffix array.
+ * @param c The input character.
+ * @param idx The output index.
+ * @return The count of matches if no error occurred, -1 otherwise.
+ */
+DIVSUFSORT_API
+saidx_t
+sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
+                const saidx_t *SA, saidx_t SAsize,
+                saint_t c, saidx_t *left);
+#endif
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _DIVSUFSORT_H */
diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort.h.cmake b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h.cmake
new file mode 100644
index 0000000..bcaba7c
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h.cmake
@@ -0,0 +1,180 @@
+/*
+ * divsufsort@W64BIT@.h for libdivsufsort@W64BIT@
+ * Copyright (c) 2003-2008 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 _DIVSUFSORT@W64BIT@_H
+#define _DIVSUFSORT@W64BIT@_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+@INCFILE@
+
+#ifndef DIVSUFSORT_API
+# ifdef DIVSUFSORT_BUILD_DLL
+#  define DIVSUFSORT_API @DIVSUFSORT_EXPORT@
+# else
+#  define DIVSUFSORT_API @DIVSUFSORT_IMPORT@
+# endif
+#endif
+
+/*- Datatypes -*/
+#ifndef SAUCHAR_T
+#define SAUCHAR_T
+typedef @SAUCHAR_TYPE@ sauchar_t;
+#endif /* SAUCHAR_T */
+#ifndef SAINT_T
+#define SAINT_T
+typedef @SAINT32_TYPE@ saint_t;
+#endif /* SAINT_T */
+#ifndef SAIDX@W64BIT@_T
+#define SAIDX@W64BIT@_T
+typedef @SAINDEX_TYPE@ saidx@W64BIT@_t;
+#endif /* SAIDX@W64BIT@_T */
+#ifndef PRIdSAINT_T
+#define PRIdSAINT_T @SAINT_PRId@
+#endif /* PRIdSAINT_T */
+#ifndef PRIdSAIDX@W64BIT@_T
+#define PRIdSAIDX@W64BIT@_T @SAINDEX_PRId@
+#endif /* PRIdSAIDX@W64BIT@_T */
+
+
+/*- Prototypes -*/
+
+/**
+ * Constructs the suffix array of a given string.
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n-1] The output array of suffixes.
+ * @param n The length of the given string.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+divsufsort@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t *SA, saidx@W64BIT@_t n);
+
+/**
+ * Constructs the burrows-wheeler transformed string of a given string.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param A[0..n-1] The temporary array. (can be NULL)
+ * @param n The length of the given string.
+ * @return The primary index if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saidx@W64BIT@_t
+divbwt@W64BIT@(const sauchar_t *T, sauchar_t *U, saidx@W64BIT@_t *A, saidx@W64BIT@_t n);
+
+/**
+ * Returns the version of the divsufsort library.
+ * @return The version number string.
+ */
+DIVSUFSORT_API
+const char *
+divsufsort@W64BIT@_version(void);
+
+
+/**
+ * Constructs the burrows-wheeler transformed string of a given string and suffix array.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param SA[0..n-1] The suffix array. (can be NULL)
+ * @param n The length of the given string.
+ * @param idx The output primary index.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+bw_transform@W64BIT@(const sauchar_t *T, sauchar_t *U,
+             saidx@W64BIT@_t *SA /* can NULL */,
+             saidx@W64BIT@_t n, saidx@W64BIT@_t *idx);
+
+/**
+ * Inverse BW-transforms a given BWTed string.
+ * @param T[0..n-1] The input string.
+ * @param U[0..n-1] The output string. (can be T)
+ * @param A[0..n-1] The temporary array. (can be NULL)
+ * @param n The length of the given string.
+ * @param idx The primary index.
+ * @return 0 if no error occurred, -1 or -2 otherwise.
+ */
+DIVSUFSORT_API
+saint_t
+inverse_bw_transform@W64BIT@(const sauchar_t *T, sauchar_t *U,
+                     saidx@W64BIT@_t *A /* can NULL */,
+                     saidx@W64BIT@_t n, saidx@W64BIT@_t idx);
+
+/**
+ * Checks the correctness of a given suffix array.
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n-1] The input suffix array.
+ * @param n The length of the given string.
+ * @param verbose The verbose mode.
+ * @return 0 if no error occurred.
+ */
+DIVSUFSORT_API
+saint_t
+sufcheck@W64BIT@(const sauchar_t *T, const saidx@W64BIT@_t *SA, saidx@W64BIT@_t n, saint_t verbose);
+
+/**
+ * Search for the pattern P in the string T.
+ * @param T[0..Tsize-1] The input string.
+ * @param Tsize The length of the given string.
+ * @param P[0..Psize-1] The input pattern string.
+ * @param Psize The length of the given pattern string.
+ * @param SA[0..SAsize-1] The input suffix array.
+ * @param SAsize The length of the given suffix array.
+ * @param idx The output index.
+ * @return The count of matches if no error occurred, -1 otherwise.
+ */
+DIVSUFSORT_API
+saidx@W64BIT@_t
+sa_search@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t Tsize,
+          const sauchar_t *P, saidx@W64BIT@_t Psize,
+          const saidx@W64BIT@_t *SA, saidx@W64BIT@_t SAsize,
+          saidx@W64BIT@_t *left);
+
+/**
+ * Search for the character c in the string T.
+ * @param T[0..Tsize-1] The input string.
+ * @param Tsize The length of the given string.
+ * @param SA[0..SAsize-1] The input suffix array.
+ * @param SAsize The length of the given suffix array.
+ * @param c The input character.
+ * @param idx The output index.
+ * @return The count of matches if no error occurred, -1 otherwise.
+ */
+DIVSUFSORT_API
+saidx@W64BIT@_t
+sa_simplesearch@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t Tsize,
+                const saidx@W64BIT@_t *SA, saidx@W64BIT@_t SAsize,
+                saint_t c, saidx@W64BIT@_t *left);
+
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _DIVSUFSORT@W64BIT@_H */
diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort_config.h b/tools/apultra_src/src/libdivsufsort/include/divsufsort_config.h
new file mode 100644
index 0000000..4054a8a
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort_config.h
@@ -0,0 +1,9 @@
+#define HAVE_STRING_H 1

+#define HAVE_STDLIB_H 1

+#define HAVE_MEMORY_H 1

+#define HAVE_STDINT_H 1

+#define INLINE inline

+

+#ifdef _MSC_VER

+#pragma warning( disable : 4244 )

+#endif /* _MSC_VER */

diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort_private.h b/tools/apultra_src/src/libdivsufsort/include/divsufsort_private.h
new file mode 100644
index 0000000..b4d97ad
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort_private.h
@@ -0,0 +1,205 @@
+/*
+ * divsufsort_private.h for libdivsufsort
+ * Copyright (c) 2003-2008 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 _DIVSUFSORT_PRIVATE_H
+#define _DIVSUFSORT_PRIVATE_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#include "divsufsort_config.h"
+#include <assert.h>
+#include <stdio.h>
+#if HAVE_STRING_H
+# include <string.h>
+#endif
+#if HAVE_STDLIB_H
+# include <stdlib.h>
+#endif
+#if HAVE_MEMORY_H
+# include <memory.h>
+#endif
+#if HAVE_STDDEF_H
+# include <stddef.h>
+#endif
+#if HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#if HAVE_INTTYPES_H
+# include <inttypes.h>
+#else
+# if HAVE_STDINT_H
+#  include <stdint.h>
+# endif
+#endif
+#if defined(BUILD_DIVSUFSORT64)
+# include "divsufsort64.h"
+# ifndef SAIDX_T
+#  define SAIDX_T
+#  define saidx_t saidx64_t
+# endif /* SAIDX_T */
+# ifndef PRIdSAIDX_T
+#  define PRIdSAIDX_T PRIdSAIDX64_T
+# endif /* PRIdSAIDX_T */
+# define divsufsort divsufsort64
+# define divbwt divbwt64
+# define divsufsort_version divsufsort64_version
+# define bw_transform bw_transform64
+# define inverse_bw_transform inverse_bw_transform64
+# define sufcheck sufcheck64
+# define sa_search sa_search64
+# define sa_simplesearch sa_simplesearch64
+# define sssort sssort64
+# define trsort trsort64
+#else
+# include "divsufsort.h"
+#endif
+
+
+/*- Constants -*/
+#if !defined(UINT8_MAX)
+# define UINT8_MAX (255)
+#endif /* UINT8_MAX */
+#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1)
+# undef ALPHABET_SIZE
+#endif
+#if !defined(ALPHABET_SIZE)
+# define ALPHABET_SIZE (UINT8_MAX + 1)
+#endif
+/* for divsufsort.c */
+#define BUCKET_A_SIZE (ALPHABET_SIZE)
+#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE)
+/* for sssort.c */
+#if defined(SS_INSERTIONSORT_THRESHOLD)
+# if SS_INSERTIONSORT_THRESHOLD < 1
+#  undef SS_INSERTIONSORT_THRESHOLD
+#  define SS_INSERTIONSORT_THRESHOLD (1)
+# endif
+#else
+# define SS_INSERTIONSORT_THRESHOLD (8)
+#endif
+#if defined(SS_BLOCKSIZE)
+# if SS_BLOCKSIZE < 0
+#  undef SS_BLOCKSIZE
+#  define SS_BLOCKSIZE (0)
+# elif 32768 <= SS_BLOCKSIZE
+#  undef SS_BLOCKSIZE
+#  define SS_BLOCKSIZE (32767)
+# endif
+#else
+# define SS_BLOCKSIZE (1024)
+#endif
+/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */
+#if SS_BLOCKSIZE == 0
+# if defined(BUILD_DIVSUFSORT64)
+#  define SS_MISORT_STACKSIZE (96)
+# else
+#  define SS_MISORT_STACKSIZE (64)
+# endif
+#elif SS_BLOCKSIZE <= 4096
+# define SS_MISORT_STACKSIZE (16)
+#else
+# define SS_MISORT_STACKSIZE (24)
+#endif
+#if defined(BUILD_DIVSUFSORT64)
+# define SS_SMERGE_STACKSIZE (64)
+#else
+# define SS_SMERGE_STACKSIZE (32)
+#endif
+/* for trsort.c */
+#define TR_INSERTIONSORT_THRESHOLD (8)
+#if defined(BUILD_DIVSUFSORT64)
+# define TR_STACKSIZE (96)
+#else
+# define TR_STACKSIZE (64)
+#endif
+
+
+/*- Macros -*/
+#ifndef SWAP
+# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0)
+#endif /* SWAP */
+#ifndef MIN
+# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b))
+#endif /* MIN */
+#ifndef MAX
+# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b))
+#endif /* MAX */
+#define STACK_PUSH(_a, _b, _c, _d)\
+  do {\
+    assert(ssize < STACK_SIZE);\
+    stack[ssize].a = (_a), stack[ssize].b = (_b),\
+    stack[ssize].c = (_c), stack[ssize++].d = (_d);\
+  } while(0)
+#define STACK_PUSH5(_a, _b, _c, _d, _e)\
+  do {\
+    assert(ssize < STACK_SIZE);\
+    stack[ssize].a = (_a), stack[ssize].b = (_b),\
+    stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\
+  } while(0)
+#define STACK_POP(_a, _b, _c, _d)\
+  do {\
+    assert(0 <= ssize);\
+    if(ssize == 0) { return; }\
+    (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
+    (_c) = stack[ssize].c, (_d) = stack[ssize].d;\
+  } while(0)
+#define STACK_POP5(_a, _b, _c, _d, _e)\
+  do {\
+    assert(0 <= ssize);\
+    if(ssize == 0) { return; }\
+    (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
+    (_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\
+  } while(0)
+/* for divsufsort.c */
+#define BUCKET_A(_c0) bucket_A[(_c0)]
+#if ALPHABET_SIZE == 256
+#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)])
+#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)])
+#else
+#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)])
+#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)])
+#endif
+
+
+/*- Private Prototypes -*/
+/* sssort.c */
+void
+sssort(const sauchar_t *Td, const saidx_t *PA,
+       saidx_t *first, saidx_t *last,
+       saidx_t *buf, saidx_t bufsize,
+       saidx_t depth, saidx_t n, saint_t lastsuffix);
+/* trsort.c */
+void
+trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth);
+
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _DIVSUFSORT_PRIVATE_H */
diff --git a/tools/apultra_src/src/libdivsufsort/include/lfs.h.cmake b/tools/apultra_src/src/libdivsufsort/include/lfs.h.cmake
new file mode 100644
index 0000000..d5b84a8
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/include/lfs.h.cmake
@@ -0,0 +1,56 @@
+/*
+ * lfs.h for libdivsufsort
+ * Copyright (c) 2003-2008 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 _LFS_H
+#define _LFS_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#ifndef __STRICT_ANSI__
+# define LFS_OFF_T @LFS_OFF_T@
+# define LFS_FOPEN @LFS_FOPEN@
+# define LFS_FTELL @LFS_FTELL@
+# define LFS_FSEEK @LFS_FSEEK@
+# define LFS_PRId  @LFS_PRID@
+#else
+# define LFS_OFF_T long
+# define LFS_FOPEN fopen
+# define LFS_FTELL ftell
+# define LFS_FSEEK fseek
+# define LFS_PRId "ld"
+#endif
+#ifndef PRIdOFF_T
+# define PRIdOFF_T LFS_PRId
+#endif
+
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _LFS_H */