Initial import of the open source release

1 files changed, 220 insertions, 0 deletions

diff --git a/tools/apultra_src/src/libdivsufsort/examples/bwt.c b/tools/apultra_src/src/libdivsufsort/examples/bwt.c
new file mode 100644
index 0000000..5a362d0
--- /dev/null
+++ b/tools/apultra_src/src/libdivsufsort/examples/bwt.c
@@ -0,0 +1,220 @@
+/*
+ * bwt.c 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.
+ */
+
+#if HAVE_CONFIG_H
+# include "config.h"
+#endif
+#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_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#if HAVE_IO_H && HAVE_FCNTL_H
+# include <io.h>
+# include <fcntl.h>
+#endif
+#include <time.h>
+#include <divsufsort.h>
+#include "lfs.h"
+
+
+static
+size_t
+write_int(FILE *fp, saidx_t n) {
+  unsigned char c[4];
+  c[0] = (unsigned char)((n >>  0) & 0xff), c[1] = (unsigned char)((n >>  8) & 0xff),
+  c[2] = (unsigned char)((n >> 16) & 0xff), c[3] = (unsigned char)((n >> 24) & 0xff);
+  return fwrite(c, sizeof(unsigned char), 4, fp);
+}
+
+static
+void
+print_help(const char *progname, int status) {
+  fprintf(stderr,
+          "bwt, a burrows-wheeler transform program, version %s.\n",
+          divsufsort_version());
+  fprintf(stderr, "usage: %s [-b num] INFILE OUTFILE\n", progname);
+  fprintf(stderr, "  -b num    set block size to num MiB [1..512] (default: 32)\n\n");
+  exit(status);
+}
+
+int
+main(int argc, const char *argv[]) {
+  FILE *fp, *ofp;
+  const char *fname, *ofname;
+  sauchar_t *T;
+  saidx_t *SA;
+  LFS_OFF_T n;
+  size_t m;
+  saidx_t pidx;
+  clock_t start,finish;
+  saint_t i, blocksize = 32, needclose = 3;
+
+  /* Check arguments. */
+  if((argc == 1) ||
+     (strcmp(argv[1], "-h") == 0) ||
+     (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
+  if((argc != 3) && (argc != 5)) { print_help(argv[0], EXIT_FAILURE); }
+  i = 1;
+  if(argc == 5) {
+    if(strcmp(argv[i], "-b") != 0) { print_help(argv[0], EXIT_FAILURE); }
+    blocksize = atoi(argv[i + 1]);
+    if(blocksize < 0) { blocksize = 1; }
+    else if(512 < blocksize) { blocksize = 512; }
+    i += 2;
+  }
+  blocksize <<= 20;
+
+  /* Open a file for reading. */
+  if(strcmp(argv[i], "-") != 0) {
+#if HAVE_FOPEN_S
+    if(fopen_s(&fp, fname = argv[i], "rb") != 0) {
+#else
+    if((fp = LFS_FOPEN(fname = argv[i], "rb")) == NULL) {
+#endif
+      fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+  } else {
+#if HAVE__SETMODE && HAVE__FILENO
+    if(_setmode(_fileno(stdin), _O_BINARY) == -1) {
+      fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+#endif
+    fp = stdin;
+    fname = "stdin";
+    needclose ^= 1;
+  }
+  i += 1;
+
+  /* Open a file for writing. */
+  if(strcmp(argv[i], "-") != 0) {
+#if HAVE_FOPEN_S
+    if(fopen_s(&ofp, ofname = argv[i], "wb") != 0) {
+#else
+    if((ofp = LFS_FOPEN(ofname = argv[i], "wb")) == NULL) {
+#endif
+      fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+  } else {
+#if HAVE__SETMODE && HAVE__FILENO
+    if(_setmode(_fileno(stdout), _O_BINARY) == -1) {
+      fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+#endif
+    ofp = stdout;
+    ofname = "stdout";
+    needclose ^= 2;
+  }
+
+  /* Get the file size. */
+  if(LFS_FSEEK(fp, 0, SEEK_END) == 0) {
+    n = LFS_FTELL(fp);
+    rewind(fp);
+    if(n < 0) {
+      fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+    if(0x20000000L < n) { n = 0x20000000L; }
+    if((blocksize == 0) || (n < blocksize)) { blocksize = (saidx_t)n; }
+  } else if(blocksize == 0) { blocksize = 32 << 20; }
+
+  /* Allocate 5blocksize bytes of memory. */
+  T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t));
+  SA = (saidx_t *)malloc(blocksize * sizeof(saidx_t));
+  if((T == NULL) || (SA == NULL)) {
+    fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
+    exit(EXIT_FAILURE);
+  }
+
+  /* Write the blocksize. */
+  if(write_int(ofp, blocksize) != 4) {
+    fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
+    perror(NULL);
+    exit(EXIT_FAILURE);
+  }
+
+  fprintf(stderr, "  BWT (blocksize %" PRIdSAINT_T ") ... ", blocksize);
+  start = clock();
+  for(n = 0; 0 < (m = fread(T, sizeof(sauchar_t), blocksize, fp)); n += m) {
+    /* Burrows-Wheeler Transform. */
+    pidx = divbwt(T, T, SA, m);
+    if(pidx < 0) {
+      fprintf(stderr, "%s (bw_transform): %s.\n",
+        argv[0],
+        (pidx == -1) ? "Invalid arguments" : "Cannot allocate memory");
+      exit(EXIT_FAILURE);
+    }
+
+    /* Write the bwted data. */
+    if((write_int(ofp, pidx) != 4) ||
+       (fwrite(T, sizeof(sauchar_t), m, ofp) != m)) {
+      fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+  }
+  if(ferror(fp)) {
+    fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
+    perror(NULL);
+    exit(EXIT_FAILURE);
+  }
+  finish = clock();
+  fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n",
+    n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
+
+  /* Close files */
+  if(needclose & 1) { fclose(fp); }
+  if(needclose & 2) { fclose(ofp); }
+
+  /* Deallocate memory. */
+  free(SA);
+  free(T);
+
+  return 0;
+}