aboutsummaryrefslogtreecommitdiffstats
path: root/examples/unbwt.c
diff options
context:
space:
mode:
Diffstat (limited to 'examples/unbwt.c')
-rw-r--r--examples/unbwt.c207
1 files changed, 207 insertions, 0 deletions
diff --git a/examples/unbwt.c b/examples/unbwt.c
new file mode 100644
index 000000000000..c0f19e97ad0f
--- /dev/null
+++ b/examples/unbwt.c
@@ -0,0 +1,207 @@
+/*
+ * unbwt.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
+read_int(FILE *fp, saidx_t *n) {
+ unsigned char c[4];
+ size_t m = fread(c, sizeof(unsigned char), 4, fp);
+ if(m == 4) {
+ *n = (c[0] << 0) | (c[1] << 8) |
+ (c[2] << 16) | (c[3] << 24);
+ }
+ return m;
+}
+
+static
+void
+print_help(const char *progname, int status) {
+ fprintf(stderr,
+ "unbwt, an inverse burrows-wheeler transform program, version %s.\n",
+ divsufsort_version());
+ fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname);
+ exit(status);
+}
+
+int
+main(int argc, const char *argv[]) {
+ FILE *fp, *ofp;
+ const char *fname, *ofname;
+ sauchar_t *T;
+ saidx_t *A;
+ LFS_OFF_T n;
+ size_t m;
+ saidx_t pidx;
+ clock_t start, finish;
+ saint_t err, blocksize, 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) { print_help(argv[0], EXIT_FAILURE); }
+
+ /* Open a file for reading. */
+ if(strcmp(argv[1], "-") != 0) {
+#if HAVE_FOPEN_S
+ if(fopen_s(&fp, fname = argv[1], "rb") != 0) {
+#else
+ if((fp = LFS_FOPEN(fname = argv[1], "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;
+ }
+
+ /* Open a file for writing. */
+ if(strcmp(argv[2], "-") != 0) {
+#if HAVE_FOPEN_S
+ if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) {
+#else
+ if((ofp = LFS_FOPEN(ofname = argv[2], "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;
+ }
+
+ /* Read the blocksize. */
+ if(read_int(fp, &blocksize) != 4) {
+ fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
+ perror(NULL);
+ exit(EXIT_FAILURE);
+ }
+
+ /* Allocate 5blocksize bytes of memory. */
+ T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t));
+ A = (saidx_t *)malloc(blocksize * sizeof(saidx_t));
+ if((T == NULL) || (A == NULL)) {
+ fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
+ exit(EXIT_FAILURE);
+ }
+
+ fprintf(stderr, "UnBWT (blocksize %" PRIdSAINT_T ") ... ", blocksize);
+ start = clock();
+ for(n = 0; (m = read_int(fp, &pidx)) != 0; n += m) {
+ /* Read blocksize bytes of data. */
+ if((m != 4) || ((m = fread(T, sizeof(sauchar_t), blocksize, fp)) == 0)) {
+ fprintf(stderr, "%s: %s `%s': ",
+ argv[0],
+ (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
+ fname);
+ perror(NULL);
+ exit(EXIT_FAILURE);
+ }
+
+ /* Inverse Burrows-Wheeler Transform. */
+ if((err = inverse_bw_transform(T, T, A, m, pidx)) != 0) {
+ fprintf(stderr, "%s (reverseBWT): %s.\n",
+ argv[0],
+ (err == -1) ? "Invalid data" : "Cannot allocate memory");
+ exit(EXIT_FAILURE);
+ }
+
+ /* Write m bytes of data. */
+ if(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(A);
+ free(T);
+
+ return 0;
+}