Added original files

COPYING

+The sais-lite copyright is as follows:
+
+Copyright (c) 2008-2010 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.

Makefile

+# Makefile for suftest and test
+
+# options
+CC						= llvm-gcc
+#CXX						= g++
+#OUTPUT_OPTION	= -o $@
+CFLAGS                          = -ffast-math -O9 -funroll-loops -DNDEBUG
+#CFLAGS				= -O3 -fomit-frame-pointer -funroll-loops
+#CXXFLAGS			= -O3 -fomit-frame-pointer
+CPPFLAGS			= -Wall -DNDEBUG
+#CPPFLAGS			= -Wall
+LDFLAGS				= 
+LDLIBS				= 
+#TARGET_ARCH		=
+
+# targets
+.PHONY: all
+all: suftest
+suftest: sais.o suftest.o
+test:
+	$(CC) -O -g -Wall test.c sais.c -o test
+	./test
+	$(RM) test test.exe
+
+distclean: clean
+clean:
+	$(RM) suftest suftest.exe test test.exe sais.o suftest.o
+
+# dependencies
+sais.o suftest.o: sais.h Makefile

README

+sais-lite-LCP-0.0.1
+----------------------
+
+This is an ad-hoc-implementation of the code described in
+
+"Inducing the LCP-Array" (http://arxiv.org/abs/1101.3448)
+
+by Johannes Fischer.
+
+It is based on Yuta Mori's sais-lite 2.4.1 (http://sites.google.com/site/yuta256),
+which, in turn, is an implementation of the  following paper:
+
+Ge Nong, Sen Zhang and Wai Hong Chan
+Two Efficient Algorithms for Linear Suffix Array Construction
+DCC 2009.
+
+To compile, type 'make'. Then run ./suftest <testfile>.
+
+----
+
+Johannes Fischer (johannes.fischer@kit.edu)
\ No newline at end of file

sais.h

+/*
+ * sais.h for sais-lite
+ * Copyright (c) 2008-2010 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 _SAIS_H
+#define _SAIS_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+/* find the suffix array SA of T[0..n-1]
+   use a working space (excluding T and SA) of at most 2n+O(lg n) */
+  int sais(const unsigned char *T, int *SA, int *LCP, int n);
+
+/* find the suffix array SA of T[0..n-1] in {0..k-1}^n
+   use a working space (excluding T and SA) of at most MAX(4k,2n) */
+int
+sais_int(const int *T, int *SA, int n, int k);
+
+/* burrows-wheeler transform */
+int
+sais_bwt(const unsigned char *T, unsigned char *U, int *A, int n);
+int
+sais_int_bwt(const int *T, int *U, int *A, int n, int k);
+
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif /* __cplusplus */
+
+#endif /* _SAIS_H */

suftest.c

+/*
+ * suftest.c for sais-lite
+ * Copyright (c) 2008-2010 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.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#include "sais.h"
+
+
+/* Checks the suffix array SA of the string T. */
+static
+int
+sufcheck(const unsigned char *T, const int *SA, int n, int verbose) {
+  int C[256];
+  int i, p, q, t;
+  int c;
+
+  if(verbose) { fprintf(stderr, "sufcheck: "); }
+  if(n == 0) {
+    if(verbose) { fprintf(stderr, "Done.\n"); }
+    return 0;
+  }
+
+  /* Check arguments. */
+  if((T == NULL) || (SA == NULL) || (n < 0)) {
+    if(verbose) { fprintf(stderr, "Invalid arguments.\n"); }
+    return -1;
+  }
+
+  /* check range: [0..n-1] */
+  for(i = 0; i < n; ++i) {
+    if((SA[i] < 0) || (n <= SA[i])) {
+      if(verbose) {
+        fprintf(stderr, "Out of the range [0,%d].\n"
+                        "  SA[%d]=%d\n",
+                        n - 1, i, SA[i]);
+      }
+      return -2;
+    }
+  }
+
+  /* check first characters. */
+  for(i = 1; i < n; ++i) {
+    if(T[SA[i - 1]] > T[SA[i]]) {
+      if(verbose) {
+        fprintf(stderr, "Suffixes in wrong order.\n"
+                        "  T[SA[%d]=%d]=%d > T[SA[%d]=%d]=%d\n",
+                        i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]);
+      }
+      return -3;
+    }
+  }
+
+  /* check suffixes. */
+  for(i = 0; i < 256; ++i) { C[i] = 0; }
+  for(i = 0; i < n; ++i) { ++C[T[i]]; }
+  for(i = 0, p = 0; i < 256; ++i) {
+    t = C[i];
+    C[i] = p;
+    p += t;
+  }
+
+  q = C[T[n - 1]];
+  C[T[n - 1]] += 1;
+  for(i = 0; i < n; ++i) {
+    p = SA[i];
+    if(0 < p) {
+      c = T[--p];
+      t = C[c];
+    } else {
+      c = T[p = n - 1];
+      t = q;
+    }
+    if((t < 0) || (p != SA[t])) {
+      if(verbose) {
+        fprintf(stderr, "Suffix in wrong position.\n"
+                        "  SA[%d]=%d or\n"
+                        "  SA[%d]=%d\n",
+                        t, (0 <= t) ? SA[t] : -1, i, SA[i]);
+      }
+      return -4;
+    }
+    if(t != q) {
+      ++C[c];
+      if((n <= C[c]) || (T[SA[C[c]]] != c)) { C[c] = -1; }
+    }
+  }
+
+  if(1 <= verbose) { fprintf(stderr, "Done.\n"); }
+  return 0;
+}
+
+static
+void
+print_help(const char *progname, int status) {
+  fprintf(stderr, "usage: %s FILE\n\n", progname);
+  exit(status);
+}
+
+int
+main(int argc, const char *argv[]) {
+  FILE *fp;
+  const char *fname;
+  unsigned char *T;
+  int *SA;
+  int *LCP;
+  long n;
+  clock_t start, finish;
+
+  /* Check arguments. */
+  if((argc == 1) ||
+     (strcmp(argv[1], "-h") == 0) ||
+     (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
+  if(argc != 2) { print_help(argv[0], EXIT_FAILURE); }
+
+  /* Open a file for reading. */
+  if((fp = fopen(fname = argv[1], "rb")) == NULL) {
+    fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
+    perror(NULL);
+    exit(EXIT_FAILURE);
+  }
+
+  /* Get the file size. */
+  if(fseek(fp, 0, SEEK_END) == 0) {
+    n = ftell(fp);
+    rewind(fp);
+    if(n < 0) {
+      fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname);
+      perror(NULL);
+      exit(EXIT_FAILURE);
+    }
+  } else {
+    fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], fname);
+    perror(NULL);
+    exit(EXIT_FAILURE);
+  }
+
+  /* Allocate 9n bytes of memory. */
+  T = (unsigned char *)malloc((size_t)n * sizeof(unsigned char));
+  SA = (int *)malloc((size_t)(n+1) * sizeof(int)); // +1 for computing LCP
+  LCP = (int *)malloc((size_t)n * sizeof(int));
+  if((T == NULL) || (SA == NULL) || (LCP == NULL)) {
+    fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
+    exit(EXIT_FAILURE);
+  }
+
+  /* Read n bytes of data. */
+  if(fread(T, sizeof(unsigned char), (size_t)n, fp) != (size_t)n) {
+    fprintf(stderr, "%s: %s `%s': ",
+      argv[0],
+      (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
+      argv[1]);
+    perror(NULL);
+    exit(EXIT_FAILURE);
+  }
+  fclose(fp);
+
+if (n < 256) printf("%s\n", T);
+T[n-1]=0;
+ /* int ii; */
+ /* for (ii=0;ii<n;++ii) printf("%i,", (int)T[ii]); printf("\n");  */
+if (n < 256) printf("%s\n", T);
+
+ int j;
+ /* for (j = 0; j < n; j++) printf("%i,", (int) T[j]); printf("\n"); */
+  
+  /* Construct the suffix array. */
+  fprintf(stderr, "%s: %ld bytes ... \n", fname, n);
+  start = clock();
+  if(sais(T, SA, LCP, (int)n) != 0) {
+    fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
+    exit(EXIT_FAILURE);
+  }
+  finish = clock();
+  fprintf(stderr, "induced: %.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC);
+
+  /* // check LCP: */
+  /* int i,l; */
+  /* for (i = 1; i < n; ++i) { */
+  /*   l = 0; */
+  /*   while (T[SA[i]+l]==T[SA[i-1]+l]) ++l; */
+  /*   if (l != LCP[i]) { */
+  /*     printf("Error at position %i\n", i); */
+  /*     printf("%i vs. %i\n", l, LCP[i]); */
+  /*     for (j = 0; j < 10; j++) printf("%c", T[SA[i]+j]); printf("\n"); */
+  /*     for (j = 0; j < 10; j++) printf("%c", T[SA[i-1]+j]); printf("\n"); */
+  /*     exit(-1); */
+  /*   } */
+  /* } */
+
+  // naive LCP:
+  start = clock();
+  int i,l;
+  for (i = 1; i < n; ++i) {
+    l = 0;
+    while (T[SA[i]+l]==T[SA[i-1]+l]) ++l;
+    LCP[i] = l;
+  }
+  finish = clock();
+  fprintf(stderr, "naive: %.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC);
+
+  /* Deallocate memory. */
+  free(SA);
+  free(LCP);
+  free(T);
+
+  return 0;
+}

test.c

+/*
+ * test.c for sais-lite
+ * Copyright (c) 2008-2010 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.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "sais.h"
+
+
+static
+int
+cmp_suf(const unsigned char *T, int n, int p1, int p2) {
+  int r, s = (p1 < p2) ? 1 : ((p1 > p2) ? -1 : 0);
+  for(r = 0; (p1 < n) && (p2 < n) && ((r = T[p1] - T[p2]) == 0); ++p1, ++p2) { }
+  return (r != 0) ? r : s;
+}
+
+int
+main(int argc, const char *argv[]) {
+  unsigned char *T1;
+  int *T3;
+  unsigned char *T1BWT;
+  int *T3BWT;
+  int *SA1;
+  int *SA3;
+  int *A;
+  int i, j, n, p1, p3;
+  unsigned int bits;
+
+  fprintf(stdout, "start test...\n");
+  for(n = 1; n <= 24; ++n) {
+    T1 = malloc(n * sizeof(unsigned char));
+    T1BWT = malloc(n * sizeof(unsigned char));
+    T3 = malloc(n * sizeof(int));
+    T3BWT = malloc(n * sizeof(int));
+    SA1 = malloc(n * sizeof(int));
+    SA3 = malloc(n * sizeof(int));
+    A = malloc(n * sizeof(int));
+    for(bits = 0; bits < (1U << n); ++bits) {
+      if((bits & 4095) == 0) {
+        fprintf(stderr, "  n=%2d : %3d%%\r", n, (int)((double)bits / (double)((1U << n) - 1) * 100.0));
+      }
+      for(i = 0; i < n; ++i) {
+        T1[i] = (bits >> i) & 1;
+        T3[i] = T1[i] * 511;
+      }
+
+      /* construct sa and bwt */
+      if(sais(T1, SA1, n) != 0) {
+        fprintf(stderr, "  n=%2d, bits=%u : failure - sais\n", n, bits);
+        exit(EXIT_FAILURE);
+      }
+      if((p1 = sais_bwt(T1, T1BWT, A, n)) < 0) {
+        fprintf(stderr, "  n=%2d, bits=%u : failure - sais_bwt\n", n, bits);
+        exit(EXIT_FAILURE);
+      }
+      if(sais_int(T3, SA3, n, 512) != 0) {
+        fprintf(stderr, "  n=%2d, bits=%u : failure - sais_int\n", n, bits);
+        exit(EXIT_FAILURE);
+      }
+      if((p3 = sais_int_bwt(T3, T3BWT, A, n, 512)) < 0) {
+        fprintf(stderr, "  n=%2d, bits=%u : failure - sais_int_bwt\n", n, bits);
+        exit(EXIT_FAILURE);
+      }
+
+      /* check SA1 */
+      for(i = 1; i < n; ++i) {
+        if(0 <= cmp_suf(T1, n, SA1[i - 1], SA1[i])) {
+          fprintf(stderr, "  n=%2d, bits=%u : failure - SA1\n", n, bits);
+          for(i = 0; i < n; ++i) {
+            fprintf(stderr, "    SA[%d]=%d: ", i, SA1[i]);
+            for(j = SA1[i]; j < n; ++j) { fprintf(stderr, "%d", T1[j]); }
+            fprintf(stderr, "\n");
+          }
+          exit(EXIT_FAILURE);
+        }
+      }
+
+      /* check SA3 */
+      for(i = 0; i < n; ++i) {
+        if(SA1[i] != SA3[i]) {
+          fprintf(stderr, "  n=%2d, bits=%u : failure - SA3\n", n, bits);
+          for(i = 0; i < n; ++i) {
+            fprintf(stderr, "    SA1[%d]=%d, SA3[%d]=%d: ", i, SA1[i], i, SA3[i]);
+            for(j = SA3[i]; j < n; ++j) { fprintf(stderr, "%d", T3[j] / 511); }
+            fprintf(stderr, "\n");
+          }
+          exit(EXIT_FAILURE);
+        }
+      }
+
+      /* check T1BWT */
+      for(i = 0, j = 0; i <= n; ++i) {
+        if(i != 0) {
+          if(SA1[i - 1] == 0) { if(p1 != i) { break; } }
+          else if(n <= j) { break; }
+          else { if(T1BWT[j++] != T1[SA1[i - 1] - 1]) { break; } }
+        } else {
+          if(T1BWT[j++] != T1[n - 1]) { break; }
+        }
+      }
+      if((i != (n + 1)) || (j != n)) {
+        fprintf(stderr, "  n=%2d, bits=%u : failure - T1BWT\n", n, bits);
+        fprintf(stderr, "    T1BWT=");
+        for(i = 0; i < n; ++i) { fprintf(stderr, "%d", T1BWT[i]); }
+        fprintf(stderr, ", p1=%d\n", p1);
+        for(i = 0; i < n; ++i) {
+          fprintf(stderr, "    SA[%d]=%d: ", i, SA1[i]);
+          for(j = SA1[i]; j < n; ++j) { fprintf(stderr, "%d", T1[j]); }
+          fprintf(stderr, " ");
+          for(j = 0; j < SA1[i]; ++j) { fprintf(stderr, "%d", T1[j]); }
+          fprintf(stderr, "\n");
+        }
+        exit(EXIT_FAILURE);
+      }
+
+      /* check T3BWT */
+      for(i = 0; i < n; ++i) { if(T1BWT[i] != T3BWT[i] / 511) { break; } }
+      if((i != n) || (p1 != p3)) {
+        fprintf(stderr, "  n=%2d, bits=%u : failure - T3BWT\n", n, bits);
+        fprintf(stderr, "    T3BWT=");
+        for(i = 0; i < n; ++i) { fprintf(stderr, "%d", T3BWT[i]); }
+        fprintf(stderr, ", p3=%d\n", p3);
+        for(i = 0; i < n; ++i) {
+          fprintf(stderr, "    SA[%d]=%d: ", i, SA3[i]);
+          for(j = SA3[i]; j < n; ++j) { fprintf(stderr, "%d", T3[j] / 511); }
+          fprintf(stderr, " ");
+          for(j = 0; j < SA3[i]; ++j) { fprintf(stderr, "%d", T3[j] / 511); }
+          fprintf(stderr, "\n");
+        }
+        exit(EXIT_FAILURE);
+      }
+
+    }
+    fprintf(stderr, "  n=%2d : success\n", n);
+    free(T1);
+    free(T1BWT);
+    free(T3);
+    free(T3BWT);
+    free(SA1);
+    free(SA3);
+    free(A);
+  }
+  fprintf(stderr, "finish test\n");
+
+  return 0;
+}