divsufsort 0.1.0

data/libdivsufsort/utils.c

@@ -0,0 +1,381 @@
+/*
+ * utils.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.
+ */
+
+#include "divsufsort_private.h"
+
+
+/*- Private Function -*/
+
+/* Binary search for inverse bwt. */
+static
+saidx_t
+binarysearch_lower(const saidx_t *A, saidx_t size, saidx_t value) {
+  saidx_t half, i;
+  for(i = 0, half = size >> 1;
+      0 < size;
+      size = half, half >>= 1) {
+    if(A[i + half] < value) {
+      i += half + 1;
+      half -= (size & 1) ^ 1;
+    }
+  }
+  return i;
+}
+
+
+/*- Functions -*/
+
+/* Burrows-Wheeler transform. */
+saint_t
+bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
+             saidx_t n, saidx_t *idx) {
+  saidx_t *A, i, j, p, t;
+  saint_t c;
+
+  /* Check arguments. */
+  if((T == NULL) || (U == NULL) || (n < 0) || (idx == NULL)) { return -1; }
+  if(n <= 1) {
+    if(n == 1) { U[0] = T[0]; }
+    *idx = n;
+    return 0;
+  }
+
+  if((A = SA) == NULL) {
+    i = divbwt(T, U, NULL, n);
+    if(0 <= i) { *idx = i; i = 0; }
+    return (saint_t)i;
+  }
+
+  /* BW transform. */
+  if(T == U) {
+    t = n;
+    for(i = 0, j = 0; i < n; ++i) {
+      p = t - 1;
+      t = A[i];
+      if(0 <= p) {
+        c = T[j];
+        U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
+        A[j] = c;
+        j++;
+      } else {
+        *idx = i;
+      }
+    }
+    p = t - 1;
+    if(0 <= p) {
+      c = T[j];
+      U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
+      A[j] = c;
+    } else {
+      *idx = i;
+    }
+  } else {
+    U[0] = T[n - 1];
+    for(i = 0; A[i] != 0; ++i) { U[i + 1] = T[A[i] - 1]; }
+    *idx = i + 1;
+    for(++i; i < n; ++i) { U[i] = T[A[i] - 1]; }
+  }
+
+  if(SA == NULL) {
+    /* Deallocate memory. */
+    free(A);
+  }
+
+  return 0;
+}
+
+/* Inverse Burrows-Wheeler transform. */
+saint_t
+inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A,
+                     saidx_t n, saidx_t idx) {
+  saidx_t C[ALPHABET_SIZE];
+  sauchar_t D[ALPHABET_SIZE];
+  saidx_t *B;
+  saidx_t i, p;
+  saint_t c, d;
+
+  /* Check arguments. */
+  if((T == NULL) || (U == NULL) || (n < 0) || (idx < 0) ||
+     (n < idx) || ((0 < n) && (idx == 0))) {
+    return -1;
+  }
+  if(n <= 1) { return 0; }
+
+  if((B = A) == NULL) {
+    /* Allocate n*sizeof(saidx_t) bytes of memory. */
+    if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; }
+  }
+
+  /* Inverse BW transform. */
+  for(c = 0; c < ALPHABET_SIZE; ++c) { C[c] = 0; }
+  for(i = 0; i < n; ++i) { ++C[T[i]]; }
+  for(c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) {
+    p = C[c];
+    if(0 < p) {
+      C[c] = i;
+      D[d++] = (sauchar_t)c;
+      i += p;
+    }
+  }
+  for(i = 0; i < idx; ++i) { B[C[T[i]]++] = i; }
+  for( ; i < n; ++i)       { B[C[T[i]]++] = i + 1; }
+  for(c = 0; c < d; ++c) { C[c] = C[D[c]]; }
+  for(i = 0, p = idx; i < n; ++i) {
+    U[i] = D[binarysearch_lower(C, d, p)];
+    p = B[p - 1];
+  }
+
+  if(A == NULL) {
+    /* Deallocate memory. */
+    free(B);
+  }
+
+  return 0;
+}
+
+/* Checks the suffix array SA of the string T. */
+saint_t
+sufcheck(const sauchar_t *T, const saidx_t *SA,
+         saidx_t n, saint_t verbose) {
+  saidx_t C[ALPHABET_SIZE];
+  saidx_t i, p, q, t;
+  saint_t c;
+
+  if(verbose) { fprintf(stderr, "sufcheck: "); }
+
+  /* Check arguments. */
+  if((T == NULL) || (SA == NULL) || (n < 0)) {
+    if(verbose) { fprintf(stderr, "Invalid arguments.\n"); }
+    return -1;
+  }
+  if(n == 0) {
+    if(verbose) { fprintf(stderr, "Done.\n"); }
+    return 0;
+  }
+
+  /* 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,%" PRIdSAIDX_T "].\n"
+                        "  SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\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[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d"
+                        " > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%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 < ALPHABET_SIZE; ++i) { C[i] = 0; }
+  for(i = 0; i < n; ++i) { ++C[T[i]]; }
+  for(i = 0, p = 0; i < ALPHABET_SIZE; ++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[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n"
+                        "  SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\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
+int
+_compare(const sauchar_t *T, saidx_t Tsize,
+         const sauchar_t *P, saidx_t Psize,
+         saidx_t suf, saidx_t *match) {
+  saidx_t i, j;
+  saint_t r;
+  for(i = suf + *match, j = *match, r = 0;
+      (i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { }
+  *match = j;
+  return (r == 0) ? -(j != Psize) : r;
+}
+
+/* Search for the pattern P in the string T. */
+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 *idx) {
+  saidx_t size, lsize, rsize, half;
+  saidx_t match, lmatch, rmatch;
+  saidx_t llmatch, lrmatch, rlmatch, rrmatch;
+  saidx_t i, j, k;
+  saint_t r;
+
+  if(idx != NULL) { *idx = -1; }
+  if((T == NULL) || (P == NULL) || (SA == NULL) ||
+     (Tsize < 0) || (Psize < 0) || (SAsize < 0)) { return -1; }
+  if((Tsize == 0) || (SAsize == 0)) { return 0; }
+  if(Psize == 0) { if(idx != NULL) { *idx = 0; } return SAsize; }
+
+  for(i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1;
+      0 < size;
+      size = half, half >>= 1) {
+    match = MIN(lmatch, rmatch);
+    r = _compare(T, Tsize, P, Psize, SA[i + half], &match);
+    if(r < 0) {
+      i += half + 1;
+      half -= (size & 1) ^ 1;
+      lmatch = match;
+    } else if(r > 0) {
+      rmatch = match;
+    } else {
+      lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
+
+      /* left part */
+      for(llmatch = lmatch, lrmatch = match, half = lsize >> 1;
+          0 < lsize;
+          lsize = half, half >>= 1) {
+        lmatch = MIN(llmatch, lrmatch);
+        r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch);
+        if(r < 0) {
+          j += half + 1;
+          half -= (lsize & 1) ^ 1;
+          llmatch = lmatch;
+        } else {
+          lrmatch = lmatch;
+        }
+      }
+
+      /* right part */
+      for(rlmatch = match, rrmatch = rmatch, half = rsize >> 1;
+          0 < rsize;
+          rsize = half, half >>= 1) {
+        rmatch = MIN(rlmatch, rrmatch);
+        r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch);
+        if(r <= 0) {
+          k += half + 1;
+          half -= (rsize & 1) ^ 1;
+          rlmatch = rmatch;
+        } else {
+          rrmatch = rmatch;
+        }
+      }
+
+      break;
+    }
+  }
+
+  if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
+  return k - j;
+}
+
+/* Search for the character c in the string T. */
+saidx_t
+sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
+                const saidx_t *SA, saidx_t SAsize,
+                saint_t c, saidx_t *idx) {
+  saidx_t size, lsize, rsize, half;
+  saidx_t i, j, k, p;
+  saint_t r;
+
+  if(idx != NULL) { *idx = -1; }
+  if((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) { return -1; }
+  if((Tsize == 0) || (SAsize == 0)) { return 0; }
+
+  for(i = j = k = 0, size = SAsize, half = size >> 1;
+      0 < size;
+      size = half, half >>= 1) {
+    p = SA[i + half];
+    r = (p < Tsize) ? T[p] - c : -1;
+    if(r < 0) {
+      i += half + 1;
+      half -= (size & 1) ^ 1;
+    } else if(r == 0) {
+      lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
+
+      /* left part */
+      for(half = lsize >> 1;
+          0 < lsize;
+          lsize = half, half >>= 1) {
+        p = SA[j + half];
+        r = (p < Tsize) ? T[p] - c : -1;
+        if(r < 0) {
+          j += half + 1;
+          half -= (lsize & 1) ^ 1;
+        }
+      }
+
+      /* right part */
+      for(half = rsize >> 1;
+          0 < rsize;
+          rsize = half, half >>= 1) {
+        p = SA[k + half];
+        r = (p < Tsize) ? T[p] - c : -1;
+        if(r <= 0) {
+          k += half + 1;
+          half -= (rsize & 1) ^ 1;
+        }
+      }
+
+      break;
+    }
+  }
+
+  if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
+  return k - j;
+}

metadata

@@ -0,0 +1,80 @@
+--- !ruby/object:Gem::Specification 
+name: divsufsort
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- winebarrel
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2008-10-22 00:00:00 +09:00
+default_executable: 
+dependencies: []
+
+description: 
+email: sgwr_dts@yahoo.co.jp
+executables: []
+
+extensions: 
+- ext/extconf.rb
+extra_rdoc_files: 
+- README.txt
+- ext/divsufsort_ruby.c
+files: 
+- ext/divsufsort.c
+- ext/divsufsort.h
+- ext/divsufsort.o
+- ext/divsufsort.so
+- ext/divsufsort_private.h
+- ext/divsufsort_ruby.c
+- ext/divsufsort_ruby.o
+- ext/extconf.rb
+- ext/lfs.h
+- ext/Makefile
+- ext/mkmf.log
+- ext/sssort.c
+- ext/sssort.o
+- ext/trsort.c
+- ext/trsort.o
+- ext/utils.c
+- ext/utils.o
+- libdivsufsort/COPYING
+- libdivsufsort/divsufsort.c
+- libdivsufsort/divsufsort.h
+- libdivsufsort/divsufsort_private.h
+- libdivsufsort/lfs.h
+- libdivsufsort/sssort.c
+- libdivsufsort/trsort.c
+- libdivsufsort/utils.c
+- README.txt
+has_rdoc: true
+homepage: http://divsufsort.rubyforge.org
+post_install_message: 
+rdoc_options: 
+- --title
+- divsufsort - Ruby bindings for libdivsufsort.
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: divsufsort
+rubygems_version: 1.2.0
+signing_key: 
+specification_version: 2
+summary: Ruby bindings for libdivsufsort.
+test_files: []
+