divsufsort 0.1.0-mswin32

data/README.txt

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+= divsufsort
+
+Copyright (c) 2008 SUGAWARA Genki <sgwr_dts@yahoo.co.jp>
+
+== Description
+
+Ruby bindings for libdivsufsort.
+
+libdivsufsort is a C API library to construct the suffix array and the Burrows-Wheeler transformed string.
+
+== Project Page
+
+http://rubyforge.org/projects/divsufsort
+
+== Install
+
+gem install divsufsort
+
+== Example
+=== Burrows-Wheeler Transform/Inverse Burrows-Wheeler Transform
+
+    require 'divsufsort'
+    include Divsufsort
+    
+    bwt = divbwt(<<-EOS)
+      London bridge is falling down,
+      Falling down, falling down,
+      London bridge is falling down,
+    My fair Lady.
+    EOS
+    
+    unbwt = inverse_bw_transform(bwt)
+
+=== Construct the suffix array
+
+    require 'divsufsort'
+    include Divsufsort
+    
+    sa = divsufsort(<<-EOS)
+      London bridge is falling down,
+      Falling down, falling down,
+      London bridge is falling down,
+      My fair Lady.
+    EOS
+
+== License
+    Copyright (c) 2008 SUGAWARA Genki <sgwr_dts@yahoo.co.jp>
+    All rights reserved.
+    
+    Redistribution and use in source and binary forms, with or without modification,
+    are permitted provided that the following conditions are met:
+    
+        * Redistributions of source code must retain the above copyright notice, 
+          this list of conditions and the following disclaimer.
+        * Redistributions in binary form must reproduce the above copyright notice, 
+          this list of conditions and the following disclaimer in the documentation 
+          and/or other materials provided with the distribution.
+        * The names of its contributors may be used to endorse or promote products 
+           derived from this software without specific prior written permission.
+    
+    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+    ANY EXPRESS OR IMPLIED WARRANTIES,
+    INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND 
+    FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
+    OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
+    EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT 
+    OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+    INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, 
+    STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY 
+    OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH 
+    DAMAGE.
+
+=== libdivsufsort
+divsufsort contains libdivsufsort.
+
+* libdivsufsort is a lightweight suffix-sorting library.
+* http://code.google.com/p/libdivsufsort/

data/ext/divsufsort_ruby.c

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+#ifdef DIVSUFSORT_EXPORTS
+#define DLLEXPORT __declspec(dllexport)
+#else
+#define DLLEXPORT
+#endif
+
+#define VERSION "0.1.0"
+
+#include "divsufsort.h"
+#include "ruby.h"
+#include "rubysig.h"
+
+#ifndef RSTRING_PTR
+#define RSTRING_PTR(s) (RSTRING(s)->ptr)
+#endif
+#ifndef RSTRING_LEN
+#define RSTRING_LEN(s) (RSTRING(s)->len)
+#endif
+
+#define RB_STR_CAT_INT(o, n) do { \
+  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); \
+  rb_str_cat((o), c, 4); \
+} while(0)
+
+#define PTR_READ_INT(p, n, x) do { \
+  unsigned char c[4]; \
+  c[0] = (unsigned char) (p)[0]; \
+  c[1] = (unsigned char) (p)[1]; \
+  c[2] = (unsigned char) (p)[2]; \
+  c[3] = (unsigned char) (p)[3]; \
+  (x) = (c[0] <<  0) | (c[1] <<  8) | (c[2] << 16) | (c[3] << 24); \
+  (p) += 4; \
+  (n) -= 4; \
+} while(0)
+
+static VALUE Divsufsort;
+
+/* */
+static VALUE divsufsort_divsufsort(VALUE self, VALUE src) {
+  VALUE dst;
+  sauchar_t *T;
+  saidx_t *SA;
+  char *p;
+  long n, i;
+  saint_t err;
+
+  Check_Type(src, T_STRING);
+  p = RSTRING_PTR(src);
+  n = RSTRING_LEN(src);
+
+  if(n >= 0x7fffffff) {
+    rb_raise(rb_eRuntimeError, "Input data is too big.");
+  }
+
+  T = (sauchar_t *) xmalloc((size_t) n * sizeof(sauchar_t));
+  SA = (saidx_t *) xmalloc((size_t) n * sizeof(saidx_t));
+  dst = rb_ary_new();
+  memcpy(T, p, (size_t) n * sizeof(sauchar_t));
+
+  TRAP_BEG;
+  err = divsufsort(T, SA, (saidx_t) n);
+  TRAP_END;
+
+  if(err != 0) {
+    xfree(SA);
+    xfree(T);
+    rb_raise(rb_eRuntimeError, "Cannot allocate memory.");
+  }
+
+  TRAP_BEG;
+  err = sufcheck(T, SA, (saidx_t) n, 0);
+  TRAP_END;
+
+  if(err != 0) {
+    xfree(SA);
+    xfree(T);
+    rb_raise(rb_eRuntimeError, "Wrong suffix array.");
+  }
+
+  for(i = 0; i < n; i++) {
+    saidx_t SA_i = SA[i];
+    rb_ary_push(dst, LONG2NUM(SA_i));
+  }
+
+  xfree(SA);
+  xfree(T);
+
+  if(err != 0) {
+    rb_raise(rb_eRuntimeError, "Cannot allocate memory.");
+  }
+
+  return dst;
+}
+
+/* */
+static VALUE divsufsort_divbwt(int argc, VALUE *argv, VALUE self) {
+  VALUE src, v_blocksize, transformed;
+  sauchar_t *T;
+  saidx_t *SA;
+  char *p;
+  long n, T_len;
+  saint_t blocksize = 32;
+  saidx_t pidx;
+
+  rb_scan_args(argc, argv, "11", &src, &v_blocksize);
+  Check_Type(src, T_STRING);
+
+  if (!NIL_P(v_blocksize)) {
+    blocksize = (saint_t) NUM2INT(v_blocksize);
+  }
+
+  blocksize <<= 20;
+  p = RSTRING_PTR(src);
+  n = RSTRING_LEN(src);
+
+  if(n > 0x20000000L) {
+    n = 0x20000000L;
+  }
+
+  if(blocksize == 0 || n < blocksize) {
+    blocksize = (saidx_t) n;
+  }
+
+  T_len = blocksize * sizeof(sauchar_t);
+  T = (sauchar_t *) xmalloc(T_len);
+  SA = (saidx_t *) xmalloc(blocksize * sizeof(saidx_t));
+  transformed = rb_str_new("", 0);
+
+  RB_STR_CAT_INT(transformed, blocksize);
+
+  while (n > 0) {
+    int m = (n < T_len) ? n : T_len;
+
+    memcpy(T, p, m);
+    p += m; n -= m;
+
+    TRAP_BEG;
+    pidx = divbwt(T, T, SA, m);
+    TRAP_END;
+
+    if(pidx < 0) {
+      break;
+    }
+
+    RB_STR_CAT_INT(transformed, pidx);
+    rb_str_cat(transformed, T, m);
+  }
+
+  xfree(SA);
+  xfree(T);
+
+  if(pidx < 0) {
+    rb_raise(rb_eRuntimeError, "bw_transform: %s.", (pidx == -1) ? "Invalid arguments" : "Cannot allocate memory");
+  }
+
+  return transformed;
+}
+
+/* */
+static VALUE divsufsort_inverse_bw_transform(VALUE self, VALUE transformed) {
+  VALUE dst;
+  sauchar_t *T;
+  saidx_t *A;
+  char *p;
+  long n;
+  saint_t blocksize;
+  int err = 0;
+
+  Check_Type(transformed, T_STRING);
+  p = RSTRING_PTR(transformed);
+  n = RSTRING_LEN(transformed);
+
+  if (n < 4) {
+    rb_raise(rb_eRuntimeError, "reverseBWT: Invalid data.\n");
+  }
+
+  PTR_READ_INT(p, n, blocksize);
+  T = (sauchar_t *) xmalloc(blocksize * sizeof(sauchar_t));
+  A = (saidx_t *) xmalloc(blocksize * sizeof(saidx_t));
+  dst = rb_str_new("", 0);
+
+  while (n > 0) {
+    int m;
+    saidx_t pidx;
+
+    if (n < 4) {
+      err = -1;
+      break;
+    }
+
+    PTR_READ_INT(p, n, pidx);
+    m = (n < blocksize) ? n : blocksize;
+    memcpy(T, p, m);
+    p += m; n -= m;
+
+    TRAP_BEG;
+    err = inverse_bw_transform(T, T, A, m, pidx);
+    TRAP_END;
+
+    if(err != 0) {
+      break;
+    }
+
+    rb_str_cat(dst, T, m);
+  }
+
+  xfree(A);
+  xfree(T);
+
+  if (err != 0) {
+    rb_raise(rb_eRuntimeError, "reverseBWT: %s.\n", (err == -1) ? "Invalid data" : "Cannot allocate memory");
+  }
+
+  return dst;
+}
+
+void DLLEXPORT Init_divsufsort() {
+  Divsufsort = rb_define_module("Divsufsort");
+  rb_define_const(Divsufsort, "VERSION", rb_str_new2(VERSION));
+  rb_define_module_function(Divsufsort, "divsufsort", divsufsort_divsufsort, 1);
+  rb_define_module_function(Divsufsort, "divbwt", divsufsort_divbwt, -1);
+  rb_define_module_function(Divsufsort, "inverse_bw_transform", divsufsort_inverse_bw_transform, 1);
+}

metadata

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+--- !ruby/object:Gem::Specification 
+name: divsufsort
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: mswin32
+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: []
+
+extra_rdoc_files: 
+- README.txt
+- ext/divsufsort_ruby.c
+files: 
+- lib/i386-mswin32/divsufsort.so
+- README.txt
+- ext/divsufsort_ruby.c
+has_rdoc: true
+homepage: http://divsufsort.rubyforge.org
+post_install_message: 
+rdoc_options: 
+- --title
+- divsufsort - Ruby bindings for libdivsufsort.
+require_paths: 
+- lib/i386-mswin32
+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: []
+