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141 lines
4.2 KiB
141 lines
4.2 KiB
# libdivsufsort
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libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.
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## News
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* 2015-03-21: The project has moved from [Google Code](http://code.google.com/p/libdivsufsort/) to [GitHub](https://github.com/y-256/libdivsufsort)
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## Introduction
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This library provides a simple and an efficient C API to construct a suffix array and a Burrows-Wheeler transformed string from a given string over a constant-size alphabet.
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The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of
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the string.
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## Build requirements
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* An ANSI C Compiler (e.g. GNU GCC)
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* [CMake](http://www.cmake.org/ "CMake") version 2.4.2 or newer
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* CMake-supported build tool
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## Building on GNU/Linux
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1. Get the source code from GitHub. You can either
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* use git to clone the repository
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```
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git clone https://github.com/y-256/libdivsufsort.git
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```
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* or download a [zip file](../../archive/master.zip) directly
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2. Create a `build` directory in the package source directory.
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```shell
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$ cd libdivsufsort
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$ mkdir build
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$ cd build
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```
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3. Configure the package for your system.
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If you want to install to a different location, change the -DCMAKE_INSTALL_PREFIX option.
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```shell
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$ cmake -DCMAKE_BUILD_TYPE="Release" \
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-DCMAKE_INSTALL_PREFIX="/usr/local" ..
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```
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4. Compile the package.
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```shell
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$ make
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```
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5. (Optional) Install the library and header files.
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```shell
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$ sudo make install
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```
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## API
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```c
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/* Data types */
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typedef int32_t saint_t;
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typedef int32_t saidx_t;
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typedef uint8_t sauchar_t;
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/*
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* Constructs the suffix array of a given string.
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* @param T[0..n-1] The input string.
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* @param SA[0..n-1] The output array or suffixes.
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* @param n The length of the given string.
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* @return 0 if no error occurred, -1 or -2 otherwise.
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*/
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saint_t
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divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n);
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/*
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* Constructs the burrows-wheeler transformed string of a given string.
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* @param T[0..n-1] The input string.
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* @param U[0..n-1] The output string. (can be T)
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* @param A[0..n-1] The temporary array. (can be NULL)
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* @param n The length of the given string.
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* @return The primary index if no error occurred, -1 or -2 otherwise.
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*/
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saidx_t
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divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n);
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```
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## Example Usage
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```c
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <divsufsort.h>
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int main() {
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// intput data
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char *Text = "abracadabra";
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int n = strlen(Text);
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int i, j;
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// allocate
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int *SA = (int *)malloc(n * sizeof(int));
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// sort
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divsufsort((unsigned char *)Text, SA, n);
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// output
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for(i = 0; i < n; ++i) {
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printf("SA[%2d] = %2d: ", i, SA[i]);
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for(j = SA[i]; j < n; ++j) {
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printf("%c", Text[j]);
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}
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printf("$\n");
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}
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// deallocate
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free(SA);
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return 0;
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}
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```
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See the [examples](examples) directory for a few other examples.
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## Benchmarks
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See [Benchmarks](https://github.com/y-256/libdivsufsort/blob/wiki/SACA_Benchmarks.md) page for details.
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## License
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libdivsufsort is released under the [MIT license](LICENSE "MIT license").
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> The MIT License (MIT)
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>
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> Copyright (c) 2003 Yuta Mori All rights reserved.
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>
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> Permission is hereby granted, free of charge, to any person obtaining a copy
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> of this software and associated documentation files (the "Software"), to deal
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> in the Software without restriction, including without limitation the rights
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> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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> copies of the Software, and to permit persons to whom the Software is
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> furnished to do so, subject to the following conditions:
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>
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> The above copyright notice and this permission notice shall be included in all
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> copies or substantial portions of the Software.
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>
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> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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> SOFTWARE.
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## Author
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* Yuta Mori
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