mirror of
https://github.com/mii443/esaxx-rs.git
synced 2025-08-22 15:05:33 +00:00
Initial commit.
This commit is contained in:
Nicolas Patry
1
.gitignore
vendored
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1
.gitignore
vendored
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@ -0,0 +1 @@
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target
|
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14
Cargo.lock
generated
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14
Cargo.lock
generated
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# This file is automatically @generated by Cargo.
|
||||
# It is not intended for manual editing.
|
||||
[[package]]
|
||||
name = "cc"
|
||||
version = "1.0.54"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "7bbb73db36c1246e9034e307d0fba23f9a2e251faa47ade70c1bd252220c8311"
|
||||
|
||||
[[package]]
|
||||
name = "esaxx-rs"
|
||||
version = "0.1.0"
|
||||
dependencies = [
|
||||
"cc",
|
||||
]
|
||||
18
Cargo.toml
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18
Cargo.toml
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|
||||
[package]
|
||||
name = "esaxx-rs"
|
||||
version = "0.1.0"
|
||||
authors = ["Nicolas Patry <patry.nicolas@protonmail.com>"]
|
||||
edition = "2018"
|
||||
description = "Wrapping around sentencepiece's esaxxx library."
|
||||
license = "Apache-2.0"
|
||||
homepage = "https://github.com/Narsil/esaxx-rs"
|
||||
documentation = "https://docs.rs/esaxx-rs"
|
||||
repository = "https://github.com/Narsil/esaxx-rs"
|
||||
readme = "README.md"
|
||||
|
||||
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
|
||||
|
||||
[dependencies]
|
||||
|
||||
[build-dependencies]
|
||||
cc = "1.0"
|
||||
33
README.md
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33
README.md
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@ -0,0 +1,33 @@
|
||||
# esaxx-rs
|
||||
|
||||
Small wrapper around sentencepiece's esaxx suffix array C++ library.
|
||||
Usage
|
||||
|
||||
```rust
|
||||
let string = "abracadabra".to_string();
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||||
let chars: Vec<_> = string.chars().collect();
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||||
let n = chars.len();
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||||
let mut sa = vec![0; n];
|
||||
let mut l = vec![0; n];
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||||
let mut r = vec![0; n];
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let mut d = vec![0; n];
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||||
let mut node_num = 0;
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||||
|
||||
let alphabet_size = 0x110000; // All UCS4 range.
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unsafe {
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esaxx_int32(
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chars.as_ptr() as *mut u32,
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||||
sa.as_mut_ptr(),
|
||||
l.as_mut_ptr(),
|
||||
r.as_mut_ptr(),
|
||||
d.as_mut_ptr(),
|
||||
n.try_into().unwrap(),
|
||||
alphabet_size,
|
||||
&mut node_num,
|
||||
);
|
||||
}
|
||||
```
|
||||
|
||||
Current version: 0.1.0
|
||||
|
||||
License: Apache
|
||||
7
README.tpl
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7
README.tpl
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|
||||
# {{crate}}
|
||||
|
||||
{{readme}}
|
||||
|
||||
Current version: {{version}}
|
||||
|
||||
License: {{license}}
|
||||
7
build.rs
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7
build.rs
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|
||||
fn main() {
|
||||
cc::Build::new()
|
||||
.cpp(true)
|
||||
.file("src/esaxx.cpp")
|
||||
.include("src")
|
||||
.compile("esaxx");
|
||||
}
|
||||
126
src/esa.hxx
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126
src/esa.hxx
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|
||||
/*
|
||||
* esa.hxx
|
||||
* Copyright (c) 2010 Daisuke Okanohara 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 _ESA_HXX
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||||
#define _ESA_HXX
|
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|
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#include <vector>
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#include <utility>
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#include <cassert>
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#include "sais.hxx"
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|
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namespace esaxx_private {
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template<typename string_type, typename sarray_type, typename index_type>
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index_type suffixtree(string_type T, sarray_type SA, sarray_type L, sarray_type R, sarray_type D, index_type n){
|
||||
if (n == 0){
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||||
return 0;
|
||||
}
|
||||
sarray_type Psi = L;
|
||||
Psi[SA[0]] = SA[n-1];
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||||
for (index_type i = 1; i < n; ++i){
|
||||
Psi[SA[i]] = SA[i-1];
|
||||
}
|
||||
|
||||
// Compare at most 2n log n charcters. Practically fastest
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||||
// "Permuted Longest-Common-Prefix Array", Juha Karkkainen, CPM 09
|
||||
sarray_type PLCP = R;
|
||||
index_type h = 0;
|
||||
for (index_type i = 0; i < n; ++i){
|
||||
index_type j = Psi[i];
|
||||
while (i+h < n && j+h < n &&
|
||||
T[i+h] == T[j+h]){
|
||||
++h;
|
||||
}
|
||||
PLCP[i] = h;
|
||||
if (h > 0) --h;
|
||||
}
|
||||
|
||||
sarray_type H = L;
|
||||
for (index_type i = 0; i < n; ++i){
|
||||
H[i] = PLCP[SA[i]];
|
||||
}
|
||||
H[0] = -1;
|
||||
|
||||
std::vector<std::pair<index_type, index_type> > S;
|
||||
S.push_back(std::make_pair((index_type)-1, (index_type)-1));
|
||||
size_t nodeNum = 0;
|
||||
for (index_type i = 0; ; ++i){
|
||||
std::pair<index_type, index_type> cur (i, (i == n) ? -1 : H[i]);
|
||||
std::pair<index_type, index_type> cand(S.back());
|
||||
while (cand.second > cur.second){
|
||||
if (i - cand.first > 1){
|
||||
L[nodeNum] = cand.first;
|
||||
R[nodeNum] = i;
|
||||
D[nodeNum] = cand.second;
|
||||
++nodeNum;
|
||||
}
|
||||
cur.first = cand.first;
|
||||
S.pop_back();
|
||||
cand = S.back();
|
||||
}
|
||||
if (cand.second < cur.second){
|
||||
S.push_back(cur);
|
||||
}
|
||||
if (i == n) break;
|
||||
S.push_back(std::make_pair(i, n - SA[i] + 1));
|
||||
}
|
||||
return nodeNum;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* @brief Build an enhanced suffix array of a given string in linear time
|
||||
* For an input text T, esaxx() builds an enhancd suffix array in linear time.
|
||||
* i-th internal node is represented as a triple (L[i], R[i], D[i]);
|
||||
* L[i] and R[i] is the left/right boundary of the suffix array as SA[L[i]....R[i]-1]
|
||||
* D[i] is the depth of the internal node
|
||||
* The number of internal node is at most N-1 and return the actual number by
|
||||
* @param T[0...n-1] The input string. (random access iterator)
|
||||
* @param SA[0...n-1] The output suffix array (random access iterator)
|
||||
* @param L[0...n-1] The output left boundary of internal node (random access iterator)
|
||||
* @param R[0...n-1] The output right boundary of internal node (random access iterator)
|
||||
* @param D[0...n-1] The output depth of internal node (random access iterator)
|
||||
* @param n The length of the input string
|
||||
* @param k The alphabet size
|
||||
* @pram nodeNum The output the number of internal node
|
||||
* @return 0 if succeded, -1 or -2 otherwise
|
||||
*/
|
||||
|
||||
template<typename string_type, typename sarray_type, typename index_type>
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||||
int esaxx(string_type T, sarray_type SA, sarray_type L, sarray_type R, sarray_type D,
|
||||
index_type n, index_type k, index_type& nodeNum) {
|
||||
if ((n < 0) || (k <= 0)) return -1;
|
||||
int err = saisxx(T, SA, n, k);
|
||||
if (err != 0){
|
||||
return err;
|
||||
}
|
||||
nodeNum = esaxx_private::suffixtree(T, SA, L, R, D, n);
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
#endif // _ESA_HXX
|
||||
|
||||
632
src/esaxx.cpp
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632
src/esaxx.cpp
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@ -0,0 +1,632 @@
|
||||
//
|
||||
// /*
|
||||
// * sais.hxx for sais-lite
|
||||
// * Copyright (c) 2008-2009 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_HXX
|
||||
// #define _SAIS_HXX 1
|
||||
// #ifdef __cplusplus
|
||||
//
|
||||
// #ifdef __INTEL_COMPILER
|
||||
// #pragma warning(disable : 383 981 1418)
|
||||
// // for icc 64-bit
|
||||
// //#define __builtin_vsnprintf(a, b, c, d) __builtin_vsnprintf(a, b, c, (char *)d)
|
||||
// #endif
|
||||
//
|
||||
// #include <iterator>
|
||||
// #ifdef _OPENMP
|
||||
// # include <omp.h>
|
||||
// #endif
|
||||
//
|
||||
// namespace saisxx_private {
|
||||
//
|
||||
// /* find the start or end of each bucket */
|
||||
// template<typename string_type, typename bucket_type, typename index_type>
|
||||
// void
|
||||
// getCounts(const string_type T, bucket_type C, index_type n, index_type k) {
|
||||
// #ifdef _OPENMP
|
||||
// bucket_type D;
|
||||
// index_type i, j, p, sum, first, last;
|
||||
// int thnum, maxthreads = omp_get_max_threads();
|
||||
// #pragma omp parallel default(shared) private(D, i, thnum, first, last)
|
||||
// {
|
||||
// thnum = omp_get_thread_num();
|
||||
// D = C + thnum * k;
|
||||
// first = n / maxthreads * thnum;
|
||||
// last = (thnum < (maxthreads - 1)) ? n / maxthreads * (thnum + 1) : n;
|
||||
// for(i = 0; i < k; ++i) { D[i] = 0; }
|
||||
// for(i = first; i < last; ++i) { ++D[T[i]]; }
|
||||
// }
|
||||
// if(1 < maxthreads) {
|
||||
// #pragma omp parallel for default(shared) private(i, j, p, sum)
|
||||
// for(i = 0; i < k; ++i) {
|
||||
// for(j = 1, p = i + k, sum = C[i]; j < maxthreads; ++j, p += k) {
|
||||
// sum += C[p];
|
||||
// }
|
||||
// C[i] = sum;
|
||||
// }
|
||||
// }
|
||||
// #else
|
||||
// index_type i;
|
||||
// for(i = 0; i < k; ++i) { C[i] = 0; }
|
||||
// for(i = 0; i < n; ++i) { ++C[T[i]]; }
|
||||
// #endif
|
||||
// }
|
||||
// template<typename bucket_type, typename index_type>
|
||||
// void
|
||||
// getBuckets(const bucket_type C, bucket_type B, index_type k, bool end) {
|
||||
// index_type i, sum = 0;
|
||||
// if(end) { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } }
|
||||
// else { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } }
|
||||
// }
|
||||
//
|
||||
// /* compute SA and BWT */
|
||||
// template<typename string_type, typename sarray_type,
|
||||
// typename bucket_type, typename index_type>
|
||||
// void
|
||||
// induceSA(string_type T, sarray_type SA, bucket_type C, bucket_type B,
|
||||
// index_type n, index_type k) {
|
||||
// typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
// sarray_type b;
|
||||
// index_type i, j;
|
||||
// char_type c0, c1;
|
||||
// /* compute SAl */
|
||||
// if(C == B) { getCounts(T, C, n, k); }
|
||||
// getBuckets(C, B, k, false); /* find starts of buckets */
|
||||
// b = SA + B[c1 = T[j = n - 1]];
|
||||
// *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
// for(i = 0; i < n; ++i) {
|
||||
// j = SA[i], SA[i] = ~j;
|
||||
// if(0 < j) {
|
||||
// if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
// *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
// }
|
||||
// }
|
||||
// /* compute SAs */
|
||||
// if(C == B) { getCounts(T, C, n, k); }
|
||||
// getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
// for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
|
||||
// if(0 < (j = SA[i])) {
|
||||
// if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
// *--b = ((j == 0) || (T[j - 1] > c1)) ? ~j : j;
|
||||
// } else {
|
||||
// SA[i] = ~j;
|
||||
// }
|
||||
// }
|
||||
// }
|
||||
// template<typename string_type, typename sarray_type,
|
||||
// typename bucket_type, typename index_type>
|
||||
// int
|
||||
// computeBWT(string_type T, sarray_type SA, bucket_type C, bucket_type B,
|
||||
// index_type n, index_type k) {
|
||||
// typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
// sarray_type b;
|
||||
// index_type i, j, pidx = -1;
|
||||
// char_type c0, c1;
|
||||
// /* compute SAl */
|
||||
// if(C == B) { getCounts(T, C, n, k); }
|
||||
// getBuckets(C, B, k, false); /* find starts of buckets */
|
||||
// b = SA + B[c1 = T[j = n - 1]];
|
||||
// *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
// for(i = 0; i < n; ++i) {
|
||||
// if(0 < (j = SA[i])) {
|
||||
// SA[i] = ~(c0 = T[--j]);
|
||||
// if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
// *b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
// } else if(j != 0) {
|
||||
// SA[i] = ~j;
|
||||
// }
|
||||
// }
|
||||
// /* compute SAs */
|
||||
// if(C == B) { getCounts(T, C, n, k); }
|
||||
// getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
// for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
|
||||
// if(0 < (j = SA[i])) {
|
||||
// SA[i] = (c0 = T[--j]);
|
||||
// if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
// *--b = ((0 < j) && (T[j - 1] > c1)) ? ~((index_type)T[j - 1]) : j;
|
||||
// } else if(j != 0) {
|
||||
// SA[i] = ~j;
|
||||
// } else {
|
||||
// pidx = i;
|
||||
// }
|
||||
// }
|
||||
// return pidx;
|
||||
// }
|
||||
//
|
||||
// /* find the suffix array SA of T[0..n-1] in {0..k}^n
|
||||
// use a working space (excluding s and SA) of at most 2n+O(1) for a constant alphabet */
|
||||
// template<typename string_type, typename sarray_type, typename index_type>
|
||||
// int
|
||||
// suffixsort(string_type T, sarray_type SA,
|
||||
// index_type fs, index_type n, index_type k,
|
||||
// bool isbwt) {
|
||||
// typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
// sarray_type RA;
|
||||
// index_type i, j, m, p, q, plen, qlen, name, pidx = 0;
|
||||
// bool diff;
|
||||
// int c;
|
||||
// #ifdef _OPENMP
|
||||
// int maxthreads = omp_get_max_threads();
|
||||
// #else
|
||||
// # define maxthreads 1
|
||||
// #endif
|
||||
// char_type c0, c1;
|
||||
//
|
||||
// /* stage 1: reduce the problem by at least 1/2
|
||||
// sort all the S-substrings */
|
||||
// if(fs < (maxthreads * k)) {
|
||||
// index_type *C, *B;
|
||||
// if((C = new index_type[maxthreads * k]) == 0) { return -2; }
|
||||
// B = (1 < maxthreads) ? C + k : C;
|
||||
// getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
// #ifdef _OPENMP
|
||||
// #pragma omp parallel for default(shared) private(i)
|
||||
// #endif
|
||||
// for(i = 0; i < n; ++i) { SA[i] = 0; }
|
||||
// for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
// if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
// else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
|
||||
// }
|
||||
// induceSA(T, SA, C, B, n, k);
|
||||
// delete [] C;
|
||||
// } else {
|
||||
// sarray_type C, B;
|
||||
// C = SA + n;
|
||||
// B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
|
||||
// getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
// #ifdef _OPENMP
|
||||
// #pragma omp parallel for default(shared) private(i)
|
||||
// #endif
|
||||
// for(i = 0; i < n; ++i) { SA[i] = 0; }
|
||||
// for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
// if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
// else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
|
||||
// }
|
||||
// induceSA(T, SA, C, B, n, k);
|
||||
// }
|
||||
//
|
||||
// /* compact all the sorted substrings into the first m items of SA
|
||||
// 2*m must be not larger than n (proveable) */
|
||||
// #ifdef _OPENMP
|
||||
// #pragma omp parallel for default(shared) private(i, j, p, c0, c1)
|
||||
// for(i = 0; i < n; ++i) {
|
||||
// p = SA[i];
|
||||
// if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
|
||||
// for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
|
||||
// if((j < n) && (c0 < c1)) { SA[i] = ~p; }
|
||||
// }
|
||||
// }
|
||||
// for(i = 0, m = 0; i < n; ++i) { if((p = SA[i]) < 0) { SA[m++] = ~p; } }
|
||||
// #else
|
||||
// for(i = 0, m = 0; i < n; ++i) {
|
||||
// p = SA[i];
|
||||
// if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
|
||||
// for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
|
||||
// if((j < n) && (c0 < c1)) { SA[m++] = p; }
|
||||
// }
|
||||
// }
|
||||
// #endif
|
||||
// j = m + (n >> 1);
|
||||
// #ifdef _OPENMP
|
||||
// #pragma omp parallel for default(shared) private(i)
|
||||
// #endif
|
||||
// for(i = m; i < j; ++i) { SA[i] = 0; } /* init the name array buffer */
|
||||
// /* store the length of all substrings */
|
||||
// for(i = n - 2, j = n, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
// if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
// else if(c != 0) { SA[m + ((i + 1) >> 1)] = j - i - 1; j = i + 1; c = 0; }
|
||||
// }
|
||||
// /* find the lexicographic names of all substrings */
|
||||
// for(i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
|
||||
// p = SA[i], plen = SA[m + (p >> 1)], diff = true;
|
||||
// if(plen == qlen) {
|
||||
// for(j = 0; (j < plen) && (T[p + j] == T[q + j]); ++j) { }
|
||||
// if(j == plen) { diff = false; }
|
||||
// }
|
||||
// if(diff != false) { ++name, q = p, qlen = plen; }
|
||||
// SA[m + (p >> 1)] = name;
|
||||
// }
|
||||
//
|
||||
// /* stage 2: solve the reduced problem
|
||||
// recurse if names are not yet unique */
|
||||
// if(name < m) {
|
||||
// RA = SA + n + fs - m;
|
||||
// for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) {
|
||||
// if(SA[i] != 0) { RA[j--] = SA[i] - 1; }
|
||||
// }
|
||||
// if(suffixsort(RA, SA, fs + n - m * 2, m, name, false) != 0) { return -2; }
|
||||
// for(i = n - 2, j = m - 1, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
// if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
// else if(c != 0) { RA[j--] = i + 1, c = 0; } /* get p1 */
|
||||
// }
|
||||
// #ifdef _OPENMP
|
||||
// #pragma omp parallel for default(shared) private(i)
|
||||
// #endif
|
||||
// for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; } /* get index in s */
|
||||
// }
|
||||
//
|
||||
// /* stage 3: induce the result for the original problem */
|
||||
// if(fs < (maxthreads * k)) {
|
||||
// index_type *B, *C;
|
||||
// if((C = new index_type[maxthreads * k]) == 0) { return -2; }
|
||||
// B = (1 < maxthreads) ? C + k : C;
|
||||
// /* put all left-most S characters into their buckets */
|
||||
// getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
// #ifdef _OPENMP
|
||||
// #pragma omp parallel for default(shared) private(i)
|
||||
// #endif
|
||||
// for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
|
||||
// for(i = m - 1; 0 <= i; --i) {
|
||||
// j = SA[i], SA[i] = 0;
|
||||
// SA[--B[T[j]]] = j;
|
||||
// }
|
||||
// if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
|
||||
// else { pidx = computeBWT(T, SA, C, B, n, k); }
|
||||
// delete [] C;
|
||||
// } else {
|
||||
// sarray_type C, B;
|
||||
// C = SA + n;
|
||||
// B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
|
||||
// /* put all left-most S characters into their buckets */
|
||||
// getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
// #ifdef _OPENMP
|
||||
// #pragma omp parallel for default(shared) private(i)
|
||||
// #endif
|
||||
// for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
|
||||
// for(i = m - 1; 0 <= i; --i) {
|
||||
// j = SA[i], SA[i] = 0;
|
||||
// SA[--B[T[j]]] = j;
|
||||
// }
|
||||
// if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
|
||||
// else { pidx = computeBWT(T, SA, C, B, n, k); }
|
||||
// }
|
||||
//
|
||||
// return pidx;
|
||||
// #ifndef _OPENMP
|
||||
// # undef maxthreads
|
||||
// #endif
|
||||
// }
|
||||
//
|
||||
// } /* namespace saisxx_private */
|
||||
//
|
||||
//
|
||||
// /**
|
||||
// * @brief Constructs the suffix array of a given string in linear time.
|
||||
// * @param T[0..n-1] The input string. (random access iterator)
|
||||
// * @param SA[0..n-1] The output array of suffixes. (random access iterator)
|
||||
// * @param n The length of the given string.
|
||||
// * @param k The alphabet size.
|
||||
// * @return 0 if no error occurred, -1 or -2 otherwise.
|
||||
// */
|
||||
// template<typename string_type, typename sarray_type, typename index_type>
|
||||
// int
|
||||
// saisxx(string_type T, sarray_type SA, index_type n, index_type k = 256) {
|
||||
// int err;
|
||||
// if((n < 0) || (k <= 0)) { return -1; }
|
||||
// if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; }
|
||||
// try { err = saisxx_private::suffixsort(T, SA, 0U, n, k, false); }
|
||||
// catch(...) { err = -2; }
|
||||
// return err;
|
||||
// }
|
||||
//
|
||||
// /**
|
||||
// * @brief Constructs the burrows-wheeler transformed string of a given string in linear time.
|
||||
// * @param T[0..n-1] The input string. (random access iterator)
|
||||
// * @param U[0..n-1] The output string. (random access iterator)
|
||||
// * @param A[0..n-1] The temporary array. (random access iterator)
|
||||
// * @param n The length of the given string.
|
||||
// * @param k The alphabet size.
|
||||
// * @return The primary index if no error occurred, -1 or -2 otherwise.
|
||||
// */
|
||||
// template<typename string_type, typename sarray_type, typename index_type>
|
||||
// index_type
|
||||
// saisxx_bwt(string_type T, string_type U, sarray_type A, index_type n, index_type k = 256) {
|
||||
// typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
// index_type i, pidx;
|
||||
// if((n < 0) || (k <= 0)) { return -1; }
|
||||
// if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
|
||||
// try {
|
||||
// pidx = saisxx_private::suffixsort(T, A, 0, n, k, true);
|
||||
// if(0 <= pidx) {
|
||||
// U[0] = T[n - 1];
|
||||
// for(i = 0; i < pidx; ++i) { U[i + 1] = (char_type)A[i]; }
|
||||
// for(i += 1; i < n; ++i) { U[i] = (char_type)A[i]; }
|
||||
// pidx += 1;
|
||||
// }
|
||||
// } catch(...) { pidx = -2; }
|
||||
// return pidx;
|
||||
// }
|
||||
//
|
||||
//
|
||||
// #endif /* __cplusplus */
|
||||
// #endif /* _SAIS_HXX */
|
||||
// /*
|
||||
// * esa.hxx
|
||||
// * Copyright (c) 2010 Daisuke Okanohara 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 _ESA_HXX
|
||||
// #define _ESA_HXX
|
||||
//
|
||||
// #include <vector>
|
||||
// #include <utility>
|
||||
// #include <cassert>
|
||||
// #include "sais.hxx"
|
||||
//
|
||||
// namespace esaxx_private {
|
||||
// template<typename string_type, typename sarray_type, typename index_type>
|
||||
// index_type suffixtree(string_type T, sarray_type SA, sarray_type L, sarray_type R, sarray_type D, index_type n){
|
||||
// if (n == 0){
|
||||
// return 0;
|
||||
// }
|
||||
// sarray_type Psi = L;
|
||||
// Psi[SA[0]] = SA[n-1];
|
||||
// for (index_type i = 1; i < n; ++i){
|
||||
// Psi[SA[i]] = SA[i-1];
|
||||
// }
|
||||
//
|
||||
// // Compare at most 2n log n charcters. Practically fastest
|
||||
// // "Permuted Longest-Common-Prefix Array", Juha Karkkainen, CPM 09
|
||||
// sarray_type PLCP = R;
|
||||
// index_type h = 0;
|
||||
// for (index_type i = 0; i < n; ++i){
|
||||
// index_type j = Psi[i];
|
||||
// while (i+h < n && j+h < n &&
|
||||
// T[i+h] == T[j+h]){
|
||||
// ++h;
|
||||
// }
|
||||
// PLCP[i] = h;
|
||||
// if (h > 0) --h;
|
||||
// }
|
||||
//
|
||||
// sarray_type H = L;
|
||||
// for (index_type i = 0; i < n; ++i){
|
||||
// H[i] = PLCP[SA[i]];
|
||||
// }
|
||||
// H[0] = -1;
|
||||
//
|
||||
// std::vector<std::pair<index_type, index_type> > S;
|
||||
// S.push_back(std::make_pair((index_type)-1, (index_type)-1));
|
||||
// size_t nodeNum = 0;
|
||||
// for (index_type i = 0; ; ++i){
|
||||
// std::pair<index_type, index_type> cur (i, (i == n) ? -1 : H[i]);
|
||||
// std::pair<index_type, index_type> cand(S.back());
|
||||
// while (cand.second > cur.second){
|
||||
// if (i - cand.first > 1){
|
||||
// L[nodeNum] = cand.first;
|
||||
// R[nodeNum] = i;
|
||||
// D[nodeNum] = cand.second;
|
||||
// ++nodeNum;
|
||||
// }
|
||||
// cur.first = cand.first;
|
||||
// S.pop_back();
|
||||
// cand = S.back();
|
||||
// }
|
||||
// if (cand.second < cur.second){
|
||||
// S.push_back(cur);
|
||||
// }
|
||||
// if (i == n) break;
|
||||
// S.push_back(std::make_pair(i, n - SA[i] + 1));
|
||||
// }
|
||||
// return nodeNum;
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// /**
|
||||
// * @brief Build an enhanced suffix array of a given string in linear time
|
||||
// * For an input text T, esaxx() builds an enhancd suffix array in linear time.
|
||||
// * i-th internal node is represented as a triple (L[i], R[i], D[i]);
|
||||
// * L[i] and R[i] is the left/right boundary of the suffix array as SA[L[i]....R[i]-1]
|
||||
// * D[i] is the depth of the internal node
|
||||
// * The number of internal node is at most N-1 and return the actual number by
|
||||
// * @param T[0...n-1] The input string. (random access iterator)
|
||||
// * @param SA[0...n-1] The output suffix array (random access iterator)
|
||||
// * @param L[0...n-1] The output left boundary of internal node (random access iterator)
|
||||
// * @param R[0...n-1] The output right boundary of internal node (random access iterator)
|
||||
// * @param D[0...n-1] The output depth of internal node (random access iterator)
|
||||
// * @param n The length of the input string
|
||||
// * @param k The alphabet size
|
||||
// * @pram nodeNum The output the number of internal node
|
||||
// * @return 0 if succeded, -1 or -2 otherwise
|
||||
// */
|
||||
//
|
||||
// template<typename string_type, typename sarray_type, typename index_type>
|
||||
// int esaxx(string_type T, sarray_type SA, sarray_type L, sarray_type R, sarray_type D,
|
||||
// index_type n, index_type k, index_type& nodeNum) {
|
||||
// if ((n < 0) || (k <= 0)) return -1;
|
||||
// int err = saisxx(T, SA, n, k);
|
||||
// if (err != 0){
|
||||
// return err;
|
||||
// }
|
||||
// nodeNum = esaxx_private::suffixtree(T, SA, L, R, D, n);
|
||||
// return 0;
|
||||
// }
|
||||
//
|
||||
//
|
||||
// #endif // _ESA_HXX
|
||||
// /*
|
||||
// * esa.hxx
|
||||
// * Copyright (c) 2010 Daisuke Okanohara 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 _ESA_HXX
|
||||
// #define _ESA_HXX
|
||||
//
|
||||
// #include <vector>
|
||||
// #include <utility>
|
||||
// #include <cassert>
|
||||
// #include "sais.hxx"
|
||||
//
|
||||
// namespace esaxx_private {
|
||||
// template<typename string_type, typename sarray_type, typename index_type>
|
||||
// index_type suffixtree(string_type T, sarray_type SA, sarray_type L, sarray_type R, sarray_type D, index_type n){
|
||||
// if (n == 0){
|
||||
// return 0;
|
||||
// }
|
||||
// sarray_type Psi = L;
|
||||
// Psi[SA[0]] = SA[n-1];
|
||||
// for (index_type i = 1; i < n; ++i){
|
||||
// Psi[SA[i]] = SA[i-1];
|
||||
// }
|
||||
//
|
||||
// // Compare at most 2n log n charcters. Practically fastest
|
||||
// // "Permuted Longest-Common-Prefix Array", Juha Karkkainen, CPM 09
|
||||
// sarray_type PLCP = R;
|
||||
// index_type h = 0;
|
||||
// for (index_type i = 0; i < n; ++i){
|
||||
// index_type j = Psi[i];
|
||||
// while (i+h < n && j+h < n &&
|
||||
// T[i+h] == T[j+h]){
|
||||
// ++h;
|
||||
// }
|
||||
// PLCP[i] = h;
|
||||
// if (h > 0) --h;
|
||||
// }
|
||||
//
|
||||
// sarray_type H = L;
|
||||
// for (index_type i = 0; i < n; ++i){
|
||||
// H[i] = PLCP[SA[i]];
|
||||
// }
|
||||
// H[0] = -1;
|
||||
//
|
||||
// std::vector<std::pair<index_type, index_type> > S;
|
||||
// S.push_back(std::make_pair((index_type)-1, (index_type)-1));
|
||||
// size_t nodeNum = 0;
|
||||
// for (index_type i = 0; ; ++i){
|
||||
// std::pair<index_type, index_type> cur (i, (i == n) ? -1 : H[i]);
|
||||
// std::pair<index_type, index_type> cand(S.back());
|
||||
// while (cand.second > cur.second){
|
||||
// if (i - cand.first > 1){
|
||||
// L[nodeNum] = cand.first;
|
||||
// R[nodeNum] = i;
|
||||
// D[nodeNum] = cand.second;
|
||||
// ++nodeNum;
|
||||
// }
|
||||
// cur.first = cand.first;
|
||||
// S.pop_back();
|
||||
// cand = S.back();
|
||||
// }
|
||||
// if (cand.second < cur.second){
|
||||
// S.push_back(cur);
|
||||
// }
|
||||
// if (i == n) break;
|
||||
// S.push_back(std::make_pair(i, n - SA[i] + 1));
|
||||
// }
|
||||
// return nodeNum;
|
||||
// }
|
||||
// }
|
||||
//
|
||||
// /**
|
||||
// * @brief Build an enhanced suffix array of a given string in linear time
|
||||
// * For an input text T, esaxx() builds an enhancd suffix array in linear time.
|
||||
// * i-th internal node is represented as a triple (L[i], R[i], D[i]);
|
||||
// * L[i] and R[i] is the left/right boundary of the suffix array as SA[L[i]....R[i]-1]
|
||||
// * D[i] is the depth of the internal node
|
||||
// * The number of internal node is at most N-1 and return the actual number by
|
||||
// * @param T[0...n-1] The input string. (random access iterator)
|
||||
// * @param SA[0...n-1] The output suffix array (random access iterator)
|
||||
// * @param L[0...n-1] The output left boundary of internal node (random access iterator)
|
||||
// * @param R[0...n-1] The output right boundary of internal node (random access iterator)
|
||||
// * @param D[0...n-1] The output depth of internal node (random access iterator)
|
||||
// * @param n The length of the input string
|
||||
// * @param k The alphabet size
|
||||
// * @pram nodeNum The output the number of internal node
|
||||
// * @return 0 if succeded, -1 or -2 otherwise
|
||||
// */
|
||||
//
|
||||
// template<typename string_type, typename sarray_type, typename index_type>
|
||||
// int esaxx(string_type T, sarray_type SA, sarray_type L, sarray_type R, sarray_type D,
|
||||
// index_type n, index_type k, index_type& nodeNum) {
|
||||
// if ((n < 0) || (k <= 0)) return -1;
|
||||
// std::count<<"Here"<<std::endl;
|
||||
// int err = saisxx(T, SA, n, k);
|
||||
// if (err != 0){
|
||||
// return err;
|
||||
// }
|
||||
// std::cout<<"suffixtree"<<std::endl;
|
||||
// nodeNum = esaxx_private::suffixtree(T, SA, L, R, D, n);
|
||||
// std::count<<"ok"<<std::endl;
|
||||
// return 0;
|
||||
// }
|
||||
//
|
||||
//
|
||||
// #endif // _ESA_HXX
|
||||
|
||||
#include "esa.hxx"
|
||||
|
||||
extern "C"{
|
||||
|
||||
int esaxx_int32(char32_t* T, int32_t* SA, int32_t* L, int32_t* R, int32_t* D,
|
||||
int32_t n, int32_t k, int32_t &nodeNum) {
|
||||
|
||||
return esaxx(T, SA, L, R, D, n, k, nodeNum);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
77
src/lib.rs
Normal file
77
src/lib.rs
Normal file
@ -0,0 +1,77 @@
|
||||
//! Small wrapper around sentencepiece's esaxx suffix array C++ library.
|
||||
//! Usage
|
||||
//!
|
||||
//! ```rust
|
||||
//! let string = "abracadabra".to_string();
|
||||
//! let chars: Vec<_> = string.chars().collect();
|
||||
//! let n = chars.len();
|
||||
//! let mut sa = vec![0; n];
|
||||
//! let mut l = vec![0; n];
|
||||
//! let mut r = vec![0; n];
|
||||
//! let mut d = vec![0; n];
|
||||
//! let mut node_num = 0;
|
||||
//!
|
||||
//! let alphabet_size = 0x110000; // All UCS4 range.
|
||||
//! unsafe {
|
||||
//! esaxx_int32(
|
||||
//! chars.as_ptr() as *mut u32,
|
||||
//! sa.as_mut_ptr(),
|
||||
//! l.as_mut_ptr(),
|
||||
//! r.as_mut_ptr(),
|
||||
//! d.as_mut_ptr(),
|
||||
//! n.try_into().unwrap(),
|
||||
//! alphabet_size,
|
||||
//! &mut node_num,
|
||||
//! );
|
||||
//! }
|
||||
//! ```
|
||||
extern "C" {
|
||||
pub fn esaxx_int32(
|
||||
// This is char32
|
||||
T: *const u32,
|
||||
SA: *mut i32,
|
||||
L: *mut i32,
|
||||
R: *mut i32,
|
||||
D: *mut i32,
|
||||
n: u32,
|
||||
k: u32,
|
||||
nodeNum: &mut u32,
|
||||
);
|
||||
}
|
||||
|
||||
#[cfg(test)]
|
||||
mod tests {
|
||||
use super::*;
|
||||
use std::convert::TryInto;
|
||||
|
||||
#[test]
|
||||
fn test_esaxx() {
|
||||
let string = "abracadabra".to_string();
|
||||
let chars: Vec<_> = string.chars().collect();
|
||||
let n = chars.len();
|
||||
let mut sa = vec![0; n];
|
||||
let mut l = vec![0; n];
|
||||
let mut r = vec![0; n];
|
||||
let mut d = vec![0; n];
|
||||
let mut node_num = 0;
|
||||
|
||||
let alphabet_size = 0x110000; // All UCS4 range.
|
||||
unsafe {
|
||||
esaxx_int32(
|
||||
chars.as_ptr() as *mut u32,
|
||||
sa.as_mut_ptr(),
|
||||
l.as_mut_ptr(),
|
||||
r.as_mut_ptr(),
|
||||
d.as_mut_ptr(),
|
||||
n.try_into().unwrap(),
|
||||
alphabet_size,
|
||||
&mut node_num,
|
||||
);
|
||||
}
|
||||
assert_eq!(node_num, 5);
|
||||
assert_eq!(sa, vec![10, 7, 0, 3, 5, 8, 1, 4, 6, 9, 2]);
|
||||
assert_eq!(l, vec![1, 0, 5, 9, 0, 0, 3, 0, 0, 0, 2]);
|
||||
assert_eq!(r, vec![3, 5, 7, 11, 11, 1, 0, 1, 0, 0, 0]);
|
||||
assert_eq!(d, vec![4, 1, 3, 2, 0, 0, 0, 0, 0, 0, 0]);
|
||||
}
|
||||
}
|
||||
366
src/sais.hxx
Normal file
366
src/sais.hxx
Normal file
@ -0,0 +1,366 @@
|
||||
/*
|
||||
* sais.hxx for sais-lite
|
||||
* Copyright (c) 2008-2009 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_HXX
|
||||
#define _SAIS_HXX 1
|
||||
#ifdef __cplusplus
|
||||
|
||||
#ifdef __INTEL_COMPILER
|
||||
#pragma warning(disable : 383 981 1418)
|
||||
// for icc 64-bit
|
||||
//#define __builtin_vsnprintf(a, b, c, d) __builtin_vsnprintf(a, b, c, (char *)d)
|
||||
#endif
|
||||
|
||||
#include <iterator>
|
||||
#ifdef _OPENMP
|
||||
# include <omp.h>
|
||||
#endif
|
||||
|
||||
namespace saisxx_private {
|
||||
|
||||
/* find the start or end of each bucket */
|
||||
template<typename string_type, typename bucket_type, typename index_type>
|
||||
void
|
||||
getCounts(const string_type T, bucket_type C, index_type n, index_type k) {
|
||||
#ifdef _OPENMP
|
||||
bucket_type D;
|
||||
index_type i, j, p, sum, first, last;
|
||||
int thnum, maxthreads = omp_get_max_threads();
|
||||
#pragma omp parallel default(shared) private(D, i, thnum, first, last)
|
||||
{
|
||||
thnum = omp_get_thread_num();
|
||||
D = C + thnum * k;
|
||||
first = n / maxthreads * thnum;
|
||||
last = (thnum < (maxthreads - 1)) ? n / maxthreads * (thnum + 1) : n;
|
||||
for(i = 0; i < k; ++i) { D[i] = 0; }
|
||||
for(i = first; i < last; ++i) { ++D[T[i]]; }
|
||||
}
|
||||
if(1 < maxthreads) {
|
||||
#pragma omp parallel for default(shared) private(i, j, p, sum)
|
||||
for(i = 0; i < k; ++i) {
|
||||
for(j = 1, p = i + k, sum = C[i]; j < maxthreads; ++j, p += k) {
|
||||
sum += C[p];
|
||||
}
|
||||
C[i] = sum;
|
||||
}
|
||||
}
|
||||
#else
|
||||
index_type i;
|
||||
for(i = 0; i < k; ++i) { C[i] = 0; }
|
||||
for(i = 0; i < n; ++i) { ++C[T[i]]; }
|
||||
#endif
|
||||
}
|
||||
template<typename bucket_type, typename index_type>
|
||||
void
|
||||
getBuckets(const bucket_type C, bucket_type B, index_type k, bool end) {
|
||||
index_type i, sum = 0;
|
||||
if(end) { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } }
|
||||
else { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } }
|
||||
}
|
||||
|
||||
/* compute SA and BWT */
|
||||
template<typename string_type, typename sarray_type,
|
||||
typename bucket_type, typename index_type>
|
||||
void
|
||||
induceSA(string_type T, sarray_type SA, bucket_type C, bucket_type B,
|
||||
index_type n, index_type k) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
sarray_type b;
|
||||
index_type i, j;
|
||||
char_type c0, c1;
|
||||
/* compute SAl */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, false); /* find starts of buckets */
|
||||
b = SA + B[c1 = T[j = n - 1]];
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
for(i = 0; i < n; ++i) {
|
||||
j = SA[i], SA[i] = ~j;
|
||||
if(0 < j) {
|
||||
if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
}
|
||||
}
|
||||
/* compute SAs */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
|
||||
if(0 < (j = SA[i])) {
|
||||
if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*--b = ((j == 0) || (T[j - 1] > c1)) ? ~j : j;
|
||||
} else {
|
||||
SA[i] = ~j;
|
||||
}
|
||||
}
|
||||
}
|
||||
template<typename string_type, typename sarray_type,
|
||||
typename bucket_type, typename index_type>
|
||||
int
|
||||
computeBWT(string_type T, sarray_type SA, bucket_type C, bucket_type B,
|
||||
index_type n, index_type k) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
sarray_type b;
|
||||
index_type i, j, pidx = -1;
|
||||
char_type c0, c1;
|
||||
/* compute SAl */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, false); /* find starts of buckets */
|
||||
b = SA + B[c1 = T[j = n - 1]];
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
for(i = 0; i < n; ++i) {
|
||||
if(0 < (j = SA[i])) {
|
||||
SA[i] = ~(c0 = T[--j]);
|
||||
if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
} else if(j != 0) {
|
||||
SA[i] = ~j;
|
||||
}
|
||||
}
|
||||
/* compute SAs */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
|
||||
if(0 < (j = SA[i])) {
|
||||
SA[i] = (c0 = T[--j]);
|
||||
if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*--b = ((0 < j) && (T[j - 1] > c1)) ? ~((index_type)T[j - 1]) : j;
|
||||
} else if(j != 0) {
|
||||
SA[i] = ~j;
|
||||
} else {
|
||||
pidx = i;
|
||||
}
|
||||
}
|
||||
return pidx;
|
||||
}
|
||||
|
||||
/* find the suffix array SA of T[0..n-1] in {0..k}^n
|
||||
use a working space (excluding s and SA) of at most 2n+O(1) for a constant alphabet */
|
||||
template<typename string_type, typename sarray_type, typename index_type>
|
||||
int
|
||||
suffixsort(string_type T, sarray_type SA,
|
||||
index_type fs, index_type n, index_type k,
|
||||
bool isbwt) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
sarray_type RA;
|
||||
index_type i, j, m, p, q, plen, qlen, name;
|
||||
int pidx = 0;
|
||||
bool diff;
|
||||
int c;
|
||||
#ifdef _OPENMP
|
||||
int maxthreads = omp_get_max_threads();
|
||||
#else
|
||||
# define maxthreads 1
|
||||
#endif
|
||||
char_type c0, c1;
|
||||
|
||||
/* stage 1: reduce the problem by at least 1/2
|
||||
sort all the S-substrings */
|
||||
if(fs < (maxthreads * k)) {
|
||||
index_type *C, *B;
|
||||
if((C = new index_type[maxthreads * k]) == 0) { return -2; }
|
||||
B = (1 < maxthreads) ? C + k : C;
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = 0; i < n; ++i) { SA[i] = 0; }
|
||||
for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
|
||||
}
|
||||
induceSA(T, SA, C, B, n, k);
|
||||
delete [] C;
|
||||
} else {
|
||||
sarray_type C, B;
|
||||
C = SA + n;
|
||||
B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = 0; i < n; ++i) { SA[i] = 0; }
|
||||
for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
|
||||
}
|
||||
induceSA(T, SA, C, B, n, k);
|
||||
}
|
||||
|
||||
/* compact all the sorted substrings into the first m items of SA
|
||||
2*m must be not larger than n (proveable) */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i, j, p, c0, c1)
|
||||
for(i = 0; i < n; ++i) {
|
||||
p = SA[i];
|
||||
if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
|
||||
for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
|
||||
if((j < n) && (c0 < c1)) { SA[i] = ~p; }
|
||||
}
|
||||
}
|
||||
for(i = 0, m = 0; i < n; ++i) { if((p = SA[i]) < 0) { SA[m++] = ~p; } }
|
||||
#else
|
||||
for(i = 0, m = 0; i < n; ++i) {
|
||||
p = SA[i];
|
||||
if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
|
||||
for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
|
||||
if((j < n) && (c0 < c1)) { SA[m++] = p; }
|
||||
}
|
||||
}
|
||||
#endif
|
||||
j = m + (n >> 1);
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = m; i < j; ++i) { SA[i] = 0; } /* init the name array buffer */
|
||||
/* store the length of all substrings */
|
||||
for(i = n - 2, j = n, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { SA[m + ((i + 1) >> 1)] = j - i - 1; j = i + 1; c = 0; }
|
||||
}
|
||||
/* find the lexicographic names of all substrings */
|
||||
for(i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
|
||||
p = SA[i], plen = SA[m + (p >> 1)], diff = true;
|
||||
if(plen == qlen) {
|
||||
for(j = 0; (j < plen) && (T[p + j] == T[q + j]); ++j) { }
|
||||
if(j == plen) { diff = false; }
|
||||
}
|
||||
if(diff != false) { ++name, q = p, qlen = plen; }
|
||||
SA[m + (p >> 1)] = name;
|
||||
}
|
||||
|
||||
/* stage 2: solve the reduced problem
|
||||
recurse if names are not yet unique */
|
||||
if(name < m) {
|
||||
RA = SA + n + fs - m;
|
||||
for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) {
|
||||
if(SA[i] != 0) { RA[j--] = SA[i] - 1; }
|
||||
}
|
||||
if(suffixsort(RA, SA, fs + n - m * 2, m, name, false) != 0) { return -2; }
|
||||
for(i = n - 2, j = m - 1, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { RA[j--] = i + 1, c = 0; } /* get p1 */
|
||||
}
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; } /* get index in s */
|
||||
}
|
||||
|
||||
/* stage 3: induce the result for the original problem */
|
||||
if(fs < (maxthreads * k)) {
|
||||
index_type *B, *C;
|
||||
if((C = new index_type[maxthreads * k]) == 0) { return -2; }
|
||||
B = (1 < maxthreads) ? C + k : C;
|
||||
/* put all left-most S characters into their buckets */
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
|
||||
for(i = m - 1; 0 <= i; --i) {
|
||||
j = SA[i], SA[i] = 0;
|
||||
SA[--B[T[j]]] = j;
|
||||
}
|
||||
if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
|
||||
else { pidx = computeBWT(T, SA, C, B, n, k); }
|
||||
delete [] C;
|
||||
} else {
|
||||
sarray_type C, B;
|
||||
C = SA + n;
|
||||
B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
|
||||
/* put all left-most S characters into their buckets */
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
|
||||
for(i = m - 1; 0 <= i; --i) {
|
||||
j = SA[i], SA[i] = 0;
|
||||
SA[--B[T[j]]] = j;
|
||||
}
|
||||
if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
|
||||
else { pidx = computeBWT(T, SA, C, B, n, k); }
|
||||
}
|
||||
|
||||
return pidx;
|
||||
#ifndef _OPENMP
|
||||
# undef maxthreads
|
||||
#endif
|
||||
}
|
||||
|
||||
} /* namespace saisxx_private */
|
||||
|
||||
|
||||
/**
|
||||
* @brief Constructs the suffix array of a given string in linear time.
|
||||
* @param T[0..n-1] The input string. (random access iterator)
|
||||
* @param SA[0..n-1] The output array of suffixes. (random access iterator)
|
||||
* @param n The length of the given string.
|
||||
* @param k The alphabet size.
|
||||
* @return 0 if no error occurred, -1 or -2 otherwise.
|
||||
*/
|
||||
template<typename string_type, typename sarray_type, typename index_type>
|
||||
int
|
||||
saisxx(string_type T, sarray_type SA, index_type n, index_type k = 256) {
|
||||
int err;
|
||||
if((n < 0) || (k <= 0)) { return -1; }
|
||||
if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; }
|
||||
try { err = saisxx_private::suffixsort(T, SA, index_type(0), n, k, false); }
|
||||
catch(...) { err = -2; }
|
||||
return err;
|
||||
}
|
||||
|
||||
/**
|
||||
* @brief Constructs the burrows-wheeler transformed string of a given string in linear time.
|
||||
* @param T[0..n-1] The input string. (random access iterator)
|
||||
* @param U[0..n-1] The output string. (random access iterator)
|
||||
* @param A[0..n-1] The temporary array. (random access iterator)
|
||||
* @param n The length of the given string.
|
||||
* @param k The alphabet size.
|
||||
* @return The primary index if no error occurred, -1 or -2 otherwise.
|
||||
*/
|
||||
template<typename string_type, typename sarray_type, typename index_type>
|
||||
index_type
|
||||
saisxx_bwt(string_type T, string_type U, sarray_type A, index_type n, index_type k = 256) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
index_type i, pidx;
|
||||
if((n < 0) || (k <= 0)) { return -1; }
|
||||
if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
|
||||
try {
|
||||
pidx = saisxx_private::suffixsort(T, A, 0, n, k, true);
|
||||
if(0 <= pidx) {
|
||||
U[0] = T[n - 1];
|
||||
for(i = 0; i < pidx; ++i) { U[i + 1] = (char_type)A[i]; }
|
||||
for(i += 1; i < n; ++i) { U[i] = (char_type)A[i]; }
|
||||
pidx += 1;
|
||||
}
|
||||
} catch(...) { pidx = -2; }
|
||||
return pidx;
|
||||
}
|
||||
|
||||
|
||||
#endif /* __cplusplus */
|
||||
#endif /* _SAIS_HXX */
|
||||
|
||||
Reference in New Issue
Block a user