1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
use super::saca::saca;
#[cfg(feature = "pack")]
use super::packed_sa::PackedSuffixArray;
use super::utils::{lcp, trunc};
#[cfg(feature = "pack")]
use std::io::{Read, Result, Write};
use std::ops::Range;
#[cfg(feature = "pack")]
use std::path::Path;
#[derive(Clone)]
pub struct SuffixArray<'s> {
s: &'s [u8],
sa: Vec<u32>,
}
impl<'s> SuffixArray<'s> {
pub fn new(s: &'s [u8]) -> Self {
let mut sa = vec![0; s.len() + 1];
saca(s, &mut sa[..]);
SuffixArray { s, sa }
}
pub fn set(&mut self, s: &'s [u8]) {
self.sa.resize(s.len() + 1, 0);
saca(s, &mut self.sa[..]);
}
pub fn fit(&mut self) {
self.sa.shrink_to_fit()
}
pub fn len(&self) -> usize {
self.s.len()
}
pub fn is_empty(&self) -> bool {
self.len() == 0
}
pub fn into_parts(self) -> (&'s [u8], Vec<u32>) {
(self.s, self.sa)
}
pub fn from_parts(s: &'s [u8], sa: Vec<u32>) -> Option<Self> {
let compose = SuffixArray { s, sa };
if compose.check_integrity() {
Some(compose)
} else {
None
}
}
pub unsafe fn unchecked_from_parts(s: &'s [u8], sa: Vec<u32>) -> Self {
SuffixArray { s, sa }
}
fn check_integrity(&self) -> bool {
if self.s.len() + 1 != self.sa.len() {
return false;
}
for i in 1..self.sa.len() {
let x = &self.s[self.sa[i - 1] as usize..];
let y = &self.s[self.sa[i] as usize..];
if x >= y {
return false;
}
}
true
}
pub fn contains(&self, sub: &[u8]) -> bool {
self.sa
.binary_search_by_key(&sub, |&i| {
trunc(&self.s[i as usize..], sub.len())
})
.is_ok()
}
pub fn search_all(&self, sub: &[u8]) -> &[u32] {
let mut i = 0;
let mut k = self.sa.len();
while i < k {
let m = i + (k - i) / 2;
if sub > &self.s[self.sa[m] as usize..] {
i = m + 1;
} else {
k = m;
}
}
let mut j = i;
k = self.sa.len();
while j < k {
let m = j + (k - j) / 2;
if self.s[self.sa[m] as usize..].starts_with(sub) {
j = m + 1;
} else {
k = m;
}
}
&self.sa[i..j]
}
pub fn search_lcp(&self, pat: &[u8]) -> Range<usize> {
let point =
self.sa.binary_search_by(|&i| self.s[i as usize..].cmp(pat));
match point {
Ok(i) => {
let j = self.sa[i] as usize;
j..self.s.len()
}
Err(i) => {
if i > 0 && i < self.sa.len() {
let j = self.sa[i - 1] as usize;
let k = self.sa[i] as usize;
let a = lcp(pat, &self.s[j..]);
let b = lcp(pat, &self.s[k..]);
if a > b {
j..j + a
} else {
k..k + b
}
} else if i == self.sa.len() {
let j = self.sa[i - 1] as usize;
let a = lcp(pat, &self.s[j..]);
j..j + a
} else {
self.s.len()..self.s.len()
}
}
}
}
#[cfg(feature = "pack")]
pub fn dump<W: Write>(&self, file: W) -> Result<()> {
let psa = PackedSuffixArray::from_sa(&self.sa[..]);
psa.dump(file)
}
#[cfg(feature = "pack")]
pub fn dump_file<P: AsRef<Path>>(&self, name: P) -> Result<()> {
use std::fs::File;
use std::io::BufWriter;
let file = BufWriter::new(File::create(name)?);
let psa = PackedSuffixArray::from_sa(&self.sa[..]);
psa.dump(file)
}
#[cfg(feature = "pack")]
pub fn dump_bytes(&self) -> Result<Vec<u8>> {
let psa = PackedSuffixArray::from_sa(&self.sa[..]);
psa.dump_bytes()
}
#[cfg(feature = "pack")]
pub unsafe fn unchecked_load<R: Read>(
s: &'s [u8],
file: R,
) -> Result<Self> {
let psa = PackedSuffixArray::load(file)?;
let sa = psa.into_sa();
Ok(Self::unchecked_from_parts(s, sa))
}
#[cfg(feature = "pack")]
pub fn load<R: Read>(s: &'s [u8], file: R) -> Result<Self> {
use std::io::{Error, ErrorKind};
let sa = unsafe { Self::unchecked_load(s, file)? };
if !sa.check_integrity() {
Err(Error::new(
ErrorKind::InvalidData,
"inconsistent suffix array",
))
} else {
Ok(sa)
}
}
#[cfg(feature = "pack")]
pub unsafe fn unchecked_load_file<P: AsRef<Path>>(
s: &'s [u8],
name: P,
) -> Result<Self> {
use std::fs::File;
use std::io::BufReader;
let file = BufReader::new(File::open(name)?);
Self::unchecked_load(s, file)
}
#[cfg(feature = "pack")]
pub fn load_file<P: AsRef<Path>>(s: &'s [u8], name: P) -> Result<Self> {
use std::io::{Error, ErrorKind};
let sa = unsafe { Self::unchecked_load_file(s, name)? };
if !sa.check_integrity() {
Err(Error::new(
ErrorKind::InvalidData,
"inconsistent suffix array",
))
} else {
Ok(sa)
}
}
#[cfg(feature = "pack")]
pub unsafe fn unchecked_load_bytes(
s: &'s [u8],
bytes: &[u8],
) -> Result<Self> {
let psa = PackedSuffixArray::load_bytes(bytes)?;
let sa = psa.into_sa();
Ok(Self::unchecked_from_parts(s, sa))
}
#[cfg(feature = "pack")]
pub fn load_bytes(s: &'s [u8], bytes: &[u8]) -> Result<Self> {
use std::io::{Error, ErrorKind};
let sa = unsafe { Self::unchecked_load_bytes(s, bytes)? };
if !sa.check_integrity() {
Err(Error::new(
ErrorKind::InvalidData,
"inconsistent suffix array",
))
} else {
Ok(sa)
}
}
}
impl<'s> From<SuffixArray<'s>> for Vec<u32> {
fn from(sa: SuffixArray<'s>) -> Vec<u32> {
sa.sa
}
}
impl<'s> AsRef<[u8]> for SuffixArray<'s> {
fn as_ref(&self) -> &[u8] {
self.s
}
}