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
// Copyright 2014-2016 Johannes Köster.
// Licensed under the MIT license (http://opensource.org/licenses/MIT)
// This file may not be copied, modified, or distributed
// except according to those terms.
//! Backward oracle matching algorithm.
//! Best-case complexity: O(n / m) with pattern of length m and text of length n.
//! Worst case complexity: O(n * m).
//!
//! # Example
//!
//! ```
//! use bio::pattern_matching::bom::BOM;
//! let text = b"ACGGCTAGGAAAAAGACTGAGGACTGAAAA";
//! let pattern = b"GAAAA";
//! let bom = BOM::new(pattern);
//! let occ: Vec<usize> = bom.find_all(text).collect();
//! assert_eq!(occ, [8, 25]);
//! ```
use crate::utils::TextSlice;
use std::borrow::Borrow;
use std::cmp::Ord;
use std::iter::repeat;
use vec_map::VecMap;
/// Backward oracle matching algorithm.
#[derive(Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
pub struct BOM {
m: usize,
table: Vec<VecMap<usize>>,
}
impl BOM {
/// Create a new instance for a given pattern.
pub fn new<C, P>(pattern: P) -> Self
where
C: Borrow<u8> + Ord,
P: IntoIterator<Item = C>,
P::IntoIter: DoubleEndedIterator + ExactSizeIterator + Clone,
{
let pattern = pattern.into_iter();
let m = pattern.len();
let maxsym = *pattern
.clone()
.max()
.expect("Expecting non-empty pattern.")
.borrow() as usize;
let mut table: Vec<VecMap<usize>> = Vec::with_capacity(m);
// init suffix table, initially all values unknown
// suff[i] is the state in which the longest suffix of
// pattern[..i+1] ends that does not end in i
let mut suff: Vec<Option<usize>> = repeat(None).take(m + 1).collect();
for (j, b) in pattern.rev().enumerate() {
let i = j + 1;
let a = *b.borrow() as usize;
let mut delta = VecMap::with_capacity(maxsym);
// reading symbol a leads into state i (this is an inner edge)
delta.insert(a, i);
// now, add edges for substrings ending with a
let mut k = suff[i - 1];
// for this iterate over the known suffixes until
// reaching an edge labelled with a or the start
while let Some(k_) = k {
if table[k_].contains_key(a) {
break;
}
table[k_].insert(a, i);
k = suff[k_];
}
// the longest suffix is either 0 or the state
// reached by the edge labelled with a
suff[i] = Some(match k {
Some(k) => *table[k].get(a).unwrap(),
None => 0,
});
table.push(delta);
}
BOM { m, table }
}
fn delta(&self, q: usize, a: u8) -> Option<usize> {
if q >= self.table.len() {
None
} else {
self.table[q].get(a as usize).copied()
}
}
/// Find all matches of the pattern in the given text. Matches are returned as an iterator over start positions.
pub fn find_all<'a>(&'a self, text: TextSlice<'a>) -> Matches<'_> {
Matches {
bom: self,
text,
window: self.m,
}
}
}
/// Iterator over start positions of matches.
#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize)]
pub struct Matches<'a> {
bom: &'a BOM,
text: TextSlice<'a>,
window: usize,
}
impl<'a> Iterator for Matches<'a> {
type Item = usize;
fn next(&mut self) -> Option<usize> {
while self.window <= self.text.len() {
let (mut q, mut j) = (Some(0), 1);
while j <= self.bom.m {
match q {
Some(q_) => {
q = self.bom.delta(q_, self.text[self.window - j]);
j += 1;
}
None => break,
}
}
// putative start position
let i = self.window - self.bom.m;
self.window += self.bom.m + 2 - j;
if q.is_some() {
// return match
return Some(i);
}
}
None
}
}
#[cfg(test)]
mod tests {
use super::BOM;
use itertools::Itertools;
#[test]
fn test_delta() {
let pattern = b"qnnnannan"; // reverse of nannannnq
let bom = BOM::new(pattern);
assert_eq!(bom.delta(0, b'n'), Some(1));
assert_eq!(bom.delta(1, b'a'), Some(2));
assert_eq!(bom.delta(2, b'n'), Some(3));
assert_eq!(bom.delta(3, b'n'), Some(4));
assert_eq!(bom.delta(4, b'a'), Some(5));
assert_eq!(bom.delta(5, b'n'), Some(6));
assert_eq!(bom.delta(6, b'n'), Some(7));
assert_eq!(bom.delta(7, b'n'), Some(8));
assert_eq!(bom.delta(8, b'q'), Some(9));
assert_eq!(bom.delta(0, b'a'), Some(2));
assert_eq!(bom.delta(0, b'q'), Some(9));
assert_eq!(bom.delta(1, b'n'), Some(4));
assert_eq!(bom.delta(1, b'q'), Some(9));
assert_eq!(bom.delta(4, b'n'), Some(8));
assert_eq!(bom.delta(4, b'q'), Some(9));
bom.delta(9, b'a');
}
#[test]
fn test_find_all() {
let text = b"dhjalkjwqnnnannanaflkjdklfj";
let pattern = b"qnnnannan";
let bom = BOM::new(pattern);
assert_eq!(bom.find_all(text).collect_vec(), [8]);
}
#[test]
fn test_find_all_at_start() {
let text = b"dhjalkjwqnnnannanaflkjdklfj";
let pattern = b"dhjalk";
let bom = BOM::new(pattern);
assert_eq!(bom.find_all(text).collect_vec(), [0]);
}
}