Module bio::pattern_matching::bndm

Backward nondeterministic DAWG matching (BNDM). Best-case complexity: O(n / m) with pattern of length m <= 64 and text of length n. Worst case complexity: O(n * m).

Example

use bio::pattern_matching::bndm;
let pattern = b"GAAAA";
let text = b"ACGGCTAGAAAAGGCTAGAAAA";
let bndm = bndm::BNDM::new(pattern);
let occ: Vec<usize> = bndm.find_all(text).collect();
assert_eq!(occ, [7, 17]);

Structs

BNDM	BNDM algorithm.
Matches	Iterator over start positions of matches.