Struct bio::pattern_matching::ukkonen::Ukkonen

pub struct Ukkonen<F> where
    F: Fn(u8, u8) -> u32,  { /* fields omitted */ }

Ukkonens algorithm.

Methods

impl<F> Ukkonen<F> where
    F: Fn(u8, u8) -> u32, 

pub fn with_capacity(m: usize, cost: F) -> Self

Initialize algorithm with given capacity and cost function.

Important traits for Matches<'a, F, C, T>

impl<'a, F, C, T> Iterator for Matches<'a, F, C, T> where
    F: 'a + Fn(u8, u8) -> u32,
    C: Borrow<u8>,
    T: Iterator<Item = C>,  type Item = (usize, usize);

pub fn find_all_end<'a, C, T>(
    &'a mut self,
    pattern: TextSlice<'a>,
    text: T,
    k: usize
) -> Matches<F, C, T::IntoIter> where
    C: Borrow<u8>,
    T: IntoIterator<Item = C>, 

Find all matches between pattern and text with up to k errors. Matches are returned as an iterator over pairs of end position and distance.