Struct bio::pattern_matching::myers::Myers

pub struct Myers<T = u64>where
    T: BitVec,{ /* private fields */ }

Myers algorithm.

Implementations

impl<T: BitVec> Myers<T>

pub fn new<'a, C, P>(pattern: P) -> Selfwhere
    C: Borrow<u8>,
    P: IntoIterator<Item = C>,
    P::IntoIter: ExactSizeIterator,

Create a new instance of Myers algorithm for a given pattern.

pub fn distance<C, I>(&self, text: I) -> T::DistTypewhere
    C: Borrow<u8>,
    I: IntoIterator<Item = C>,

Calculate the global distance of the pattern to the given text.

pub fn find_all_end<C, I>(
    &self,
    text: I,
    max_dist: T::DistType
) -> Matches<'_, T, C, I::IntoIter> where
    C: Borrow<u8>,
    I: IntoIterator<Item = C>,

Finds all matches of pattern in the given text up to a given maximum distance. Matches are returned as an iterator over pairs of end position and distance.

pub fn find_best_end<C, I>(&self, text: I) -> (usize, T::DistType)where
    C: Borrow<u8>,
    I: IntoIterator<Item = C>,

Find the best match of the pattern in the given text. if multiple end positions have the same distance, the first is returned.

pub fn find_all<'a, C, I>(
    &'a mut self,
    text: I,
    max_dist: T::DistType
) -> FullMatches<'a, T, C, I::IntoIter> where
    C: Borrow<u8>,
    I: IntoIterator<Item = C>,
    I::IntoIter: ExactSizeIterator,

Finds all matches of pattern in the given text up to a given maximum distance. In contrast to find_all_end, matches are returned as an iterator over ranges of (start, end, distance). Note that the end coordinate is not included in the range and thus and thus greater by one compared to the end index returned by find_all_end().

pub fn find_all_lazy<'a, C, I>(
    &'a mut self,
    text: I,
    max_dist: T::DistType
) -> LazyMatches<'a, T, C, I::IntoIter> where
    C: Borrow<u8>,
    I: IntoIterator<Item = C>,
    I::IntoIter: ExactSizeIterator,

As find_all_end, this function returns an iterator over tuples of (end, distance). Additionally, it keeps the data necessary for later obtaining the starting positions and/or the alignment path at any position that was already searched.