Struct bio::pattern_matching::myers::long::Myers

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

Myers algorithm.

Implementations

impl<T: BitVec> Myers<T>

pub fn distance<C, I>(&self, text: I) -> usizewhere 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: usize ) -> 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, usize)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<C, I>( &mut self, text: I, max_dist: usize ) -> FullMatches<'_, 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<C, I>( &mut self, text: I, max_dist: usize ) -> LazyMatches<'_, 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.

impl<T: BitVec> Myers<T>

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

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

Trait Implementations

impl<T> Clone for Myers<T>where T: BitVec + Clone,

fn clone(&self) -> Myers<T>

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl<T> Debug for Myers<T>where T: BitVec + Debug,

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<T> Default for Myers<T>where T: BitVec + Default,

fn default() -> Myers<T>

Returns the “default value” for a type.

impl<T> Hash for Myers<T>where T: BitVec + Hash,

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl<T> Ord for Myers<T>where T: BitVec + Ord,

fn cmp(&self, other: &Myers<T>) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Selfwhere Self: Sized + PartialOrd<Self>,

Restrict a value to a certain interval.

impl<T> PartialEq<Myers<T>> for Myers<T>where T: BitVec + PartialEq,

fn eq(&self, other: &Myers<T>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<T> PartialOrd<Myers<T>> for Myers<T>where T: BitVec + PartialOrd,

fn partial_cmp(&self, other: &Myers<T>) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl<T> Eq for Myers<T>where T: BitVec + Eq,

impl<T> StructuralEq for Myers<T>where T: BitVec,

impl<T> StructuralPartialEq for Myers<T>where T: BitVec,