Struct bio::alphabets::RankTransform

pub struct RankTransform {
    pub ranks: SymbolRanks,
}

Tools based on transforming the alphabet symbols to their lexicographical ranks.

Fields

ranks: SymbolRanks

Methods

impl RankTransform

pub fn new(alphabet: &Alphabet) -> Self

Construct a new RankTransform.

pub fn get(&self, a: u8) -> u8

Get the rank of symbol a.

pub fn transform<C, T>(&self, text: T) -> Vec<u8> where
    C: Borrow<u8>,
    T: IntoIterator<Item = C>, 

Transform a given text.

Important traits for QGrams<'a, C, T>

impl<'a, C, T> Iterator for QGrams<'a, C, T> where
    C: Borrow<u8>,
    T: Iterator<Item = C>,  type Item = usize;

pub fn qgrams<C, T>(&self, q: u32, text: T) -> QGrams<C, T::IntoIter> where
    C: Borrow<u8>,
    T: IntoIterator<Item = C>, 

Iterate over q-grams (substrings of length q) of given text. The q-grams are encoded as usize by storing the symbol ranks in log2(|A|) bits (with |A| being the alphabet size).

If q is larger than usize::BITS / log2(|A|), this method fails with an assertion.

pub fn alphabet(&self) -> Alphabet

Restore alphabet from transform.

Trait Implementations

impl Serialize for RankTransform

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl<'de> Deserialize<'de> for RankTransform

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.