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

fn new(alphabet: &Alphabet) -> Self

Construct a new RankTransform.

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

Get the rank of symbol a.

fn transform<'a, T: IntoTextIterator<'a>>(&self, text: T) -> Vec<u8>

Transform a given text.

fn qgrams<'a, T: IntoTextIterator<'a>>(&'a self, q: u32, text: T) -> QGrams<T::IntoIter>

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.

fn alphabet(&self) -> Alphabet

Restore alphabet from transform.