Struct bio::data_structures::bwt::Occ

pub struct Occ { /* fields omitted */ }

An occurence array implementation.

Methods

impl Occ

fn new(bwt: &BWTSlice, k: usize, alphabet: &Alphabet) -> Self

Calculate occ array with sampling from BWT of length n. Time complexity: O(n). Space complexity: O(n / k * A) with A being the alphabet size. Alphabet size is determined on the fly from the BWT. For large texts, it is therefore advisable to transform the text before calculating the BWT (see alphabets::rank_transform).

Arguments

• bwt - the BWT
• k - the sampling rate: every k-th entry will be stored

fn get(&self, bwt: &BWTSlice, r: usize, a: u8) -> usize

Get occurrence count of symbol a in BWT[..r+1]. Complexity: O(k).