Struct bio::data_structures::bwt::Occ

pub struct Occ { /* private fields */ }

An occurrence array implementation.

Implementations

impl Occ

pub fn new(bwt: &BWTSlice, k: u32, 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

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

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

Trait Implementations

impl<'de> Deserialize<'de> for Occ

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

Deserialize this value from the given Serde deserializer.

impl Serialize for Occ

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

Serialize this value into the given Serde serializer.