Struct bio::data_structures::qgram_index::QGramIndex

pub struct QGramIndex { /* fields omitted */ }

A classical, flexible, q-gram index implementation.

Methods

impl QGramIndex

pub fn new(q: u32, text: &[u8], alphabet: &Alphabet) -> Self

Create a new q-gram index. The q has to be smaller than b / log2(|A|) with |A| being the alphabet size and b the number bits with the usize data type.

pub fn with_max_count(     q: u32,     text: &[u8],     alphabet: &Alphabet,     max_count: usize ) -> Self

Create a new q-gram index, only considering q-grams that occur at most max_count times. The q has to be smaller than b / log2(|A|) with |A| being the alphabet size and b the number bits with the usize data type.

pub fn q(&self) -> u32

The used q.

Important traits for &'a [u8]

impl<'a> Read for &'a [u8]impl<'a> Write for &'a mut [u8]

pub fn qgram_matches(&self, qgram: usize) -> &[usize]

Return text positions with matching q-gram. Complexity O(1).

Important traits for Vec<u8>

impl Write for Vec<u8>

pub fn matches(&self, pattern: &[u8], min_count: usize) -> Vec<Match>

Return matches of the given pattern. Complexity O(m + k) for pattern of length m and k being the number of matching q-grams.

Important traits for Vec<u8>

impl Write for Vec<u8>

pub fn exact_matches(&self, pattern: &[u8]) -> Vec<ExactMatch>

Return exact matches (substrings) of the given pattern. Complexity O(m + k) for pattern of length m and k being the number of matching q-grams.