Struct bio::data_structures::qgram_index::QGramIndex

pub struct QGramIndex { /* private fields */ }

A classical, flexible, q-gram index implementation.

Implementations

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.

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

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

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.

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.

Trait Implementations

impl<'de> Deserialize<'de> for QGramIndex

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

Deserialize this value from the given Serde deserializer.

impl Serialize for QGramIndex

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

Serialize this value into the given Serde serializer.