Struct bio::data_structures::qgram_index::QGramIndex

pub struct QGramIndex { /* private fields */ }

A classical, flexible, q-gram index implementation.

Uses |alphabet|^q + k words of memory, where k is the number of q-grams in the text with count at most max_count (if specified).

Implementations

impl QGramIndex

pub fn new<'a, T, I>(q: u32, text: T, alphabet: &Alphabet) -> Selfwhere I: Iterator<Item = &'a u8> + ExactSizeIterator + Clone, T: IntoIterator<Item = &'a u8, IntoIter = I> + Sized,

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<'a, T, I>( q: u32, text: T, alphabet: &Alphabet, max_count: usize ) -> Selfwhere I: Iterator<Item = &'a u8> + ExactSizeIterator + Clone, T: IntoIterator<Item = &'a u8, IntoIter = I> + Sized,

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, matching in at least min_count q-grams. Complexity O(m + k) for pattern of length m and k being the number of matching q-grams.

A match is a substring of pattern and a corresponding substring of the text that share at least min_count 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.

An exact match is a substring of pattern occurring in the text of length at least q.

Trait Implementations

impl Clone for QGramIndex

fn clone(&self) -> QGramIndex

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for QGramIndex

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for QGramIndex

fn default() -> QGramIndex

Returns the “default value” for a type.

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 Hash for QGramIndex

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for QGramIndex

fn cmp(&self, other: &QGramIndex) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Selfwhere Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Selfwhere Self: Sized + PartialOrd<Self>,

Restrict a value to a certain interval.

impl PartialEq<QGramIndex> for QGramIndex

fn eq(&self, other: &QGramIndex) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd<QGramIndex> for QGramIndex

fn partial_cmp(&self, other: &QGramIndex) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

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.

impl Eq for QGramIndex

impl StructuralEq for QGramIndex

impl StructuralPartialEq for QGramIndex