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. The specified alphabet must match the alphabet of the text and its BWT. For large texts, it is 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 Clone for Occ

fn clone(&self) -> Occ

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Occ

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

Formats the value using the given formatter.

impl Default for Occ

fn default() -> Occ

Returns the “default value” for a type.

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 Hash for Occ

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 Occ

fn cmp(&self, other: &Occ) -> 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<Occ> for Occ

fn eq(&self, other: &Occ) -> 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<Occ> for Occ

fn partial_cmp(&self, other: &Occ) -> 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 Occ

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 Occ

impl StructuralEq for Occ

impl StructuralPartialEq for Occ