Struct bio::alphabets::RankTransform

pub struct RankTransform {
    pub ranks: SymbolRanks,
}

Tools based on transforming the alphabet symbols to their lexicographical ranks.

Lexicographical rank is computed using u8 representations, i.e. ASCII codes, of the input characters. For example, assuming that the alphabet consists of the symbols A, C, G, and T, this will yield ranks 0, 1, 2, 3 for them, respectively.

RankTransform can be used in to perform bit encoding for texts over a given alphabet via bio::data_structures::bitenc.

Fields

ranks: SymbolRanks

Implementations

impl RankTransform

pub fn new(alphabet: &Alphabet) -> Self

Construct a new RankTransform.

Complexity: O(n), where n is the number of symbols in the alphabet.

Example

use bio::alphabets;

let dna_alphabet = alphabets::Alphabet::new(b"acgtACGT");
let dna_ranks = alphabets::RankTransform::new(&dna_alphabet);

pub fn get(&self, a: u8) -> u8

Get the rank of symbol a.

This method panics for characters not contained in the alphabet.

Complexity: O(1)

Example

use bio::alphabets;

let dna_alphabet = alphabets::Alphabet::new(b"acgtACGT");
let dna_ranks = alphabets::RankTransform::new(&dna_alphabet);
assert_eq!(dna_ranks.get(65), 0); // "A"
assert_eq!(dna_ranks.get(116), 7); // "t"

pub fn transform<C, T>(&self, text: T) -> Vec<u8>where C: Borrow<u8>, T: IntoIterator<Item = C>,

Transform a given text into a vector of rank values.

Complexity: O(n), where n is the length of the text.

Example

use bio::alphabets;

let dna_alphabet = alphabets::Alphabet::new(b"ACGTacgt");
let dna_ranks = alphabets::RankTransform::new(&dna_alphabet);
let text = b"aAcCgGtT";
assert_eq!(dna_ranks.transform(text), vec![4, 0, 5, 1, 6, 2, 7, 3]);

pub fn qgrams<C, T>(&self, q: u32, text: T) -> QGrams<'_, C, T::IntoIter> where C: Borrow<u8>, T: IntoIterator<Item = C>,

Iterate over q-grams (substrings of length q) of given text. The q-grams are encoded as usize by storing the symbol ranks in log2(|A|) bits (with |A| being the alphabet size).

If q is larger than usize::BITS / log2(|A|), this method fails with an assertion.

Complexity: O(n), where n is the length of the text.

Example

use bio::alphabets;

let dna_alphabet = alphabets::Alphabet::new(b"ACGTacgt");
let dna_ranks = alphabets::RankTransform::new(&dna_alphabet);

let q_grams: Vec<usize> = dna_ranks.qgrams(2, b"ACGT").collect();
assert_eq!(q_grams, vec![1, 10, 19]);

pub fn alphabet(&self) -> Alphabet

Restore alphabet from transform.

Complexity: O(n), where n is the number of symbols in the alphabet.

Example

use bio::alphabets;

let dna_alphabet = alphabets::Alphabet::new(b"acgtACGT");
let dna_ranks = alphabets::RankTransform::new(&dna_alphabet);
assert_eq!(dna_ranks.alphabet().symbols, dna_alphabet.symbols);

pub fn get_width(&self) -> usize

Compute the number of bits required to encode the largest rank value.

For example, the alphabet b"ACGT" with 4 symbols has the maximal rank 3, which can be encoded in 2 bits.

This value can be used to create a data_structures::bitenc::BitEnc bit encoding tailored to the given alphabet.

Complexity: O(n), where n is the number of symbols in the alphabet.

Example

use bio::alphabets;

let dna_alphabet = alphabets::Alphabet::new(b"ACGT");
let dna_ranks = alphabets::RankTransform::new(&dna_alphabet);
assert_eq!(dna_ranks.get_width(), 2);
let dna_n_alphabet = alphabets::Alphabet::new(b"ACGTN");
let dna_n_ranks = alphabets::RankTransform::new(&dna_n_alphabet);
assert_eq!(dna_n_ranks.get_width(), 3);

Trait Implementations

impl Clone for RankTransform

fn clone(&self) -> RankTransform

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for RankTransform

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

Formats the value using the given formatter.

impl Default for RankTransform

fn default() -> RankTransform

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for RankTransform

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

Deserialize this value from the given Serde deserializer.

impl Hash for RankTransform

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 RankTransform

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

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

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

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 RankTransform

impl StructuralEq for RankTransform

impl StructuralPartialEq for RankTransform