Enum AmbiNuc 

#[repr(u8)]
pub enum AmbiNuc {
    A = 1,
    C = 2,
    G = 4,
    T = 8,
    R = 5,
    Y = 10,
    M = 3,
    K = 12,
    W = 9,
    S = 6,
    B = 14,
    D = 13,
    H = 11,
    V = 7,
    N = 15,
}

Ambiguous nucleotide

Note that AmbiNuc always represents at least one possible nucleotide; there is no such thing as an empty/null AmbiNuc.

For details, see: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representation

Beware that AmbiNuc’s order isn’t alphabetic.

Variants

A = 1

Adenine

C = 2

Cytosine

G = 4

Guanine

T = 8

Thymine

R = 5

A/G: puRine

Y = 10

C/T: pYrimidines

M = 3

A/C: aMino groups

K = 12

G/T: Ketones

W = 9

A/T: Weak interaction

S = 6

C/G: Strong interaction

B = 14

C/G/T: Not A (B comes after A)

D = 13

A/G/T: Not C (D comes after C)

H = 11

A/C/T: Not G (H comes after G)

V = 7

A/C/G: Not T (V comes after U/T)

N = 15

A/C/G/T: Nucleic acid

Implementations

impl AmbiNuc

pub const ALL: [Self; 15]

All AmbiNucs sorted in ascending order

pub const fn complement(self) -> Self

Return ambiguous nucleotide containing complements for each potential value.

use nucs::AmbiNuc;

assert_eq!(AmbiNuc::A.complement(), AmbiNuc::T);
assert_eq!(AmbiNuc::C.complement(), AmbiNuc::G);
assert_eq!(AmbiNuc::G.complement(), AmbiNuc::C);
assert_eq!(AmbiNuc::T.complement(), AmbiNuc::A);

// D -> A|G|T -> T|C|A -> H
assert_eq!(AmbiNuc::D.complement(), AmbiNuc::H);

pub const fn to_str(self) -> &'static str

Return uppercase string representation

Examples

use nucs::AmbiNuc;

assert_eq!(AmbiNuc::A.to_str(), "A");
assert_eq!(AmbiNuc::N.to_str(), "N");

pub const fn from_ascii(ascii: u8) -> Result<Self, ParseSymbolError>

Construct from ASCII representation

Errors

Returns ParseSymbolError if the given byte isn’t A, B, C, D, G, H, K, M, N, R, S, T, V, W or Y (case-insensitve).

Examples

use nucs::AmbiNuc;

assert_eq!(AmbiNuc::from_ascii(b'A'), Ok(AmbiNuc::A));
assert!(AmbiNuc::from_ascii(b'E').is_err());

pub const fn to_ascii(self) -> u8

Return uppercase ASCII representation

Examples

use nucs::AmbiNuc;

assert_eq!(AmbiNuc::A.to_ascii(), b'A');
assert_eq!(AmbiNuc::N.to_ascii(), b'N');

pub fn iter(self) -> Copied<Iter<'static, Nuc>>

Return iterator of Nucs that this ambiguous nucleotide could be.

The iterator is guaranteed to return things in sorted order and without duplicates, and its contents are guaranteed to recompose into this AmbiNuc via BitOr.

Examples

use nucs::{AmbiNuc, Nuc};

assert!(AmbiNuc::B.iter().eq(Nuc::lit(b"CGT")));

pub const fn lit<const N: usize>(literal: &[u8; N]) -> [AmbiNuc; N]

Construct AmbiNuc array from literal without allocating.

Examples

use nucs::AmbiNuc;

let dna1 = AmbiNuc::lit(b"NASTYGRAM");
// ...is shorthand for...
use AmbiNuc::{N, A, S, T, Y, G, R, M};
let dna2 = [N, A, S, T, Y, G, R, A, M];

assert_eq!(dna1, dna2);

Panics

This panics if the supplied literal isn’t valid. Whitespace is NOT allowed because the returned array must have the same length.

Trait Implementations

impl AsMut<AmbiNuc> for AmbiNuc

fn as_mut(&mut self) -> &mut AmbiNuc

Converts this type into a mutable reference of the (usually inferred) input type.

impl AsRef<AmbiNuc> for AmbiNuc

fn as_ref(&self) -> &AmbiNuc

Converts this type into a shared reference of the (usually inferred) input type.

impl BitOr<&AmbiNuc> for &Nuc

type Output = AmbiNuc

The resulting type after applying the | operator.

fn bitor(self, rhs: &AmbiNuc) -> Self::Output

Performs the | operation.

impl BitOr<&Nuc> for &AmbiNuc

type Output = AmbiNuc

The resulting type after applying the | operator.

fn bitor(self, rhs: &Nuc) -> Self::Output

Performs the | operation.

impl BitOr<AmbiNuc> for Nuc

type Output = AmbiNuc

The resulting type after applying the | operator.

fn bitor(self, rhs: AmbiNuc) -> Self::Output

Performs the | operation.

impl BitOr<Nuc> for AmbiNuc

type Output = AmbiNuc

The resulting type after applying the | operator.

fn bitor(self, rhs: Nuc) -> Self::Output

Performs the | operation.

impl BitOr for &AmbiNuc

type Output = AmbiNuc

The resulting type after applying the | operator.

fn bitor(self, rhs: &AmbiNuc) -> Self::Output

Performs the | operation.

impl BitOr for AmbiNuc

type Output = AmbiNuc

The resulting type after applying the | operator.

fn bitor(self, rhs: AmbiNuc) -> Self::Output

Performs the | operation.

impl BitOrAssign<&AmbiNuc> for AmbiNuc

fn bitor_assign(&mut self, rhs: &AmbiNuc)

Performs the |= operation.

impl BitOrAssign<&Nuc> for AmbiNuc

fn bitor_assign(&mut self, rhs: &Nuc)

Performs the |= operation.

impl BitOrAssign<Nuc> for AmbiNuc

fn bitor_assign(&mut self, rhs: Nuc)

Performs the |= operation.

impl BitOrAssign for AmbiNuc

fn bitor_assign(&mut self, rhs: AmbiNuc)

Performs the |= operation.

impl Clone for AmbiNuc

fn clone(&self) -> AmbiNuc

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AmbiNuc

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

Formats the value using the given formatter.

impl Display for AmbiNuc

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

Formats the value using the given formatter.

impl From<Nuc> for AmbiNuc

fn from(nuc: Nuc) -> Self

Converts to this type from the input type.

impl FromStr for AmbiNuc

type Err = ParseSymbolError

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl Hash for AmbiNuc

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 IntoIterator for &AmbiNuc

type IntoIter = Copied<Iter<'static, Nuc>>

Which kind of iterator are we turning this into?

type Item = Nuc

The type of the elements being iterated over.

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl IntoIterator for AmbiNuc

type IntoIter = Copied<Iter<'static, Nuc>>

Which kind of iterator are we turning this into?

type Item = Nuc

The type of the elements being iterated over.

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl Nucleotide for AmbiNuc

const ALL: &[Self]

All possible nucleotides in ascending order

type Amino = AmbiAmino

Amino acid; either Amino or AmbiAmino

fn complement(self) -> Self

Return this nucleotide’s complement.

fn translate<G: GeneticCode>(codon: [Self; 3], genetic_code: G) -> Self::Amino

Translate a codon into an amino acid

impl Ord for AmbiNuc

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

This method returns an Ordering between self and other.

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

where Self: Sized,

Compares and returns the maximum of two values.

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

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq<AmbiNuc> for Nuc

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

Tests for self and other values to be equal, and is used by ==.

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

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

impl PartialEq<Nuc> for AmbiNuc

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

Tests for self and other values to be equal, and is used by ==.

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

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

impl PartialEq for AmbiNuc

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

Tests for self and other values to be equal, and is used by ==.

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

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

impl PartialOrd<AmbiNuc> for Nuc

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

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

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

Tests less than (for self and other) and is used by the < operator.

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

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

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

Tests greater than (for self and other) and is used by the > operator.

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

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

impl PartialOrd<Nuc> for AmbiNuc

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

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

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

Tests less than (for self and other) and is used by the < operator.

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

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

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

Tests greater than (for self and other) and is used by the > operator.

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

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

impl PartialOrd for AmbiNuc

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

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

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

Tests less than (for self and other) and is used by the < operator.

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

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

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

Tests greater than (for self and other) and is used by the > operator.

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

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

impl Symbol for AmbiNuc

type Concrete = Nuc

Concrete symbols, i.e. Nuc or Amino

type Ambiguous = AmbiNuc

Ambiguous symbols, i.e. AmbiNuc or AmbiAmino

fn to_str(self) -> &'static str

Return uppercase string representation

fn from_ascii(ascii: u8) -> Result<Self, ParseSymbolError>

Construct from (case-insensitive) ASCII representation

fn to_ascii(self) -> u8

Return uppercase ASCII representation

fn lit<const N: usize>(literal: &[u8; N]) -> [Self; N]

Construct array from literal without allocating.

impl TryFrom<AmbiNuc> for Nuc

type Error = AmbiNuc

The type returned in the event of a conversion error.

fn try_from(nuc: AmbiNuc) -> Result<Self, Self::Error>

Performs the conversion.

impl Copy for AmbiNuc

impl Eq for AmbiNuc

impl StructuralPartialEq for AmbiNuc