Struct Dna

pub struct Dna;

The standard DNA alphabet composed of 4 deoxyribonucleotides and a wildcard.

Trait Implementations

impl Alphabet for Dna

type Symbol = Nucleotide

type K = UInt<UInt<UInt<UTerm, B1>, B0>, B1>

fn symbols() -> &'static [Nucleotide]

Get all the symbols of this alphabet.

fn as_str() -> &'static str

Get a string with all symbols from this alphabet.

fn default_symbol() -> Self::Symbol

Get the default symbol for this alphabet.

impl Clone for Dna

fn clone(&self) -> Dna

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Dna

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

Formats the value using the given formatter.

impl Default for Dna

fn default() -> Dna

Returns the “default value” for a type.

impl PartialEq for Dna

fn eq(&self, other: &Dna) -> 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 Score<u8, Dna, <Avx2 as Backend>::Lanes> for Pipeline<Dna, Avx2>

fn score_rows_into<S, M>( &self, pssm: M, seq: S, rows: Range<usize>, scores: &mut StripedScores<u8, <Avx2 as Backend>::Lanes>, )

where S: AsRef<StripedSequence<Dna, <Avx2 as Backend>::Lanes>>, M: AsRef<DenseMatrix<u8, <Dna as Alphabet>::K>>,

Compute the PSSM scores into the given striped score matrix.

fn score_into<S, M>(&self, pssm: M, seq: S, scores: &mut StripedScores<T, C>)

where S: AsRef<StripedSequence<A, C>>, M: AsRef<DenseMatrix<T, A::K>>,

Compute the PSSM scores into the given striped score matrix.

fn score<S, M>(&self, pssm: M, seq: S) -> StripedScores<T, C>

where S: AsRef<StripedSequence<A, C>>, M: AsRef<DenseMatrix<T, A::K>>,

Compute the PSSM scores for every sequence positions.

impl Score<u8, Dna, <Dispatch as Backend>::Lanes> for Pipeline<Dna, Dispatch>

fn score_rows_into<S, M>( &self, pssm: M, seq: S, rows: Range<usize>, scores: &mut StripedScores<u8, <Dispatch as Backend>::Lanes>, )

where S: AsRef<StripedSequence<Dna, <Dispatch as Backend>::Lanes>>, M: AsRef<DenseMatrix<u8, <Dna as Alphabet>::K>>,

Compute the PSSM scores into the given striped score matrix.

fn score_into<S, M>(&self, pssm: M, seq: S, scores: &mut StripedScores<T, C>)

where S: AsRef<StripedSequence<A, C>>, M: AsRef<DenseMatrix<T, A::K>>,

Compute the PSSM scores into the given striped score matrix.

fn score<S, M>(&self, pssm: M, seq: S) -> StripedScores<T, C>

where S: AsRef<StripedSequence<A, C>>, M: AsRef<DenseMatrix<T, A::K>>,

Compute the PSSM scores for every sequence positions.

impl<C> Score<u8, Dna, C> for Pipeline<Dna, Neon>

where C: PositiveLength + MultipleOf<U16>,

fn score_rows_into<S, M>( &self, pssm: M, seq: S, rows: Range<usize>, scores: &mut StripedScores<u8, C>, )

where S: AsRef<StripedSequence<Dna, C>>, M: AsRef<DenseMatrix<u8, <Dna as Alphabet>::K>>,

Compute the PSSM scores into the given striped score matrix.

fn score_into<S, M>(&self, pssm: M, seq: S, scores: &mut StripedScores<T, C>)

where S: AsRef<StripedSequence<A, C>>, M: AsRef<DenseMatrix<T, A::K>>,

Compute the PSSM scores into the given striped score matrix.

fn score<S, M>(&self, pssm: M, seq: S) -> StripedScores<T, C>

where S: AsRef<StripedSequence<A, C>>, M: AsRef<DenseMatrix<T, A::K>>,

Compute the PSSM scores for every sequence positions.

impl Copy for Dna

impl Eq for Dna

impl StructuralPartialEq for Dna