Struct EncodedSequence

pub struct EncodedSequence<A: Alphabet> { /* private fields */ }

A biological sequence encoded with an alphabet.

Implementations

impl<A: Alphabet> EncodedSequence<A>

pub fn new(data: Vec<A::Symbol>) -> Self

Create a new encoded sequence.

pub fn encode<S: AsRef<[u8]>>(sequence: S) -> Result<Self, InvalidSymbol>

Create a new encoded sequence from a textual representation.

Note

Uses platform-accelerated implementation when available.

pub fn sample<R: Rng>(rng: R, background: Background<A>, length: usize) -> Self

Sample a new random sequence from the given background frequencies.

pub fn len(&self) -> usize

Return the number of symbols in the sequence.

pub fn is_empty(&self) -> bool

Check whether the sequence is empty.

pub fn iter(&self) -> <&[A::Symbol] as IntoIterator>::IntoIter

Iterate over the symbols in the sequence.

pub fn to_striped<C>(&self) -> StripedSequence<A, C>

where C: StrictlyPositive + ArrayLength, Pipeline<A, Dispatch>: Stripe<A, C>,

Convert the encoded sequence to a striped matrix.

Note

Uses platform-accelerated implementation when available.

Trait Implementations

impl<A: Alphabet> AsRef<[<A as Alphabet>::Symbol]> for EncodedSequence<A>

fn as_ref(&self) -> &[A::Symbol]

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

impl<A: Alphabet> AsRef<EncodedSequence<A>> for EncodedSequence<A>

fn as_ref(&self) -> &Self

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

impl<A: Clone + Alphabet> Clone for EncodedSequence<A>

where A::Symbol: Clone,

fn clone(&self) -> EncodedSequence<A>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<A: Debug + Alphabet> Debug for EncodedSequence<A>

where A::Symbol: Debug,

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

Formats the value using the given formatter.

impl<A: Alphabet> Default for EncodedSequence<A>

fn default() -> Self

Returns the “default value” for a type.

impl<A: Alphabet> Display for EncodedSequence<A>

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

Formats the value using the given formatter.

impl<A: Alphabet, C: PositiveLength> From<EncodedSequence<A>> for StripedSequence<A, C>

where Pipeline<A, Dispatch>: Stripe<A, C>,

fn from(encoded: EncodedSequence<A>) -> Self

Converts to this type from the input type.

impl<A: Alphabet> From<Vec<<A as Alphabet>::Symbol>> for EncodedSequence<A>

fn from(data: Vec<A::Symbol>) -> Self

Converts to this type from the input type.

impl<A: Alphabet> FromIterator<<A as Alphabet>::Symbol> for EncodedSequence<A>

fn from_iter<T>(iter: T) -> Self

where T: IntoIterator<Item = A::Symbol>,

Creates a value from an iterator.

impl<A: Alphabet> FromIterator<EncodedSequence<A>> for Result<CountMatrix<A>, InvalidData>

fn from_iter<I>(iter: I) -> Self

where I: IntoIterator<Item = EncodedSequence<A>>,

Creates a value from an iterator.

impl<A: Alphabet> FromStr for EncodedSequence<A>

type Err = InvalidSymbol

The associated error which can be returned from parsing.

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

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

impl<A: Alphabet> Index<usize> for EncodedSequence<A>

type Output = <A as Alphabet>::Symbol

The returned type after indexing.

fn index(&self, index: usize) -> &Self::Output

Performs the indexing (container[index]) operation.

impl<'a, A: Alphabet> IntoIterator for &'a EncodedSequence<A>

type Item = &'a <A as Alphabet>::Symbol

The type of the elements being iterated over.

type IntoIter = Iter<'a, <A as Alphabet>::Symbol>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl<A, S> PartialEq<S> for EncodedSequence<A>

where A: Alphabet, S: AsRef<[<A as Alphabet>::Symbol]>,

fn eq(&self, other: &S) -> 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<A: Alphabet> SymbolCount<A> for EncodedSequence<A>

fn count_symbol(&self, symbol: <A as Alphabet>::Symbol) -> usize

fn count_symbols(&self) -> GenericArray<usize, A::K>