Struct StripedSequence

pub struct StripedSequence<A: Alphabet, C: PositiveLength = DefaultColumns> { /* private fields */ }

An encoded sequence stored in a striped matrix with a fixed column count.

Implementations

impl<A: Alphabet, C: PositiveLength> StripedSequence<A, C>

pub fn new( data: DenseMatrix<A::Symbol, C>, length: usize, ) -> Result<Self, InvalidData>

Create a new striped sequence from the given dense matrix.

Errors

Returns InvalidData when the DenseMatrix given as input stores less symbols than the given length.

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

Get the length of the sequence.

pub fn is_empty(&self) -> bool

Check whether the sequence is empty.

pub fn wrap(&self) -> usize

Get the number of wrapping rows in the striped matrix.

pub fn matrix(&self) -> &DenseMatrix<A::Symbol, C>

Get an immutable reference over the underlying matrix storing the sequence.

pub fn into_matrix(self) -> DenseMatrix<A::Symbol, C>

Extract the underlying matrix where the striped sequence is stored.

pub fn configure(&mut self, motif: &ScoringMatrix<A>)

Reconfigure the striped sequence for searching with a motif.

pub fn configure_wrap(&mut self, m: usize)

Add wrap-around rows for a motif of length m.

Trait Implementations

impl<A: Alphabet, C: PositiveLength> AsRef<DenseMatrix<<A as Alphabet>::Symbol, C>> for StripedSequence<A, C>

fn as_ref(&self) -> &DenseMatrix<A::Symbol, C>

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

impl<A: Alphabet, C: PositiveLength> AsRef<StripedSequence<A, C>> for StripedSequence<A, C>

fn as_ref(&self) -> &Self

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

impl<A: Clone + Alphabet, C: Clone + PositiveLength> Clone for StripedSequence<A, C>

where A::Symbol: Clone,

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

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<A: Alphabet, C: PositiveLength> Debug for StripedSequence<A, C>

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

Formats the value using the given formatter.

impl<A: Alphabet, C: PositiveLength> Default for StripedSequence<A, C>

fn default() -> Self

Returns the “default value” for a type.

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, C: PositiveLength> From<StripedSequence<A, C>> for DenseMatrix<A::Symbol, C>

fn from(striped: StripedSequence<A, C>) -> Self

Converts to this type from the input type.

impl<A: Alphabet, C: PositiveLength> Index<usize> for StripedSequence<A, C>

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: Alphabet, C: PositiveLength> SymbolCount<A> for StripedSequence<A, C>

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

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