Struct lightmotif::pwm::CountMatrix

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

A matrix storing symbol occurrences at each position.

Implementations

impl<A: Alphabet> CountMatrix<A>

pub fn new(data: DenseMatrix<u32, A::K>) -> Result<Self, InvalidData>

Create a new count matrix from the given data.

The matrix must contain count data, for sequences of the same length, i.e. rows should all sum to the same value.

pub fn from_sequences<'seq, I>(sequences: I) -> Result<Self, InvalidData>

where I: IntoIterator, <I as IntoIterator>::Item: AsRef<EncodedSequence<A>>,

Create a new count matrix from the given sequences.

pub fn to_freq<P>(&self, pseudo: P) -> FrequencyMatrix<A>

where P: Into<Pseudocounts<A>>,

Build a probability matrix from this count matrix using pseudo-counts.

pub fn counts(&self) -> &DenseMatrix<u32, A::K>

The raw counts from the count matrix.

impl<A: ComplementableAlphabet> CountMatrix<A>

pub fn reverse_complement(&self) -> Self

Get the reverse-complement of this count matrix.

Trait Implementations

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

fn as_ref(&self) -> &Self

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

impl<A: Alphabet> AsRef<DenseMatrix<u32, <A as Alphabet>::K>> for CountMatrix<A>

fn as_ref(&self) -> &DenseMatrix<u32, A::K>

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

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

where A::K: Clone,

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

Returns a copy of the value.

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

Performs copy-assignment from source.

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

where A::K: Debug,

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

Formats the value using the given formatter.

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

type Output = <DenseMatrix<u32, <A as Alphabet>::K> as Index<usize>>::Output

The returned type after indexing.

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

Performs the indexing (container[index]) operation.

impl<A: PartialEq + Alphabet> PartialEq for CountMatrix<A>

where A::K: PartialEq,

fn eq(&self, other: &CountMatrix<A>) -> 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<A: Eq + Alphabet> Eq for CountMatrix<A>

where A::K: Eq,

impl<A: Alphabet> StructuralEq for CountMatrix<A>

impl<A: Alphabet> StructuralPartialEq for CountMatrix<A>