Struct Pssm 

pub struct Pssm<const N: usize> { /* private fields */ }

A Position-Specific Scoring Matrix (PSSM) with a fixed alphabet size.

Scores are stored as log-odds ratios relative to background frequencies.

Implementations

impl<const N: usize> Pssm<N>

pub fn from_counts( counts: &[[f64; N]], pseudocount: f64, background: [f64; N], ) -> Result<Self>

Build a PSSM from a count matrix.

Each row of counts represents one position; each column is a symbol. A pseudocount is added to every cell before converting to frequencies. Scores are computed as ln(freq / background).

Errors

Returns an error if counts is empty or any background entry is zero.

pub fn len(&self) -> usize

Number of positions in the motif.

pub fn is_empty(&self) -> bool

Returns true if the PSSM has zero positions.

pub fn score( &self, seq: &[u8], mapping: &dyn Fn(u8) -> Option<usize>, ) -> Result<f64>

Score a sequence window against this PSSM.

seq must be exactly [self.len()] bytes. The mapping function converts each byte to an alphabet index in 0..N.

Errors

Returns an error if seq.len() != self.len() or if mapping returns None for any byte.

pub fn scan( &self, seq: &[u8], threshold: f64, mapping: &dyn Fn(u8) -> Option<usize>, ) -> Vec<(usize, f64)>

Slide the PSSM across seq and return all hits at or above threshold.

Returns (position, score) pairs. Positions with unmapped characters are silently skipped.

pub fn information_content(&self) -> Vec<f64>

Information content (bits) at each position.

IC_j = sum_c freq_c * log2(freq_c / bg_c) where frequencies are recovered from the stored log-odds scores.

pub fn max_score(&self) -> f64

Maximum possible score (sum of the best symbol at each position).

pub fn min_score(&self) -> f64

Minimum possible score (sum of the worst symbol at each position).

Trait Implementations

impl<const N: usize> Clone for Pssm<N>

fn clone(&self) -> Pssm<N>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<const N: usize> Debug for Pssm<N>

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

Formats the value using the given formatter.