Struct KmerClassifier 

pub struct KmerClassifier { /* private fields */ }

K-mer based taxonomic classifier (Kraken-style).

Maps k-mer hashes to sets of taxon ids. Classification of a query sequence takes the LCA of all k-mer hits.

Implementations

impl KmerClassifier

pub fn new(taxonomy: TaxonomyTree, k: usize) -> Self

Create a new classifier with the given taxonomy and k-mer size.

pub fn add_reference(&mut self, sequence: &[u8], taxon_id: usize)

Index a reference sequence under the given taxon id.

Extracts all k-mers, hashes them, and associates them with taxon_id.

pub fn classify(&self, sequence: &[u8]) -> Option<usize>

Classify a query sequence by k-mer matching.

For each k-mer in the query, looks up matching taxa. Returns the LCA of all matched taxa, preferring deeper (more specific) assignments. Returns None if no k-mers match.

Trait Implementations

impl Clone for KmerClassifier

fn clone(&self) -> KmerClassifier

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for KmerClassifier

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

Formats the value using the given formatter.