Struct Encoder 

pub struct Encoder<const K: usize>
where
    Kmer<K>: KmerBits,
{ /* private fields */ }

Encoder for building SPSS from DNA sequences

Accumulates sequences, encodes them to 2-bit format, tracks offsets, and builds the final SPSS structure.

IMPORTANT: Bases are packed contiguously across sequences without byte-boundary padding. This means base_idx / 4 always gives the correct byte and (base_idx % 4) * 2 gives the correct bit offset within that byte.

Implementations

impl<const K: usize> Encoder<K>

where Kmer<K>: KmerBits,

pub fn new() -> Self

Create a new encoder

pub fn add_sequence(&mut self, sequence: &[u8]) -> Result<()>

Add a DNA sequence to the encoder

Bases are packed contiguously into the byte buffer without padding between sequences, so decode_kmer can use simple base_idx/4 arithmetic.

Arguments

• sequence - DNA sequence (A, C, G, T only)

Errors

Returns error if sequence contains invalid characters or is too short

pub fn num_kmers(&self) -> u64

Get the current number of k-mers

pub fn num_strings(&self) -> u64

Get the current number of strings

pub fn build(self, m: usize) -> SpectrumPreservingStringSet

Build the final SpectrumPreservingStringSet

Consumes the encoder and returns the SPSS.

Trait Implementations

impl<const K: usize> Default for Encoder<K>

where Kmer<K>: KmerBits,

fn default() -> Self

Returns the “default value” for a type.