Struct SequenceEncoder 

pub struct SequenceEncoder { /* private fields */ }

A struct for encoding biological sequences into a compact, bit-packed format.

The SequenceEncoder is designed to efficiently encode sequences using a specified alphabet type (e.g., DNA, protein, or ASCII). It uses a bit buffer to pack symbols into bytes, minimizing memory usage while maintaining fast encoding performance.

Fields

• encoding_array - A lookup table that maps input bytes to their encoded values.
• bits_per_symbol - The number of bits used to represent each symbol in the sequence.
• encoded_sequence - A vector that stores the resulting bit-packed sequence.
• bit_pos - The current bit position in the encoded sequence.
• buffer - An internal bit buffer used for packing symbols into bytes.
• buffer_bits - The number of bits currently stored in the buffer.

Usage

1. Create a new SequenceEncoder using the new method.
2. Add sequence chunks with the update method.
3. Call the finalize method to retrieve the encoded sequence as a Vec<u8>.

Implementations

impl SequenceEncoder

pub fn new(alphabet_type: AlphabetType, length: usize) -> Self

pub fn update(&mut self, sequence: &[u8])

pub fn finalize(self) -> Vec<u8>