Struct RectangularBinaryMatrix 

pub struct RectangularBinaryMatrix { /* private fields */ }

A rectangular binary matrix over GF(2), used by Jellyfish for hash position computation.

The matrix has dimensions rows × cols where rows ≤ 64. It is stored in column-major format: each column is a single u64 word. Matrix-vector multiplication is done using XOR operations.

This is used to compute the expected position of a k-mer in the binary/sorted file format, enabling efficient binary search for random access queries.

Implementations

impl RectangularBinaryMatrix

pub fn new(rows: usize, cols: usize, columns: Vec<u64>) -> Result<Self>

Create a new matrix with the given dimensions and column data.

pub fn identity(size: usize) -> Self

Create an identity matrix.

pub fn from_json(value: &Value) -> Result<Self>

Parse a matrix from the JSON header representation.

In the Jellyfish header, a matrix is stored as an array of integers representing the column values, preceded by dimension information.

pub fn rows(&self) -> usize

Number of rows.

pub fn cols(&self) -> usize

Number of columns.

pub fn is_identity(&self) -> bool

Whether this is an identity matrix.

pub fn times(&self, vector: &[u64]) -> u64

Multiply this matrix by a vector (given as packed u64 words).

The vector represents the k-mer’s packed bits. The result is a u64 hash position value.

Trait Implementations

impl Clone for RectangularBinaryMatrix

fn clone(&self) -> RectangularBinaryMatrix

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for RectangularBinaryMatrix

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

Formats the value using the given formatter.