Struct SparseDistanceMatrix 

pub struct SparseDistanceMatrix<'a> {
    pub n_distances: usize,
    pub knn: usize,
    /* private fields */
}

A sparse distance matrix with a maximum of knn distances for each sample.

In self-query mode (one database), query_names is None and ref_names is used for both row iteration and column index lookup.

In cross-query mode (two databases), query_names holds the query genome names (one per row) and ref_names holds the reference genome names (indexed by the stored neighbour index inside each distance item).

Fields

n_distances: usize

Total number of distances

knn: usize

Maximum number of distances kept per sample: k smallest distances

Implementations

impl<'a> SparseDistanceMatrix<'a>

pub fn new(ref_sketches: &'a MultiSketch, knn: usize, jaccard: DistType) -> Self

Self-query constructor: one database, rows and columns are the same set.

pub fn new_cross_query( ref_sketches: &'a MultiSketch, query_sketches: &'a MultiSketch, knn: usize, jaccard: DistType, ) -> Self

Cross-query constructor: two databases. Rows are query genomes; column indices index into the reference genome list.

pub fn dists_as_ref(&self) -> &DistVec

Reference/borrow of underlying distance storage

pub fn dists_mut(&mut self) -> &mut DistVec

Mutable reference to the underlying distance storage

Trait Implementations

impl Display for SparseDistanceMatrix<'_>

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

Formats the value using the given formatter.

impl<'a> Distances<'a> for SparseDistanceMatrix<'a>

fn jaccard(&self) -> &DistType

Distance type

fn n_samples(&self) -> (usize, Option<usize>)

The number of reference and query (if set) samples

fn shape(&self) -> (usize, usize)

The (rows, columns) of the underlying data (C-order/row-major)

fn ani(&self) -> bool

Whether calculating ANI

fn k_vals(&self) -> Option<(usize, f64)>

If calcualting Jaccard distances, the index of the k-mer, and the k-mer as a float

fn n_dist_cols(&self) -> usize

Number of distance columns in the output

fn sketch_names(sketches: &'a MultiSketch) -> Vec<&'a str>

Names of the sketch files in the distance matrix