Struct NamedMatrix

pub struct NamedMatrix { /* private fields */ }

A named matrix for storing pairwise distances/scores with sequence names

Examples

let names = vec!["seq1".to_string(), "seq2".to_string(), "seq3".to_string()];
let mut matrix = NamedMatrix::new(names);

// Set some values
matrix.set(0, 1, 0.5);
matrix.set(0, 2, 0.7);
matrix.set(1, 2, 0.3);

// Get values
assert_eq!(matrix.size(), 3);
assert_eq!(matrix.get(0, 1), 0.5);
assert_eq!(matrix.get(1, 0), 0.5);  // Symmetric matrix

Implementations

impl NamedMatrix

pub fn new(names: Vec<String>) -> Self

pub fn size(&self) -> usize

pub fn get(&self, row: usize, col: usize) -> f32

pub fn set(&mut self, row: usize, col: usize, value: f32)

pub fn get_names(&self) -> Vec<&String>

pub fn get_by_name(&self, name1: &str, name2: &str) -> Option<f32>

Get matrix value by sequence names

let names = vec!["seq1".to_string(), "seq2".to_string()];
let mut matrix = NamedMatrix::new(names);
matrix.set(0, 1, 0.5);

assert_eq!(matrix.get_by_name("seq1", "seq2"), Some(0.5));
assert_eq!(matrix.get_by_name("seq1", "seq3"), None);  // Non-existent name

pub fn set_by_name( &mut self, name1: &str, name2: &str, value: f32, ) -> Result<(), String>

Set matrix value by sequence names

let names = vec!["seq1".to_string(), "seq2".to_string()];
let mut matrix = NamedMatrix::new(names);

assert!(matrix.set_by_name("seq1", "seq2", 0.5).is_ok());
assert_eq!(matrix.get_by_name("seq1", "seq2"), Some(0.5));
assert!(matrix.set_by_name("seq1", "seq3", 0.5).is_err());  // Non-existent name

pub fn from_pair_scores(infile: &str, same: f32, missing: f32) -> Self

pub fn from_relaxed_phylip(infile: &str) -> Self

Creates a new matrix from a relaxed PHYLIP format file

let matrix = NamedMatrix::from_relaxed_phylip("input.phy");

Trait Implementations

impl Debug for NamedMatrix

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

Formats the value using the given formatter.