Struct AAMatrix 

pub struct AAMatrix { /* private fields */ }

Amino acid scoring matrix.

Supports characters A to Z. Lowercase characters are uppercased.

Implementations

impl AAMatrix

pub const fn new_simple(match_score: i8, mismatch_score: i8) -> Self

Create a simple matrix with a certain match and mismatch score.

pub fn from_tsv(tsv: &str, aa_order: &str) -> Self

Create an AAMatrix from a tab-separated table with no headers.

Use aa_order to pass in the amino acids in order.

Trait Implementations

impl Clone for AAMatrix

fn clone(&self) -> AAMatrix

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AAMatrix

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

Formats the value using the given formatter.

impl Matrix for AAMatrix

const NULL: u8 = 91u8

Byte to use as padding.

fn new() -> Self

Create a new matrix with default (usually nonsense) values.

fn set(&mut self, a: u8, b: u8, score: i8)

Set the score for a pair of bytes.

fn get(&self, a: u8, b: u8) -> i8

Get the score for a pair of bytes.

fn as_ptr(&self, i: usize) -> *const i8

Get the pointer for a specific index.

unsafe fn get_scores(&self, c: u8, v: HalfSimd, _right: bool) -> Simd

Get the scores for a certain byte and a certain SIMD vector of bytes.

fn convert_char(c: u8) -> u8

Convert a byte to a better storage format that makes retrieving scores easier.

impl PartialEq for AAMatrix

fn eq(&self, other: &AAMatrix) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl StructuralPartialEq for AAMatrix