Struct AAProfile 

pub struct AAProfile { /* private fields */ }

Amino acid position specific scoring matrix.

Supports characters A to Z. Lowercase characters are uppercased.

Trait Implementations

impl Clone for AAProfile

fn clone(&self) -> AAProfile

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AAProfile

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

Formats the value using the given formatter.

impl PartialEq for AAProfile

fn eq(&self, other: &AAProfile) -> 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 Profile for AAProfile

const NULL: u8

Byte to use as padding.

fn new(str_len: usize, block_size: usize, gap_extend: i8) -> Self

Create a new profile of a specific length, with default (large negative) values.

fn from_bytes( b: &[u8], block_size: usize, match_score: i8, mismatch_score: i8, gap_open_C: i8, gap_close_C: i8, gap_open_R: i8, gap_extend: i8, ) -> Self

Create a new profile from a byte string.

fn len(&self) -> usize

Get the length of the profile.

fn clear(&mut self, str_len: usize, block_size: usize)

Clear the profile so it can be reused for profile lengths less than or equal to the length this struct was created with.

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

Set the score for a position and byte.

fn set_all( &mut self, order: &[u8], scores: &[i8], left_shift: usize, right_shift: usize, )

Set the scores for all positions in the position specific scoring matrix.

fn set_all_rev( &mut self, order: &[u8], scores: &[i8], left_shift: usize, right_shift: usize, )

Set the scores for all positions in reverse in the position specific scoring matrix.

fn set_gap_open_C(&mut self, i: usize, gap: i8)

Set the gap open cost for a column.

fn set_gap_close_C(&mut self, i: usize, gap: i8)

Set the gap close cost for a column.

fn set_gap_open_R(&mut self, i: usize, gap: i8)

Set the gap open cost for a row.

fn set_all_gap_open_C(&mut self, gap: i8)

Set the gap open cost for all column transitions.

fn set_all_gap_close_C(&mut self, gap: i8)

Set the gap close cost for all column transitions.

fn set_all_gap_open_R(&mut self, gap: i8)

Set the gap open cost for all row transitions.

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

Get the score for a position and byte.

fn get_gap_extend(&self) -> i8

Get the gap extend cost.

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

Get the pointer for a specific index.

fn as_ptr_aa(&self, a: usize) -> *const i16

Get the pointer for a specific amino acid.

unsafe fn get_scores_pos(&self, i: usize, v: HalfSimd, _right: bool) -> Simd

Get the scores for a certain SIMD vector of bytes at a specific position in the profile.

unsafe fn get_scores_aa(&self, i: usize, c: u8, _right: bool) -> Simd

Get the scores for a certain byte starting at a specific position in the profile.

unsafe fn get_gap_open_right_C(&self, i: usize) -> Simd

Get the gap open cost for a column.

unsafe fn get_gap_close_right_C(&self, i: usize) -> Simd

Get the gap close cost for a column.

unsafe fn get_gap_open_right_R(&self, i: usize) -> Simd

Get the gap open cost for a row.

unsafe fn get_gap_open_down_C(&self, i: usize) -> Simd

Get the gap open cost for a column.

unsafe fn get_gap_close_down_C(&self, i: usize) -> Simd

Get the gap close cost for a column.

unsafe fn get_gap_open_down_R(&self, i: usize) -> Simd

Get the gap open cost for a row.

fn convert_char(c: u8) -> u8

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

impl StructuralPartialEq for AAProfile