Struct bio::alignment::pairwise::Scoring

pub struct Scoring<F: MatchFunc> {
    pub gap_open: i32,
    pub gap_extend: i32,
    pub match_fn: F,
    pub match_scores: Option<(i32, i32)>,
    pub xclip_prefix: i32,
    pub xclip_suffix: i32,
    pub yclip_prefix: i32,
    pub yclip_suffix: i32,
}

Expand description

Details of scoring are encapsulated in this structure. An affine gap score model is used so that the gap score for a length ‘k’ is: GapScore(k) = gap_open + gap_extend * k

Fields

gap_open: i32gap_extend: i32match_fn: Fmatch_scores: Option<(i32, i32)>xclip_prefix: i32xclip_suffix: i32yclip_prefix: i32yclip_suffix: i32

Implementations

impl Scoring<MatchParams>

pub fn from_scores(
    gap_open: i32,
    gap_extend: i32,
    match_score: i32,
    mismatch_score: i32
) -> Self

Create new Scoring instance with given gap open, gap extend penalties match and mismatch scores. The clip penalties are set to MIN_SCORE by default

Arguments

gap_open - the score for opening a gap (should not be positive)
gap_extend - the score for extending a gap (should not be positive)
match_score - the score for a match
mismatch_score - the score for a mismatch

impl<F: MatchFunc> Scoring<F>

pub fn new(gap_open: i32, gap_extend: i32, match_fn: F) -> Self

Create new Scoring instance with given gap open, gap extend penalties and the score function. The clip penalties are set to MIN_SCORE by default

Arguments

gap_open - the score for opening a gap (should not be positive)
gap_extend - the score for extending a gap (should not be positive)
match_fn - function that returns the score for substitutions (also see bio::scores)

pub fn xclip(self, penalty: i32) -> Self

Sets the prefix and suffix clipping penalties for x to the input value

Arguments

penalty - Clipping penalty for x (both prefix and suffix, should not be positive)

pub fn yclip(self, penalty: i32) -> Self

Sets the prefix and suffix clipping penalties for y to the input value

Arguments

penalty - Clipping penalty for y (both prefix and suffix, should not be positive)

Trait Implementations

impl<F: Clone + MatchFunc> Clone for Scoring<F>

fn clone(&self) -> Scoring<F>

Returns a copy of the value. Read more

1.0.0 · source

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

Performs copy-assignment from source. Read more

impl<F: Debug + MatchFunc> Debug for Scoring<F>

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

Formats the value using the given formatter. Read more

Auto Trait Implementations

impl<F> RefUnwindSafe for Scoring<F>where
F: RefUnwindSafe,

impl<F> Send for Scoring<F>where
F: Send,

impl<F> Sync for Scoring<F>where
F: Sync,

impl<F> Unpin for Scoring<F>where
F: Unpin,

impl<F> UnwindSafe for Scoring<F>where
F: UnwindSafe,

Blanket Implementations

impl<T> Any for Twhere
T: 'static + ?Sized,

fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

impl<T> Borrow<T> for Twhere
T: ?Sized,

const: unstable · source

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

impl<T> BorrowMut<T> for Twhere
T: ?Sized,

const: unstable · source

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

impl<T> From<T> for T

const: unstable · source

fn from(t: T) -> T

Returns the argument unchanged.

impl<T, U> Into<U> for Twhere
U: From<T>,

const: unstable · source

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

impl<T> ToOwned for Twhere
T: Clone,

type Owned = T

The resulting type after obtaining ownership.

fn to_owned(&self) -> T

Creates owned data from borrowed data, usually by cloning. Read more

fn clone_into(&self, target: &mut T)

Uses borrowed data to replace owned data, usually by cloning. Read more

impl<T, U> TryFrom<U> for Twhere
U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

Performs the conversion.

impl<T, U> TryInto<U> for Twhere
U: TryFrom<T>,

type Error = <U as TryFrom<T>>::Error

The type returned in the event of a conversion error.

const: unstable · source

fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

Performs the conversion.