Struct bio::alignment::pairwise::Scoring

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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

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impl Scoring<MatchParams>

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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

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impl<F: MatchFunc> Scoring<F>

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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 (see also bio::alignment::pairwise::Scoring)

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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)

use bio::alignment::pairwise::{Scoring, MIN_SCORE};
let scoring = Scoring::from_scores(0, -2, 1, -2).xclip(-5);
assert!(scoring.xclip_prefix == -5);
assert!(scoring.yclip_prefix == MIN_SCORE);
assert!(scoring.xclip_suffix == -5);
assert!(scoring.yclip_suffix == MIN_SCORE);

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

Sets the prefix clipping penalty for x to the input value

Arguments

penalty - Prefix clipping penalty for x (should not be positive)

Example

use bio::alignment::pairwise::{Scoring, MIN_SCORE};
let scoring = Scoring::from_scores(0, -2, 1, -2).xclip_prefix(-5);
assert!(scoring.xclip_prefix == -5);
assert!(scoring.yclip_prefix == MIN_SCORE);
assert!(scoring.xclip_suffix == MIN_SCORE);
assert!(scoring.yclip_suffix == MIN_SCORE);

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

Sets the suffix clipping penalty for x to the input value

Arguments

penalty - Suffix clipping penalty for x (should not be positive)

use bio::alignment::pairwise::{Scoring, MIN_SCORE};
let scoring = Scoring::from_scores(0, -2, 1, -2).xclip_suffix(-5);
assert!(scoring.xclip_prefix == MIN_SCORE);
assert!(scoring.yclip_prefix == MIN_SCORE);
assert!(scoring.xclip_suffix == -5);
assert!(scoring.yclip_suffix == MIN_SCORE);

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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)

use bio::alignment::pairwise::{Scoring, MIN_SCORE};
let scoring = Scoring::from_scores(0, -2, 1, -2).yclip(-5);
assert!(scoring.xclip_prefix == MIN_SCORE);
assert!(scoring.yclip_prefix == -5);
assert!(scoring.xclip_suffix == MIN_SCORE);
assert!(scoring.yclip_suffix == -5);

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

Sets the prefix clipping penalty for y to the input value

Arguments

penalty - Prefix clipping penalty for y (should not be positive)

use bio::alignment::pairwise::{Scoring, MIN_SCORE};
let scoring = Scoring::from_scores(0, -2, 1, -2).yclip_prefix(-5);
assert!(scoring.xclip_prefix == MIN_SCORE);
assert!(scoring.yclip_prefix == -5);
assert!(scoring.xclip_suffix == MIN_SCORE);
assert!(scoring.yclip_suffix == MIN_SCORE);

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

Sets the suffix clipping penalty for y to the input value

Arguments

penalty - Suffix clipping penalty for y (should not be positive)

use bio::alignment::pairwise::{Scoring, MIN_SCORE};
let scoring = Scoring::from_scores(0, -2, 1, -2).yclip_suffix(-5);
assert!(scoring.xclip_prefix == MIN_SCORE);
assert!(scoring.yclip_prefix == MIN_SCORE);
assert!(scoring.xclip_suffix == MIN_SCORE);
assert!(scoring.yclip_suffix == -5);

Trait Implementations

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

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

Returns a copy of the value. Read more

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

Performs copy-assignment from source. Read more

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

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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,

pub fn into(self) -> U

Performs the conversion.

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impl<T> Same<T> for T

type Output = T

Should always be Self

impl<SS, SP> SupersetOf<SS> for SP where
SS: SubsetOf<SP>,

pub fn to_subset(&self) -> Option<SS>

The inverse inclusion map: attempts to construct self from the equivalent element of its superset. Read more

pub fn is_in_subset(&self) -> bool

Checks if self is actually part of its subset T (and can be converted to it).

pub fn to_subset_unchecked(&self) -> SS

Use with care! Same as self.to_subset but without any property checks. Always succeeds.

pub fn from_subset(element: &SS) -> SP

The inclusion map: converts self to the equivalent element of its superset.

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impl<T> ToOwned for T where
T: Clone,

type Owned = T

The resulting type after obtaining ownership.

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pub fn to_owned(&self) -> T

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

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

🔬 This is a nightly-only experimental API. (toowned_clone_into)

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

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

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

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

Performs the conversion.

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

type Error = >::Error

The type returned in the event of a conversion error.

const: unstable · source

pub fn try_into(self) -> Result<U, >::Error>

Performs the conversion.

Struct bio::alignment::pairwise::Scoring

Fields

Implementations

impl Scoring<MatchParams>

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

impl<F: MatchFunc> Scoring<F>

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

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

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

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

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

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

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

Trait Implementations

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

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

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

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

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

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 T where T: 'static + ?Sized,

pub fn type_id(&self) -> TypeId

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

pub fn borrow(&self) -> &T

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

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

impl<T> From<T> for T

pub fn from(t: T) -> T

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

pub fn into(self) -> U

impl<T> Same<T> for T

type Output = T

impl<SS, SP> SupersetOf<SS> for SP where SS: SubsetOf<SP>,

pub fn to_subset(&self) -> Option<SS>

pub fn is_in_subset(&self) -> bool

pub fn to_subset_unchecked(&self) -> SS

pub fn from_subset(element: &SS) -> SP

impl<T> ToOwned for T where T: Clone,

type Owned = T

pub fn to_owned(&self) -> T

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

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

type Error = Infallible

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

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

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

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

impl<V, T> VZip<V> for T where V: MultiLane<T>,

pub fn vzip(self) -> V

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

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,

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

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

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

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

impl<SS, SP> SupersetOf<SS> for SP where
SS: SubsetOf<SP>,

impl<T> ToOwned for T where
T: Clone,

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

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

impl<V, T> VZip<V> for T where
V: MultiLane<T>,