Struct bio::stats::pairhmm::PairHMM

pub struct PairHMM { /* private fields */ }

Expand description

A pair Hidden Markov Model for comparing sequences x and y as described by Durbin, R., Eddy, S., Krogh, A., & Mitchison, G. (1998). Biological Sequence Analysis. Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.

Implementations

impl PairHMM

pub fn new() -> Self

pub fn prob_related<G, E>(
    &mut self,
    gap_params: &G,
    emission_params: &E,
    max_edit_dist: Option<usize>
) -> LogProbwhere
    G: GapParameters + StartEndGapParameters,
    E: EmissionParameters,

Calculate the probability of sequence x being related to y via any alignment.

Arguments

gap_params - parameters for opening or extending gaps
emission_params - parameters for emission
max_edit_dist - maximum edit distance to consider; if not None, perform banded alignment

Trait Implementations

impl Default for PairHMM

fn default() -> Self

Returns the “default value” for a type. Read more

Auto Trait Implementations

impl RefUnwindSafe for PairHMM

impl Send for PairHMM

impl Sync for PairHMM

impl Unpin for PairHMM

impl UnwindSafe for PairHMM

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, 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.