Struct bio::stats::pairhmm::PairHMM[−][src]

pub struct PairHMM { /* fields omitted */ }

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`[src]

`pub fn new<G>(gap_params: &G) -> Self where G: GapParameters,` [src]

`pub fn prob_related<E, A>( &mut self, emission_params: &E, alignment_mode: &A, max_edit_dist: Option<usize> ) -> LogProb where E: EmissionParameters, A: StartEndGapParameters,` [src]

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 Clone for PairHMM`[src]

`fn clone(&self) -> PairHMM`[src]

`pub fn clone_from(&mut self, source: &Self)`1.0.0 [src]

`impl Debug for PairHMM`[src]

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

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 T where T: 'static + ?Sized,` [src]

`pub fn type_id(&self) -> TypeId`[src]

`impl<T> Borrow<T> for T where T: ?Sized,` [src]

`pub fn borrow(&self) -> &T`[src]

`impl<T> BorrowMut<T> for T where T: ?Sized,` [src]

`pub fn borrow_mut(&mut self) -> &mut T`[src]

`impl<T> From<T> for T`[src]

`pub fn from(t: T) -> T`[src]

`impl<T, U> Into for T where U: From<T>,` [src]

`pub fn into(self) -> U`[src]

`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>`

`pub fn is_in_subset(&self) -> bool`

`pub unsafe fn to_subset_unchecked(&self) -> SS`

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

`impl<T> ToOwned for T where T: Clone,` [src]

`type Owned = T`

The resulting type after obtaining ownership.

`pub fn to_owned(&self) -> T`[src]

`pub fn clone_into(&self, target: &mut T)`[src]

`impl<T, U> TryFrom for T where U: Into<T>,` [src]

`type Error = Infallible`

The type returned in the event of a conversion error.

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

`impl<T, U> TryInto for T where U: TryFrom<T>,` [src]

`type Error = >::Error`

The type returned in the event of a conversion error.

`pub fn try_into(self) -> Result<U, >::Error>`[src]

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

`pub fn vzip(self) -> V`

Struct bio::stats::pairhmm::PairHMM⎘[−][src]

Implementations

impl PairHMM[src]

pub fn new<G>(gap_params: &G) -> Self where G: GapParameters, [src]

pub fn prob_related<E, A>( &mut self, emission_params: &E, alignment_mode: &A, max_edit_dist: Option<usize>) -> LogProb where E: EmissionParameters, A: StartEndGapParameters, [src]

Arguments

Trait Implementations

impl Clone for PairHMM[src]

fn clone(&self) -> PairHMM[src]

pub fn clone_from(&mut self, source: &Self)1.0.0[src]

impl Debug for PairHMM[src]

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

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 T where T: 'static + ?Sized, [src]

pub fn type_id(&self) -> TypeId[src]

impl<T> Borrow<T> for T where T: ?Sized, [src]

pub fn borrow(&self) -> &T[src]

impl<T> BorrowMut<T> for T where T: ?Sized, [src]

pub fn borrow_mut(&mut self) -> &mut T[src]

impl<T> From<T> for T[src]

pub fn from(t: T) -> T[src]

impl<T, U> Into<U> for T where U: From<T>, [src]

pub fn into(self) -> U[src]

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 unsafe fn to_subset_unchecked(&self) -> SS

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

impl<T> ToOwned for T where T: Clone, [src]

type Owned = T

pub fn to_owned(&self) -> T[src]

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

impl<T, U> TryFrom<U> for T where U: Into<T>, [src]

type Error = Infallible

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

impl<T, U> TryInto<U> for T where U: TryFrom<T>, [src]

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

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

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

pub fn vzip(self) -> V