Struct SharedProfiles 

pub struct SharedProfiles<'a, const M: usize, const N: usize, const O: usize, const S: usize> { /* private fields */ }

A lazily-evaluated set of striped alignment profiles which can be shared across threads.

This is an abstraction around StripedProfile, providing convenience methods for automatically increasing the integer width and rerunning the alignment when overflow occurs. This only supports the unsigned version of the algorithm.

When sharing between threads is not needed, consider using LocalProfiles instead.

Parameters

• 'a: The lifetime of the stored sequence, the WeightMatrix, and the alphabet (ByteIndexMap). An owned sequence can also be stored.
• M: The number of SIMD lanes for i8 profiles
• N: The number of SIMD lanes for i16 profiles
• O: The number of SIMD lanes for i32 profiles
• S: The size of the alphabet (usually 5 for DNA including N)

Implementations

impl<'a, const M: usize, const N: usize, const O: usize, const S: usize> SharedProfiles<'a, M, N, O, S>

pub fn new( seq: impl Into<Cow<'a, [u8]>>, matrix: &'a WeightMatrix<'a, i8, S>, gap_open: i8, gap_extend: i8, ) -> Result<Self, ProfileError>

Creates an empty SharedProfiles.

Usually you instead want to use new_with_w128, new_with_w256, or new_with_w512, based on the SIMD register width of your target. See Picking the Register Width for more details.

Errors

• ProfileError::EmptySequence if seq is empty
• ProfileError::GapOpenOutOfRange if gap_open is not between -127 and 0, inclusive
• ProfileError::GapExtendOutOfRange if gap_extend is not between -127 and 0, inclusive
• ProfileError::BadGapWeights if gap_extend is less than gap_open

impl<'a, const S: usize> SharedProfiles<'a, 16, 8, 4, S>

pub fn new_with_w128( seq: impl Into<Cow<'a, [u8]>>, matrix: &'a WeightMatrix<'_, i8, S>, gap_open: i8, gap_extend: i8, ) -> Result<SharedProfiles<'a, 16, 8, 4, S>, ProfileError>

Creates an empty SharedProfiles optimized for 128-bit SIMD width.

This sets M=16, N=8, and O=4 for i8, i16, and i32 profiles respectively.

Errors

Same as SharedProfiles::new.

impl<'a, const S: usize> SharedProfiles<'a, 32, 16, 8, S>

pub fn new_with_w256( seq: impl Into<Cow<'a, [u8]>>, matrix: &'a WeightMatrix<'_, i8, S>, gap_open: i8, gap_extend: i8, ) -> Result<SharedProfiles<'a, 32, 16, 8, S>, ProfileError>

Creates an empty SharedProfiles optimized for 256-bit SIMD width.

This sets M=32, N=16, and O=8 for i8, i16, and i32 profiles respectively.

Errors

Same as SharedProfiles::new.

impl<'a, const S: usize> SharedProfiles<'a, 64, 32, 16, S>

pub fn new_with_w512( seq: impl Into<Cow<'a, [u8]>>, matrix: &'a WeightMatrix<'_, i8, S>, gap_open: i8, gap_extend: i8, ) -> Result<SharedProfiles<'a, 64, 32, 16, S>, ProfileError>

Creates an empty SharedProfiles optimized for 512-bit SIMD width.

This sets M=64, N=32, and O=16 for i8, i16, and i32 profiles respectively.

Errors

Same as SharedProfiles::new.

Trait Implementations

impl<'a, const M: usize, const N: usize, const O: usize, const S: usize> Clone for SharedProfiles<'a, M, N, O, S>

fn clone(&self) -> SharedProfiles<'a, M, N, O, S>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<'a, const M: usize, const N: usize, const O: usize, const S: usize> Debug for SharedProfiles<'a, M, N, O, S>

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

Formats the value using the given formatter.

impl<const M: usize, const N: usize, const O: usize, const S: usize> Eq for SharedProfiles<'_, M, N, O, S>

impl<const M: usize, const N: usize, const O: usize, const S: usize> Hash for SharedProfiles<'_, M, N, O, S>

fn hash<H: Hasher>(&self, state: &mut H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl<const M: usize, const N: usize, const O: usize, const S: usize> PartialEq for SharedProfiles<'_, M, N, O, S>

fn eq(&self, other: &Self) -> bool

Equality operator ==.

fn ne(&self, other: &Rhs) -> bool

Inequality operator !=.

impl<'a, const M: usize, const N: usize, const O: usize, const S: usize> ProfileSets<'a, M, N, O, S> for SharedProfiles<'a, M, N, O, S>

fn get_i8(&self) -> &StripedProfile<'a, i8, M, S>

Gets or initializes StripedProfile with elements of i8 and M SIMD lanes and returns a reference to the field.

fn get_i16(&self) -> &StripedProfile<'a, i16, N, S>

Gets or initializes StripedProfile with elements of i16 and N SIMD lanes and returns a reference to the field.

fn get_i32(&self) -> &StripedProfile<'a, i32, O, S>

Gets or initializes StripedProfile with elements of i32 and O SIMD lanes and returns a reference to the field.

fn sequence(&self) -> &[u8]

Retrieves the sequence from which the profiles are built.

fn gap_open(&self) -> i8

Retrieves the gap open score being used.

fn gap_extend(&self) -> i8

Retrieves the gap extend score being used.

fn matrix(&self) -> &WeightMatrix<'a, i8, S>

Retrieves the weight matrix being used.

fn sw_score_from_i8<T>(&self, seq: &T) -> MaybeAligned<u32>

where T: AsRef<[u8]> + ?Sized,

Lazily execute StripedProfile::sw_score starting with the i8 profile.

fn sw_score_from_i16<T>(&self, seq: &T) -> MaybeAligned<u32>

where T: AsRef<[u8]> + ?Sized,

Lazily execute StripedProfile::sw_score starting with the i16 profile, skipping the i8 profile.

fn sw_score_from_i32<T>(&self, seq: &T) -> MaybeAligned<u32>

where T: AsRef<[u8]> + ?Sized,

Execute StripedProfile::sw_score with the i32 profile, skipping the i8 and i16 profiles.

fn sw_align_from_i8<T>(&self, seq: SeqSrc<&T>) -> MaybeAligned<Alignment<u32>>

where T: AsRef<[u8]> + ?Sized,

Lazily execute StripedProfile::sw_align starting with the i8 profile.

fn sw_align_from_i16<T>(&self, seq: SeqSrc<&T>) -> MaybeAligned<Alignment<u32>>

where T: AsRef<[u8]> + ?Sized,

Lazily execute StripedProfile::sw_align starting with the i16 profile, skipping the i8 profile.

fn sw_align_from_i32<T>(&self, seq: SeqSrc<&T>) -> MaybeAligned<Alignment<u32>>

where T: AsRef<[u8]> + ?Sized,

Execute StripedProfile::sw_align with the i32 profile, skipping the i8 and i16 profiles.

fn sw_align_from_i8_3pass<T>( &self, seq: SeqSrc<&T>, ) -> MaybeAligned<Alignment<u32>>

where T: AsRef<[u8]> + ?Sized,

Lazily executes a 3-pass version of Smith-Waterman local alignment, starting with an i8 profile.

fn sw_align_from_i16_3pass<T>( &self, seq: SeqSrc<&T>, ) -> MaybeAligned<Alignment<u32>>

where T: AsRef<[u8]> + ?Sized,

Lazily executes a 3-pass version of Smith-Waterman local alignment, starting with an i16 profile.

fn sw_align_from_i32_3pass<T>( &self, seq: SeqSrc<&T>, ) -> MaybeAligned<Alignment<u32>>

where T: AsRef<[u8]> + ?Sized,

Lazily executes a 3-pass version of Smith-Waterman local alignment using an i32 profile.

fn sw_score_ranges_from_i8<T>( &self, seq: SeqSrc<&T>, ) -> MaybeAligned<ScoreAndRanges<u32>>

where T: AsRef<[u8]> + ?Sized,

Lazily execute StripedProfile::sw_score_ranges starting with the i8 profile.

fn sw_score_ranges_from_i16<T>( &self, seq: SeqSrc<&T>, ) -> MaybeAligned<ScoreAndRanges<u32>>

where T: AsRef<[u8]> + ?Sized,

Lazily execute StripedProfile::sw_score_ranges starting with the i16 profile, skipping the i8 profile.

fn sw_score_ranges_from_i32<T>( &self, seq: SeqSrc<&T>, ) -> MaybeAligned<ScoreAndRanges<u32>>

where T: AsRef<[u8]> + ?Sized,

Execute StripedProfile::sw_score_ranges with the i32 profile, skipping the i8 and i16 profiles.

impl<const M: usize, const N: usize, const O: usize, const S: usize> SequenceReadable for SharedProfiles<'_, M, N, O, S>

fn sequence_bytes(&self) -> &[u8]

Get the sequence from the struct as a byte slice.