Struct LcsArray

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pub struct LcsArray { /* private fields */ }
Expand description

An array that stores the lengths of the longest common suffixes of consecutive k-mers in colexicographic order.

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impl LcsArray

An LCS array implementation using ceil(log(k)) bits per element.

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pub fn new(v: IntVector) -> Self

Construct from a pre-built LCS array stored in an IntVector.

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pub fn access(&self, i: usize) -> usize

Access the LCS value at position i.

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pub fn len(&self) -> usize

Returns the number of elements in the LCS array.

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pub fn is_empty(&self) -> bool

Returns true iff the length of the array is zero.

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pub fn size_in_bytes(&self) -> usize

Returns the number of bytes used by the LCS array.

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pub fn serialize<W: Write>(&self, out: &mut W) -> Result<usize>

Serialize the LCS array to the given writer. The array can then later be loaded with LcsArray::load. Returns number of bytes written.

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pub fn load<R: Read>(input: &mut R) -> Result<Self>

Load an LCS array that was previously serialized with LcsArray::serialize.

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pub fn from_sbwt<SS: SubsetSeq + Sync>( sbwt: &SbwtIndex<SS>, n_threads: usize, ) -> Self

Build an LCS array using the given SBWT index. This runs an O(nk) time algorithm, where n is the number of k-mers in the padded spectrum encoded in the SBWT, and k is the length of the k-mers. The algorithm works by inverting the SBWT column by column, which takes 2n bytes of extra working space. The algorithm is described in the paper Longest Common Prefix Arrays for Succinct k-spectra.

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impl Clone for LcsArray

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fn clone(&self) -> LcsArray

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 ContractLeft for LcsArray

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fn contract_left(&self, I: Range<usize>, target_len: usize) -> Range<usize>

Expands the interval by scanning left and right until the LCS value is less than target_len. This has worst case time complexity equal to the length of LCS array, but if used on short intervals, the performance is typically quite good.

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impl Debug for LcsArray

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

Formats the value using the given formatter. Read more
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impl PartialEq for LcsArray

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

Tests for self and other values to be equal, and is used by ==.
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fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.
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impl Eq for LcsArray

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impl StructuralPartialEq for LcsArray

Auto Trait Implementations§

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

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more
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impl<T> Borrow<T> for T
where T: ?Sized,

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fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more
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impl<T> BorrowMut<T> for T
where T: ?Sized,

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

Mutably borrows from an owned value. Read more
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impl<T> CloneToUninit for T
where T: Clone,

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unsafe fn clone_to_uninit(&self, dest: *mut u8)

🔬This is a nightly-only experimental API. (clone_to_uninit)
Performs copy-assignment from self to dest. Read more
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impl<T> Conv for T

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fn conv<T>(self) -> T
where Self: Into<T>,

Converts self into T using Into<T>. Read more
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impl<T> FmtForward for T

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fn fmt_binary(self) -> FmtBinary<Self>
where Self: Binary,

Causes self to use its Binary implementation when Debug-formatted.
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fn fmt_display(self) -> FmtDisplay<Self>
where Self: Display,

Causes self to use its Display implementation when Debug-formatted.
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fn fmt_lower_exp(self) -> FmtLowerExp<Self>
where Self: LowerExp,

Causes self to use its LowerExp implementation when Debug-formatted.
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fn fmt_lower_hex(self) -> FmtLowerHex<Self>
where Self: LowerHex,

Causes self to use its LowerHex implementation when Debug-formatted.
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fn fmt_octal(self) -> FmtOctal<Self>
where Self: Octal,

Causes self to use its Octal implementation when Debug-formatted.
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fn fmt_pointer(self) -> FmtPointer<Self>
where Self: Pointer,

Causes self to use its Pointer implementation when Debug-formatted.
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fn fmt_upper_exp(self) -> FmtUpperExp<Self>
where Self: UpperExp,

Causes self to use its UpperExp implementation when Debug-formatted.
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fn fmt_upper_hex(self) -> FmtUpperHex<Self>
where Self: UpperHex,

Causes self to use its UpperHex implementation when Debug-formatted.
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fn fmt_list(self) -> FmtList<Self>
where &'a Self: for<'a> IntoIterator,

Formats each item in a sequence. Read more
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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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

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fn into(self) -> U

Calls U::from(self).

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

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impl<T> IntoEither for T

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fn into_either(self, into_left: bool) -> Either<Self, Self>

Converts self into a Left variant of Either<Self, Self> if into_left is true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more
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fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
where F: FnOnce(&Self) -> bool,

Converts self into a Left variant of Either<Self, Self> if into_left(&self) returns true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more
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impl<T> Pipe for T
where T: ?Sized,

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fn pipe<R>(self, func: impl FnOnce(Self) -> R) -> R
where Self: Sized,

Pipes by value. This is generally the method you want to use. Read more
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fn pipe_ref<'a, R>(&'a self, func: impl FnOnce(&'a Self) -> R) -> R
where R: 'a,

Borrows self and passes that borrow into the pipe function. Read more
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fn pipe_ref_mut<'a, R>(&'a mut self, func: impl FnOnce(&'a mut Self) -> R) -> R
where R: 'a,

Mutably borrows self and passes that borrow into the pipe function. Read more
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fn pipe_borrow<'a, B, R>(&'a self, func: impl FnOnce(&'a B) -> R) -> R
where Self: Borrow<B>, B: 'a + ?Sized, R: 'a,

Borrows self, then passes self.borrow() into the pipe function. Read more
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fn pipe_borrow_mut<'a, B, R>( &'a mut self, func: impl FnOnce(&'a mut B) -> R, ) -> R
where Self: BorrowMut<B>, B: 'a + ?Sized, R: 'a,

Mutably borrows self, then passes self.borrow_mut() into the pipe function. Read more
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fn pipe_as_ref<'a, U, R>(&'a self, func: impl FnOnce(&'a U) -> R) -> R
where Self: AsRef<U>, U: 'a + ?Sized, R: 'a,

Borrows self, then passes self.as_ref() into the pipe function.
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fn pipe_as_mut<'a, U, R>(&'a mut self, func: impl FnOnce(&'a mut U) -> R) -> R
where Self: AsMut<U>, U: 'a + ?Sized, R: 'a,

Mutably borrows self, then passes self.as_mut() into the pipe function.
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fn pipe_deref<'a, T, R>(&'a self, func: impl FnOnce(&'a T) -> R) -> R
where Self: Deref<Target = T>, T: 'a + ?Sized, R: 'a,

Borrows self, then passes self.deref() into the pipe function.
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fn pipe_deref_mut<'a, T, R>( &'a mut self, func: impl FnOnce(&'a mut T) -> R, ) -> R
where Self: DerefMut<Target = T> + Deref, T: 'a + ?Sized, R: 'a,

Mutably borrows self, then passes self.deref_mut() into the pipe function.
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impl<T> Pointable for T

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const ALIGN: usize

The alignment of pointer.
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type Init = T

The type for initializers.
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unsafe fn init(init: <T as Pointable>::Init) -> usize

Initializes a with the given initializer. Read more
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unsafe fn deref<'a>(ptr: usize) -> &'a T

Dereferences the given pointer. Read more
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unsafe fn deref_mut<'a>(ptr: usize) -> &'a mut T

Mutably dereferences the given pointer. Read more
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unsafe fn drop(ptr: usize)

Drops the object pointed to by the given pointer. Read more
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impl<T> Tap for T

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fn tap(self, func: impl FnOnce(&Self)) -> Self

Immutable access to a value. Read more
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fn tap_mut(self, func: impl FnOnce(&mut Self)) -> Self

Mutable access to a value. Read more
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fn tap_borrow<B>(self, func: impl FnOnce(&B)) -> Self
where Self: Borrow<B>, B: ?Sized,

Immutable access to the Borrow<B> of a value. Read more
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fn tap_borrow_mut<B>(self, func: impl FnOnce(&mut B)) -> Self
where Self: BorrowMut<B>, B: ?Sized,

Mutable access to the BorrowMut<B> of a value. Read more
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fn tap_ref<R>(self, func: impl FnOnce(&R)) -> Self
where Self: AsRef<R>, R: ?Sized,

Immutable access to the AsRef<R> view of a value. Read more
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fn tap_ref_mut<R>(self, func: impl FnOnce(&mut R)) -> Self
where Self: AsMut<R>, R: ?Sized,

Mutable access to the AsMut<R> view of a value. Read more
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fn tap_deref<T>(self, func: impl FnOnce(&T)) -> Self
where Self: Deref<Target = T>, T: ?Sized,

Immutable access to the Deref::Target of a value. Read more
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fn tap_deref_mut<T>(self, func: impl FnOnce(&mut T)) -> Self
where Self: DerefMut<Target = T> + Deref, T: ?Sized,

Mutable access to the Deref::Target of a value. Read more
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fn tap_dbg(self, func: impl FnOnce(&Self)) -> Self

Calls .tap() only in debug builds, and is erased in release builds.
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fn tap_mut_dbg(self, func: impl FnOnce(&mut Self)) -> Self

Calls .tap_mut() only in debug builds, and is erased in release builds.
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fn tap_borrow_dbg<B>(self, func: impl FnOnce(&B)) -> Self
where Self: Borrow<B>, B: ?Sized,

Calls .tap_borrow() only in debug builds, and is erased in release builds.
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fn tap_borrow_mut_dbg<B>(self, func: impl FnOnce(&mut B)) -> Self
where Self: BorrowMut<B>, B: ?Sized,

Calls .tap_borrow_mut() only in debug builds, and is erased in release builds.
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fn tap_ref_dbg<R>(self, func: impl FnOnce(&R)) -> Self
where Self: AsRef<R>, R: ?Sized,

Calls .tap_ref() only in debug builds, and is erased in release builds.
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fn tap_ref_mut_dbg<R>(self, func: impl FnOnce(&mut R)) -> Self
where Self: AsMut<R>, R: ?Sized,

Calls .tap_ref_mut() only in debug builds, and is erased in release builds.
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fn tap_deref_dbg<T>(self, func: impl FnOnce(&T)) -> Self
where Self: Deref<Target = T>, T: ?Sized,

Calls .tap_deref() only in debug builds, and is erased in release builds.
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fn tap_deref_mut_dbg<T>(self, func: impl FnOnce(&mut T)) -> Self
where Self: DerefMut<Target = T> + Deref, T: ?Sized,

Calls .tap_deref_mut() only in debug builds, and is erased in release builds.
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impl<T> ToOwned for T
where T: Clone,

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type Owned = T

The resulting type after obtaining ownership.
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fn to_owned(&self) -> T

Creates owned data from borrowed data, usually by cloning. Read more
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fn clone_into(&self, target: &mut T)

Uses borrowed data to replace owned data, usually by cloning. Read more
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impl<T> TryConv for T

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fn try_conv<T>(self) -> Result<T, Self::Error>
where Self: TryInto<T>,

Attempts to convert self into T using TryInto<T>. Read more
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impl<T, U> TryFrom<U> for T
where U: Into<T>,

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type Error = Infallible

The type returned in the event of a conversion error.
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fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

Performs the conversion.
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impl<T, U> TryInto<U> for T
where U: TryFrom<T>,

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

The type returned in the event of a conversion error.
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fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

Performs the conversion.
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impl<V, T> VZip<V> for T
where V: MultiLane<T>,

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fn vzip(self) -> V

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impl<T> Erased for T