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.
Implementations§
Source§impl LcsArray
An LCS array implementation using ceil(log(k)) bits per element.
impl LcsArray
An LCS array implementation using ceil(log(k)) bits per element.
Sourcepub fn size_in_bytes(&self) -> usize
pub fn size_in_bytes(&self) -> usize
Returns the number of bytes used by the LCS array.
Sourcepub fn serialize<W: Write>(&self, out: &mut W) -> Result<usize>
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.
Sourcepub fn load<R: Read>(input: &mut R) -> Result<Self>
pub fn load<R: Read>(input: &mut R) -> Result<Self>
Load an LCS array that was previously serialized with LcsArray::serialize.
Sourcepub fn from_sbwt<SS: SubsetSeq + Sync>(
sbwt: &SbwtIndex<SS>,
n_threads: usize,
) -> Self
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.
Trait Implementations§
Source§impl ContractLeft for LcsArray
impl ContractLeft for LcsArray
Source§fn contract_left(&self, I: Range<usize>, target_len: usize) -> Range<usize>
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.
impl Eq for LcsArray
impl StructuralPartialEq for LcsArray
Auto Trait Implementations§
impl Freeze for LcsArray
impl RefUnwindSafe for LcsArray
impl Send for LcsArray
impl Sync for LcsArray
impl Unpin for LcsArray
impl UnwindSafe for LcsArray
Blanket Implementations§
Source§impl<T> BorrowMut<T> for Twhere
T: ?Sized,
impl<T> BorrowMut<T> for Twhere
T: ?Sized,
Source§fn borrow_mut(&mut self) -> &mut T
fn borrow_mut(&mut self) -> &mut T
Source§impl<T> CloneToUninit for Twhere
T: Clone,
impl<T> CloneToUninit for Twhere
T: Clone,
Source§impl<T> FmtForward for T
impl<T> FmtForward for T
Source§fn fmt_binary(self) -> FmtBinary<Self>where
Self: Binary,
fn fmt_binary(self) -> FmtBinary<Self>where
Self: Binary,
self
to use its Binary
implementation when Debug
-formatted.Source§fn fmt_display(self) -> FmtDisplay<Self>where
Self: Display,
fn fmt_display(self) -> FmtDisplay<Self>where
Self: Display,
self
to use its Display
implementation when
Debug
-formatted.Source§fn fmt_lower_exp(self) -> FmtLowerExp<Self>where
Self: LowerExp,
fn fmt_lower_exp(self) -> FmtLowerExp<Self>where
Self: LowerExp,
self
to use its LowerExp
implementation when
Debug
-formatted.Source§fn fmt_lower_hex(self) -> FmtLowerHex<Self>where
Self: LowerHex,
fn fmt_lower_hex(self) -> FmtLowerHex<Self>where
Self: LowerHex,
self
to use its LowerHex
implementation when
Debug
-formatted.Source§fn fmt_octal(self) -> FmtOctal<Self>where
Self: Octal,
fn fmt_octal(self) -> FmtOctal<Self>where
Self: Octal,
self
to use its Octal
implementation when Debug
-formatted.Source§fn fmt_pointer(self) -> FmtPointer<Self>where
Self: Pointer,
fn fmt_pointer(self) -> FmtPointer<Self>where
Self: Pointer,
self
to use its Pointer
implementation when
Debug
-formatted.Source§fn fmt_upper_exp(self) -> FmtUpperExp<Self>where
Self: UpperExp,
fn fmt_upper_exp(self) -> FmtUpperExp<Self>where
Self: UpperExp,
self
to use its UpperExp
implementation when
Debug
-formatted.Source§fn fmt_upper_hex(self) -> FmtUpperHex<Self>where
Self: UpperHex,
fn fmt_upper_hex(self) -> FmtUpperHex<Self>where
Self: UpperHex,
self
to use its UpperHex
implementation when
Debug
-formatted.Source§impl<T> IntoEither for T
impl<T> IntoEither for T
Source§fn into_either(self, into_left: bool) -> Either<Self, Self>
fn into_either(self, into_left: bool) -> Either<Self, Self>
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 moreSource§fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
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 moreSource§impl<T> Pipe for Twhere
T: ?Sized,
impl<T> Pipe for Twhere
T: ?Sized,
Source§fn pipe<R>(self, func: impl FnOnce(Self) -> R) -> Rwhere
Self: Sized,
fn pipe<R>(self, func: impl FnOnce(Self) -> R) -> Rwhere
Self: Sized,
Source§fn pipe_ref<'a, R>(&'a self, func: impl FnOnce(&'a Self) -> R) -> Rwhere
R: 'a,
fn pipe_ref<'a, R>(&'a self, func: impl FnOnce(&'a Self) -> R) -> Rwhere
R: 'a,
self
and passes that borrow into the pipe function. Read moreSource§fn pipe_ref_mut<'a, R>(&'a mut self, func: impl FnOnce(&'a mut Self) -> R) -> Rwhere
R: 'a,
fn pipe_ref_mut<'a, R>(&'a mut self, func: impl FnOnce(&'a mut Self) -> R) -> Rwhere
R: 'a,
self
and passes that borrow into the pipe function. Read moreSource§fn pipe_borrow<'a, B, R>(&'a self, func: impl FnOnce(&'a B) -> R) -> R
fn pipe_borrow<'a, B, R>(&'a self, func: impl FnOnce(&'a B) -> R) -> R
Source§fn pipe_borrow_mut<'a, B, R>(
&'a mut self,
func: impl FnOnce(&'a mut B) -> R,
) -> R
fn pipe_borrow_mut<'a, B, R>( &'a mut self, func: impl FnOnce(&'a mut B) -> R, ) -> R
Source§fn pipe_as_ref<'a, U, R>(&'a self, func: impl FnOnce(&'a U) -> R) -> R
fn pipe_as_ref<'a, U, R>(&'a self, func: impl FnOnce(&'a U) -> R) -> R
self
, then passes self.as_ref()
into the pipe function.Source§fn pipe_as_mut<'a, U, R>(&'a mut self, func: impl FnOnce(&'a mut U) -> R) -> R
fn pipe_as_mut<'a, U, R>(&'a mut self, func: impl FnOnce(&'a mut U) -> R) -> R
self
, then passes self.as_mut()
into the pipe
function.Source§fn pipe_deref<'a, T, R>(&'a self, func: impl FnOnce(&'a T) -> R) -> R
fn pipe_deref<'a, T, R>(&'a self, func: impl FnOnce(&'a T) -> R) -> R
self
, then passes self.deref()
into the pipe function.Source§impl<T> Pointable for T
impl<T> Pointable for T
Source§impl<T> Tap for T
impl<T> Tap for T
Source§fn tap_borrow<B>(self, func: impl FnOnce(&B)) -> Self
fn tap_borrow<B>(self, func: impl FnOnce(&B)) -> Self
Borrow<B>
of a value. Read moreSource§fn tap_borrow_mut<B>(self, func: impl FnOnce(&mut B)) -> Self
fn tap_borrow_mut<B>(self, func: impl FnOnce(&mut B)) -> Self
BorrowMut<B>
of a value. Read moreSource§fn tap_ref<R>(self, func: impl FnOnce(&R)) -> Self
fn tap_ref<R>(self, func: impl FnOnce(&R)) -> Self
AsRef<R>
view of a value. Read moreSource§fn tap_ref_mut<R>(self, func: impl FnOnce(&mut R)) -> Self
fn tap_ref_mut<R>(self, func: impl FnOnce(&mut R)) -> Self
AsMut<R>
view of a value. Read moreSource§fn tap_deref<T>(self, func: impl FnOnce(&T)) -> Self
fn tap_deref<T>(self, func: impl FnOnce(&T)) -> Self
Deref::Target
of a value. Read moreSource§fn tap_deref_mut<T>(self, func: impl FnOnce(&mut T)) -> Self
fn tap_deref_mut<T>(self, func: impl FnOnce(&mut T)) -> Self
Deref::Target
of a value. Read moreSource§fn tap_dbg(self, func: impl FnOnce(&Self)) -> Self
fn tap_dbg(self, func: impl FnOnce(&Self)) -> Self
.tap()
only in debug builds, and is erased in release builds.Source§fn tap_mut_dbg(self, func: impl FnOnce(&mut Self)) -> Self
fn tap_mut_dbg(self, func: impl FnOnce(&mut Self)) -> Self
.tap_mut()
only in debug builds, and is erased in release
builds.Source§fn tap_borrow_dbg<B>(self, func: impl FnOnce(&B)) -> Self
fn tap_borrow_dbg<B>(self, func: impl FnOnce(&B)) -> Self
.tap_borrow()
only in debug builds, and is erased in release
builds.Source§fn tap_borrow_mut_dbg<B>(self, func: impl FnOnce(&mut B)) -> Self
fn tap_borrow_mut_dbg<B>(self, func: impl FnOnce(&mut B)) -> Self
.tap_borrow_mut()
only in debug builds, and is erased in release
builds.Source§fn tap_ref_dbg<R>(self, func: impl FnOnce(&R)) -> Self
fn tap_ref_dbg<R>(self, func: impl FnOnce(&R)) -> Self
.tap_ref()
only in debug builds, and is erased in release
builds.Source§fn tap_ref_mut_dbg<R>(self, func: impl FnOnce(&mut R)) -> Self
fn tap_ref_mut_dbg<R>(self, func: impl FnOnce(&mut R)) -> Self
.tap_ref_mut()
only in debug builds, and is erased in release
builds.Source§fn tap_deref_dbg<T>(self, func: impl FnOnce(&T)) -> Self
fn tap_deref_dbg<T>(self, func: impl FnOnce(&T)) -> Self
.tap_deref()
only in debug builds, and is erased in release
builds.