[−][src]Struct debruijn::kmer::VarIntKmer
A fixed-length Kmer sequence that may not fill the bits of T
side: L R bases: 0 0 0 A C G T T bits: H ........ L bit : 14 12 10 8 6 4 2 0
sorting the integer will give a lexicographic sorting of the corresponding string.
kmers that don't fill storage
are always aligned to the least signifcant bits
Fields
storage: T
phantom: PhantomData<KS>
Implementations
impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> VarIntKmer<T, KS>
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Trait Implementations
impl<T: Clone + PrimInt + FromPrimitive + IntHelp, KS: Clone + KmerSize> Clone for VarIntKmer<T, KS>
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fn clone(&self) -> VarIntKmer<T, KS>
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fn clone_from(&mut self, source: &Self)
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impl<T: Copy + PrimInt + FromPrimitive + IntHelp, KS: Copy + KmerSize> Copy for VarIntKmer<T, KS>
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impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> Debug for VarIntKmer<T, KS>
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impl<'de, T: PrimInt + FromPrimitive + IntHelp, KS: KmerSize> Deserialize<'de> for VarIntKmer<T, KS> where
T: Deserialize<'de>,
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T: Deserialize<'de>,
fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
__D: Deserializer<'de>,
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__D: Deserializer<'de>,
impl<T: Eq + PrimInt + FromPrimitive + IntHelp, KS: Eq + KmerSize> Eq for VarIntKmer<T, KS>
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impl<T: Hash + PrimInt + FromPrimitive + IntHelp, KS: Hash + KmerSize> Hash for VarIntKmer<T, KS>
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fn hash<__H: Hasher>(&self, state: &mut __H)
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fn hash_slice<H>(data: &[Self], state: &mut H) where
H: Hasher,
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H: Hasher,
impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> Kmer for VarIntKmer<T, KS>
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fn empty() -> Self
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fn k() -> usize
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fn to_u64(&self) -> u64
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fn from_u64(v: u64) -> Self
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fn extend_left(&self, v: u8) -> Self
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Shift the base v into the left end of the kmer
fn extend_right(&self, v: u8) -> Self
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fn extend(&self, v: u8, dir: Dir) -> Self
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fn get_extensions(&self, exts: Exts, dir: Dir) -> Vec<Self>
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fn min_rc_flip(&self) -> (Self, bool)
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fn min_rc(&self) -> Self
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fn is_palindrome(&self) -> bool
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fn from_bytes(bytes: &[u8]) -> Self
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fn from_ascii(bytes: &[u8]) -> Self
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fn to_string(&self) -> String
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fn kmers_from_bytes(str: &[u8]) -> Vec<Self>
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fn kmers_from_ascii(str: &[u8]) -> Vec<Self>
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impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> Mer for VarIntKmer<T, KS>
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fn len(&self) -> usize
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fn get(&self, pos: usize) -> u8
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Get the letter at the given position.
fn set_mut(&mut self, pos: usize, v: u8)
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fn set_slice_mut(&mut self, pos: usize, n_bases: usize, value: u64)
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Set a slice of bases in the kmer, using the packed representation in value. Sets n_bases, starting at pos. Incoming bases must always be packed into the upper-most bits of the value.
fn rc(&self) -> Self
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Return the reverse complement of this kmer
fn at_count(&self) -> u32
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fn gc_count(&self) -> u32
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fn iter<'a>(&'a self) -> MerIter<'a, Self>
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impl<T: Ord + PrimInt + FromPrimitive + IntHelp, KS: Ord + KmerSize> Ord for VarIntKmer<T, KS>
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fn cmp(&self, other: &VarIntKmer<T, KS>) -> Ordering
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#[must_use]fn max(self, other: Self) -> Self
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#[must_use]fn min(self, other: Self) -> Self
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#[must_use]fn clamp(self, min: Self, max: Self) -> Self
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impl<T: PartialEq + PrimInt + FromPrimitive + IntHelp, KS: PartialEq + KmerSize> PartialEq<VarIntKmer<T, KS>> for VarIntKmer<T, KS>
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fn eq(&self, other: &VarIntKmer<T, KS>) -> bool
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fn ne(&self, other: &VarIntKmer<T, KS>) -> bool
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impl<T: PartialOrd + PrimInt + FromPrimitive + IntHelp, KS: PartialOrd + KmerSize> PartialOrd<VarIntKmer<T, KS>> for VarIntKmer<T, KS>
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fn partial_cmp(&self, other: &VarIntKmer<T, KS>) -> Option<Ordering>
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fn lt(&self, other: &VarIntKmer<T, KS>) -> bool
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fn le(&self, other: &VarIntKmer<T, KS>) -> bool
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fn gt(&self, other: &VarIntKmer<T, KS>) -> bool
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fn ge(&self, other: &VarIntKmer<T, KS>) -> bool
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impl<T: PrimInt + FromPrimitive + IntHelp, KS: KmerSize> Serialize for VarIntKmer<T, KS> where
T: Serialize,
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T: Serialize,
fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
__S: Serializer,
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__S: Serializer,
impl<T: PrimInt + FromPrimitive + IntHelp, KS: KmerSize> StructuralEq for VarIntKmer<T, KS>
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impl<T: PrimInt + FromPrimitive + IntHelp, KS: KmerSize> StructuralPartialEq for VarIntKmer<T, KS>
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Auto Trait Implementations
impl<T, KS> RefUnwindSafe for VarIntKmer<T, KS> where
KS: RefUnwindSafe,
T: RefUnwindSafe,
KS: RefUnwindSafe,
T: RefUnwindSafe,
impl<T, KS> Send for VarIntKmer<T, KS> where
KS: Send,
T: Send,
KS: Send,
T: Send,
impl<T, KS> Sync for VarIntKmer<T, KS> where
KS: Sync,
T: Sync,
KS: Sync,
T: Sync,
impl<T, KS> Unpin for VarIntKmer<T, KS> where
KS: Unpin,
T: Unpin,
KS: Unpin,
T: Unpin,
impl<T, KS> UnwindSafe for VarIntKmer<T, KS> where
KS: UnwindSafe,
T: UnwindSafe,
KS: UnwindSafe,
T: UnwindSafe,
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized,
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T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized,
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T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
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T: ?Sized,
fn borrow_mut(&mut self) -> &mut T
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impl<T> DeserializeOwned for T where
T: for<'de> Deserialize<'de>,
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T: for<'de> Deserialize<'de>,
impl<T> From<T> for T
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impl<T, U> Into<U> for T where
U: From<T>,
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U: From<T>,
impl<T> MerImmut for T where
T: Mer + Clone,
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T: Mer + Clone,
fn set(&self, pos: usize, val: u8) -> Self
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fn set_slice(&self, pos: usize, nbases: usize, bits: u64) -> Self
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impl<T> ToOwned for T where
T: Clone,
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T: Clone,
type Owned = T
The resulting type after obtaining ownership.
fn to_owned(&self) -> T
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fn clone_into(&self, target: &mut T)
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impl<T, U> TryFrom<U> for T where
U: Into<T>,
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U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>
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impl<T, U> TryInto<U> for T where
U: TryFrom<T>,
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U: TryFrom<T>,