Struct debruijn::vmer::Lmer

pub struct Lmer<A: Array> { /* fields omitted */ }

Store a variable-length DNA sequence in a packed 2-bit encoding, up 92bp in length The length of the sequence is stored in the lower 8 bits of storage

Trait Implementations

impl<A: Clone + Array> Clone for Lmer<A>

fn clone(&self) -> Lmer<A>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<A: Copy + Array> Copy for Lmer<A>

impl<A: Array<Item = u64> + Copy + Eq + Ord + Hash> Debug for Lmer<A>

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

Formats the value using the given formatter.

impl<'de, A: Array> Deserialize<'de> for Lmer<A> where
    A: Deserialize<'de>, 

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl<A: Eq + Array> Eq for Lmer<A>

impl<A: Hash + Array> Hash for Lmer<A>

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, 

Feeds a slice of this type into the given [Hasher].

impl<A: Array<Item = u64> + Copy + Eq + Ord + Hash> Mer for Lmer<A>

fn len(&self) -> usize

The length of the DNA string

fn get(&self, pos: usize) -> u8

Get the base at position pos

fn set_mut(&mut self, pos: usize, val: u8)

Return a new Lmer with position pos set to base val

fn set_slice_mut(&mut self, pos: usize, n_bases: usize, value: u64)

Set nbases positions in the sequence, starting at pos. Values must be packed into the upper-most bits of value.

fn rc(&self) -> Self

Return a new object containing the reverse complement of the sequence

fn iter<'a>(&'a self) -> MerIter<'a, Self>

Iterate over the bases in the sequence

fn at_count(&self) -> u32

Count the number of A/T bases in the kmer

fn gc_count(&self) -> u32

Count the number of G/C bases in the kmer

impl<A: Ord + Array> Ord for Lmer<A>

fn cmp(&self, other: &Lmer<A>) -> Ordering

This method returns an [Ordering] between self and other.

#[must_use]fn max(self, other: Self) -> Self

Compares and returns the maximum of two values.

#[must_use]fn min(self, other: Self) -> Self

Compares and returns the minimum of two values.

#[must_use]fn clamp(self, min: Self, max: Self) -> Self

🔬 This is a nightly-only experimental API. (clamp)

Restrict a value to a certain interval.

impl<A: PartialEq + Array> PartialEq<Lmer<A>> for Lmer<A>

fn eq(&self, other: &Lmer<A>) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Lmer<A>) -> bool

This method tests for !=.

impl<A: PartialOrd + Array> PartialOrd<Lmer<A>> for Lmer<A>

fn partial_cmp(&self, other: &Lmer<A>) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Lmer<A>) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Lmer<A>) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Lmer<A>) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Lmer<A>) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl<A: Array> Serialize for Lmer<A> where
    A: Serialize, 

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl<A: Array> StructuralEq for Lmer<A>

impl<A: Array> StructuralPartialEq for Lmer<A>

impl<A: Array<Item = u64> + Copy + Eq + Ord + Hash> Vmer for Lmer<A>

fn max_len() -> usize

Maximum sequence length that can be stored in this type

fn new(len: usize) -> Lmer<A>

Initialize an blank Lmer of length len. Will initially represent all A's.

fn get_kmer<K: Kmer>(&self, pos: usize) -> K

Get the kmer starting at position pos

fn from_slice(seq: &[u8]) -> Self

Create a Vmer from a sequence of bytes

fn first_kmer<K: Kmer>(&self) -> K

Get the first Kmer from the sequence

fn last_kmer<K: Kmer>(&self) -> K

Get the last kmer in the sequence

fn both_term_kmer<K: Kmer>(&self) -> (K, K)

Get the terminal kmer of the sequence, on the both side of the sequence

fn term_kmer<K: Kmer>(&self, dir: Dir) -> K

Get the terminal kmer of the sequence, on the side of the sequence given by dir

fn iter_kmers<K: Kmer>(&self) -> KmerIter<K, Self>

Iterate over the kmers in the sequence

fn iter_kmer_exts<K: Kmer>(&self, seq_exts: Exts) -> KmerExtsIter<K, Self>

Iterate over the kmers and their extensions, given the extensions of the whole sequence