Struct debruijn::DnaBytes

pub struct DnaBytes(pub Vec<u8>);

A newtype wrapper around a Vec<u8> with implementations of the Mer and Vmer traits.

Tuple Fields

0: Vec<u8>

Trait Implementations

impl Clone for DnaBytes

fn clone(&self) -> DnaBytes

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for DnaBytes

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

Formats the value using the given formatter.

impl Mer for DnaBytes

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

Set base at pos to 2-bit encoded base val

fn set_slice_mut(&mut self, _pos: usize, _nbases: 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 len(&self) -> usize

Length of DNA sequence

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

Get 2-bit encoded base at position pos

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 Ord for DnaBytes

fn cmp(&self, other: &DnaBytes) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

Restrict a value to a certain interval.

impl PartialEq<DnaBytes> for DnaBytes

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

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

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

This method tests for !=.

impl PartialOrd<DnaBytes> for DnaBytes

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

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

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

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

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

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

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

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

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

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

impl Vmer for DnaBytes

fn new(len: usize) -> Self

Create a new sequence with length len, initialized to all A’s

fn max_len() -> usize

Maximum sequence length that can be stored in this type

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

Efficiently extract a Kmer from the sequence

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

impl Eq for DnaBytes

impl StructuralEq for DnaBytes

impl StructuralPartialEq for DnaBytes