Struct debruijn::DnaSlice

pub struct DnaSlice<'a>(pub &'a [u8]);

A newtype wrapper around a &[u8] with implementations

Trait Implementations

impl<'a> Mer for DnaSlice<'a>

fn len(&self) -> usize

Length of DNA sequence

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

Get 2-bit encoded base at position pos

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

Important traits for MerIter<'a, M>

impl<'a, M: 'a + Mer> Iterator for MerIter<'a, M> type Item = u8;

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

Iterate over the bases in the sequence

impl<'a> Vmer for DnaSlice<'a>

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

Important traits for KmerIter<'a, K, D>

impl<'a, K: Kmer, D: Mer> Iterator for KmerIter<'a, K, D> type Item = K;

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

Iterate over the kmers in the sequence

Important traits for KmerExtsIter<'a, K, D>

impl<'a, K: Kmer, D: Mer> Iterator for KmerExtsIter<'a, K, D> type Item = (K, Exts);

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<'a> PartialEq<DnaSlice<'a>> for DnaSlice<'a>

fn eq(&self, other: &DnaSlice<'a>) -> bool

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

fn ne(&self, other: &DnaSlice<'a>) -> bool

This method tests for !=.

impl<'a> Ord for DnaSlice<'a>

fn cmp(&self, other: &DnaSlice<'a>) -> 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

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

Restrict a value to a certain interval.

impl<'a> Eq for DnaSlice<'a>

impl<'a> PartialOrd<DnaSlice<'a>> for DnaSlice<'a>

fn partial_cmp(&self, other: &DnaSlice<'a>) -> Option<Ordering>

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

fn lt(&self, other: &DnaSlice<'a>) -> bool

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

fn le(&self, other: &DnaSlice<'a>) -> bool

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

fn gt(&self, other: &DnaSlice<'a>) -> bool

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

fn ge(&self, other: &DnaSlice<'a>) -> bool

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

impl<'a> Debug for DnaSlice<'a>

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

Formats the value using the given formatter.