Struct debruijn::dna_string::DnaStringSlice

pub struct DnaStringSlice<'a> {
    pub dna_string: &'a DnaString,
    pub start: usize,
    pub length: usize,
    pub is_rc: bool,
}

An immutable slice into a DnaString

Fields

dna_string: &'a DnaString

start: usize

length: usize

is_rc: bool

Implementations

impl<'a> DnaStringSlice<'a>

pub fn is_palindrome(&self) -> bool

pub fn bytes(&self) -> Vec<u8>

pub fn ascii(&self) -> Vec<u8>

pub fn to_dna_string(&self) -> String

pub fn to_string(&self) -> String

pub fn to_owned(&self) -> DnaString

pub fn slice(&self, start: usize, end: usize) -> DnaStringSlice<'_>

Get slice containing the interval [start, end) of self

pub fn hamming_dist(&self, other: &DnaStringSlice<'_>) -> u32

Compute the Hamming distance between this DNA string and another

Trait Implementations

impl<'a> Clone for DnaStringSlice<'a>

fn clone(&self) -> DnaStringSlice<'a>

Returns a copy of the value.

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

Performs copy-assignment from source.

impl<'a> Debug for DnaStringSlice<'a>

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

Formats the value using the given formatter.

impl<'a> IntoIterator for &'a DnaStringSlice<'a>

type Item = u8

The type of the elements being iterated over.

type IntoIter = MerIter<'a, DnaStringSlice<'a>>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl<'a> Mer for DnaStringSlice<'a>

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

Get the base at position i.

fn set_mut(&mut self, _: usize, _: u8)

Set the base as position i.

fn len(&self) -> usize

Length of DNA sequence

fn set_slice_mut(&mut self, _: usize, _: usize, _: u64)

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

fn rc(&self) -> DnaStringSlice<'a>

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> PartialEq<DnaStringSlice<'a>> for DnaStringSlice<'a>

fn eq(&self, other: &DnaStringSlice<'_>) -> bool

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

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

This method tests for !=.

impl<'a> Vmer for DnaStringSlice<'a>

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

Get the kmer starting at position pos

fn new(_: 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 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<'a> Eq for DnaStringSlice<'a>