Trait Mer 

pub trait Mer: Sized + Debug {
    // Required methods
    fn len(&self) -> usize;
    fn get(&self, pos: usize) -> u8;
    fn set_mut(&mut self, pos: usize, val: u8);
    fn set_slice_mut(&mut self, pos: usize, nbases: usize, value: u64);
    fn rc(&self) -> Self;

    // Provided methods
    fn iter<'a>(&'a self) -> MerIter<'a, Self>  { ... }
    fn at_count(&self) -> u32 { ... }
    fn gc_count(&self) -> u32 { ... }
}

Trait for interacting with DNA sequences

Required Methods

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

Provided Methods

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

Dyn Compatibility

This trait is not dyn compatible.

In older versions of Rust, dyn compatibility was called "object safety".

Implementors

impl Mer for DnaBytes

impl Mer for DnaString

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

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

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

impl<T: PrimInt + FromPrimitive + Hash + IntHelp, KS: KmerSize> Mer for VarIntKmer<T, KS>

impl<T: PrimInt + FromPrimitive + Hash + IntHelp> Mer for IntKmer<T>