Trait SuffixArray 

pub trait SuffixArray {
    // Required methods
    fn get(&self, index: usize) -> Option<usize>;
    fn len(&self) -> usize;
    fn is_empty(&self) -> bool;

    // Provided method
    fn sample<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>>(
        &self,
        text: &[u8],
        bwt: DBWT,
        less: DLess,
        occ: DOcc,
        sampling_rate: usize,
    ) -> SampledSuffixArray<DBWT, DLess, DOcc> { ... }
}

A trait exposing general functionality of suffix arrays.

Required Methods

fn get(&self, index: usize) -> Option<usize>

fn len(&self) -> usize

fn is_empty(&self) -> bool

Provided Methods

fn sample<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>>( &self, text: &[u8], bwt: DBWT, less: DLess, occ: DOcc, sampling_rate: usize, ) -> SampledSuffixArray<DBWT, DLess, DOcc>

Sample the suffix array with the given sample rate.

Arguments

• text - text that the suffix array is built on
• bwt - the corresponding BWT
• less - the corresponding less array
• occ - the corresponding occ table
• sampling_rate - if sampling rate is k, every k-th entry will be kept

Example

use bio::alphabets::dna;
use bio::data_structures::bwt::{bwt, less, Occ};
use bio::data_structures::suffix_array::{suffix_array, SuffixArray};

let text = b"ACGCGAT$";
let alphabet = dna::n_alphabet();
let sa = suffix_array(text);
let bwt = bwt(text, &sa);
let less = less(&bwt, &alphabet);
let occ = Occ::new(&bwt, 3, &alphabet);
let sampled = sa.sample(text, &bwt, &less, &occ, 2);

for i in 0..sa.len() {
    assert_eq!(sa.get(i), sampled.get(i));
}

Dyn Compatibility

This trait is not dyn compatible.

In older versions of Rust, dyn compatibility was called "object safety", so this trait is not object safe.

Implementors

impl SuffixArray for RawSuffixArray

impl<DBWT: Borrow<BWT>, DLess: Borrow<Less>, DOcc: Borrow<Occ>> SuffixArray for SampledSuffixArray<DBWT, DLess, DOcc>