Struct bio_types::annot::refids::RefIDSet

pub struct RefIDSet<R> { /* fields omitted */ }

Data structure for interning sequence names efficiently.

The structure is parameterized over the reference type R used to intern strings. Typically, this would be Rc for single-threaded access or Arc for multi-threaded access. These reference types provide fast, reference-counted cloning with no new allocation, which can make sequence location calculations faster as well as reducing the memory footprint required.

use std::rc::Rc;
use bio_types::strand::ReqStrand;
use bio_types::annot::contig::Contig;
use bio_types::annot::loc::Loc;
use bio_types::annot::refids::RefIDSet;
let mut refids: RefIDSet<Rc<String>> = RefIDSet::new();
let pau8 = Contig::new(refids.intern("chrI"), 1807, 2170 - 1807, ReqStrand::Reverse);
{
  let chr_i = refids.intern("chrI");
  // One reference for the RefIDSet itself, one for the pau8 Contig, one for chr_i
  assert_eq!(Rc::strong_count(&chr_i), 3);
}
let seo1 = Contig::new(refids.intern("chrI"), 7235, 9017 - 7235, ReqStrand::Reverse);
let tda8 = Contig::new(refids.intern("chrI"), 13363, 13744 - 13363, ReqStrand::Reverse);
{
  let chr_i = refids.intern("chrI");
  assert_eq!(Rc::strong_count(&chr_i), 5);
}
let seo1_beginning = seo1.first_pos();
let seo1_ending = seo1.last_pos();
{
  let chr_i = refids.intern("chrI");
  assert_eq!(Rc::strong_count(&chr_i), 7);
}

Methods

impl<R> RefIDSet<R>

pub fn new() -> Self

Create a new, empty table of interned reference names

pub fn intern(&mut self, id: &str) -> R where
    R: Deref<Target = String> + From<String> + Clone, 

Intern a reference name.

This returns a shared reference of type R for the name. This reference will be shared with any other intern calls for the same name. The name is given originally as a reference, and it will be cloned into an owned String only when the name is new for the data type.