Struct rust_lapper::Lapper

pub struct Lapper<T: Eq + Clone> {
    pub intervals: Vec<Interval<T>>,
    pub overlaps_merged: bool,
    // some fields omitted
}

Primary object of the library. The public intervals holds all the intervals and can be used for iterating / pulling values out of the tree.

Fields

intervals: Vec<Interval<T>>

List of intervasl

overlaps_merged: bool

Whether or not overlaps have been merged

Methods

impl<T: Eq + Clone> Lapper<T>

pub fn new(intervals: Vec<Interval<T>>) -> Self

Create a new instance of Lapper by passing in a vector of Intervals. This vector will immediately be sorted by start order.

use rust_lapper::{Lapper, Interval};
let data = (0..20).step_by(5)
                  .map(|x| Interval{start: x, stop: x + 10, val: true})
                  .collect::<Vec<Interval<bool>>>();
let lapper = Lapper::new(data);

pub fn len(&self) -> usize

Get the number over intervals in Lapper

use rust_lapper::{Lapper, Interval};
let data = (0..20).step_by(5)
                  .map(|x| Interval{start: x, stop: x + 10, val: true})
                  .collect::<Vec<Interval<bool>>>();
let lapper = Lapper::new(data);
assert_eq!(lapper.len(), 4);

pub fn is_empty(&self) -> bool

Check if lapper is empty

use rust_lapper::{Lapper, Interval};
let data: Vec<Interval<bool>> = vec![];
let lapper = Lapper::new(data);
assert_eq!(lapper.is_empty(), true);

pub fn cov(&self) -> u32

Get the number of positions covered by the intervals in Lapper. This provides immutable access if it has already been set, or on the fly calculation.

use rust_lapper::{Lapper, Interval};
let data = (0..20).step_by(5)
                  .map(|x| Interval{start: x, stop: x + 10, val: true})
                  .collect::<Vec<Interval<bool>>>();
let lapper = Lapper::new(data);
assert_eq!(lapper.cov(), 25);

pub fn set_cov(&mut self) -> u32

Get the number fo positions covered by the intervals in Lapper and store it. If you are going to be using the coverage, you should set it to avoid calculating it over and over.

Important traits for IterLapper<'a, T>

impl<'a, T: Eq + Clone> Iterator for IterLapper<'a, T> type Item = &'a Interval<T>;

pub fn iter(&self) -> IterLapper<T>

Return an iterator over the intervals in Lapper

pub fn merge_overlaps(&mut self)

Merge any intervals that overlap with eachother within the Lapper. This is an easy way to speed up queries.

pub fn lower_bound(start: u32, intervals: &[Interval<T>]) -> usize

Determine the first index that we should start checking for overlaps for via a binary search.

pub fn bsearch_seq(key: u32, elems: &[u32]) -> usize

pub fn union_and_intersect(&self, other: &Self) -> (u32, u32)

Find the union and the intersect of two lapper objects. Union: The set of positions found in both lappers Intersect: The number of positions where both lappers intersect. Note that a position only counts one time, multiple Intervals covering the same position don't add up.

use rust_lapper::{Lapper, Interval};
type Iv = Interval<u32>;
let data1: Vec<Iv> = vec![
    Iv{start: 70, stop: 120, val: 0}, // max_len = 50
    Iv{start: 10, stop: 15, val: 0}, // exact overlap
    Iv{start: 12, stop: 15, val: 0}, // inner overlap
    Iv{start: 14, stop: 16, val: 0}, // overlap end
    Iv{start: 68, stop: 71, val: 0}, // overlap start
];
let data2: Vec<Iv> = vec![

    Iv{start: 10, stop: 15, val: 0},
    Iv{start: 40, stop: 45, val: 0},
    Iv{start: 50, stop: 55, val: 0},
    Iv{start: 60, stop: 65, val: 0},
    Iv{start: 70, stop: 75, val: 0},
];

let (mut lapper1, mut lapper2) = (Lapper::new(data1), Lapper::new(data2)) ;
// Should be the same either way it's calculated
let (union, intersect) = lapper1.union_and_intersect(&lapper2);
assert_eq!(intersect, 10);
assert_eq!(union, 73);
let (union, intersect) = lapper2.union_and_intersect(&lapper1);
assert_eq!(intersect, 10);
assert_eq!(union, 73);
lapper1.merge_overlaps();
lapper1.set_cov();
lapper2.merge_overlaps();
lapper2.set_cov();

// Should be the same either way it's calculated
let (union, intersect) = lapper1.union_and_intersect(&lapper2);
assert_eq!(intersect, 10);
assert_eq!(union, 73);
let (union, intersect) = lapper2.union_and_intersect(&lapper1);
assert_eq!(intersect, 10);
assert_eq!(union, 73);

pub fn intersect(&self, other: &Self) -> u32

Find the intersect of two lapper objects. Intersect: The number of positions where both lappers intersect. Note that a position only counts one time, multiple Intervals covering the same position don't add up

pub fn union(&self, other: &Self) -> u32

Find the union of two lapper objects.

Important traits for IterDepth<'a, T>

impl<'a, T: Eq + Clone> Iterator for IterDepth<'a, T> type Item = Interval<u32>;

pub fn depth(&self) -> IterDepth<T>

Return the contiguous intervals of coverage, val represents the number of intervals covering the returned interval.

Examples

use rust_lapper::{Lapper, Interval};
let data = (0..20).step_by(5)
                  .map(|x| Interval{start: x, stop: x + 10, val: true})
                  .collect::<Vec<Interval<bool>>>();
let lapper = Lapper::new(data);
assert_eq!(lapper.depth().collect::<Vec<Interval<u32>>>(), vec![
            Interval { start: 0, stop: 5, val: 1 },
            Interval { start: 5, stop: 20, val: 2 },
            Interval { start: 20, stop: 25, val: 1 }]);

pub fn count(&self, start: u32, stop: u32) -> usize

Count all intervals that overlap start .. stop. This performs two binary search in order to find all the excluded elements, and then deduces the intersection from there. See BITS for more details.

use rust_lapper::{Lapper, Interval};
let lapper = Lapper::new((0..100).step_by(5)
                                .map(|x| Interval{start: x, stop: x+2 , val: true})
                                .collect::<Vec<Interval<bool>>>());
assert_eq!(lapper.count(5, 11), 2);

Important traits for IterFind<'a, T>

impl<'a, T: Eq + Clone> Iterator for IterFind<'a, T> type Item = &'a Interval<T>;

pub fn find(&self, start: u32, stop: u32) -> IterFind<T>

Find all intervals that overlap start .. stop

use rust_lapper::{Lapper, Interval};
let lapper = Lapper::new((0..100).step_by(5)
                                .map(|x| Interval{start: x, stop: x+2 , val: true})
                                .collect::<Vec<Interval<bool>>>());
assert_eq!(lapper.find(5, 11).count(), 2);

Important traits for IterFind<'a, T>

impl<'a, T: Eq + Clone> Iterator for IterFind<'a, T> type Item = &'a Interval<T>;

pub fn seek<'a>(
    &'a self,
    start: u32,
    stop: u32,
    cursor: &mut usize
) -> IterFind<'a, T>

Find all intevals that overlap start .. stop. This method will work when queries to this lapper are in sorted (start) order. It uses a linear search from the last query instead of a binary search. A reference to a cursor must be passed in. This reference will be modified and should be reused in the next query. This allows seek to not need to make the lapper object mutable, and thus use the same lapper accross threads.

use rust_lapper::{Lapper, Interval};
let lapper = Lapper::new((0..100).step_by(5)
                                .map(|x| Interval{start: x, stop: x+2 , val: true})
                                .collect::<Vec<Interval<bool>>>());
let mut cursor = 0;
for i in lapper.iter() {
   assert_eq!(lapper.seek(i.start, i.stop, &mut cursor).count(), 1);
}

Trait Implementations

impl<T: Eq + Clone> IntoIterator for Lapper<T>

type Item = Interval<T>

The type of the elements being iterated over.

type IntoIter = IntoIter<Self::Item>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl<'a, T: Eq + Clone> IntoIterator for &'a Lapper<T>

type Item = &'a Interval<T>

The type of the elements being iterated over.

type IntoIter = Iter<'a, Interval<T>>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Iter<'a, Interval<T>>

Creates an iterator from a value.

impl<'a, T: Eq + Clone> IntoIterator for &'a mut Lapper<T>

type Item = &'a mut Interval<T>

The type of the elements being iterated over.

type IntoIter = IterMut<'a, Interval<T>>

Which kind of iterator are we turning this into?

fn into_iter(self) -> IterMut<'a, Interval<T>>

Creates an iterator from a value.

impl<T: Debug + Eq + Clone> Debug for Lapper<T>

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

Formats the value using the given formatter.