Struct rust_lapper::Lapper [−][src]
pub struct Lapper<I, T> where
I: PrimInt + Unsigned + Ord + Clone + Send + Sync,
T: Eq + Clone + Send + Sync, { pub intervals: Vec<Interval<I, T>>, pub overlaps_merged: bool, // some fields omitted }
Expand description
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<I, T>>
List of intervals
overlaps_merged: bool
Whether or not overlaps have been merged
Implementations
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<usize, bool>>>(); let lapper = Lapper::new(data);
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<usize, bool>>>(); let lapper = Lapper::new(data); assert_eq!(lapper.len(), 4);
Check if lapper is empty
use rust_lapper::{Lapper, Interval}; let data: Vec<Interval<usize, bool>> = vec![]; let lapper = Lapper::new(data); assert_eq!(lapper.is_empty(), true);
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<usize, bool>>>(); let lapper = Lapper::new(data); assert_eq!(lapper.cov(), 25);
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.
Return an iterator over the intervals in Lapper
Merge any intervals that overlap with eachother within the Lapper. This is an easy way to speed up queries.
Determine the first index that we should start checking for overlaps for via a binary
search.
Assumes that the maximum interval length in intervals
has been subtracted from
start
, otherwise the result is undefined
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, 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);
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
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<usize, bool>>>(); let lapper = Lapper::new(data); assert_eq!(lapper.depth().collect::<Vec<Interval<usize, usize>>>(), vec![ Interval { start: 0, stop: 5, val: 1 }, Interval { start: 5, stop: 20, val: 2 }, Interval { start: 20, stop: 25, val: 1 }]);
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<usize, bool>>>()); assert_eq!(lapper.count(5, 11), 2);
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<usize, bool>>>()); assert_eq!(lapper.find(5, 11).count(), 2);
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<usize, bool>>>()); let mut cursor = 0; for i in lapper.iter() { assert_eq!(lapper.seek(i.start, i.stop, &mut cursor).count(), 1); }
Trait Implementations
Auto Trait Implementations
impl<I, T> RefUnwindSafe for Lapper<I, T> where
I: RefUnwindSafe,
T: RefUnwindSafe,
impl<I, T> UnwindSafe for Lapper<I, T> where
I: UnwindSafe,
T: UnwindSafe,
Blanket Implementations
Mutably borrows from an owned value. Read more