pub struct Lapper<I, T>{
pub intervals: Vec<Interval<I, T>>,
pub overlaps_merged: bool,
/* private fields */
}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: boolWhether or not overlaps have been merged
Implementations§
Source§impl<I, T> Lapper<I, T>
impl<I, T> Lapper<I, T>
Sourcepub fn new(intervals: Vec<Interval<I, T>>) -> Self
pub fn new(intervals: Vec<Interval<I, 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<usize, bool>>>();
let lapper = Lapper::new(data);Sourcepub fn insert(&mut self, elem: Interval<I, T>)
pub fn insert(&mut self, elem: Interval<I, T>)
Insert a new interval after the Lapper has been created. This is very inefficient and should be avoided if possible.
SIDE EFFECTS: This clears cov() and overlaps_merged meaning that those will have to be recomputed after a insert
use rust_lapper::{Lapper, Interval};
let data : Vec<Interval<usize, usize>>= vec!{
Interval{start:0, stop:5, val:1},
Interval{start:6, stop:10, val:2},
};
let mut lapper = Lapper::new(data);
lapper.insert(Interval{start:0, stop:20, val:5});
assert_eq!(lapper.len(), 3);
assert_eq!(lapper.find(1,3).collect::<Vec<&Interval<usize,usize>>>(),
vec![
&Interval{start:0, stop:5, val:1},
&Interval{start:0, stop:20, val:5},
]
);
Sourcepub fn len(&self) -> usize
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<usize, bool>>>();
let lapper = Lapper::new(data);
assert_eq!(lapper.len(), 4);Sourcepub fn is_empty(&self) -> bool
pub fn is_empty(&self) -> bool
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);Sourcepub fn cov(&self) -> I
pub fn cov(&self) -> I
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);Sourcepub fn set_cov(&mut self) -> I
pub fn set_cov(&mut self) -> I
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.
Sourcepub fn iter(&self) -> IterLapper<'_, I, T> ⓘ
pub fn iter(&self) -> IterLapper<'_, I, T> ⓘ
Return an iterator over the intervals in Lapper
Sourcepub fn merge_overlaps(&mut self)
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.
Sourcepub fn lower_bound(start: I, intervals: &[Interval<I, T>]) -> usize
pub fn lower_bound(start: I, intervals: &[Interval<I, T>]) -> usize
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
pub fn bsearch_seq<K>(key: K, elems: &[K]) -> usizewhere
K: PartialEq + PartialOrd,
pub fn bsearch_seq_ref<K>(key: &K, elems: &[K]) -> usizewhere
K: PartialEq + PartialOrd,
Sourcepub fn union_and_intersect(&self, other: &Self) -> (I, I)
pub fn union_and_intersect(&self, other: &Self) -> (I, I)
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);Sourcepub fn intersect(&self, other: &Self) -> I
pub fn intersect(&self, other: &Self) -> I
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
Sourcepub fn depth(&self) -> IterDepth<'_, I, T> ⓘ
pub fn depth(&self) -> IterDepth<'_, I, 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<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 }]);Sourcepub fn count(&self, start: I, stop: I) -> usize
pub fn count(&self, start: I, stop: I) -> 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<usize, bool>>>());
assert_eq!(lapper.count(5, 11), 2);Sourcepub fn find(&self, start: I, stop: I) -> IterFind<'_, I, T> ⓘ
pub fn find(&self, start: I, stop: I) -> IterFind<'_, I, 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<usize, bool>>>());
assert_eq!(lapper.find(5, 11).count(), 2);Sourcepub fn seek<'a>(
&'a self,
start: I,
stop: I,
cursor: &mut usize,
) -> IterFind<'a, I, T> ⓘ
pub fn seek<'a>( &'a self, start: I, stop: I, cursor: &mut usize, ) -> IterFind<'a, I, 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<usize, bool>>>());
let mut cursor = 0;
for i in lapper.iter() {
assert_eq!(lapper.seek(i.start, i.stop, &mut cursor).count(), 1);
}