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use crate::traits::{ChromBounds, Coordinates, Overlap, ValueBounds};
pub trait StrandedOverlap<C, T>: Coordinates<C, T>
where
Self: Sized,
C: ChromBounds,
T: ValueBounds,
{
/// Returns true if the current interval overlaps the other
/// and both intervals are on the same chromosome and strand.
///
/// Considers all three of:
/// 1. The chromosome
/// 2. The strand
/// 3. The interval overlap
///
/// ```text
/// (Self) |-------->
/// (Other) |-------->
///
/// or
///
/// (Self) <--------|
/// (Other) <--------|
/// ```
fn stranded_overlaps<I: Coordinates<C, T>>(&self, other: &I) -> bool {
self.bounded_strand(other) && self.overlaps(other)
}
/// Returns true if the current interval overlaps the other by at least `bases`
/// and both intervals are on the same chromosome and strand.
///
/// Considers all three of:
/// 1. The chromosome
/// 2. The strand
/// 3. The interval overlap
///
/// ```text
/// (Self) |-------->
/// (Other) |-------->
/// ```
/// or
/// ```text
/// (Self) <--------
/// (Other) <--------
/// ```
fn stranded_overlaps_by<I: Coordinates<C, T>>(&self, other: &I, bases: T) -> bool {
self.stranded_overlap_size(other)
.is_some_and(|n| n >= bases)
}
/// Returns true if the current interval overlaps the other by exactly `bases`
/// and both intervals are on the same chromosome and strand.
fn stranded_overlaps_by_exactly<I: Coordinates<C, T>>(&self, other: &I, bases: T) -> bool {
self.stranded_overlap_size(other) == Some(bases)
}
/// Returns the size of the overlap between the current interval and the other
/// if the intervals are on the same chromosome and strand.
fn stranded_overlap_size<I: Coordinates<C, T>>(&self, other: &I) -> Option<T> {
if self.bounded_strand(other) {
self.overlap_size(other)
} else {
None
}
}
/// Returns true if the current interval starts the other and
/// both intervals are on the same strand
/// ```text
/// (Self) |-------->
/// (Other) |----------------->
/// ```
/// # Example
/// ```
/// use bedrs::{StrandedBed3, Strand, Coordinates, Overlap, StrandedOverlap};
/// let interval1 = StrandedBed3::new(1, 100, 200, Strand::Forward);
/// let interval2 = StrandedBed3::new(1, 100, 400, Strand::Forward);
/// let interval3 = StrandedBed3::new(1, 100, 400, Strand::Reverse);
/// assert!(interval1.stranded_starts(&interval2));
/// assert!(!interval1.stranded_starts(&interval3));
/// ```
fn stranded_starts<I: Coordinates<C, T>>(&self, other: &I) -> bool {
self.bounded_strand(other) && self.starts(other)
}
/// Returns true if the current interval ends the other and
/// both intervals are on the same strand
/// ```text
/// (Self) |-------->
/// (Other) |----------------->
/// ```
/// # Example
/// ```
/// use bedrs::{StrandedBed3, Strand, Coordinates, Overlap, StrandedOverlap};
/// let interval1 = StrandedBed3::new(1, 300, 400, Strand::Forward);
/// let interval2 = StrandedBed3::new(1, 100, 400, Strand::Forward);
/// let interval3 = StrandedBed3::new(1, 100, 400, Strand::Reverse);
/// assert!(interval1.stranded_ends(&interval2));
/// assert!(!interval1.stranded_ends(&interval3));
/// ```
fn stranded_ends<I: Coordinates<C, T>>(&self, other: &I) -> bool {
self.bounded_strand(other) && self.ends(other)
}
/// Returns true if the current interval equals the other and they are on the same strand
/// considers both the interval overlap and the chromosome.
/// ```text
/// (Self) |-------->
/// (Other) |-------->
/// ```
/// # Example
/// ```
/// use bedrs::{StrandedBed3, Strand, Coordinates, Overlap, StrandedOverlap};
/// let interval1 = StrandedBed3::new(1, 100, 200, Strand::Forward);
/// let interval2 = StrandedBed3::new(1, 100, 200, Strand::Forward);
/// let interval3 = StrandedBed3::new(1, 100, 200, Strand::Reverse);
/// assert!(interval1.stranded_equals(&interval2));
/// assert!(!interval1.stranded_equals(&interval3));
/// ```
fn stranded_equals<I: Coordinates<C, T>>(&self, other: &I) -> bool {
self.bounded_strand(other) && self.equals(other)
}
/// Returns true if the current interval is during the other and
/// both intervals are on the same strand -
/// ```text
/// (Self) |---->
/// (Other) |-------->
/// ```
/// # Example
/// ```
/// use bedrs::{StrandedBed3, Strand, Coordinates, Overlap, StrandedOverlap};
/// let interval1 = StrandedBed3::new(1, 150, 160, Strand::Forward);
/// let interval2 = StrandedBed3::new(1, 100, 200, Strand::Forward);
/// let interval3 = StrandedBed3::new(1, 100, 200, Strand::Reverse);
/// assert!(interval1.stranded_during(&interval2));
/// assert!(!interval1.stranded_during(&interval3));
/// ```
fn stranded_during<I: Coordinates<C, T>>(&self, other: &I) -> bool {
self.bounded_strand(other) && self.during(other)
}
/// Returns true if the current interval contains the other and
/// both intervals are on the same strand -
///
/// ```text
/// (Self) |-------->
/// (Other) |---->
/// ```
///
/// # Example
///
/// ```
/// use bedrs::{StrandedBed3, Strand, Coordinates, Overlap, StrandedOverlap};
///
/// let interval1 = StrandedBed3::new(1, 100, 200, Strand::Forward);
/// let interval2 = StrandedBed3::new(1, 150, 160, Strand::Forward);
/// let interval3 = StrandedBed3::new(1, 150, 160, Strand::Reverse);
///
/// assert!(interval1.stranded_contains(&interval2));
/// assert!(!interval1.stranded_contains(&interval3));
/// ```
fn stranded_contains<I: Coordinates<C, T>>(&self, other: &I) -> bool {
self.bounded_strand(other) && self.contains(other)
}
/// Returns true if the current interval is contained by the other and
/// both intervals are on the same strand -
///
/// ```text
/// (Self) |---->
/// (Other) |-------->
///
/// or
/// (Self) <----|
/// (Other) <--------|
/// ```
///
/// # Example
///
/// ```
/// use bedrs::{StrandedBed3, Strand, Coordinates, Overlap, StrandedOverlap};
///
/// let interval1 = StrandedBed3::new(1, 150, 160, Strand::Forward);
/// let interval2 = StrandedBed3::new(1, 100, 200, Strand::Forward);
/// let interval3 = StrandedBed3::new(1, 100, 200, Strand::Reverse);
///
/// assert!(interval1.stranded_contained_by(&interval2));
/// assert!(!interval1.stranded_contained_by(&interval3));
/// ```
fn stranded_contained_by<I: Coordinates<C, T>>(&self, other: &I) -> bool {
other.stranded_contains(self)
}
/// Returns true if the current interval borders the other and
/// both intervals are on the same strand -
///
/// ```text
/// (Self) |-------->
/// (Other) |-------->
///
/// or
/// (Self) <--------|
/// (Other) <--------|
/// ```
///
/// # Example
///
/// ```
/// use bedrs::{StrandedBed3, Strand, Coordinates, Overlap, StrandedOverlap};
///
/// let interval1 = StrandedBed3::new(1, 100, 200, Strand::Forward);
/// let interval2 = StrandedBed3::new(1, 200, 300, Strand::Forward);
/// let interval3 = StrandedBed3::new(1, 200, 300, Strand::Reverse);
///
/// assert!(interval1.stranded_borders(&interval2));
/// assert!(!interval1.stranded_borders(&interval3));
/// ```
fn stranded_borders<I: Coordinates<C, T>>(&self, other: &I) -> bool {
self.bounded_strand(other) && self.borders(other)
}
}
#[cfg(test)]
mod testing {
use super::*;
use crate::{Strand, StrandedBed3};
#[test]
fn test_same_overlaps() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 250, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 250, Strand::Reverse);
assert!(iv_a.stranded_overlaps(&iv_b));
assert!(!iv_a.stranded_overlaps(&iv_c));
}
#[test]
fn test_same_overlaps_by() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 250, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 250, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 170, 250, Strand::Forward);
let iv_e = StrandedBed3::new(1, 170, 250, Strand::Reverse);
assert!(iv_a.stranded_overlaps_by(&iv_b, 50));
assert!(!iv_a.stranded_overlaps_by(&iv_c, 50));
assert!(!iv_a.stranded_overlaps_by(&iv_d, 50));
assert!(!iv_a.stranded_overlaps_by(&iv_e, 50));
}
#[test]
fn test_same_overlaps_by_exactly() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 250, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 250, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 170, 250, Strand::Forward);
let iv_e = StrandedBed3::new(1, 170, 250, Strand::Reverse);
assert!(iv_a.stranded_overlaps_by_exactly(&iv_b, 50));
assert!(!iv_a.stranded_overlaps_by_exactly(&iv_c, 50));
assert!(!iv_a.stranded_overlaps_by_exactly(&iv_d, 50));
assert!(!iv_a.stranded_overlaps_by_exactly(&iv_e, 50));
assert!(iv_a.stranded_overlaps_by_exactly(&iv_d, 30));
assert!(!iv_a.stranded_overlaps_by_exactly(&iv_e, 30));
}
#[test]
fn test_same_overlap_size() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 250, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 250, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 170, 250, Strand::Forward);
let iv_e = StrandedBed3::new(1, 170, 250, Strand::Reverse);
assert_eq!(iv_a.stranded_overlap_size(&iv_b), Some(50));
assert_eq!(iv_a.stranded_overlap_size(&iv_c), None);
assert_eq!(iv_a.stranded_overlap_size(&iv_d), Some(30));
assert_eq!(iv_a.stranded_overlap_size(&iv_e), None);
}
#[test]
fn test_same_starts() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 250, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 250, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 100, 250, Strand::Forward);
let iv_e = StrandedBed3::new(1, 100, 250, Strand::Reverse);
assert!(!iv_a.stranded_starts(&iv_b));
assert!(!iv_a.stranded_starts(&iv_c));
assert!(iv_a.stranded_starts(&iv_d));
assert!(!iv_a.stranded_starts(&iv_e));
}
#[test]
fn test_same_ends() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 250, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 250, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 50, 200, Strand::Forward);
let iv_e = StrandedBed3::new(1, 50, 200, Strand::Reverse);
assert!(!iv_a.stranded_ends(&iv_b));
assert!(!iv_a.stranded_ends(&iv_c));
assert!(iv_a.stranded_ends(&iv_d));
assert!(!iv_a.stranded_ends(&iv_e));
}
#[test]
fn test_same_equals() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 250, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 250, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_e = StrandedBed3::new(1, 100, 200, Strand::Reverse);
assert!(!iv_a.stranded_equals(&iv_b));
assert!(!iv_a.stranded_equals(&iv_c));
assert!(iv_a.stranded_equals(&iv_d));
assert!(!iv_a.stranded_equals(&iv_e));
}
#[test]
fn test_same_during() {
let iv_a = StrandedBed3::new(1, 150, 160, Strand::Forward);
let iv_b = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_c = StrandedBed3::new(1, 100, 200, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 100, 160, Strand::Forward);
let iv_e = StrandedBed3::new(1, 100, 160, Strand::Reverse);
let iv_f = StrandedBed3::new(1, 150, 200, Strand::Forward);
let iv_g = StrandedBed3::new(1, 150, 200, Strand::Reverse);
assert!(iv_a.stranded_during(&iv_b));
assert!(!iv_a.stranded_during(&iv_c));
assert!(!iv_a.stranded_during(&iv_d));
assert!(!iv_a.stranded_during(&iv_e));
assert!(!iv_a.stranded_during(&iv_f));
assert!(!iv_a.stranded_during(&iv_g));
}
#[test]
fn test_same_contains() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 150, 160, Strand::Forward);
let iv_c = StrandedBed3::new(1, 150, 160, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 100, 160, Strand::Forward);
let iv_e = StrandedBed3::new(1, 100, 160, Strand::Reverse);
let iv_f = StrandedBed3::new(1, 150, 200, Strand::Forward);
let iv_g = StrandedBed3::new(1, 150, 200, Strand::Reverse);
let in_set = [iv_b, iv_d, iv_f];
let out_set = [iv_c, iv_e, iv_g];
for iv in in_set {
assert!(iv_a.stranded_contains(&iv));
}
for iv in out_set {
assert!(!iv_a.stranded_contains(&iv));
}
}
#[test]
fn test_same_contained_by() {
let iv_a = StrandedBed3::new(1, 150, 160, Strand::Forward);
let iv_b = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_c = StrandedBed3::new(1, 100, 200, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 100, 160, Strand::Forward);
let iv_e = StrandedBed3::new(1, 100, 160, Strand::Reverse);
let iv_f = StrandedBed3::new(1, 150, 200, Strand::Forward);
let iv_g = StrandedBed3::new(1, 150, 200, Strand::Reverse);
assert!(iv_a.stranded_contained_by(&iv_b));
assert!(!iv_a.stranded_contained_by(&iv_c));
assert!(iv_a.stranded_contained_by(&iv_d));
assert!(!iv_a.stranded_contained_by(&iv_e));
assert!(iv_a.stranded_contained_by(&iv_f));
assert!(!iv_a.stranded_contained_by(&iv_g));
}
#[test]
fn test_same_borders() {
let iv_a = StrandedBed3::new(1, 100, 200, Strand::Forward);
let iv_b = StrandedBed3::new(1, 200, 300, Strand::Forward);
let iv_c = StrandedBed3::new(1, 200, 300, Strand::Reverse);
let iv_d = StrandedBed3::new(1, 50, 100, Strand::Forward);
let iv_e = StrandedBed3::new(1, 50, 100, Strand::Reverse);
let iv_f = StrandedBed3::new(1, 199, 300, Strand::Forward);
let iv_g = StrandedBed3::new(1, 199, 300, Strand::Reverse);
let iv_h = StrandedBed3::new(1, 50, 101, Strand::Forward);
let iv_i = StrandedBed3::new(1, 50, 101, Strand::Reverse);
let iv_j = StrandedBed3::new(1, 201, 300, Strand::Forward);
let iv_k = StrandedBed3::new(1, 201, 300, Strand::Reverse);
let iv_l = StrandedBed3::new(1, 50, 99, Strand::Forward);
let iv_m = StrandedBed3::new(1, 50, 99, Strand::Reverse);
let in_set = [iv_b, iv_d];
let out_set = [iv_c, iv_e, iv_f, iv_g, iv_h, iv_i, iv_j, iv_k, iv_l, iv_m];
for iv in in_set {
assert!(iv_a.stranded_borders(&iv));
}
for iv in out_set {
assert!(!iv_a.stranded_borders(&iv));
}
}
}