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// Copyright (C) 2024 Philipp Benner
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the “Software”), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.
use std::cmp::Ordering;
use std::collections::HashMap;
use crate::granges::GRanges;
use crate::granges_find_endpoint::{EndPoint, EndPointList};
/* -------------------------------------------------------------------------- */
#[derive(Debug)]
pub struct FindNearestHits {
pub query_hits : Vec<usize>,
pub subject_hits: Vec<usize>,
pub distances : Vec<i64>,
}
/* -------------------------------------------------------------------------- */
impl FindNearestHits {
fn new(query_hits: Vec<usize>, subject_hits: Vec<usize>, distances: Vec<i64>) -> Self {
FindNearestHits {
query_hits,
subject_hits,
distances,
}
}
fn len(&self) -> usize {
self.query_hits.len()
}
fn sort(&mut self) {
let mut r : Vec<FindNearestHitsItem> = (0..self.len()).map(
|i| FindNearestHitsItem{
query_hit : self. query_hits[i],
subject_hit: self.subject_hits[i],
distance : self. distances[i]}
).collect();
r.sort();
for i in 0..self.len() {
self. query_hits[i] = r[i].query_hit;
self.subject_hits[i] = r[i].subject_hit;
self. distances[i] = r[i].distance;
}
}
}
/* -------------------------------------------------------------------------- */
#[derive(Debug)]
pub struct FindNearestHitsItem {
pub query_hit : usize,
pub subject_hit: usize,
pub distance : i64,
}
/* -------------------------------------------------------------------------- */
impl PartialEq for FindNearestHitsItem {
fn eq(&self, other: &Self) -> bool {
self.query_hit == other.query_hit &&
self.subject_hit == other.subject_hit &&
self.distance == other.distance
}
}
impl Eq for FindNearestHitsItem {}
impl PartialOrd for FindNearestHitsItem {
fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
Some(self.cmp(other))
}
}
impl Ord for FindNearestHitsItem {
fn cmp(&self, other: &Self) -> Ordering {
if self.query_hit == other.query_hit {
if self.distance == other.distance {
self.subject_hit.cmp(&other.subject_hit)
} else {
self.distance.cmp(&other.distance)
}
} else {
self.query_hit.cmp(&other.query_hit)
}
}
}
/* -------------------------------------------------------------------------- */
impl GRanges {
pub fn find_nearest(query: &GRanges, subject: &GRanges, k: usize) -> FindNearestHits {
let n = query .num_rows();
let m = subject.num_rows();
let mut query_hits = Vec::new();
let mut subject_hits = Vec::new();
let mut distances = Vec::new();
let mut rmap: HashMap<String, EndPointList> = HashMap::new();
for i in 0..n {
let start = EndPoint::new(query.ranges[i].from, i, true);
let end = EndPoint::new(query.ranges[i].to , i, true);
start.borrow_mut().end = Some(end .clone());
end .borrow_mut().start = Some(start.clone());
let entry = rmap.entry(query.seqnames[i].clone()).or_insert(EndPointList::new());
entry.push(start);
entry.push(end);
}
for i in 0..m {
let start = EndPoint::new(subject.ranges[i].from, i, false);
let end = EndPoint::new(subject.ranges[i].to , i, false);
start.borrow_mut().end = Some(end .clone());
end .borrow_mut().start = Some(start.clone());
let entry = rmap.entry(subject.seqnames[i].clone()).or_insert(EndPointList::new());
entry.push(start);
entry.push(end);
}
for (_, entry) in rmap.iter_mut() {
entry.sort();
}
for (_, mut entry) in rmap.iter_mut() {
EndPointList::find_overlaps_entry(&mut query_hits, &mut subject_hits, &mut entry);
for _ in 0..query_hits.len() {
distances.push(0);
}
for i in 0..entry.len() {
let r = &entry[i];
// loop over query start regions
if r.is_query() && !r.is_end() {
let mut i1 = i as i64 - 1;
let mut i2 = i as i64 + 1;
// find k nearest neighbors
for _ in 0..k {
if i1 < 0 && (i2 as usize) >= entry.len() {
break;
}
// find next subject end to the left
for _ in 0..entry.len() {
if !(i1 >= 0) {
break;
}
if !entry[i1 as usize].is_query() && entry[i1 as usize].is_end() {
break;
}
i1 -= 1;
}
// find next subject start to the right (and drop overlaps)
for _ in 0..entry.len() {
if !((i2 as usize) < entry.len()) {
break;
}
if !entry[i2 as usize].is_query() && entry[i2 as usize].is_start() && entry[i2 as usize].get_position() > r.get_end() {
break;
}
i2 += 1;
}
// are there two elements to compare?
let mut ir = -1;
let mut dr = -1;
if i1 >= 0 && i2 < entry.len() as i64 {
let (d1, s1) = EndPoint::distance(&r, &entry[i1 as usize]);
let (d2, s2) = EndPoint::distance(&r, &entry[i2 as usize]);
if d1 <= d2 {
dr = d1*s1; ir = i1; i1 -= 1;
} else {
dr = d2*s2; ir = i2; i2 += 1;
}
} else {
if i1 >= 0 {
let (d1, s1) = EndPoint::distance(&r, &entry[i1 as usize]);
dr = d1*s1; ir = i1; i1 -= 1;
}
if (i2 as usize) < entry.len() {
let (d2, s2) = EndPoint::distance(&r, &entry[i2 as usize]);
dr = d2*s2; ir = i2; i2 += 1;
}
}
if ir != -1 {
query_hits .push(entry[i as usize].src_idx());
subject_hits.push(entry[ir as usize].src_idx());
distances .push(dr);
}
}
}
}
}
let mut find_nearest_hits = FindNearestHits::new(query_hits, subject_hits, distances);
find_nearest_hits.sort();
find_nearest_hits
}
}
/* -------------------------------------------------------------------------- */
#[cfg(test)]
mod tests {
use crate::granges::GRanges;
#[test]
fn test_nearest() {
let r_query = GRanges::new(
vec!["chr4", "chr4"].iter().map(|&x| x.into()).collect(),
vec![600, 850],
vec![950, 950],
vec![]
);
let r_subjects = GRanges::new(
vec!["chr4", "chr4", "chr4", "chr4"].iter().map(|&x| x.into()).collect(),
vec![100, 200, 300, 400],
vec![900, 300, 700, 600],
vec![]
);
let rq = vec![0, 0, 0, 0, 1, 1, 1];
let rs = vec![0, 2, 3, 1, 0, 2, 3];
let rd = vec![0, 0, 0, 300, 0, 150, 250];
let r = GRanges::find_nearest(&r_query, &r_subjects, 2);
assert!(r.query_hits .len() == rq.len());
assert!(r.subject_hits.len() == rs.len());
assert!(r.distances .len() == rd.len());
for i in 0..rd.len() {
assert!(rq[i] == r.query_hits [i]);
assert!(rs[i] == r.subject_hits[i]);
assert!(rd[i] == r.distances [i]);
}
}
}