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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::collections::HashMap;
use crate::kmer_class::{union_kmer_classes, KmerClass, KmerClassId};
/* -------------------------------------------------------------------------- */
#[derive(Clone, Debug, Default, PartialEq, Eq)]
pub struct KmerCounts {
pub kmers: Vec<KmerClass>,
pub counts: HashMap<KmerClassId, usize>,
}
/* -------------------------------------------------------------------------- */
impl KmerCounts {
pub fn len(&self) -> usize {
self.kmers.len()
}
pub fn is_empty(&self) -> bool {
self.kmers.is_empty()
}
pub fn n(&self) -> usize {
self.counts.len()
}
pub fn at(&self, i: usize) -> usize {
self.counts.get(&self.kmers[i].id()).copied().unwrap_or(0)
}
pub fn get_count(&self, kmer: &KmerClass) -> usize {
self.counts.get(&kmer.id()).copied().unwrap_or(0)
}
pub fn get_kmer(&self, i: usize) -> &KmerClass {
&self.kmers[i]
}
pub fn iter(&self) -> KmerCountsIterator<'_> {
KmerCountsIterator { counts: self, i: 0 }
}
pub fn set_kmers(&mut self, kmers: Vec<KmerClass>) {
let mut counts = HashMap::new();
for kmer in &kmers {
if let Some(count) = self.counts.get(&kmer.id()) {
counts.insert(kmer.id(), *count);
}
}
self.kmers = kmers;
self.counts = counts;
}
}
/* -------------------------------------------------------------------------- */
#[derive(Clone, Debug, Default, PartialEq, Eq)]
pub struct KmerCountsList {
pub kmers: Vec<KmerClass>,
pub counts: Vec<HashMap<KmerClassId, usize>>,
}
/* -------------------------------------------------------------------------- */
impl KmerCountsList {
pub fn new(counts: Vec<KmerCounts>) -> Self {
let result = Self::default();
result.append(counts)
}
pub fn append(mut self, args: Vec<KmerCounts>) -> Self {
if args.is_empty() {
return self;
}
let mut slices: Vec<&[KmerClass]> = Vec::with_capacity(args.len() + 1);
slices.push(&self.kmers);
for counts in &args {
slices.push(&counts.kmers);
}
self.kmers = union_kmer_classes(&slices);
for counts in args {
self.counts.push(counts.counts);
}
self
}
pub fn len(&self) -> usize {
self.counts.len()
}
pub fn is_empty(&self) -> bool {
self.counts.is_empty()
}
pub fn at(&self, i: usize) -> KmerCounts {
KmerCounts {
kmers: self.kmers.clone(),
counts: self.counts[i].clone(),
}
}
pub fn slice(&self, i: usize, j: usize) -> Self {
Self {
kmers: self.kmers.clone(),
counts: self.counts[i..j].to_vec(),
}
}
pub fn set_kmers(&mut self, kmers: Vec<KmerClass>) {
for counts in &mut self.counts {
let mut filtered = HashMap::new();
for kmer in &kmers {
if let Some(value) = counts.get(&kmer.id()) {
filtered.insert(kmer.id(), *value);
}
}
*counts = filtered;
}
self.kmers = kmers;
}
}
/* -------------------------------------------------------------------------- */
#[derive(Clone, Debug)]
pub struct KmerCountsIterator<'a> {
counts: &'a KmerCounts,
i: usize,
}
/* -------------------------------------------------------------------------- */
impl<'a> KmerCountsIterator<'a> {
pub fn ok(&self) -> bool {
self.i < self.counts.len()
}
pub fn get_kmer(&self) -> &KmerClass {
&self.counts.kmers[self.i]
}
pub fn get_count(&self) -> usize {
self.counts.at(self.i)
}
pub fn get_index(&self) -> usize {
self.i
}
pub fn next(&mut self) {
self.i += 1;
}
}