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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 std::fmt;
use crate::alphabet::ComplementableAlphabet;
use crate::kmer::Kmer;
/* -------------------------------------------------------------------------- */
#[derive(Clone, Copy, Debug, PartialEq, Eq, Hash, PartialOrd, Ord)]
pub struct KmerClassId {
pub k: usize,
pub i: usize,
}
/* -------------------------------------------------------------------------- */
#[derive(Clone, Debug, PartialEq, Eq)]
pub struct KmerClass {
pub k: usize,
pub i: usize,
pub elements: Vec<String>,
}
/* -------------------------------------------------------------------------- */
impl KmerClass {
pub fn new(k: usize, i: usize, elements: Vec<String>) -> Self {
Self { k, i, elements }
}
pub fn id(&self) -> KmerClassId {
KmerClassId {
k: self.k,
i: self.i,
}
}
pub fn matches<A: ComplementableAlphabet>(&self, other: &KmerClass, alphabet: &A) -> bool {
for left in &self.elements {
for right in &other.elements {
if Kmer::from(left.as_str()).matches(&Kmer::from(right.as_str()), alphabet) {
return true;
}
}
}
false
}
pub fn count_ambiguous<A: ComplementableAlphabet>(&self, alphabet: &A) -> usize {
self.elements
.first()
.map(|sequence| {
sequence
.bytes()
.filter(|base| alphabet.is_ambiguous(*base).unwrap_or(false))
.count()
})
.unwrap_or(0)
}
pub fn count_wildcard<A: ComplementableAlphabet>(&self, alphabet: &A) -> usize {
self.elements
.first()
.map(|sequence| {
sequence
.bytes()
.filter(|base| alphabet.is_wildcard(*base).unwrap_or(false))
.count()
})
.unwrap_or(0)
}
pub fn string(&self) -> String {
self.to_string()
}
}
/* -------------------------------------------------------------------------- */
impl Ord for KmerClass {
fn cmp(&self, other: &Self) -> Ordering {
self.id().cmp(&other.id())
}
}
impl PartialOrd for KmerClass {
fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
Some(self.cmp(other))
}
}
impl fmt::Display for KmerClass {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
f.write_str(&self.elements.join("|"))
}
}
/* -------------------------------------------------------------------------- */
pub type KmerClassSet = HashMap<KmerClassId, Vec<String>>;
pub(crate) fn union_kmer_classes(slices: &[&[KmerClass]]) -> Vec<KmerClass> {
let mut set: KmerClassSet = HashMap::new();
for slice in slices {
for class in *slice {
set.insert(class.id(), class.elements.clone());
}
}
let mut kmers: Vec<_> = set
.into_iter()
.map(|(id, elements)| KmerClass::new(id.k, id.i, elements))
.collect();
kmers.sort();
kmers
}