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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::fmt;
use std::cmp::Ordering;
use crate::granges::GRanges;
use crate::error::ArgumentError;
/* -------------------------------------------------------------------------- */
impl GRanges {
pub fn sorted_indices(&self, name: &str, reverse: bool) -> Result<Vec<usize>, ArgumentError> {
let mut indices: Vec<usize> = (0..self.num_rows()).collect();
match name {
"seqnames" => {
indices.sort_by(|&i, &j| {
let cmp = self.seqnames[i].cmp(&self.seqnames[j]);
if reverse {
cmp.reverse()
} else {
cmp
}
});
Ok(indices)
}
"ranges" => {
indices.sort_by(|&i, &j| {
let cmp = self.ranges[i].from.cmp(&self.ranges[j].from);
if cmp == Ordering::Equal {
self.ranges[i].to.cmp(&self.ranges[j].to)
} else if reverse {
cmp.reverse()
} else {
cmp
}
});
Ok(indices)
}
"strand" => {
indices.sort_by(|&i, &j| {
let cmp = self.strand[i].cmp(&self.strand[j]);
if reverse {
cmp.reverse()
} else {
cmp
}
});
Ok(indices)
}
_ => Err(ArgumentError("Invalid sort name".to_string())),
}
}
pub fn sort(&self, name: &str, reverse: bool) -> Result<Self, ArgumentError> {
if name.is_empty() {
let mut l = GRangesSort::new(self);
if reverse {
l.indices.sort_by(|&i, &j| j.cmp(&i));
} else {
l.indices.sort();
}
let indices = l.indices.clone();
Ok(self.subset(&indices))
} else {
let j = self.sorted_indices(name, reverse)?;
Ok(self.subset(&j))
}
}
}
/* -------------------------------------------------------------------------- */
struct GRangesSort<'a> {
granges: &'a GRanges,
indices: Vec<usize>,
}
impl<'a> GRangesSort<'a> {
fn new(granges: &'a GRanges) -> Self {
let indices: Vec<usize> = (0..granges.num_rows()).collect();
GRangesSort { granges, indices }
}
}
impl<'a> fmt::Display for GRangesSort<'a> {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(f, "GRangesSort(indices={:?})", self.indices)
}
}
impl<'a> PartialEq for GRangesSort<'a> {
fn eq(&self, other: &Self) -> bool {
self.indices == other.indices
}
}
impl<'a> Eq for GRangesSort<'a> {}
impl<'a> PartialOrd for GRangesSort<'a> {
fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
Some(self.cmp(other))
}
}
impl<'a> Ord for GRangesSort<'a> {
fn cmp(&self, other: &Self) -> Ordering {
let n = self.granges.num_rows();
for i in 0..n {
let cmp = self.granges.seqnames[self.indices[i]].cmp(&self.granges.seqnames[other.indices[i]]);
if cmp != Ordering::Equal {
return cmp;
}
}
Ordering::Equal
}
}