bio_types/
genome.rs

1use std::cmp;
2use std::ops::Range;
3
4#[cfg(feature = "serde")]
5use serde::{Deserialize, Serialize};
6
7pub type Position = u64;
8pub type Length = u64;
9
10pub trait AbstractInterval {
11    /// Identifier for a genomic contig, e.g., a chromosome
12    fn contig(&self) -> &str;
13    /// Interval on the contig
14    fn range(&self) -> Range<Position>;
15    /// Return true if interval contains given locus.
16    fn contains<L>(&self, locus: L) -> bool
17    where
18        L: AbstractLocus,
19    {
20        self.contig() == locus.contig()
21            && locus.pos() >= self.range().start
22            && locus.pos() < self.range().end
23    }
24}
25#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
26#[derive(new, Debug, PartialEq, Eq, Clone, Hash)]
27pub struct Interval {
28    contig: String,
29    range: Range<Position>,
30}
31
32impl PartialOrd for Interval {
33    fn partial_cmp(&self, other: &Self) -> Option<cmp::Ordering> {
34        Some(self.contig.cmp(&other.contig).then_with(|| {
35            self.range
36                .start
37                .cmp(&other.range.start)
38                .then_with(|| self.range.end.cmp(&other.range.end))
39        }))
40    }
41}
42
43impl Ord for Interval {
44    fn cmp(&self, other: &Self) -> cmp::Ordering {
45        self.partial_cmp(other).unwrap()
46    }
47}
48
49impl Interval {
50    /// Mutable reference to interval on the contig
51    pub fn range_mut(&mut self) -> &mut Range<Position> {
52        &mut self.range
53    }
54}
55
56impl AbstractInterval for Interval {
57    fn contig(&self) -> &str {
58        &self.contig
59    }
60
61    fn range(&self) -> Range<Position> {
62        self.range.clone()
63    }
64}
65
66pub trait AbstractLocus {
67    /// Identifier for a genomic contig, e.g., a chromosome
68    fn contig(&self) -> &str;
69    /// Position on the contig
70    fn pos(&self) -> Position;
71}
72
73#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
74#[derive(new, Debug, PartialEq, Eq, PartialOrd, Ord, Clone, Hash)]
75pub struct Locus {
76    contig: String,
77    pos: Position,
78}
79
80impl Locus {
81    /// Mutable reference to position.
82    pub fn pos_mut(&mut self) -> &mut Position {
83        &mut self.pos
84    }
85}
86
87impl AbstractLocus for Locus {
88    fn contig(&self) -> &str {
89        &self.contig
90    }
91
92    fn pos(&self) -> Position {
93        self.pos
94    }
95}
bio_types/genome.rs

bio_types/
genome.rs
