5550351717

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Build # 5550351717

Build Type

Pull #63

github

Committed by

web-flow

Commit Message

Merge be9eac796 into 907b3d9da

Pull Request Pull Request #63: fix: pretty print with suffix xclip or yclip

Run Details

2 of 2 new or added lines in 1 file covered. (100.0%)

474 of 746 relevant lines covered (63.54%)

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0.0

/src/genome.rs

use std::cmp;
use std::ops::Range;

#[cfg(feature = "serde")]
use serde::{Deserialize, Serialize};

pub type Position = u64;
pub type Length = u64;

pub trait AbstractInterval {
    /// Identifier for a genomic contig, e.g., a chromosome
    fn contig(&self) -> &str;
    /// Interval on the contig
    fn range(&self) -> Range<Position>;
    /// Return true if interval contains given locus.
    fn contains<L>(&self, locus: L) -> bool
    where
        L: AbstractLocus,
    {
        self.contig() == locus.contig()
            && locus.pos() >= self.range().start
            && locus.pos() < self.range().end
    }
}
#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
#[derive(new, Debug, PartialEq, Eq, Clone, Hash)]
pub struct Interval {
    contig: String,
    range: Range<Position>,
}

impl PartialOrd for Interval {
    fn partial_cmp(&self, other: &Self) -> Option<cmp::Ordering> {
        Some(self.contig.cmp(&other.contig).then_with(|| {
            self.range
                .start
                .cmp(&other.range.start)
                .then_with(|| self.range.end.cmp(&other.range.end))
        }))
    }
}

impl Ord for Interval {
    fn cmp(&self, other: &Self) -> cmp::Ordering {
        self.partial_cmp(other).unwrap()
    }
}

impl Interval {
    /// Mutable reference to interval on the contig
    pub fn range_mut(&mut self) -> &mut Range<Position> {
        &mut self.range
    }
}

impl AbstractInterval for Interval {
    fn contig(&self) -> &str {
        &self.contig
    }

    fn range(&self) -> Range<Position> {
        self.range.clone()
    }
}

pub trait AbstractLocus {
    /// Identifier for a genomic contig, e.g., a chromosome
    fn contig(&self) -> &str;
    /// Position on the contig
    fn pos(&self) -> Position;
}

#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
#[derive(new, Debug, PartialEq, Eq, PartialOrd, Ord, Clone, Hash)]
pub struct Locus {
    contig: String,
    pos: Position,
}

impl Locus {
    /// Mutable reference to position.
    pub fn pos_mut(&mut self) -> &mut Position {
        &mut self.pos
    }
}

impl AbstractLocus for Locus {
    fn contig(&self) -> &str {
        &self.contig
    }

    fn pos(&self) -> Position {
        self.pos
    }
}

1	use std::cmp;
2	use std::ops::Range;
3
4	#[cfg(feature = "serde")]
5	use serde::{Deserialize, Serialize};
6
7	pub type Position = u64;
8	pub type Length = u64;
9
10	pub 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)]
27	pub struct Interval {
28	contig: String,
29	range: Range<Position>,
30	}
31
32	impl 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
43	impl Ord for Interval {
44	fn cmp(&self, other: &Self) -> cmp::Ordering {	×
45	self.partial_cmp(other).unwrap()	×
46	}
47	}
48
49	impl 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
56	impl 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
66	pub 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)]
75	pub struct Locus {
76	contig: String,
77	pos: Position,
78	}
79
80	impl Locus {
81	/// Mutable reference to position.
82	pub fn pos_mut(&mut self) -> &mut Position {	×
83	&mut self.pos	×
84	}
85	}
86
87	impl AbstractLocus for Locus {
88	fn contig(&self) -> &str {	×
89	&self.contig	×
90	}
91
92	fn pos(&self) -> Position {	×
93	self.pos	×
94	}
95	}

rust-bio / rust-bio-types / 5550351717

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