sfs-core 0.1.0

Core implementation of tools for working with site frequency spectra
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137

use std::{fmt, ops::Deref};

mod removed_axis;
pub(crate) use removed_axis::RemovedAxis;

mod strides;
pub use strides::Strides;

/// An axis index for an array.
#[derive(Clone, Copy, Debug, Eq, Hash, Ord, PartialEq, PartialOrd)]
pub struct Axis(pub usize);

impl Deref for Axis {
    type Target = usize;

    fn deref(&self) -> &Self::Target {
        &self.0
    }
}

/// An N-dimensional array shape.
#[derive(Clone, Debug, Eq, Hash, PartialEq)]
pub struct Shape(pub Vec<usize>);

impl Shape {
    /// The number of dimensions of an array with the corresponding shape.
    pub fn dimensions(&self) -> usize {
        self.0.len()
    }

    /// The number of elements of an array with the corresponding shape.
    pub fn elements(&self) -> usize {
        self.iter().product()
    }

    pub(crate) fn index_from_flat_unchecked(&self, mut flat: usize) -> Vec<usize> {
        let mut n = self.elements();
        let mut index = vec![0; self.len()];
        for (i, v) in self.iter().enumerate() {
            n /= v;
            index[i] = flat / n;
            flat %= n;
        }
        index
    }

    pub(crate) fn index_sum_from_flat_unchecked(&self, mut flat: usize) -> usize {
        let mut n = self.elements();
        let mut sum = 0;
        for v in self.iter() {
            n /= v;
            sum += flat / n;
            flat %= n;
        }
        sum
    }

    pub(crate) fn remove_axis(&self, axis: Axis) -> RemovedAxis<Self> {
        RemovedAxis::new(self, axis)
    }

    pub(crate) fn strides(&self) -> Strides {
        let mut strides = vec![1; self.len()];

        for (i, v) in self.iter().enumerate().skip(1).rev() {
            strides.iter_mut().take(i).for_each(|stride| *stride *= v)
        }

        Strides(strides)
    }
}

impl AsRef<[usize]> for Shape {
    fn as_ref(&self) -> &[usize] {
        self
    }
}

impl Deref for Shape {
    type Target = [usize];

    fn deref(&self) -> &Self::Target {
        &self.0
    }
}

impl From<Vec<usize>> for Shape {
    fn from(shape: Vec<usize>) -> Self {
        Self(shape)
    }
}

impl<const N: usize> From<[usize; N]> for Shape {
    fn from(shape: [usize; N]) -> Self {
        Self(shape.to_vec())
    }
}

impl From<usize> for Shape {
    fn from(shape: usize) -> Self {
        Self(vec![shape])
    }
}

impl fmt::Display for Shape {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        write!(f, "{}", self[0])?;
        for v in self.iter().skip(1) {
            write!(f, "/{v}")?;
        }
        Ok(())
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_index_from_flat_unchecked() {
        let shape = Shape(vec![3, 3, 4]);

        assert_eq!(shape.index_from_flat_unchecked(0), vec![0, 0, 0]);
        assert_eq!(shape.index_from_flat_unchecked(1), vec![0, 0, 1]);
        assert_eq!(shape.index_from_flat_unchecked(3), vec![0, 0, 3]);
        assert_eq!(shape.index_from_flat_unchecked(4), vec![0, 1, 0]);
        assert_eq!(shape.index_from_flat_unchecked(35), vec![2, 2, 3]);
    }

    #[test]
    fn test_strides() {
        let shape = Shape(vec![6, 3, 7]);
        let strides = shape.strides();

        assert_eq!(strides, Strides(vec![21, 7, 1]));
    }
}