rsomics_bioenv/
dm.rs

1use std::io::BufRead;
2
3use rsomics_common::{Result, RsomicsError};
4
5/// A square, symmetric distance matrix with sample ids, in row-major order.
6pub struct DistanceMatrix {
7    pub ids: Vec<String>,
8    pub data: Vec<f64>,
9    pub n: usize,
10}
11
12impl DistanceMatrix {
13    pub fn read<R: BufRead>(reader: R, source: &str) -> Result<Self> {
14        let mut lines = reader.lines();
15
16        let header = lines
17            .next()
18            .ok_or_else(|| RsomicsError::InvalidInput(format!("{source}: empty matrix")))?
19            .map_err(RsomicsError::Io)?;
20
21        // lsmat header: a leading empty cell, then the column ids.
22        let ids: Vec<String> = header
23            .split('\t')
24            .skip(1)
25            .map(str::trim)
26            .map(str::to_owned)
27            .collect();
28        let n = ids.len();
29        if n < 3 {
30            return Err(RsomicsError::InvalidInput(format!(
31                "{source}: need at least 3 ids, found {n}"
32            )));
33        }
34
35        let mut data = vec![0.0f64; n * n];
36        let mut row = 0;
37        for line in lines {
38            let line = line.map_err(RsomicsError::Io)?;
39            if line.is_empty() {
40                continue;
41            }
42            if row >= n {
43                return Err(RsomicsError::InvalidInput(format!(
44                    "{source}: more rows than the {n} ids in the header"
45                )));
46            }
47            let mut fields = line.split('\t');
48            let rid = fields.next().unwrap_or("").trim();
49            if rid != ids[row] {
50                return Err(RsomicsError::InvalidInput(format!(
51                    "{source}: row {row} id '{rid}' != header id '{}'",
52                    ids[row]
53                )));
54            }
55            let mut col = 0;
56            for f in fields {
57                if col >= n {
58                    return Err(RsomicsError::InvalidInput(format!(
59                        "{source}: row {row} has more than {n} values"
60                    )));
61                }
62                data[row * n + col] = f.trim().parse::<f64>().map_err(|_| {
63                    RsomicsError::InvalidInput(format!(
64                        "{source}: row {row} col {col}: not a number: '{f}'"
65                    ))
66                })?;
67                col += 1;
68            }
69            if col != n {
70                return Err(RsomicsError::InvalidInput(format!(
71                    "{source}: row {row} has {col} values, expected {n}"
72                )));
73            }
74            row += 1;
75        }
76        if row != n {
77            return Err(RsomicsError::InvalidInput(format!(
78                "{source}: {row} data rows, expected {n}"
79            )));
80        }
81
82        Ok(DistanceMatrix { ids, data, n })
83    }
84
85    /// Upper-triangle (i<j) entries in row-major order — skbio's condensed form.
86    pub fn condensed(&self) -> Vec<f64> {
87        let n = self.n;
88        let mut v = Vec::with_capacity(n * (n - 1) / 2);
89        for i in 0..n {
90            for j in (i + 1)..n {
91                v.push(self.data[i * n + j]);
92            }
93        }
94        v
95    }
96}
rsomics_bioenv/dm.rs

rsomics_bioenv/
dm.rs
