koth-ms 0.10.0

High-performance LC-MS feature finder for timsTOF and mzML data
Documentation 
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use super::*;
use crate::config::{FileConfig, HillsConfig};
use crate::models::{Peak, Spectrum};

fn spec(scan_index: usize, rt: f64, mzs: &[f32]) -> Spectrum {
    Spectrum {
        scan_index,
        retention_time: rt,
        peaks: mzs
            .iter()
            .map(|&mz| Peak {
                mz,
                intensity: 1000.0,
                ion_mobility: 0.0,
            })
            .collect(),
        ms_level: 1,
        isolation_window: None,
        faims_cv: None,
    }
}

fn default_cfgs(max_gap: usize) -> (HillsConfig, FileConfig) {
    let mut h = HillsConfig::default();
    h.max_gap = max_gap;
    h.split_hills = false;
    h.min_scans = 3;
    (h, FileConfig::default())
}

/// Regression: with `max_gap = 0`, a hill that matches the same m/z in N
/// consecutive scans must be retained (previously a stale-cleanup off-by-one
/// killed every hill before it could extend past 1 scan).
#[test]
fn max_gap_zero_retains_consecutive_hill() {
    let (h, f) = default_cfgs(0);
    let mut det = HillDetector::new(&h, &f);
    for i in 0..5 {
        det.process_scan(&spec(i, i as f64 * 0.1, &[500.0]));
    }
    let hills = det.finish();
    assert_eq!(hills.len(), 1, "expected 1 hill, got {}", hills.len());
    assert_eq!(hills[0].n_scans, 5);
    assert_eq!(hills[0].skipped_scans, 0);
}

/// With `max_gap = 0`, a one-scan gap must terminate the hill.
#[test]
fn max_gap_zero_disallows_gaps() {
    let (h, f) = default_cfgs(0);
    let mut det = HillDetector::new(&h, &f);
    for i in 0..3 {
        det.process_scan(&spec(i, i as f64 * 0.1, &[500.0]));
    }
    det.process_scan(&spec(3, 0.3, &[]));
    for i in 4..7 {
        det.process_scan(&spec(i, i as f64 * 0.1, &[500.0]));
    }
    let hills = det.finish();
    assert_eq!(
        hills.len(),
        2,
        "expected 2 hills split across the gap, got {}",
        hills.len()
    );
    for hl in &hills {
        assert_eq!(hl.skipped_scans, 0);
    }
}

/// With `max_gap = 1`, a single missed scan must be bridged.
#[test]
fn max_gap_one_bridges_single_miss() {
    let (h, f) = default_cfgs(1);
    let mut det = HillDetector::new(&h, &f);
    for i in 0..2 {
        det.process_scan(&spec(i, i as f64 * 0.1, &[500.0]));
    }
    det.process_scan(&spec(2, 0.2, &[])); // miss
    for i in 3..5 {
        det.process_scan(&spec(i, i as f64 * 0.1, &[500.0]));
    }
    let hills = det.finish();
    assert_eq!(
        hills.len(),
        1,
        "expected 1 bridged hill, got {}",
        hills.len()
    );
    assert_eq!(hills[0].skipped_scans, 1);
}

/// With `max_gap = 1`, two consecutive missed scans must split the hill.
#[test]
fn max_gap_one_splits_at_two_misses() {
    let (h, f) = default_cfgs(1);
    let mut det = HillDetector::new(&h, &f);
    for i in 0..3 {
        det.process_scan(&spec(i, i as f64 * 0.1, &[500.0]));
    }
    det.process_scan(&spec(3, 0.3, &[])); // miss
    det.process_scan(&spec(4, 0.4, &[])); // miss
    for i in 5..8 {
        det.process_scan(&spec(i, i as f64 * 0.1, &[500.0]));
    }
    let hills = det.finish();
    assert_eq!(hills.len(), 2, "expected 2 hills, got {}", hills.len());
}