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Merge pull request #8 from theGreatHerrLebert/david@rustdf
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fixing tests
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@theGreatHerrLebert
theGreatHerrLebert authored Sep 21, 2023
2 parents 6d8d09a + 3cf38c2 commit f55f82e
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Showing 2 changed files with 33 additions and 33 deletions.
2 changes: 1 addition & 1 deletion mscore/src/lib.rs
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
pub mod mz_spectrum;
pub use {mz_spectrum::MzSpectrum, mz_spectrum::TOFMzSpectrum, mz_spectrum::ImsSpectrum, mz_spectrum::TimsSpectrum, mz_spectrum::ImsFrame, mz_spectrum::TimsFrame, mz_spectrum::MsType};
pub use {mz_spectrum::MzSpectrum, mz_spectrum::IndexedMzSpectrum, mz_spectrum::ImsSpectrum, mz_spectrum::TimsSpectrum, mz_spectrum::ImsFrame, mz_spectrum::TimsFrame, mz_spectrum::MsType};
64 changes: 32 additions & 32 deletions mscore/src/mz_spectrum.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -189,34 +189,34 @@ impl std::ops::Add for MzSpectrum {
}
}

/// Represents a Time-Of-Flight (TOF) mass spectrum with corresponding m/z values and intensities.
/// Represents a mass spectrum with associated m/z indices, m/z values, and intensities
#[derive(Clone)]
pub struct TOFMzSpectrum {
pub tof: Vec<i32>,
pub struct IndexedMzSpectrum {
pub index: Vec<i32>,
pub mz: Vec<f64>,
pub intensity: Vec<f64>,
}

impl TOFMzSpectrum {
impl IndexedMzSpectrum {
/// Creates a new `TOFMzSpectrum` instance.
///
/// # Arguments
///
/// * `tof` - A vector containing the time-of-flight values.
/// * `index` - A vector containing the mz index, e.g., time-of-flight values.
/// * `mz` - A vector containing the m/z values.
/// * `intensity` - A vector containing the intensity values.
///
/// # Examples
///
/// ```
/// use mscore::TOFMzSpectrum;
///
/// let spectrum = TOFMzSpectrum::new(vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// use mscore::IndexedMzSpectrum;
///
/// let spectrum = IndexedMzSpectrum::new(vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// ```
pub fn new(tof: Vec<i32>, mz: Vec<f64>, intensity: Vec<f64>) -> Self {
TOFMzSpectrum {tof, mz, intensity}
IndexedMzSpectrum { index: tof, mz, intensity}
}
/// Bins the spectrum based on a given m/z resolution, summing intensities and averaging TOF values
/// Bins the spectrum based on a given m/z resolution, summing intensities and averaging index values
/// for m/z values that fall into the same bin.
///
/// # Arguments
Expand All @@ -226,21 +226,21 @@ impl TOFMzSpectrum {
/// # Examples
///
/// ```
/// use mscore::TOFMzSpectrum;
///
/// let spectrum = TOFMzSpectrum::new(vec![1000, 2000], vec![100.42, 100.43], vec![50.0, 60.0]);
/// use mscore::IndexedMzSpectrum;
///
/// let spectrum = IndexedMzSpectrum::new(vec![1000, 2000], vec![100.42, 100.43], vec![50.0, 60.0]);
/// let binned_spectrum = spectrum.to_resolution(1);
///
///
/// assert_eq!(binned_spectrum.mz, vec![100.4]);
/// assert_eq!(binned_spectrum.intensity, vec![110.0]);
/// assert_eq!(binned_spectrum.tof, vec![1500]);
/// assert_eq!(binned_spectrum.index, vec![1500]);
/// ```
pub fn to_resolution(&self, resolution: u32) -> TOFMzSpectrum {
pub fn to_resolution(&self, resolution: u32) -> IndexedMzSpectrum {

let mut mz_bins: BTreeMap<i64, (f64, Vec<i64>)> = BTreeMap::new();
let factor = 10f64.powi(resolution as i32);

for ((mz, intensity), tof_val) in self.mz.iter().zip(self.intensity.iter()).zip(&self.tof) {
for ((mz, intensity), tof_val) in self.mz.iter().zip(self.intensity.iter()).zip(&self.index) {
let key = (mz * factor).round() as i64;
let entry = mz_bins.entry(key).or_insert((0.0, Vec::new()));
entry.0 += *intensity;
Expand All @@ -255,18 +255,18 @@ impl TOFMzSpectrum {
(sum as f64 / count as f64).round() as i32
}).collect();

TOFMzSpectrum { mz, intensity, tof }
IndexedMzSpectrum { mz, intensity, index: tof }
}
}

impl fmt::Display for TOFMzSpectrum {
impl fmt::Display for IndexedMzSpectrum {
fn fmt(&self, f: &mut Formatter<'_>) -> fmt::Result {
let (mz, i) = self.mz.iter()
.zip(&self.intensity)
.max_by(|a, b| a.1.partial_cmp(&b.1).unwrap_or(std::cmp::Ordering::Equal))
.unwrap();

write!(f, "TOFMzSpectrum(data points: {}, max by intensity:({}, {}))", self.mz.len(), format!("{:.3}", mz), i)
write!(f, "IndexedMzSpectrum(data points: {}, max by intensity:({}, {}))", self.mz.len(), format!("{:.3}", mz), i)
}
}

Expand Down Expand Up @@ -312,7 +312,7 @@ pub struct TimsSpectrum {
pub scan_id: i32,
pub retention_time: f64,
pub inv_mobility: f64,
pub spectrum: TOFMzSpectrum,
pub spectrum: IndexedMzSpectrum,
}

impl TimsSpectrum {
Expand All @@ -329,11 +329,11 @@ impl TimsSpectrum {
/// # Examples
///
/// ```
/// use mscore::{TimsSpectrum, TOFMzSpectrum};
/// use mscore::{TimsSpectrum, IndexedMzSpectrum};
///
/// let spectrum = TimsSpectrum::new(1, 1, 100.0, 0.1, TOFMzSpectrum::new(vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]));
/// let spectrum = TimsSpectrum::new(1, 1, 100.0, 0.1, IndexedMzSpectrum::new(vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]));
/// ```
pub fn new(frame_id: i32, scan_id: i32, retention_time: f64, inv_mobility: f64, spectrum: TOFMzSpectrum) -> Self {
pub fn new(frame_id: i32, scan_id: i32, retention_time: f64, inv_mobility: f64, spectrum: IndexedMzSpectrum) -> Self {
TimsSpectrum { frame_id, scan_id, retention_time, inv_mobility, spectrum }
}
}
Expand Down Expand Up @@ -412,7 +412,7 @@ impl TimsFrame {
/// use mscore::MsType;
/// use mscore::TimsFrame;
///
/// let frame = TimsFrame::new(1, MsType::PRECURSOR, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// ```
pub fn new(frame_id: i32, ms_type: MsType, retention_time: f64, scan: Vec<i32>, inv_mobility: Vec<f64>, tof: Vec<i32>, mz: Vec<f64>, intensity: Vec<f64>) -> Self {
TimsFrame { frame_id, ms_type, retention_time, scan, inv_mobility, tof, mz, intensity }
Expand All @@ -424,9 +424,9 @@ impl TimsFrame {
/// # Examples
///
/// ```
/// use mscore::{TimsSpectrum, TimsFrame};
/// use mscore::{TimsSpectrum, TimsFrame, MsType};
///
/// let frame = TimsFrame::new(1, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// let ims_spectrum = frame.to_ims_frame();
/// ```
pub fn to_ims_frame(&self) -> ImsFrame {
Expand All @@ -439,9 +439,9 @@ impl TimsFrame {
/// # Examples
///
/// ```
/// use mscore::{TimsSpectrum, TimsFrame};
/// use mscore::{TimsSpectrum, TimsFrame, MsType};
///
/// let frame = TimsFrame::new(1, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// let tims_spectra = frame.to_tims_spectra();
/// ```
pub fn to_tims_spectra(&self) -> Vec<TimsSpectrum> {
Expand All @@ -463,7 +463,7 @@ impl TimsFrame {
let mut tims_spectra: Vec<TimsSpectrum> = Vec::new();

for (scan, (inv_mobility, tof, mz, intensity)) in spectra {
let spectrum = TOFMzSpectrum::new(tof, mz, intensity);
let spectrum = IndexedMzSpectrum::new(tof, mz, intensity);
tims_spectra.push(TimsSpectrum::new(self.frame_id, scan, self.retention_time, inv_mobility, spectrum));
}

Expand All @@ -476,9 +476,9 @@ impl TimsFrame {
/// # Examples
///
/// ```
/// use mscore::{TimsSpectrum, TimsFrame};
/// use mscore::{TimsSpectrum, TimsFrame, MsType};
///
/// let frame = TimsFrame::new(1, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
/// let ims_spectra = frame.to_ims_spectra();
/// ```
pub fn to_ims_spectra(&self) -> Vec<ImsSpectrum> {
Expand Down

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