CHORE: grouped ms data together

MannLabs · Apr 8, 2024 · 8c39a9e · 8c39a9e
1 parent 0211d13
commit 8c39a9e
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Showing 10 changed files with 22 additions and 20 deletions.
diff --git a/src/calibration.rs b/src/calibration.rs
@@ -1,6 +1,6 @@
 use crate::{
     converters::{ConvertableDomain, Tof2MzConverter},
-    spectra::RawSpectrum,
+    data::spectra::RawSpectrum,
     Precursor,
 };
 

diff --git a/src/data.rs b/src/data.rs
@@ -0,0 +1,9 @@
+pub mod acquisition;
+pub mod frames;
+pub mod precursors;
+pub mod spectra;
+
+pub use acquisition::AcquisitionType;
+pub use frames::{Frame, FrameType};
+pub use precursors::{Precursor, QuadrupoleEvent};
+pub use spectra::Spectrum;
diff --git a/src/acquisition.rs → src/data/acquisition.rs b/src/acquisition.rs → src/data/acquisition.rs
@@ -3,5 +3,6 @@
 pub enum AcquisitionType {
     DDAPASEF,
     DIAPASEF,
+    PRMPASEF,
     Unknown,
 }
diff --git a/src/frames.rs → src/data/frames.rs b/src/frames.rs → src/data/frames.rs
@@ -1,4 +1,4 @@
-use crate::acquisition::AcquisitionType;
+use crate::AcquisitionType;
 
 /// A frame with all unprocessed data as it was acquired.
 #[derive(Debug, PartialEq, Default)]

diff --git a/src/precursors.rs → src/data/precursors.rs b/src/precursors.rs → src/data/precursors.rs
diff --git a/src/spectra.rs → src/data/spectra.rs b/src/spectra.rs → src/data/spectra.rs
@@ -1,8 +1,7 @@
 use crate::{
     converters::{ConvertableDomain, Tof2MzConverter},
-    precursors::QuadrupoleEvent,
     vec_utils::{filter_with_mask, find_sparse_local_maxima_mask},
-    Precursor,
+    Precursor, QuadrupoleEvent,
 };
 
 pub struct RawSpectrumProcessor {

diff --git a/src/file_readers/frame_readers/tdf_reader.rs b/src/file_readers/frame_readers/tdf_reader.rs
@@ -1,6 +1,5 @@
 use {
     crate::{
-        acquisition::AcquisitionType,
         converters::{
             ConvertableDomain, Frame2RtConverter, Scan2ImConverter,
             Tof2MzConverter,
@@ -12,7 +11,7 @@ use {
             },
             ReadableFrames,
         },
-        Frame, FrameType,
+        AcquisitionType, Frame, FrameType,
     },
     rayon::prelude::*,
     std::path::Path,

diff --git a/src/file_readers/spectrum_readers/dda_reader.rs b/src/file_readers/spectrum_readers/dda_reader.rs
@@ -3,15 +3,14 @@ mod precursors;
 use crate::{
     calibration::Tof2MzCalibrator,
     converters::Tof2MzConverter,
+    data::spectra::RawSpectrum,
+    data::spectra::{self, RawSpectrumProcessor},
     file_readers::{
         frame_readers::{tdf_reader::TDFReader, ReadableFrames},
         ReadableSpectra,
     },
-    frames::Frame,
-    spectra::RawSpectrum,
-    spectra::{self, RawSpectrumProcessor},
     vec_utils::group_and_sum,
-    Spectrum,
+    Frame, Spectrum,
 };
 
 use rayon::prelude::*;

diff --git a/src/file_readers/spectrum_readers/mini_tdf_reader.rs b/src/file_readers/spectrum_readers/mini_tdf_reader.rs
@@ -1,4 +1,4 @@
-use crate::file_readers::FileFormatError;
+use crate::{file_readers::FileFormatError, QuadrupoleEvent};
 use std::fs;
 use {
     crate::{
@@ -9,7 +9,6 @@ use {
             },
             ReadableSpectra,
         },
-        precursors::QuadrupoleEvent,
         Precursor, Spectrum,
     },
     rayon::prelude::*,

diff --git a/src/lib.rs b/src/lib.rs
@@ -21,24 +21,20 @@
 //!     * *.ms2spectrum.bin
 //!     * *.ms2spectrum.parquet
 
-mod acquisition;
 mod calibration;
 mod converters;
+mod data;
 mod errors;
 mod file_readers;
-mod frames;
-mod precursors;
-mod spectra;
 mod vec_utils;
 
 pub use crate::{
-    acquisition::AcquisitionType,
     converters::{
         ConvertableDomain, Frame2RtConverter, Scan2ImConverter, Tof2MzConverter,
     },
+    data::{
+        AcquisitionType, Frame, FrameType, Precursor, QuadrupoleEvent, Spectrum,
+    },
     errors::*,
     file_readers::FileReader,
-    frames::{Frame, FrameType},
-    precursors::{Precursor, QuadrupoleEvent},
-    spectra::Spectrum,
 };