Merge pull request #4 from MannLabs/separate_frame_channels

Separate frame channels
MannLabs · Oct 19, 2023 · d9d009a · d9d009a
2 parents 81e4999 + 1ed2d54
commit d9d009a
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Showing 7 changed files with 70 additions and 22 deletions.
diff --git a/src/acquisition.rs b/src/acquisition.rs
@@ -0,0 +1,5 @@
+#[derive(Debug, PartialEq, Clone, Copy)]
+pub enum AcquisitionType {
+    DDAPASEF,
+    DIAPASEF,
+}
diff --git a/src/file_readers/frame_readers.rs b/src/file_readers/frame_readers.rs
@@ -10,6 +10,10 @@ pub trait ReadableFrames {
     fn read_single_frame(&self, index: usize) -> Frame;
 
     fn read_all_frames(&self) -> Vec<Frame>;
+
+    fn read_ms1_frames(&self) -> Vec<Frame>;
+
+    fn read_ms2_frames(&self) -> Vec<Frame>;
 }
 
 impl FileFormat {
@@ -35,4 +39,12 @@ impl ReadableFrames for FileFormat {
     fn read_all_frames(&self) -> Vec<Frame> {
         self.unwrap_frame_reader().read_all_frames()
     }
+
+    fn read_ms1_frames(&self) -> Vec<Frame> {
+        self.unwrap_frame_reader().read_ms1_frames()
+    }
+
+    fn read_ms2_frames(&self) -> Vec<Frame> {
+        self.unwrap_frame_reader().read_ms2_frames()
+    }
 }
diff --git a/src/file_readers/frame_readers/tdf_reader.rs b/src/file_readers/frame_readers/tdf_reader.rs
@@ -1,5 +1,6 @@
 use {
     crate::{
+        acquisition::AcquisitionType,
         converters::{
             ConvertableIndex, Frame2RtConverter, Scan2ImConverter,
             Tof2MzConverter,
@@ -26,6 +27,7 @@ pub struct TDFReader {
     pub im_converter: Scan2ImConverter,
     pub mz_converter: Tof2MzConverter,
     pub frame_table: FrameTable,
+    frame_types: Vec<FrameType>,
 }
 
 impl TDFReader {
@@ -42,6 +44,16 @@ impl TDFReader {
             String::from(&file_name),
             frame_table.offsets.clone(),
         );
+        let frame_types: Vec<FrameType> = frame_table
+            .msms_type
+            .iter()
+            .map(|msms_type| match msms_type {
+                0 => FrameType::MS1,
+                8 => FrameType::MS2(AcquisitionType::DDAPASEF),
+                9 => FrameType::MS2(AcquisitionType::DIAPASEF),
+                _ => FrameType::Unknown,
+            })
+            .collect();
         Self {
             path: path.to_string(),
             tdf_bin_reader: tdf_bin_reader,
@@ -50,6 +62,7 @@ impl TDFReader {
             mz_converter: Tof2MzConverter::from_sql(&tdf_sql_reader),
             frame_table: frame_table,
             tdf_sql_reader: tdf_sql_reader,
+            frame_types: frame_types,
         }
     }
 
@@ -65,13 +78,7 @@ impl ReadableFrames for TDFReader {
             Frame::read_from_file(&self.tdf_bin_reader, index);
         frame.rt = self.rt_converter.convert(index as u32);
         frame.index = self.frame_table.id[index];
-        let msms_type = self.frame_table.msms_type[index];
-        frame.frame_type = match msms_type {
-            0 => FrameType::MS1,
-            8 => FrameType::MS2DDA,
-            9 => FrameType::MS2DIA,
-            _ => FrameType::Unknown,
-        };
+        frame.frame_type = self.frame_types[index];
         frame
     }
 
@@ -81,4 +88,24 @@ impl ReadableFrames for TDFReader {
             .map(|index| self.read_single_frame(index))
             .collect()
     }
+
+    fn read_ms1_frames(&self) -> Vec<Frame> {
+        (0..self.tdf_bin_reader.size())
+            .into_par_iter()
+            .map(|index| match self.frame_types[index] {
+                FrameType::MS1 => self.read_single_frame(index),
+                _ => Frame::default(),
+            })
+            .collect()
+    }
+
+    fn read_ms2_frames(&self) -> Vec<Frame> {
+        (0..self.tdf_bin_reader.size())
+            .into_par_iter()
+            .map(|index| match self.frame_types[index] {
+                FrameType::MS2(_) => self.read_single_frame(index),
+                _ => Frame::default(),
+            })
+            .collect()
+    }
 }
diff --git a/src/file_readers/spectrum_readers/dda_reader.rs b/src/file_readers/spectrum_readers/dda_reader.rs
@@ -26,21 +26,21 @@ pub struct DDASpectrumReader {
     pub path_name: String,
     precursor_reader: PrecursorReader,
     mz_reader: Tof2MzConverter,
-    frames: Vec<Frame>,
+    ms2_frames: Vec<Frame>,
 }
 
 impl DDASpectrumReader {
     pub fn new(path_name: String) -> Self {
         let tdf_reader: TDFReader = TDFReader::new(&path_name.to_string());
         let mz_reader: Tof2MzConverter = tdf_reader.mz_converter;
-        let frames: Vec<Frame> = tdf_reader.read_all_frames();
+        let ms2_frames: Vec<Frame> = tdf_reader.read_ms2_frames();
         let precursor_reader: PrecursorReader =
             PrecursorReader::new(&tdf_reader);
         Self {
             path_name,
             precursor_reader,
             mz_reader,
-            frames,
+            ms2_frames,
         }
     }
 
@@ -53,21 +53,21 @@ impl DDASpectrumReader {
         for &index in selection.iter() {
             let frame: usize =
                 self.precursor_reader.pasef_frames.frame[index] - 1;
-            if self.frames[frame].intensities.len() == 0 {
+            if self.ms2_frames[frame].intensities.len() == 0 {
                 continue;
             }
             let scan_start: usize =
                 self.precursor_reader.pasef_frames.scan_start[index];
             let scan_end: usize =
                 self.precursor_reader.pasef_frames.scan_end[index];
             let offset_start: usize =
-                self.frames[frame].scan_offsets[scan_start] as usize;
+                self.ms2_frames[frame].scan_offsets[scan_start] as usize;
             let offset_end: usize =
-                self.frames[frame].scan_offsets[scan_end] as usize;
+                self.ms2_frames[frame].scan_offsets[scan_end] as usize;
             let tof_selection: &[u32] =
-                &self.frames[frame].tof_indices[offset_start..offset_end];
+                &self.ms2_frames[frame].tof_indices[offset_start..offset_end];
             let intensity_selection: &[u32] =
-                &self.frames[frame].intensities[offset_start..offset_end];
+                &self.ms2_frames[frame].intensities[offset_start..offset_end];
             tof_indices.extend(tof_selection);
             intensities.extend(intensity_selection);
         }

diff --git a/src/frames.rs b/src/frames.rs
@@ -1,3 +1,5 @@
+use crate::acquisition::AcquisitionType;
+
 #[derive(Debug, PartialEq, Default)]
 pub struct Frame {
     pub scan_offsets: Vec<u64>,
@@ -8,11 +10,10 @@ pub struct Frame {
     pub frame_type: FrameType,
 }
 
-#[derive(Debug, PartialEq)]
+#[derive(Debug, PartialEq, Clone, Copy)]
 pub enum FrameType {
     MS1,
-    MS2DDA,
-    MS2DIA,
+    MS2(AcquisitionType),
     Unknown,
 }
 

diff --git a/src/lib.rs b/src/lib.rs
@@ -18,6 +18,7 @@
 //!     * analysis.tdf
 //!     * analysis.tdf_bin
 
+mod acquisition;
 mod calibration;
 mod converters;
 mod errors;
@@ -28,6 +29,7 @@ mod spectra;
 mod vec_utils;
 
 pub use crate::{
+    acquisition::AcquisitionType,
     errors::*,
     file_readers::FileReader,
     frames::{Frame, FrameType},

diff --git a/tests/frame_readers.rs b/tests/frame_readers.rs
@@ -1,5 +1,5 @@
 use std::path::Path;
-use timsrust::{FileReader, Frame, FrameType};
+use timsrust::{AcquisitionType, FileReader, Frame, FrameType};
 
 fn get_local_directory() -> &'static Path {
     Path::new(std::file!())
@@ -15,7 +15,8 @@ fn tdf_reader_frames() {
         .to_str()
         .unwrap()
         .to_string();
-    let frames: Vec<Frame> = FileReader::new(file_path).unwrap().read_all_frames();
+    let frames: Vec<Frame> =
+        FileReader::new(file_path).unwrap().read_all_frames();
     let expected: Vec<Frame> = vec![
         Frame {
             scan_offsets: vec![0, 1, 3, 6, 10],
@@ -31,7 +32,7 @@ fn tdf_reader_frames() {
             intensities: (10..36).map(|x| (x + 1) * 2).collect(),
             index: 2,
             rt: 0.2,
-            frame_type: FrameType::MS2DDA,
+            frame_type: FrameType::MS2(AcquisitionType::DDAPASEF),
         },
         Frame {
             scan_offsets: vec![0, 9, 19, 30, 42],
@@ -47,7 +48,7 @@ fn tdf_reader_frames() {
             intensities: (78..136).map(|x| (x + 1) * 2).collect(),
             index: 4,
             rt: 0.4,
-            frame_type: FrameType::MS2DDA,
+            frame_type: FrameType::MS2(AcquisitionType::DDAPASEF),
         },
     ];
     for i in 0..frames.len() {