Merge pull request #29 from MannLabs/develop

Develop

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "timsrust"
-version = "0.4.0"
+version = "0.4.1"
 edition = "2021"
 description = "A crate to read Bruker timsTOF data"
 license = "Apache-2.0"
@@ -22,11 +22,14 @@ thiserror = "1.0.0"
 memmap2 = "0.9.3"
 rusqlite = { version = "0.31.0", features = ["bundled"], optional = true}
 parquet = { version = "42.0.0", optional = true }
+serde = { version = "1.0.209", features = ["derive"], optional = true }
+serde_json = { version = "1.0.127", optional = true }
 
 [features]
 tdf = ["rusqlite"]
 minitdf = ["parquet"]
-default = ["tdf", "minitdf"]
+default = ["tdf", "minitdf", "serialize"]
+serialize = ["serde", "serde_json"]
 
 [dev-dependencies]
 criterion = { version = "0.5.1", features = ["html_reports"] }

src/domain_converters/scan_to_im.rs

@@ -1,5 +1,9 @@
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
+
 /// A converter from Scan -> (inversed) ion mobility.
 #[derive(Debug, Default, Clone, Copy, PartialEq)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct Scan2ImConverter {
     scan_intercept: f64,
     scan_slope: f64,

src/domain_converters/tof_to_mz.rs

@@ -1,7 +1,10 @@
 use linreg::linear_regression;
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
 
 /// A converter from TOF -> m/z.
 #[derive(Debug, Default, Clone, Copy, PartialEq)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct Tof2MzConverter {
     tof_intercept: f64,
     tof_slope: f64,

src/io/readers/frame_reader.rs

@@ -112,6 +112,7 @@ impl FrameReader {
     }
 
     pub fn get(&self, index: usize) -> Result<Frame, FrameReaderError> {
+        // NOTE: get does it by 0-offsetting the vec, not by Frame index!!!
         let mut frame = self.frames[index].clone();
         let offset = self.offsets[index];
         let blob = self.tdf_bin_reader.get(offset)?;

src/io/readers/precursor_reader.rs

@@ -93,7 +93,7 @@ impl PrecursorReaderBuilder {
     }
 }
 
-trait PrecursorReaderTrait: Sync {
+trait PrecursorReaderTrait: Sync + Send {
     fn get(&self, index: usize) -> Option<Precursor>;
     fn len(&self) -> usize;
 }

src/io/readers/quad_settings_reader.rs

@@ -1,3 +1,5 @@
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
 use std::path::Path;
 
 use crate::{
@@ -151,6 +153,7 @@ type ScanSpanStep = (usize, usize);
 /// 100 and step 80 between their in the scan number.
 ///
 #[derive(Debug, Copy, Clone)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub enum QuadWindowExpansionStrategy {
     None,
     Even(usize),
@@ -171,6 +174,7 @@ pub enum FrameWindowSplittingStrategy {
 }
 
 #[derive(Debug, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub enum FrameWindowSplittingConfiguration {
     Quadrupole(QuadWindowExpansionStrategy),
     Window(QuadWindowExpansionStrategy),

src/io/readers/spectrum_reader.rs

@@ -8,6 +8,8 @@ use core::fmt;
 #[cfg(feature = "minitdf")]
 use minitdf::{MiniTDFSpectrumReader, MiniTDFSpectrumReaderError};
 use rayon::iter::{IntoParallelIterator, ParallelIterator};
+#[cfg(feature = "serialize")]
+use serde::{Deserialize, Serialize};
 use std::path::{Path, PathBuf};
 #[cfg(feature = "tdf")]
 use tdf::{TDFSpectrumReader, TDFSpectrumReaderError};
@@ -64,7 +66,7 @@ impl SpectrumReader {
         spectra
     }
 
-    pub fn calibrate(&mut self) {
+    fn calibrate(&mut self) {
         self.spectrum_reader.calibrate();
     }
 }
@@ -116,7 +118,7 @@ impl SpectrumReaderBuilder {
     }
 }
 
-trait SpectrumReaderTrait: Sync {
+trait SpectrumReaderTrait: Sync + Send {
     fn get(&self, index: usize) -> Result<Spectrum, SpectrumReaderError>;
     fn get_path(&self) -> PathBuf;
     fn len(&self) -> usize;
@@ -135,7 +137,8 @@ pub enum SpectrumReaderError {
     SpectrumReaderFileError(PathBuf),
 }
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct SpectrumProcessingParams {
     pub smoothing_window: u32,
     pub centroiding_window: u32,
@@ -154,7 +157,8 @@ impl Default for SpectrumProcessingParams {
     }
 }
 
-#[derive(Debug, Default, Clone)]
+#[derive(Debug, Default, Clone, Copy)]
+#[cfg_attr(feature = "serialize", derive(Serialize, Deserialize))]
 pub struct SpectrumReaderConfig {
     pub spectrum_processing_params: SpectrumProcessingParams,
     #[cfg(feature = "tdf")]

src/io/readers/spectrum_reader/tdf/raw_spectra.rs

@@ -135,7 +135,7 @@ impl RawSpectrumReader {
     }
 }
 
-pub trait RawSpectrumReaderTrait: Sync {
+pub trait RawSpectrumReaderTrait: Sync + Send {
     fn get(&self, index: usize) -> Result<RawSpectrum, RawSpectrumReaderError>;
     fn len(&self) -> usize;
 }