CHORE: moved spectrum reader config serialization to timsrust

crates/sage-cli/src/input.rs

@@ -1,11 +1,10 @@
 use anyhow::{ensure, Context};
 use clap::ArgMatches;
-use sage_cloudpath::CloudPath;
+use sage_cloudpath::{tdf::BrukerSpectrumProcessor, CloudPath};
 use sage_core::{
     database::{Builder, Parameters},
     lfq::LfqSettings,
     mass::Tolerance,
-    spectrum::BrukerSpectrumProcessor,
     tmt::Isobaric,
 };
 use serde::{Deserialize, Serialize};

crates/sage-cli/src/main.rs

@@ -218,7 +218,11 @@ impl Runner {
                         path_lower.ends_with(ext)
                     }
                 }) {
-                    sage_cloudpath::util::read_tdf(path, file_id, scorer.bruker_spectrum_processor)
+                    sage_cloudpath::util::read_tdf(
+                        path,
+                        file_id,
+                        self.parameters.bruker_spectrum_processor,
+                    )
                 } else {
                     sage_cloudpath::util::read_mzml(path, file_id, sn)
                 };
@@ -268,7 +272,6 @@ impl Runner {
             report_psms: self.parameters.report_psms,
             wide_window: self.parameters.wide_window,
             annotate_matches: self.parameters.annotate_matches,
-            bruker_spectrum_processor: self.parameters.bruker_spectrum_processor,
         };
 
         //Collect all results into a single container

crates/sage-cli/tests/integration.rs

@@ -1,7 +1,7 @@
 use sage_core::database::Builder;
 use sage_core::mass::Tolerance;
 use sage_core::scoring::Scorer;
-use sage_core::spectrum::{BrukerSpectrumProcessor, SpectrumProcessor};
+use sage_core::spectrum::SpectrumProcessor;
 
 #[test]
 fn integration() -> anyhow::Result<()> {
@@ -32,7 +32,6 @@ fn integration() -> anyhow::Result<()> {
         report_psms: 1,
         wide_window: false,
         annotate_matches: false,
-        bruker_spectrum_processor: BrukerSpectrumProcessor::default(),
     };
 
     let psm = scorer.score(&processed);

crates/sage-cloudpath/Cargo.toml

@@ -23,7 +23,7 @@ log = "0.4.0"
 once_cell = "1.0"
 tokio = { version = "1.0", features = ["fs", "io-util", "rt", "macros"] }
 quick-xml = { version = "0.31.0", features = ["async-tokio"] }
-timsrust = { version = "0.4.0"}
+timsrust = { version = "0.4.1"}
 rayon = "1.5"
 reqwest = { version = "0.11", features = ["json", "rustls-tls"], default-features = false }
 regex = "1.6"

crates/sage-cloudpath/src/tdf.rs

@@ -1,11 +1,10 @@
 use rayon::prelude::*;
 use sage_core::{
     mass::Tolerance,
-    spectrum::{
-        BrukerSpectrumProcessor, FrameWindowSplittingStrategy, QuadWindowExpansionStrategy,
-    },
     spectrum::{Precursor, RawSpectrum, Representation},
 };
+use serde::{Deserialize, Serialize};
+use timsrust::readers::SpectrumReaderConfig;
 
 pub struct TdfReader;
 
@@ -18,9 +17,7 @@ impl TdfReader {
     ) -> Result<Vec<RawSpectrum>, timsrust::TimsRustError> {
         let spectrum_reader = timsrust::readers::SpectrumReader::build()
             .with_path(path_name.as_ref())
-            .with_config(Self::parse_bruker_spectrum_config(
-                bruker_spectrum_processor,
-            ))
+            .with_config(bruker_spectrum_processor.spectrum_reader_config)
             .finalize()?;
         let spectra: Vec<RawSpectrum> = (0..spectrum_reader.len())
             .into_par_iter()
@@ -69,67 +66,9 @@ impl TdfReader {
         precursor.inverse_ion_mobility = Option::from(dda_precursor.im as f32);
         precursor
     }
+}
 
-    fn parse_bruker_spectrum_config(
-        config: BrukerSpectrumProcessor,
-    ) -> timsrust::readers::SpectrumReaderConfig {
-        let mut spectrum_processing_params = timsrust::readers::SpectrumProcessingParams::default();
-        if let Some(smoothing_window) = config.smoothing_window {
-            spectrum_processing_params.smoothing_window = smoothing_window;
-        }
-        if let Some(centroiding_window) = config.centroiding_window {
-            spectrum_processing_params.centroiding_window = centroiding_window;
-        }
-        if let Some(calibration_tolerance) = config.calibration_tolerance {
-            spectrum_processing_params.calibration_tolerance = calibration_tolerance;
-        }
-        if let Some(calibrate) = config.calibrate {
-            spectrum_processing_params.calibrate = calibrate;
-        }
-        let frame_splitting_params: timsrust::readers::FrameWindowSplittingConfiguration;
-        if let Some(dia_strategy) = config.dia_strategy {
-            frame_splitting_params = match dia_strategy {
-                FrameWindowSplittingStrategy::Quadrupole(q) => {
-                    timsrust::readers::FrameWindowSplittingConfiguration::Quadrupole(match q {
-                        QuadWindowExpansionStrategy::None => {
-                            timsrust::readers::QuadWindowExpansionStrategy::None
-                        }
-                        QuadWindowExpansionStrategy::Even(n) => {
-                            timsrust::readers::QuadWindowExpansionStrategy::Even(n)
-                        }
-                        QuadWindowExpansionStrategy::UniformScan(x) => {
-                            timsrust::readers::QuadWindowExpansionStrategy::UniformScan(x)
-                        }
-                        QuadWindowExpansionStrategy::UniformMobility(x) => {
-                            timsrust::readers::QuadWindowExpansionStrategy::UniformMobility(x, None)
-                        }
-                    })
-                }
-                FrameWindowSplittingStrategy::Window(q) => {
-                    timsrust::readers::FrameWindowSplittingConfiguration::Window(match q {
-                        QuadWindowExpansionStrategy::None => {
-                            timsrust::readers::QuadWindowExpansionStrategy::None
-                        }
-
-                        QuadWindowExpansionStrategy::Even(n) => {
-                            timsrust::readers::QuadWindowExpansionStrategy::Even(n)
-                        }
-
-                        QuadWindowExpansionStrategy::UniformScan(x) => {
-                            timsrust::readers::QuadWindowExpansionStrategy::UniformScan(x)
-                        }
-                        QuadWindowExpansionStrategy::UniformMobility(x) => {
-                            timsrust::readers::QuadWindowExpansionStrategy::UniformMobility(x, None)
-                        }
-                    })
-                }
-            };
-        } else {
-            frame_splitting_params = timsrust::readers::FrameWindowSplittingConfiguration::default()
-        }
-        timsrust::readers::SpectrumReaderConfig {
-            spectrum_processing_params,
-            frame_splitting_params,
-        }
-    }
+#[derive(Clone, Copy, Serialize, Deserialize, Default)]
+pub struct BrukerSpectrumProcessor {
+    pub spectrum_reader_config: SpectrumReaderConfig,
 }

crates/sage-cloudpath/src/util.rs

@@ -1,5 +1,5 @@
-use crate::{read_and_execute, Error};
-use sage_core::spectrum::{BrukerSpectrumProcessor, RawSpectrum};
+use crate::{read_and_execute, tdf::BrukerSpectrumProcessor, Error};
+use sage_core::spectrum::RawSpectrum;
 use serde::Serialize;
 use tokio::io::AsyncReadExt;
 

crates/sage/src/scoring.rs

@@ -2,7 +2,7 @@ use crate::database::{IndexedDatabase, PeptideIx};
 use crate::heap::bounded_min_heapify;
 use crate::ion_series::{IonSeries, Kind};
 use crate::mass::{Tolerance, NEUTRON, PROTON};
-use crate::spectrum::{BrukerSpectrumProcessor, Precursor, ProcessedSpectrum};
+use crate::spectrum::{Precursor, ProcessedSpectrum};
 use serde::Serialize;
 use std::ops::AddAssign;
 use std::sync::atomic::{AtomicUsize, Ordering};
@@ -191,7 +191,6 @@ pub struct Scorer<'db> {
     // the precursor tolerance window based on MS2 isolation window and charge
     pub wide_window: bool,
     pub annotate_matches: bool,
-    pub bruker_spectrum_processor: BrukerSpectrumProcessor,
 }
 
 #[inline(always)]

crates/sage/src/spectrum.rs

@@ -1,5 +1,3 @@
-use serde::{Deserialize, Serialize};
-
 use crate::database::binary_search_slice;
 use crate::mass::{Tolerance, NEUTRON, PROTON};
 
@@ -359,32 +357,6 @@ impl SpectrumProcessor {
     }
 }
 
-#[derive(Clone, Copy, Serialize, Deserialize, Default)]
-pub struct BrukerSpectrumProcessor {
-    pub smoothing_window: Option<u32>,
-    pub centroiding_window: Option<u32>,
-    pub calibration_tolerance: Option<f64>,
-    pub calibrate: Option<bool>,
-    pub dia_strategy: Option<FrameWindowSplittingStrategy>,
-}
-
-type ScanSpanStep = (usize, usize);
-type MobilitySpanStep = (f64, f64);
-
-#[derive(Debug, Copy, Clone, Serialize, Deserialize)]
-pub enum QuadWindowExpansionStrategy {
-    None,
-    Even(usize),
-    UniformMobility(MobilitySpanStep),
-    UniformScan(ScanSpanStep),
-}
-
-#[derive(Debug, Clone, Copy, Serialize, Deserialize)]
-pub enum FrameWindowSplittingStrategy {
-    Quadrupole(QuadWindowExpansionStrategy),
-    Window(QuadWindowExpansionStrategy),
-}
-
 #[cfg(test)]
 mod test {
     use super::*;