Update to timsrust 0.4

compomics · Dec 7, 2024 · e5ad3d6 · e5ad3d6
1 parent c02400f
commit e5ad3d6
Show file tree

Hide file tree

Showing 2 changed files with 27 additions and 26 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -14,7 +14,7 @@ thermo = ["mzdata/thermo"]
 
 [dependencies]
 mzdata = "0.39.0"
-timsrust = "0.3.0"
+timsrust = "0.4.1"
 
 [dependencies.pyo3]
 version = "0.23.3"

diff --git a/src/parse_timsrust.rs b/src/parse_timsrust.rs
@@ -3,8 +3,8 @@ use std::collections::HashMap;
 use crate::ms2_spectrum::MS2Spectrum;
 use crate::precursor::Precursor;
 
-impl From<timsrust::ms_data::Precursor> for Precursor {
-    fn from(precursor: timsrust::ms_data::Precursor) -> Self {
+impl From<timsrust::Precursor> for Precursor {
+    fn from(precursor: timsrust::Precursor) -> Self {
         Precursor {
             mz: precursor.mz,
             rt: precursor.rt,
@@ -15,8 +15,8 @@ impl From<timsrust::ms_data::Precursor> for Precursor {
     }
 }
 
-impl From<timsrust::ms_data::Spectrum> for MS2Spectrum {
-    fn from(spectrum: timsrust::ms_data::Spectrum) -> Self {
+impl From<timsrust::Spectrum> for MS2Spectrum {
+    fn from(spectrum: timsrust::Spectrum) -> Self {
         MS2Spectrum::new(
             spectrum.index.to_string(),
             spectrum.mz_values.iter().map(|mz| *mz as f32).collect(),
@@ -25,7 +25,7 @@ impl From<timsrust::ms_data::Spectrum> for MS2Spectrum {
                 .iter()
                 .map(|intensity| *intensity as f32)
                 .collect(),
-            Some(Precursor::from(spectrum.precursor)),
+            spectrum.precursor.map(Precursor::from),
         )
     }
 }
@@ -34,35 +34,36 @@ impl From<timsrust::ms_data::Spectrum> for MS2Spectrum {
 pub fn parse_precursor_info(
     spectrum_path: &str,
 ) -> Result<HashMap<String, Precursor>, std::io::Error> {
-    let reader = timsrust::FileReader::new(spectrum_path)
+    let reader = timsrust::readers::SpectrumReader::new(spectrum_path)
         .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
 
-    Ok(reader
-        .read_all_spectra()
+    let spectra = reader
+        .get_all()
         .into_iter()
-        .filter(|spectrum| {
-            matches!(
-                spectrum.precursor,
-                timsrust::ms_data::Precursor { .. }
-            )
-        })
-        .map(|spectrum| {
-            (
-                spectrum.index.to_string(),
-                Precursor::from(spectrum.precursor),
-            )
+        .collect::<Result<Vec<_>, _>>()
+        .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
+
+    let precursor_info = spectra
+        .into_iter()
+        .filter_map(|spectrum| match spectrum.precursor {
+            Some(precursor) => Some((spectrum.index.to_string(), Precursor::from(precursor))),
+            None => None,
         })
-        .collect::<HashMap<String, Precursor>>())
+        .collect::<HashMap<_, _>>();
+
+    Ok(precursor_info)
 }
 
 /// Read MS2 spectra from spectrum files with timsrust
 pub fn read_ms2_spectra(spectrum_path: &str) -> Result<Vec<MS2Spectrum>, std::io::Error> {
-    let reader = timsrust::FileReader::new(spectrum_path)
+    let reader = timsrust::readers::SpectrumReader::new(spectrum_path)
         .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
 
-    Ok(reader
-        .read_all_spectra()
+    let spectra = reader
+        .get_all()
         .into_iter()
-        .map(MS2Spectrum::from)
-        .collect())
+        .collect::<Result<Vec<_>, _>>()
+        .map_err(|e| std::io::Error::new(std::io::ErrorKind::Other, e.to_string()))?;
+
+    Ok(spectra.into_iter().map(MS2Spectrum::from).collect())
 }