From 86da407d889c37f4b3e0aa564d7040600e70d45d Mon Sep 17 00:00:00 2001
From: Kevin Velghe <kevin.velghe@ugent.be>
Date: Tue, 13 Aug 2024 19:03:28 +0200
Subject: [PATCH] use mz_read to parse precursor info

---
 src/lib.rs          |  2 +-
 src/parse_mzdata.rs | 28 ++++------------------------
 2 files changed, 5 insertions(+), 25 deletions(-)

diff --git a/src/lib.rs b/src/lib.rs
index b78771b..f8bc25d 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -20,7 +20,7 @@ pub fn get_precursor_info(spectrum_path: String) -> PyResult<HashMap<String, Pre
 
     let precursors = match file_type {
         SpectrumFileType::MascotGenericFormat | SpectrumFileType::MzML => {
-            parse_mzdata::parse_precursor_info(&spectrum_path, file_type)
+            parse_mzdata::parse_precursor_info(&spectrum_path)
         }
         SpectrumFileType::BrukerRaw => parse_timsrust::parse_precursor_info(&spectrum_path),
         // SpectrumFileType::ThermoRaw => parse_with_mzdata_thermo(&spectrum_path, file_type),
diff --git a/src/parse_mzdata.rs b/src/parse_mzdata.rs
index 5717d1a..ded832d 100644
--- a/src/parse_mzdata.rs
+++ b/src/parse_mzdata.rs
@@ -1,11 +1,8 @@
 use std::collections::HashMap;
-use std::fs::File;
 
-use mzdata::io::{MGFReader, MzMLReader};
 use mzdata::params::ParamValue;
 use mzdata::mz_read;
 
-use crate::file_types::SpectrumFileType;
 use crate::ms2_spectrum::MS2Spectrum;
 use crate::precursor::Precursor;
 
@@ -51,32 +48,15 @@ impl From<mzdata::spectrum::MultiLayerSpectrum> for MS2Spectrum {
 /// Parse precursor info from spectrum files with mzdata
 pub fn parse_precursor_info(
     spectrum_path: &str,
-    file_type: SpectrumFileType,
 ) -> Result<HashMap<String, Precursor>, std::io::Error> {
-    let file = File::open(spectrum_path)?;
-    match file_type {
-        SpectrumFileType::MascotGenericFormat => Ok(MGFReader::new(file)
-            .filter_map(|spectrum| {
-                spectrum.description.precursor.as_ref()?;
-                Some((spectrum.description.id.clone(), Precursor::from(&spectrum)))
-            })
-            .collect::<HashMap<String, Precursor>>()),
-
-        SpectrumFileType::MzML => Ok(MzMLReader::new(file)
+    mz_read!(spectrum_path.as_ref(), reader => {
+        reader.filter(|spectrum| spectrum.description.ms_level == 2)
             .filter_map(|spectrum| {
-                if spectrum.description.ms_level != 2 {
-                    return None;
-                }
                 spectrum.description.precursor.as_ref()?;
                 Some((spectrum.description.id.clone(), Precursor::from(&spectrum)))
             })
-            .collect::<HashMap<String, Precursor>>()),
-
-        _ => Err(std::io::Error::new(
-            std::io::ErrorKind::InvalidInput,
-            "Unsupported file type for mzdata",
-        )),
-    }
+            .collect::<HashMap<String, Precursor>>()
+    })
 }
 
 /// Read MS2 spectra from spectrum files with mzdata