Merge pull request #12 from vijay-gnanasambandan-bruker/adding_collis…

…ion_energy_in_precursor Adding collision energy in precursor.
MannLabs · Jan 3, 2024 · be40423 · be40423
2 parents c587617 + a987472
commit be40423
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Showing 4 changed files with 23 additions and 4 deletions.
diff --git a/src/file_readers/common/sql_reader.rs b/src/file_readers/common/sql_reader.rs
@@ -12,21 +12,27 @@ pub struct SqlReader {
 }
 
 impl SqlReader {
-    fn read_column_from_table<
-        T: rusqlite::types::FromSql + std::default::Default,
-    >(
+    fn read_column_from_table<T: rusqlite::types::FromSql + Default>(
         &self,
         column_name: &str,
         table_name: &str,
     ) -> Vec<T> {
-        let connection: Connection = get_sql_connection(&self.path);
         let column_names: Vec<String> =
             self.get_table_columns(table_name).unwrap();
         let order_by: String = column_names.join(", ");
         let query: String = format!(
             "SELECT {} FROM {} ORDER BY {}",
             column_name, table_name, order_by
         );
+
+        self.get_data_from_sql(&query)
+    }
+
+    pub fn get_data_from_sql<T: rusqlite::types::FromSql + Default>(
+        &self,
+        query: &String,
+    ) -> Vec<T> {
+        let connection: Connection = get_sql_connection(&self.path);
         let mut stmt: Statement = connection.prepare(&query).unwrap();
         let rows = stmt
             .query_map(

diff --git a/src/file_readers/spectrum_readers/dda_reader/precursors.rs b/src/file_readers/spectrum_readers/dda_reader/precursors.rs
@@ -23,12 +23,18 @@ pub struct PrecursorReader {
 
 impl PrecursorReader {
     pub fn new(tdf_reader: &TDFReader) -> Self {
+        let select_collision_energy_sql = String::from(
+            "SELECT CollisionEnergy FROM PasefFrameMsMsInfo GROUP BY Precursor",
+        );
         let pasef_frames: PasefFrameMsMsTable =
             PasefFrameMsMsTable::from_sql(&tdf_reader.tdf_sql_reader);
         let im_reader: Scan2ImConverter = tdf_reader.im_converter;
         let precursor_table: PrecursorTable =
             PrecursorTable::from_sql(&tdf_reader.tdf_sql_reader);
         let retention_times: Vec<f64> = tdf_reader.frame_table.rt.clone();
+        let collision_energies = tdf_reader
+            .tdf_sql_reader
+            .get_data_from_sql(&select_collision_energy_sql);
         let precursors: Vec<Precursor> = (0..precursor_table.mz.len())
             .into_par_iter()
             .map(|index| {
@@ -42,6 +48,7 @@ impl PrecursorReader {
                     intensity: precursor_table.intensity[index],
                     index: index + 1, //TODO?
                     frame_index: frame_id,
+                    collision_energy: collision_energies[index],
                 }
             })
             .collect();

diff --git a/src/precursors.rs b/src/precursors.rs
@@ -8,6 +8,7 @@ pub struct Precursor {
     pub intensity: f64,
     pub index: usize,
     pub frame_index: usize,
+    pub collision_energy: f64,
 }
 
 /// A type of quadrupole selection.

diff --git a/tests/spectrum_readers.rs b/tests/spectrum_readers.rs
@@ -29,6 +29,7 @@ fn minitdf_reader() {
                 intensity: 0.0,
                 index: 1,
                 frame_index: 1,
+                collision_energy: 0.0,
             }),
             index: 0,
         },
@@ -43,6 +44,7 @@ fn minitdf_reader() {
                 intensity: 0.0,
                 index: 2,
                 frame_index: 2,
+                collision_energy: 0.0,
             }),
             index: 1,
         },
@@ -74,6 +76,7 @@ fn tdf_reader_dda() {
                 intensity: 10.0,
                 index: 1,
                 frame_index: 1,
+                collision_energy: 0.0,
             }),
             index: 0,
         },
@@ -88,6 +91,7 @@ fn tdf_reader_dda() {
                 intensity: 10.0,
                 index: 2,
                 frame_index: 1,
+                collision_energy: 0.0,
             }),
             index: 1,
         },
@@ -102,6 +106,7 @@ fn tdf_reader_dda() {
                 intensity: 10.0,
                 index: 3,
                 frame_index: 3,
+                collision_energy: 0.0,
             }),
             index: 2,
         },