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Adding collision energy in precursor. #12

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merged 5 commits into from
Jan 3, 2024
Merged

Adding collision energy in precursor. #12

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1e734b8
Merge pull request #11 from MannLabs/develop
sander-willems-bruker Nov 6, 2023
cda1a5d
Adding collision energy in precursor.
vijay-gnanasambandan-bruker Dec 19, 2023
08cc654
fix: removed unused variable and fixed typo mistake.
vijay-gnanasambandan-bruker Dec 19, 2023
fbbbdd3
fix: review comment updates
vijay-gnanasambandan-bruker Dec 21, 2023
a987472
tests: added default value in precursor object.
vijay-gnanasambandan-bruker Dec 22, 2023
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14 changes: 10 additions & 4 deletions src/file_readers/common/sql_reader.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -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>(
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Very minimal change, check if if it formatted right by running cargo fmt. Normally thse kind sof changes are done automaticaly. (I evne set up my editor (VSCode with rust-analyzer extension) to run cargo fmt automatically on saving)

&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
);

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I like that you adhere to the boy scout rule here and leave things better than you found them. Good addition to improve code readability, thanks!

self.get_data_from_sql(&query)
}

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(
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2 changes: 2 additions & 0 deletions src/file_readers/common/sql_reader/tables/pasef_frame_msms.rs
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Expand Up @@ -9,6 +9,7 @@ pub struct PasefFrameMsMsTable {
pub mz_width: Vec<f64>,
pub collision_energy: Vec<f64>,
pub precursor: Vec<usize>,
pub collision_energy_by_precursor: Vec<f64>,
}

impl ReadableFromSql for PasefFrameMsMsTable {
Expand All @@ -28,6 +29,7 @@ impl ReadableFromSql for PasefFrameMsMsTable {
.read_column_from_table("CollisionEnergy", table_name),
precursor: sql_reader
.read_column_from_table("Precursor", table_name),
collision_energy_by_precursor: sql_reader.get_data_from_sql(&"select CollisionEnergy from PasefFrameMsMsInfo group by Precursor".to_string()),
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I think this conflicts with the setup of this class. It should just use the read_from_table structure to ensure the length of the array and the order is consistent with the rest of the table. Parsing it for a specific use case should happen at the appropriate spot, not here.

}
}
}
2 changes: 2 additions & 0 deletions src/file_readers/spectrum_readers/dda_reader/precursors.rs
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Expand Up @@ -29,6 +29,7 @@ impl PrecursorReader {
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_energy = &pasef_frames.collision_energy_by_precursor;
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Make this plural collision_energies to improve readability

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This is probably yhe place to do group by precursor you currently do in the table loading.

let precursors: Vec<Precursor> = (0..precursor_table.mz.len())
.into_par_iter()
.map(|index| {
Expand All @@ -42,6 +43,7 @@ impl PrecursorReader {
intensity: precursor_table.intensity[index],
index: index + 1, //TODO?
frame_index: frame_id,
collision_energy: collision_energy[index],
}
})
.collect();
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1 change: 1 addition & 0 deletions src/precursors.rs
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Expand Up @@ -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.
Expand Down