Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Adding collision energy in precursor. #12

Merged
merged 5 commits into from
Jan 3, 2024
Merged

Adding collision energy in precursor. #12

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 10 additions & 4 deletions src/file_readers/common/sql_reader.rs
View file
Open in desktop
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>(
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
);

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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)
}

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(
Expand Down
7 changes: 7 additions & 0 deletions src/file_readers/spectrum_readers/dda_reader/precursors.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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| {
Expand All @@ -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();
Expand Down
1 change: 1 addition & 0 deletions src/precursors.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
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
5 changes: 5 additions & 0 deletions tests/spectrum_readers.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ fn minitdf_reader() {
intensity: 0.0,
index: 1,
frame_index: 1,
collision_energy: 0.0,
}),
index: 0,
},
Expand All @@ -43,6 +44,7 @@ fn minitdf_reader() {
intensity: 0.0,
index: 2,
frame_index: 2,
collision_energy: 0.0,
}),
index: 1,
},
Expand Down Expand Up @@ -74,6 +76,7 @@ fn tdf_reader_dda() {
intensity: 10.0,
index: 1,
frame_index: 1,
collision_energy: 0.0,
}),
index: 0,
},
Expand All @@ -88,6 +91,7 @@ fn tdf_reader_dda() {
intensity: 10.0,
index: 2,
frame_index: 1,
collision_energy: 0.0,
}),
index: 1,
},
Expand All @@ -102,6 +106,7 @@ fn tdf_reader_dda() {
intensity: 10.0,
index: 3,
frame_index: 3,
collision_energy: 0.0,
}),
index: 2,
},
Expand Down