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FEAT: updated TdfReader to use frameReader instead
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,124 +1,54 @@ | ||
| use { | ||
| crate::{ | ||
| domain_converters::{ | ||
| ConvertableDomain, Frame2RtConverter, Scan2ImConverter, | ||
| Tof2MzConverter, | ||
| }, | ||
| file_readers::{ | ||
| common::{ | ||
| ms_data_blobs::ReadableFromBinFile, | ||
| sql_reader::{FrameTable, ReadableFromSql, SqlReader}, | ||
| }, | ||
| ReadableFrames, | ||
| }, | ||
| io::readers::common::tdf_blobs::TdfBlobReader, | ||
| ms_data::{AcquisitionType, Frame, MSLevel, QuadrupoleSettings}, | ||
| use crate::{ | ||
| domain_converters::{Frame2RtConverter, Scan2ImConverter, Tof2MzConverter}, | ||
| file_readers::{ | ||
| common::sql_reader::{ReadableFromSql, SqlReader}, | ||
| ReadableFrames, | ||
| }, | ||
| rayon::prelude::*, | ||
| std::{path::Path, sync::Arc}, | ||
| io::readers::frame_reader::FrameReader, | ||
| ms_data::Frame, | ||
| }; | ||
|
|
||
| #[derive(Debug)] | ||
| pub struct TDFReader { | ||
| pub path: String, | ||
| frame_reader: FrameReader, | ||
| pub tdf_sql_reader: SqlReader, | ||
| tdf_bin_reader: TdfBlobReader, | ||
| pub rt_converter: Frame2RtConverter, | ||
| pub im_converter: Scan2ImConverter, | ||
| pub mz_converter: Tof2MzConverter, | ||
| pub frame_table: FrameTable, | ||
| pub acquisition: AcquisitionType, | ||
| ms_levels: Vec<MSLevel>, | ||
| } | ||
|
|
||
| impl TDFReader { | ||
| pub fn new(path: &String) -> Self { | ||
| let tdf_sql_reader: SqlReader = SqlReader { | ||
| path: String::from(path), | ||
| }; | ||
| let frame_table: FrameTable = FrameTable::from_sql(&tdf_sql_reader); | ||
| let file_name: String = Path::new(&path) | ||
| .join("analysis.tdf_bin") | ||
| .to_string_lossy() | ||
| .to_string(); | ||
| let tdf_bin_reader: TdfBlobReader = TdfBlobReader::new( | ||
| String::from(&file_name), | ||
| frame_table.offsets.iter().map(|x| *x as usize).collect(), | ||
| ) | ||
| .unwrap(); | ||
| let ms_levels: Vec<MSLevel> = frame_table | ||
| .msms_type | ||
| .iter() | ||
| .map(|msms_type| match msms_type { | ||
| 0 => MSLevel::MS1, | ||
| 8 => MSLevel::MS2, | ||
| 9 => MSLevel::MS2, | ||
| _ => MSLevel::Unknown, | ||
| }) | ||
| .collect(); | ||
| let mut acquisition = AcquisitionType::Unknown; | ||
| if frame_table.msms_type.contains(&8) { | ||
| acquisition = AcquisitionType::DDAPASEF; | ||
| } else if frame_table.msms_type.contains(&9) { | ||
| acquisition = AcquisitionType::DIAPASEF; | ||
| } | ||
| let frame_reader: FrameReader = FrameReader::new(&path); | ||
| Self { | ||
| path: path.to_string(), | ||
| tdf_bin_reader: tdf_bin_reader, | ||
| rt_converter: Self::get_rt_converter(&frame_table), | ||
| rt_converter: Frame2RtConverter::from_values( | ||
| frame_reader.sql_frames.iter().map(|x| x.rt).collect(), | ||
| ), | ||
| im_converter: Scan2ImConverter::from_sql(&tdf_sql_reader), | ||
| mz_converter: Tof2MzConverter::from_sql(&tdf_sql_reader), | ||
| frame_table: frame_table, | ||
| tdf_sql_reader: tdf_sql_reader, | ||
| ms_levels: ms_levels, | ||
| acquisition: acquisition, | ||
| frame_reader: frame_reader, | ||
| } | ||
| } | ||
|
|
||
| fn get_rt_converter(frame_table: &FrameTable) -> Frame2RtConverter { | ||
| let retention_times: Vec<f64> = frame_table.rt.clone(); | ||
| Frame2RtConverter::from_values(retention_times) | ||
| } | ||
| } | ||
|
|
||
| impl ReadableFrames for TDFReader { | ||
| fn read_single_frame(&self, index: usize) -> Frame { | ||
| let mut frame: Frame = | ||
| Frame::read_from_file(&self.tdf_bin_reader, index); | ||
| frame.rt = self.rt_converter.convert(index as u32); | ||
| frame.index = self.frame_table.id[index]; | ||
| frame.ms_level = self.ms_levels[index]; | ||
| frame.acquisition_type = self.acquisition; | ||
| if frame.ms_level == MSLevel::MS2 { | ||
| frame.quadrupole_settings = Arc::new(QuadrupoleSettings::default()); | ||
| } | ||
| frame | ||
| self.frame_reader.get(index) | ||
| } | ||
|
|
||
| fn read_all_frames(&self) -> Vec<Frame> { | ||
| (0..self.tdf_bin_reader.len()) | ||
| .into_par_iter() | ||
| .map(|index| self.read_single_frame(index)) | ||
| .collect() | ||
| self.frame_reader.collect(|_| true) | ||
| } | ||
|
|
||
| fn read_all_ms1_frames(&self) -> Vec<Frame> { | ||
| (0..self.tdf_bin_reader.len()) | ||
| .into_par_iter() | ||
| .map(|index| match self.ms_levels[index] { | ||
| MSLevel::MS1 => self.read_single_frame(index), | ||
| _ => Frame::default(), | ||
| }) | ||
| .collect() | ||
| self.frame_reader.collect(|x| x.msms_type == 0) | ||
| } | ||
|
|
||
| fn read_all_ms2_frames(&self) -> Vec<Frame> { | ||
| (0..self.tdf_bin_reader.len()) | ||
| .into_par_iter() | ||
| .map(|index| match self.ms_levels[index] { | ||
| MSLevel::MS2 => self.read_single_frame(index), | ||
| _ => Frame::default(), | ||
| }) | ||
| .collect() | ||
| self.frame_reader.collect(|x| x.msms_type != 0) | ||
| } | ||
| } |
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