Struct TimsFrame

pub struct TimsFrame {
    pub frame_id: i32,
    pub ms_type: MsType,
    pub scan: Vec<i32>,
    pub tof: Vec<i32>,
    pub ims_frame: ImsFrame,
}

Fields

frame_id: i32

ms_type: MsType

scan: Vec<i32>

tof: Vec<i32>

ims_frame: ImsFrame

Implementations

impl TimsFrame

pub fn new( frame_id: i32, ms_type: MsType, retention_time: f64, scan: Vec<i32>, mobility: Vec<f64>, tof: Vec<i32>, mz: Vec<f64>, intensity: Vec<f64>, ) -> Self

Creates a new TimsFrame instance.

Arguments

• frame_id - index of frame in TDF raw file.
• ms_type - The type of frame.
• retention_time - The retention time in seconds.
• scan - A vector of scan IDs.
• mobility - A vector of inverse ion mobilities.
• tof - A vector of time-of-flight values.
• mz - A vector of m/z values.
• intensity - A vector of intensity values.

Examples

use mscore::data::spectrum::MsType;
use mscore::timstof::frame::TimsFrame;
use mscore::timstof::frame::ImsFrame;

let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);

pub fn get_ims_frame(&self) -> ImsFrame

Convert a given TimsFrame to an ImsFrame.

Examples

use mscore::data::spectrum::MsType;
use mscore::timstof::frame::TimsFrame;

let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
let ims_spectrum = frame.get_ims_frame();

pub fn to_tims_spectra(&self) -> Vec<TimsSpectrum>

Convert a given TimsFrame to a vector of TimsSpectrum.

Examples

use mscore::data::spectrum::MsType;
use mscore::timstof::frame::TimsFrame;

let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
let tims_spectra = frame.to_tims_spectra();

pub fn filter_ranged( &self, mz_min: f64, mz_max: f64, scan_min: i32, scan_max: i32, inv_mob_min: f64, inv_mob_max: f64, intensity_min: f64, intensity_max: f64, ) -> TimsFrame

Filter a given TimsFrame by m/z, scan, and intensity.

Arguments

• mz_min - The minimum m/z value.
• mz_max - The maximum m/z value.
• scan_min - The minimum scan value.
• scan_max - The maximum scan value.
• intensity_min - The minimum intensity value.
• intensity_max - The maximum intensity value.

Examples

use mscore::data::spectrum::MsType;
use mscore::timstof::frame::TimsFrame;

let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
let filtered_frame = frame.filter_ranged(100.0, 200.0, 1, 2, 0.0, 1.6, 50.0, 60.0);

pub fn top_n(&self, n: usize) -> TimsFrame

pub fn to_windows_indexed( &self, window_length: f64, overlapping: bool, min_peaks: usize, min_intensity: f64, ) -> (Vec<i32>, Vec<i32>, Vec<TimsSpectrum>)

pub fn to_windows( &self, window_length: f64, overlapping: bool, min_peaks: usize, min_intensity: f64, ) -> Vec<TimsSpectrum>

pub fn from_windows(windows: Vec<TimsSpectrum>) -> TimsFrame

pub fn from_tims_spectra(spectra: Vec<TimsSpectrum>) -> TimsFrame

pub fn to_dense_windows( &self, window_length: f64, overlapping: bool, min_peaks: usize, min_intensity: f64, resolution: i32, ) -> (Vec<f64>, Vec<i32>, Vec<i32>, usize, usize)

pub fn to_indexed_mz_spectrum(&self) -> IndexedMzSpectrum

pub fn generate_random_sample(&self, take_probability: f64) -> TimsFrame

pub fn to_noise_annotated_tims_frame(&self) -> TimsFrameAnnotated

pub fn get_inverse_mobility_along_scan_marginal(&self) -> f64

pub fn get_mobility_mean_and_variance(&self) -> (f64, f64)

Calculate the weighted mean and variance of inv_mob values based on their intensities.

Trait Implementations

impl Add for TimsFrame

type Output = TimsFrame

The resulting type after applying the + operator.

fn add(self, other: Self) -> TimsFrame

Performs the + operation.

impl<'__de> BorrowDecode<'__de> for TimsFrame

fn borrow_decode<__D: BorrowDecoder<'__de>>( decoder: &mut __D, ) -> Result<Self, DecodeError>

Attempt to decode this type with the given BorrowDecode.

impl Clone for TimsFrame

fn clone(&self) -> TimsFrame

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for TimsFrame

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Decode for TimsFrame

fn decode<__D: Decoder>(decoder: &mut __D) -> Result<Self, DecodeError>

Attempt to decode this type with the given Decode.

impl Default for TimsFrame

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for TimsFrame

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Display for TimsFrame

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Encode for TimsFrame

fn encode<__E: Encoder>(&self, encoder: &mut __E) -> Result<(), EncodeError>

Encode a given type.

impl Serialize for TimsFrame

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl ToResolution for TimsFrame

Convert a given TimsFrame to a vector of TimsSpectrum.

Arguments

• resolution - The resolution to which the m/z values should be rounded.

Examples

use mscore::data::spectrum::MsType;
use mscore::timstof::frame::TimsFrame;
use mscore::timstof::spectrum::TimsSpectrum;
use mscore::data::spectrum::IndexedMzSpectrum;
use mscore::data::spectrum::ToResolution;

let frame = TimsFrame::new(1, MsType::Precursor, 100.0, vec![1, 2], vec![0.1, 0.2], vec![1000, 2000], vec![100.5, 200.5], vec![50.0, 60.0]);
let low_res_frame = frame.to_resolution(1);

fn to_resolution(&self, resolution: i32) -> TimsFrame

impl Vectorized<TimsFrameVectorized> for TimsFrame

fn vectorized(&self, resolution: i32) -> TimsFrameVectorized