Struct mzdata::spectrum::RawSpectrum

pub struct RawSpectrum {
    pub description: SpectrumDescription,
    pub arrays: BinaryArrayMap,
}

Represents a spectrum that hasn’t been processed yet, with only data arrays, potentially no discrete peaks.

Fields

description: SpectrumDescription

The spectrum metadata describing acquisition conditions and details.

arrays: BinaryArrayMap

The data arrays describing the m/z, intensity, and potentially other measured properties

Implementations

impl<'transient, 'lifespan: 'transient> RawSpectrum

pub fn new(description: SpectrumDescription, arrays: BinaryArrayMap) -> Self

pub fn into_centroid<C>( self ) -> Result<CentroidSpectrumType<C>, SpectrumConversionError>

where C: BuildFromArrayMap + CentroidLike + Default,

Convert a spectrum into a CentroidSpectrumType

pub fn mzs(&'lifespan self) -> Cow<'transient, [f64]>

pub fn intensities(&'lifespan self) -> Cow<'transient, [f32]>

pub fn mzs_mut(&mut self) -> Result<&mut [f64], ArrayRetrievalError>

pub fn intensities_mut(&mut self) -> Result<&mut [f32], ArrayRetrievalError>

pub fn decode_all_arrays(&mut self) -> Result<(), ArrayRetrievalError>

pub fn into_spectrum<C, D: DeconvolutedCentroidLike + Default>( self ) -> Result<MultiLayerSpectrum<C, D>, SpectrumConversionError>

where C: BuildFromArrayMap + CentroidLike + Default,

Convert a spectrum into a Spectrum

pub fn denoise(&mut self, scale: f32) -> Result<(), SpectrumProcessingError>

pub fn pick_peaks_with_into( self, peak_picker: &PeakPicker ) -> Result<MultiLayerSpectrum<CentroidPeak, DeconvolutedPeak>, SpectrumProcessingError>

pub fn pick_peaks_into( self, signal_to_noise_threshold: f32 ) -> Result<MultiLayerSpectrum<CentroidPeak, DeconvolutedPeak>, SpectrumProcessingError>

pub fn pick_peaks_in_intervals_into( self, signal_to_noise_threshold: f32, intervals: &[(f64, f64)] ) -> Result<MultiLayerSpectrum<CentroidPeak, DeconvolutedPeak>, SpectrumProcessingError>

Trait Implementations

impl Clone for RawSpectrum

fn clone(&self) -> RawSpectrum

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for RawSpectrum

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

Formats the value using the given formatter.

impl Default for RawSpectrum

fn default() -> RawSpectrum

Returns the “default value” for a type.

impl<C, D> From<MultiLayerSpectrum<C, D>> for RawSpectrum

where C: BuildFromArrayMap + BuildArrayMapFrom + CentroidLike + Default, D: BuildFromArrayMap + BuildArrayMapFrom + DeconvolutedCentroidLike + Default,

fn from(spectrum: MultiLayerSpectrum<C, D>) -> RawSpectrum

Converts to this type from the input type.

impl<'a> From<MzMLSpectrumBuilder<'a>> for RawSpectrum

fn from(val: MzMLSpectrumBuilder<'a>) -> Self

Converts to this type from the input type.

impl<C, D> From<RawSpectrum> for MultiLayerSpectrum<C, D>

where C: BuildFromArrayMap + CentroidLike + Default, D: BuildFromArrayMap + DeconvolutedCentroidLike + Default,

fn from(spectrum: RawSpectrum) -> MultiLayerSpectrum<C, D>

Converts to this type from the input type.

impl ParamDescribed for RawSpectrum

fn params(&self) -> &[Param]

fn params_mut(&mut self) -> &mut ParamList

fn add_param(&mut self, param: Param)

fn remove_param(&mut self, index: usize) -> Param

fn get_param_by_name(&self, name: &str) -> Option<&Param>

fn get_param_by_curie(&self, curie: &CURIE) -> Option<&Param>

fn get_param_by_accession(&self, accession: &str) -> Option<&Param>

impl SpectrumLike for RawSpectrum

fn description(&self) -> &SpectrumDescription

The method to access the spectrum description itself, which supplies the data for most other methods on this trait.

fn description_mut(&mut self) -> &mut SpectrumDescription

The method to access the spectrum descript itself, mutably.

fn peaks(&self) -> RefPeakDataLevel<'_, CentroidPeak, DeconvolutedPeak>

Retrieve the most processed representation of the mass spectrum’s signal

fn raw_arrays(&self) -> Option<&BinaryArrayMap>

fn into_peaks_and_description( self ) -> (PeakDataLevel<CentroidPeak, DeconvolutedPeak>, SpectrumDescription)

fn acquisition(&self) -> &Acquisition

Access the acquisition information for this spectrum.

fn precursor(&self) -> Option<&Precursor>

Access the precursor information, if it exists.

fn precursor_iter(&self) -> impl Iterator<Item = &Precursor>

Iterate over all precursors of the spectrum

fn precursor_mut(&mut self) -> Option<&mut Precursor>

Mutably access the precursor information, if it exists

fn precursor_iter_mut(&mut self) -> impl Iterator<Item = &mut Precursor>

Iterate over all precursors of the spectrum mutably

fn start_time(&self) -> f64

A shortcut method to retrieve the scan start time of a spectrum

fn ms_level(&self) -> u8

Access the MS exponentiation level

fn id(&self) -> &str

Access the native ID string for the spectrum

fn index(&self) -> usize

Access the index of the spectrum in the source file

fn signal_continuity(&self) -> SignalContinuity

Access a description of how raw the signal is, whether a profile spectrum is available or only centroids are present.

fn polarity(&self) -> ScanPolarity

fn params(&self) -> &ParamList

fn ion_mobility(&self) -> Option<f64>

Access the point measure of ion mobility associated with the scan if present. This is distinct from having a frame-level scan across the ion mobility dimension.

fn has_ion_mobility(&self) -> bool

Check if this spectrum has a point measure of ion mobility. This is distinct from having a frame-level scan across the ion mobility dimension.

impl<C> TryFrom<RawSpectrum> for CentroidSpectrumType<C>

where C: BuildFromArrayMap + CentroidLike + Default,

type Error = SpectrumConversionError

The type returned in the event of a conversion error.

fn try_from( spectrum: RawSpectrum ) -> Result<CentroidSpectrumType<C>, Self::Error>

Performs the conversion.