Struct 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. A raw spectrum may still be centroided, but the peaks still need to be decoded.

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> RawSpectrum

where 'lifespan: 'transient,

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

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

where C: BuildFromArrayMap + CentroidLike,

Convert a spectrum into a CentroidSpectrumType.

Errors

This operation returns SpectrumConversionError::NotCentroided if the SpectrumLike::signal_continuity != SignalContinuity::Centroid.

See also

To pick peaks from profile data, see RawSpectrum::pick_peaks_into

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

Access the m/z array.

Panics

This function will panic if ArrayType::MZArray is not present in RawSpectrum::arrays

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

Access the intensity array.

Panics

This function will panic if ArrayType::IntensityArray is not present in RawSpectrum::arrays

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>

Explicitly decode any DataArray that is encoded or compressed still so that they are ready for use.

See also

BinaryArrayMap::decode_all_arrays

pub fn into_spectrum<C, D>( self, ) -> Result<MultiLayerSpectrum<C, D>, SpectrumConversionError>

where C: BuildFromArrayMap + CentroidLike, D: DeconvolutedCentroidLike,

Convert a spectrum into a MultiLayerSpectrum.

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

Apply a local denoising algorithm to the signal that is suitable for profile mode data using mzsignal::denoise.

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

where C: CentroidPeakAdapting + BuildFromArrayMap + From<FittedPeak>, D: DeconvolutedPeakAdapting + BuildFromArrayMap,

pick peaks with peak_picker and convert this spectrum into a MultiLayerSpectrum with a centroid peak list as well as raw data arrays.

See also

MultiLayerSpectrum::pick_peaks_with

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

where C: CentroidPeakAdapting + BuildFromArrayMap + From<FittedPeak>, D: DeconvolutedPeakAdapting + BuildFromArrayMap,

Pick peaks with a minimum signal-to-noise threshold and convert this spectrum into a MultiLayerSpectrum with a centroid peak list as well as raw data arrays.

See also

RawSpectrum::pick_peaks_with_into

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

where C: CentroidPeakAdapting + BuildFromArrayMap + From<FittedPeak>, D: DeconvolutedPeakAdapting + BuildFromArrayMap,

Pick peaks in the specified m/z ranges with a minimum signal-to-noise threshold and convert this spectrum into a MultiLayerSpectrum with a centroid peak list as well as raw data arrays.

See also

MultiLayerSpectrum::pick_peaks_in_intervals

impl RawSpectrum

pub fn description(&self) -> &SpectrumDescription

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

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

The method to access the spectrum descript itself, mutably.

pub fn acquisition(&self) -> &Acquisition

Access the acquisition information for this spectrum.

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

Access the precursor information, if it exists.

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

Iterate over all precursors of the spectrum

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

Mutably access the (first) precursor information, if it exists

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

Iterate over all precursors of the spectrum mutably

pub fn start_time(&self) -> f64

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

pub fn ms_level(&self) -> u8

Access the MS exponentiation level

pub fn id(&self) -> &str

Access the native ID string for the spectrum

pub fn index(&self) -> usize

Access the index of the spectrum in the source file

pub 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.

pub fn polarity(&self) -> ScanPolarity

Access a description of the spectrum polarity

pub 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.

pub 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.

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

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

pub fn into_peaks_and_description(self) -> (PeakDataLevel, SpectrumDescription)

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

Obtain a reference to the BinaryArrayMap if one is available for the peak information. This may not be the most refined version of the peak signal if it has been processed further.

pub fn has_ion_mobility_dimension(&self) -> bool

Check if this spectrum has an ion mobility dimension/array. This is distinct from having a scan-level point measure of ion mobility.

pub fn update_summaries(&mut self)

Compute and update the the total ion current, base peak, and m/z range for the spectrum based upon its current peak data.

Uses RefPeakDataLevel::fetch_summaries

Trait Implementations

impl Clone for RawSpectrum

fn clone(&self) -> RawSpectrum

Returns a duplicate 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<(), Error>

Formats the value using the given formatter.

impl Default for RawSpectrum

fn default() -> RawSpectrum

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for RawSpectrum

fn deserialize<__D>( __deserializer: __D, ) -> Result<RawSpectrum, <__D as Deserializer<'de>>::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

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

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

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

Converts to this type from the input type.

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

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

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

Converts to this type from the input type.

impl ParamDescribed for RawSpectrum

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

Obtain an immutable slice over the encapsulated Param list

fn params_mut(&mut self) -> &mut Vec<Param>

Obtain an mutable slice over the encapsulated Param list

fn add_param(&mut self, param: Param)

Add a new Param to the entity

fn extend_params(&mut self, it: impl IntoIterator<Item = Param>)

Add all parameters from an iterator of Param to the entity

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

Remove the ith Param from the entity.

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

Find the first Param whose name matches name

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

Find the first Param whose CURIE matches curie

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

Find the first Param whose Param::accession matches accession

fn iter_params(&self) -> Iter<'_, Param>

Iterate over the encapsulated parameter list

fn iter_params_mut(&mut self) -> IterMut<'_, Param>

Iterate mutably over the encapsulated parameter list

impl Serialize for RawSpectrum

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

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl<C, D> SpectrumLike<C, D> for RawSpectrum

where C: CentroidLike, D: DeconvolutedCentroidLike,

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<'_, C, D>

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

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

Obtain a reference to the BinaryArrayMap if one is available for the peak information. This may not be the most refined version of the peak signal if it has been processed further.

fn into_peaks_and_description( self, ) -> (PeakDataLevel<C, D>, SpectrumDescription)

Consume the spectrum, decomposing it into the SpectrumDescription and an owning PeakDataLevel.

fn acquisition(&self) -> &Acquisition

Access the acquisition information for this spectrum.

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

Access the (first) precursor information, if it exists.

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

Iterate over all precursors of the spectrum

fn precursor_count(&self) -> usize

The number of precursor levels recorded

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

Mutably access the (first) precursor information, if it exists

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

Iterate over all precursors of the spectrum mutably

fn add_precursor(&mut self, precursor: Precursor)

Add a precursor to the list of precursors for this spectrum.

fn remove_precursor(&mut self, index: usize) -> Precursor

Remove the precursor entry at index in the precursor list.

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

Access a description of the spectrum polarity

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.

fn has_ion_mobility_dimension(&self) -> bool

Check if this spectrum has an ion mobility dimension/array. This is distinct from having a scan-level point measure of ion mobility.

fn has_ion_mobility_class(&self) -> HasIonMobility

A single point of entry for checking if ion mobility is present.

fn spectrum_type(&self) -> Option<SpectrumType>

Find the type of spectrum described.

fn set_spectrum_type(&mut self, spectrum_type: SpectrumType)

Set the kind of spectrum represented.

fn update_summaries(&mut self)

Compute and update the the total ion current, base peak, and m/z range for the spectrum based upon its current peak data.

impl<C, D> TryFrom<MultiLayerIonMobilityFrame<C, D>> for RawSpectrum

where C: FeatureLike<MZ, IonMobility> + BuildArrayMap3DFrom, D: FeatureLike<Mass, IonMobility> + KnownCharge + BuildArrayMap3DFrom,

A MultiLayerIonMobilityFrame can be converted to RawSpectrum by flattening the feature data into a BinaryArrayMap.

type Error = ArrayRetrievalError

The type returned in the event of a conversion error.

fn try_from( value: MultiLayerIonMobilityFrame<C, D>, ) -> Result<RawSpectrum, <RawSpectrum as TryFrom<MultiLayerIonMobilityFrame<C, D>>>::Error>

Performs the conversion.

impl<CFeat, DFeat> TryFrom<RawSpectrum> for MultiLayerIonMobilityFrame<CFeat, DFeat>

where CFeat: FeatureLike<MZ, IonMobility>, DFeat: FeatureLike<Mass, IonMobility> + KnownCharge,

RawSpectrum instances can be converted to MultiLayerIonMobilityFrame by using BinaryArrayMap3D::stack on the flat RawSpectrum::arrays.

Errors

This will fail if BinaryArrayMap3D::stack fails

type Error = ArrayRetrievalError

The type returned in the event of a conversion error.

fn try_from( value: RawSpectrum, ) -> Result<MultiLayerIonMobilityFrame<CFeat, DFeat>, <MultiLayerIonMobilityFrame<CFeat, DFeat> as TryFrom<RawSpectrum>>::Error>

Performs the conversion.

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

where C: CentroidLike + BuildFromArrayMap,

type Error = SpectrumConversionError

The type returned in the event of a conversion error.

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

Performs the conversion.