Trait SpectrumLike

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pub trait SpectrumLike<C: CentroidLike = CentroidPeak, D: DeconvolutedCentroidLike = DeconvolutedPeak>: ParamDescribed {
Show 26 methods    // Required methods
    fn description(&self) -> &SpectrumDescription;
    fn description_mut(&mut self) -> &mut SpectrumDescription;
    fn peaks(&self) -> RefPeakDataLevel<'_, C, D>;
    fn into_peaks_and_description(
        self,
    ) -> (PeakDataLevel<C, D>, SpectrumDescription);
    fn raw_arrays(&self) -> Option<&BinaryArrayMap>;

    // Provided methods
    fn acquisition(&self) -> &Acquisition { ... }
    fn precursor(&self) -> Option<&Precursor> { ... }
    fn precursor_iter(
        &self,
    ) -> impl Iterator<Item = &Precursor> + ExactSizeIterator { ... }
    fn precursor_count(&self) -> usize { ... }
    fn precursor_mut(&mut self) -> Option<&mut Precursor> { ... }
    fn precursor_iter_mut(
        &mut self,
    ) -> impl Iterator<Item = &mut Precursor> + ExactSizeIterator { ... }
    fn add_precursor(&mut self, precursor: Precursor) { ... }
    fn remove_precursor(&mut self, index: usize) -> Precursor { ... }
    fn start_time(&self) -> f64 { ... }
    fn ms_level(&self) -> u8 { ... }
    fn id(&self) -> &str { ... }
    fn index(&self) -> usize { ... }
    fn signal_continuity(&self) -> SignalContinuity { ... }
    fn polarity(&self) -> ScanPolarity { ... }
    fn ion_mobility(&self) -> Option<f64> { ... }
    fn has_ion_mobility(&self) -> bool { ... }
    fn has_ion_mobility_dimension(&self) -> bool { ... }
    fn has_ion_mobility_class(&self) -> HasIonMobility { ... }
    fn spectrum_type(&self) -> Option<SpectrumType> { ... }
    fn set_spectrum_type(&mut self, spectrum_type: SpectrumType) { ... }
    fn update_summaries(&mut self) { ... }
}

Expand description

A trait for providing a uniform delegated access to spectrum metadata

Required Methods§

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fn description(&self) -> &SpectrumDescription

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

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

The method to access the spectrum descript itself, mutably.

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fn peaks(&self) -> RefPeakDataLevel<'_, C, D>

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

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

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

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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.

Provided Methods§

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fn acquisition(&self) -> &Acquisition

Access the acquisition information for this spectrum.

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

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

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

Iterate over all precursors of the spectrum

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fn precursor_count(&self) -> usize

The number of precursor levels recorded

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

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

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

Iterate over all precursors of the spectrum mutably

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fn add_precursor(&mut self, precursor: Precursor)

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

Precursors beyond the first one correspond to lower exponentiated spectra, e.g. for an MS3 spectrum the first precursor is the MS2 product ion that was selected, and the second precursor corresponds to the original MS1 ion that was chosen for MS2.

Higher order precursors may be accessed with SpectrumLike::precursor_iter.

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

Remove the precursor entry at index in the precursor list.

Care should be taken if you are attempting to re-order precursors. It may be simpler to use SpectrumLike::precursor_iter_mut to re-arrange entries.

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fn start_time(&self) -> f64

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

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fn ms_level(&self) -> u8

Access the MS exponentiation level

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fn id(&self) -> &str

Access the native ID string for the spectrum

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fn index(&self) -> usize

Access the index of the spectrum in the source file

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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.

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fn polarity(&self) -> ScanPolarity

Access a description of the spectrum polarity

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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.

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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.

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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.

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fn has_ion_mobility_class(&self) -> HasIonMobility

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

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

Find the type of spectrum described.

A spectrum in mzdata is usually a mass spectrum of some sort, but that’s not guaranteed to be the case. mzdata can handle non-MS spectra, but little of the signal processing machinery it provides currently supports those other kinds of data.

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