Struct MultiLayerIonMobilityFrame 

pub struct MultiLayerIonMobilityFrame<C = Feature<MZ, IonMobility>, D = ChargedFeature<Mass, IonMobility>>
where
    C: FeatureLike<MZ, IonMobility>,
    D: FeatureLike<Mass, IonMobility> + KnownCharge,
{
    pub arrays: Option<BinaryArrayMap3D>,
    pub features: Option<FeatureMap<MZ, IonMobility, C>>,
    pub deconvoluted_features: Option<FeatureMap<Mass, IonMobility, D>>,
    pub description: IonMobilityFrameDescription,
}

An ion mobility dimension-equivalent of MultiLayerSpectrum.

An ion mobility frame is just like a mass spectrum, except the signal is spread across multiple ion mobility “points”. This means that instead producing “points” in the mass coordinate system, this produces traces-over-time or “features”.

An ion mobility frames can usually be inter-converted with spectra.

Fields

arrays: Option<BinaryArrayMap3D>

The raw data arrays, split by ion mobility point

features: Option<FeatureMap<MZ, IonMobility, C>>

The (potentially absent) m/z coordinate feature map

deconvoluted_features: Option<FeatureMap<Mass, IonMobility, D>>

The (potentially absent) neutral mass coordinate feature map

description: IonMobilityFrameDescription

Implementations

impl<C, D> MultiLayerIonMobilityFrame<C, D>

where C: FeatureLike<MZ, IonMobility> + BuildFromArrayMap3D, D: FeatureLike<Mass, IonMobility> + KnownCharge + BuildFromArrayMap3D,

pub fn try_build_features( &mut self, ) -> Result<RefFeatureDataLevel<'_, C, D>, SpectrumConversionError>

Try to build extracted feature maps from the raw BinaryArrayMap3D

This fails if the BinaryArrayMap3D is not present, or if the required arrays for C and D are absent.

impl<C, D> MultiLayerIonMobilityFrame<C, D>

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

pub fn new( arrays: Option<BinaryArrayMap3D>, features: Option<FeatureMap<MZ, IonMobility, C>>, deconvoluted_features: Option<FeatureMap<Mass, IonMobility, D>>, description: IonMobilityFrameDescription, ) -> MultiLayerIonMobilityFrame<C, D>

Create a new MultiLayerIonMobilityFrame from a IonMobilityFrameDescription and any/all/none of the different levels of processing details for signal data.

impl<C, D> MultiLayerIonMobilityFrame<C, D>

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

When mzsignal is available, MultiLayerIonMobilityFrame supports performing feature extraction to construct ion mobility-distributed traces in the m/z dimension similar to MultiLayerSpectrum::pick_peaks.

pub fn extract_features_with<E>( &mut self, error_tolerance: Tolerance, min_length: usize, maximum_gap_size: f64, peak_picker: Option<PeakPicker>, ) -> Result<(), ArrayRetrievalError>

where E: MapState<CentroidPeak, MZ, IonMobility, FeatureType = C> + Default,

Extract features using the provided MapState type to build the C-type features directly.

If the m/z dimension is not centroided, this will pick peaks for each ion mobility slice as well.

Arguments

• error_tolerance: The mass accuracy error accepted in the m/z dimension between members of the same feature or trace.
• min_length: The minimum number of time points a feature must contain to be kept in the solution.
• maximum_gap_size: The maximum time period between m/z observations to tolerate within a feature.
• peak_picker: A configured PeakPicker instance to use to centroid profile m/z spectra. If not provided, the default configuration will be used.

Type Arguments

• E: a MapState implementing type that will control how FeatureExtracterType can construct features.

If the m/z dimension is not centroided, this will pick peaks for each ion mobility slice as well.

Note

This requires directly specifying the extraction type to use which opens up a wide range of customization options. For the simple cases and for convenience, see MultiLayerIonMobilityFrame::extract_features_simple.

impl<D> MultiLayerIonMobilityFrame<Feature<MZ, IonMobility>, D>

where D: FeatureLike<Mass, IonMobility> + KnownCharge,

A simplified API for feature extraction is available for the basic Feature type where the default MapState type is known.

pub fn extract_features_simple( &mut self, error_tolerance: Tolerance, min_length: usize, maximum_gap_size: f64, peak_picker: Option<PeakPicker>, ) -> Result<(), ArrayRetrievalError>

Extract features using the default algorithm.

Arguments

• error_tolerance: The mass accuracy error accepted in the m/z dimension between members of the same feature or trace.
• min_length: The minimum number of time points a feature must contain to be kept in the solution.
• maximum_gap_size: The maximum time period between m/z observations to tolerate within a feature.
• peak_picker: A configured PeakPicker instance to use to centroid profile m/z spectra. If not provided, the default configuration will be used.

If the m/z dimension is not centroided, this will pick peaks for each ion mobility slice as well.

Trait Implementations

impl<C, D> Clone for MultiLayerIonMobilityFrame<C, D>

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

fn clone(&self) -> MultiLayerIonMobilityFrame<C, D>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<C, D> Debug for MultiLayerIonMobilityFrame<C, D>

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

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

Formats the value using the given formatter.

impl<C, D> Default for MultiLayerIonMobilityFrame<C, D>

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

fn default() -> MultiLayerIonMobilityFrame<C, D>

Returns the “default value” for a type.

impl<'de, C, D> Deserialize<'de> for MultiLayerIonMobilityFrame<C, D>

where C: FeatureLike<MZ, IonMobility> + Deserialize<'de>, D: FeatureLike<Mass, IonMobility> + KnownCharge + Deserialize<'de>,

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

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl<C, D> IonMobilityFrameLike<C, D> for MultiLayerIonMobilityFrame<C, D>

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

fn description(&self) -> &IonMobilityFrameDescription

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 IonMobilityFrameDescription

The method to access the spectrum descript itself, mutably.

fn raw_arrays(&self) -> Option<&BinaryArrayMap3D>

Obtain a reference to the BinaryArrayMap3D if one is available for the feature information. This may not be the most refined version of the feature signal if it has been processed further.

fn features(&self) -> RefFeatureDataLevel<'_, C, D>

Retrieve the most processed representation of the ion mobility frame’s signal

fn into_features_and_parts( self, ) -> (FeatureDataLevel<C, D>, IonMobilityFrameDescription)

Consume the ion mobility frame, decomposing it into the IonMobilityFrameDescription and an owning FeatureDataLevel.

fn ion_mobility_unit(&self) -> Unit

The unit of measure of the ion mobility dimension

fn ion_mobility_unit_mut(&mut self) -> &mut Unit

Get a mutable reference to the ion mobility dimension’s unit

fn acquisition(&self) -> &Acquisition

Access the acquisition information for this frame.

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

Access the precursor information, if it exists.

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

Iterate over all precursors of the frame

fn precursor_count(&self) -> usize

The number of precursor levels recorded

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> + ExactSizeIterator

Iterate over all precursors of the frame mutably

fn add_precursor(&mut self, precursor: Precursor)

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

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

impl<C, D> ParamDescribed for MultiLayerIonMobilityFrame<C, D>

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

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<C, D> Serialize for MultiLayerIonMobilityFrame<C, D>

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

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> 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, CPeak, DPeak> TryFrom<MultiLayerIonMobilityFrame<CFeat, DFeat>> for MultiLayerSpectrum<CPeak, DPeak>

where CFeat: FeatureLike<MZ, IonMobility> + BuildArrayMap3DFrom, DFeat: FeatureLike<Mass, IonMobility> + KnownCharge + BuildArrayMap3DFrom, CPeak: CentroidLike + BuildFromArrayMap, DPeak: DeconvolutedCentroidLike + BuildFromArrayMap,

A MultiLayerIonMobilityFrame can be converted to MultiLayerSpectrum 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<CFeat, DFeat>, ) -> Result<MultiLayerSpectrum<CPeak, DPeak>, <MultiLayerSpectrum<CPeak, DPeak> as TryFrom<MultiLayerIonMobilityFrame<CFeat, DFeat>>>::Error>

Performs the conversion.

impl<CFeat, DFeat, CPeak, DPeak> TryFrom<MultiLayerSpectrum<CPeak, DPeak>> for MultiLayerIonMobilityFrame<CFeat, DFeat>

where CFeat: FeatureLike<MZ, IonMobility>, DFeat: FeatureLike<Mass, IonMobility> + KnownCharge, CPeak: CentroidLike, DPeak: DeconvolutedCentroidLike,

MultiLayerSpectrum instances can be converted to MultiLayerIonMobilityFrame by using BinaryArrayMap3D::stack on the flat MultiLayerSpectrum::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: MultiLayerSpectrum<CPeak, DPeak>, ) -> Result<MultiLayerIonMobilityFrame<CFeat, DFeat>, <MultiLayerIonMobilityFrame<CFeat, DFeat> as TryFrom<MultiLayerSpectrum<CPeak, DPeak>>>::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.