Trait mzdata::io::SpectrumSource

pub trait SpectrumSource<C: CentroidLike + Default = CentroidPeak, D: DeconvolutedCentroidLike + Default = DeconvolutedPeak, S: SpectrumLike<C, D> = MultiLayerSpectrum<C, D>>: Iterator<Item = S> {
    // Required methods
    fn reset(&mut self);
    fn get_spectrum_by_id(&mut self, id: &str) -> Option<S>;
    fn get_spectrum_by_index(&mut self, index: usize) -> Option<S>;
    fn get_index(&self) -> &OffsetIndex;
    fn set_index(&mut self, index: OffsetIndex);

    // Provided methods
    fn get_spectrum_by_time(&mut self, time: f64) -> Option<S> { ... }
    fn len(&self) -> usize { ... }
    fn is_empty(&self) -> bool { ... }
    fn _offset_of_id(&self, id: &str) -> Option<u64> { ... }
    fn _offset_of_index(&self, index: usize) -> Option<u64> { ... }
    fn _offset_of_time(&mut self, time: f64) -> Option<u64> { ... }
    fn iter(&mut self) -> SpectrumIterator<'_, C, D, S, Self> 
       where Self: Sized { ... }
    fn groups(
        &mut self
    ) -> SpectrumGroupingIterator<SpectrumIterator<'_, C, D, S, Self>, C, D, S> 
       where Self: Sized { ... }
    fn into_groups(self) -> SpectrumGroupingIterator<Self, C, D, S> 
       where Self: Sized { ... }
}

A base trait defining the behaviors of a source of spectra.

A SpectrumSource

Required Methods

fn reset(&mut self)

fn get_spectrum_by_id(&mut self, id: &str) -> Option<S>

Retrieve a spectrum by it’s native ID

fn get_spectrum_by_index(&mut self, index: usize) -> Option<S>

Retrieve a spectrum by it’s integer index

fn get_index(&self) -> &OffsetIndex

Access the spectrum offset index to enumerate all spectra by ID

fn set_index(&mut self, index: OffsetIndex)

Set the spectrum offset index. This method shouldn’t be needed if not writing a new adapter

Provided Methods

fn get_spectrum_by_time(&mut self, time: f64) -> Option<S>

Retrieve a spectrum by its scan start time Considerably more complex than seeking by ID or index, this involves a binary search over the spectrum index and assumes that spectra are stored in chronological order.

fn len(&self) -> usize

Retrieve the number of spectra in source file

fn is_empty(&self) -> bool

fn _offset_of_id(&self, id: &str) -> Option<u64>

Helper method to support seeking to an ID

fn _offset_of_index(&self, index: usize) -> Option<u64>

Helper method to support seeking to an index

fn _offset_of_time(&mut self, time: f64) -> Option<u64>

Helper method to support seeking to a specific time. Considerably more complex than seeking by ID or index.

fn iter(&mut self) -> SpectrumIterator<'_, C, D, S, Self>

where Self: Sized,

Open a new iterator over this stream.

fn groups( &mut self ) -> SpectrumGroupingIterator<SpectrumIterator<'_, C, D, S, Self>, C, D, S>

where Self: Sized,

Create a new SpectrumIterator over self and use that state to drive a SpectrumGroupIterator

fn into_groups(self) -> SpectrumGroupingIterator<Self, C, D, S>

where Self: Sized,

Consume self to create a SpectrumGroupIterator. This is ideal for non-rewindable streams like io::stdin which don’t implement io::Seek

Implementors

impl<'lifespan, C: CentroidLike + Default, D: DeconvolutedCentroidLike + Default, S: SpectrumLike<C, D>, R: SpectrumSource<C, D, S>> SpectrumSource<C, D, S> for SpectrumIterator<'lifespan, C, D, S, R>

impl<C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> SpectrumSource<C, D> for MzMLbReaderType<C, D>

They can also be used to fetch specific spectra by ID, index, or start time when the underlying file stream supports io::Seek.

impl<C: CentroidLike + Default + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + Default + From<DeconvolutedPeak> + BuildFromArrayMap, R: Read + Seek> SpectrumSource<C, D> for MZReaderType<R, C, D>

impl<C: CentroidLike + Default + From<CentroidPeak>, D: DeconvolutedCentroidLike + Default> SpectrumSource<C, D> for ThermoRawReaderType<C, D>

impl<C: CentroidLike + Default, D: DeconvolutedCentroidLike + Default, S: SpectrumLike<C, D> + Clone> SpectrumSource<C, D, S> for MemorySpectrumSource<C, D, S>

impl<C: CentroidLike + Default, D: DeconvolutedCentroidLike + Default, S: SpectrumLike<C, D>, I: Iterator<Item = S>> SpectrumSource<C, D, S> for StreamingSpectrumIterator<C, D, S, I>

impl<R: SeekRead, C: CentroidPeakAdapting + BuildFromArrayMap, D: DeconvolutedPeakAdapting + BuildFromArrayMap> SpectrumSource<C, D> for MzMLReaderType<R, C, D>

They can also be used to fetch specific spectra by ID, index, or start time when the underlying file stream supports io::Seek.

impl<R: SeekRead, C: CentroidPeakAdapting, D: DeconvolutedPeakAdapting> SpectrumSource<C, D> for MGFReaderType<R, C, D>