Trait SpectrumSource

pub trait SpectrumSource<C = CentroidPeak, D = DeconvolutedPeak, S = MultiLayerSpectrum<C, D>>: Iterator<Item = S>
where
    C: CentroidLike,
    D: DeconvolutedCentroidLike,
    S: SpectrumLike<C, D>,
{
    // Required methods
    fn reset(&mut self);
    fn detail_level(&self) -> &DetailLevel;
    fn set_detail_level(&mut self, detail_level: DetailLevel);
    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 get_group_by_index(
        &mut self,
        index: usize,
    ) -> Option<SpectrumGroup<C, D, S>>
       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 is the basis for many data access methods in mzdata.

Required Methods

fn reset(&mut self)

Rewind the current position of the source to the beginning

fn detail_level(&self) -> &DetailLevel

Get the DetailLevel the reader currently uses

fn set_detail_level(&mut self, detail_level: DetailLevel)

Set the DetailLevel for the reader, changing the amount of work done immediately on loading a spectrum.

Note

Not all readers support all detail levels, and the behavior when requesting one of those levels will depend upon the underlying reader.

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, usually by getting the length of the index. If the index isn’t initialized, this will be 0.

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 get_group_by_index(&mut self, index: usize) -> Option<SpectrumGroup<C, D, S>>

where Self: Sized,

Get the nth SpectrumGroup from this source

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 SpectrumGroupingIterator

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

where Self: Sized,

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

Implementors

impl<C, D, R> SpectrumSource<C, D> for MZReaderType<R, C, D>

where C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap, R: Read + Seek,

impl<C, D, S> SpectrumSource<C, D, S> for MemorySpectrumSource<C, D, S>

where C: CentroidLike, D: DeconvolutedCentroidLike, S: SpectrumLike<C, D> + Clone,

impl<C, D, S, I> SpectrumSource<C, D, S> for StreamingSpectrumIterator<C, D, S, I>

where C: CentroidLike, D: DeconvolutedCentroidLike, S: SpectrumLike<C, D>, I: Iterator<Item = S>,

impl<C, D, S, R> SpectrumSource<C, D, S> for SpectrumIterator<'_, C, D, S, R>

where C: CentroidLike, D: DeconvolutedCentroidLike, S: SpectrumLike<C, D>, R: SpectrumSource<C, D, S>,