Enum AsyncMZReaderType 

#[non_exhaustive]
pub enum AsyncMZReaderType<R: AsyncRead + AsyncSeek + Unpin + Send, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap + Send + Sync = CentroidPeak, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap + Send + Sync = DeconvolutedPeak> {
    MzML(AsyncMzMLReaderType<R, C, D>),
    MGF(AsyncMGFReaderType<R, C, D>),
}

Variants (Non-exhaustive)

Non-exhaustive enums could have additional variants added in future. Therefore, when matching against variants of non-exhaustive enums, an extra wildcard arm must be added to account for any future variants.

MzML(AsyncMzMLReaderType<R, C, D>)

MGF(AsyncMGFReaderType<R, C, D>)

Implementations

impl<R: AsyncRead + AsyncSeek + Unpin + Send, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap + Send + Sync, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap + Send + Sync> AsyncMZReaderType<R, C, D>

pub fn builder() -> AsyncMZReaderBuilder<C, D>

pub fn as_format(&self) -> MassSpectrometryFormat

Get the file format for this reader

pub async fn open_read_seek(source: R) -> Result<AsyncMZReaderType<R, C, D>>

Trait Implementations

impl<R: AsyncRead + AsyncSeek + Unpin + Send, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap + Send + Sync + 'static, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap + Send + Sync + 'static> AsyncIntoIonMobilityFrameSource<C, D> for AsyncMZReaderType<R, C, D>

Unlike the synchronous MZReaderType, every variant here is converted through AsyncGeneric3DIonMobilityFrameSource. There is no dispatch-based async ion mobility type yet do to lack of native support for async reading in existing formats.

type IonMobilityFrameSource<CF: FeatureLike<MZ, IonMobility> + Send + Sync, DF: FeatureLike<Mass, IonMobility> + KnownCharge + Send + Sync> = AsyncGeneric3DIonMobilityFrameSource<C, D, AsyncMZReaderType<R, C, D>, CF, DF>

The AsyncIonMobilityFrameSource-implementing type for this AsyncSpectrumSource.

async fn try_into_frame_source<CF: FeatureLike<MZ, IonMobility> + Send + Sync, DF: FeatureLike<Mass, IonMobility> + KnownCharge + Send + Sync>( self, ) -> Result<Self::IonMobilityFrameSource<CF, DF>, IntoIonMobilityFrameSourceError>

Attempt to convert the AsyncSpectrumSource into an AsyncIonMobilityFrameSource, returning IntoIonMobilityFrameSourceError if it is not possible

async fn into_frame_source<CF: FeatureLike<MZ, IonMobility> + Send + Sync, DF: FeatureLike<Mass, IonMobility> + KnownCharge + Send + Sync>( self, ) -> Self::IonMobilityFrameSource<CF, DF>

Call AsyncIntoIonMobilityFrameSource::try_into_frame_source, panicking if an error is returned.

async fn has_ion_mobility(&mut self) -> Option<HasIonMobility>

Reads a sparse 1% of the entries from the AsyncSpectrumSource, testing for the presence of ion mobility data.

impl<C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap + Send + Sync + 'static, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap + Send + Sync + 'static> AsyncMZFileReader<C, D> for AsyncMZReaderType<File, C, D>

Available on crate feature async only.

async fn construct_index_from_stream(&mut self) -> u64

An on-trait method of constructing an index. Assumed to be a trivial wrapper.

async fn open_path<P>(path: P) -> Result<Self>

where P: Into<PathBuf>,

The preferred method of opening a file from a path-like object. This method will open the file at the provided path, test whether there is an accompanied index file next to it on the file system, and if not, build one and save it or otherwise read in the index.

async fn open_file(source: File) -> Result<Self>

Given a regular file, construct a new instance without indexing.

impl<R: AsyncRead + AsyncSeek + Unpin + Send, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap + Send + Sync + 'static, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap + Send + Sync + 'static> AsyncRandomAccessSpectrumIterator<C, D> for AsyncMZReaderType<R, C, D>

async fn start_from_id( &mut self, id: &str, ) -> Result<&mut Self, SpectrumAccessError>

async fn start_from_index( &mut self, index: usize, ) -> Result<&mut Self, SpectrumAccessError>

async fn start_from_time( &mut self, time: f64, ) -> Result<&mut Self, SpectrumAccessError>

impl<R: AsyncRead + AsyncSeek + Unpin + Send, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap + Send + Sync + 'static, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap + Send + Sync + 'static> AsyncSpectrumSource<C, D> for AsyncMZReaderType<R, C, D>

async 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.

async fn get_spectrum_by_id( &mut self, id: &str, ) -> Option<MultiLayerSpectrum<C, D>>

Retrieve a spectrum by it’s native ID

async fn get_spectrum_by_index( &mut self, index: usize, ) -> Option<MultiLayerSpectrum<C, D>>

Retrieve a spectrum by it’s integer index

async fn get_spectrum_by_time( &mut self, time: f64, ) -> Option<MultiLayerSpectrum<C, D>>

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 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

async fn read_next(&mut self) -> Option<MultiLayerSpectrum<C, D>>

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

async 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 as_stream(&mut self) -> impl SpectrumStream<C, D, S> + Unpin + '_

Wrap this source in a Stream over its spectra

impl<R: AsyncRead + AsyncSeek + Unpin + Send, C: CentroidLike + From<CentroidPeak> + BuildFromArrayMap + Send + Sync + 'static, D: DeconvolutedCentroidLike + From<DeconvolutedPeak> + BuildFromArrayMap + Send + Sync + 'static> MSDataFileMetadata for AsyncMZReaderType<R, C, D>

fn data_processings(&self) -> &Vec<DataProcessing>

The series of DataProcessing workflows applied to spectra in this data file.

fn instrument_configurations(&self) -> &HashMap<u32, InstrumentConfiguration>

A mapping over different InstrumentConfiguration modes that spectra were acquired under.

fn file_description(&self) -> &FileDescription

A description of the contents and the sources for this mass spectrometry data file.

fn softwares(&self) -> &Vec<Software>

The series of Software applied to the data file to apply different DataProcessing methods.

fn samples(&self) -> &Vec<Sample>

A list of sample descriptions that were measured in this data file if available.

fn data_processings_mut(&mut self) -> &mut Vec<DataProcessing>

Mutably access the DataProcessing list for this data file

fn instrument_configurations_mut( &mut self, ) -> &mut HashMap<u32, InstrumentConfiguration>

Mutably access the InstrumentConfiguration mapping for this data file

fn file_description_mut(&mut self) -> &mut FileDescription

Mutably access the FileDescription description of the contents and the sources for this mass spectrometry data file.

fn softwares_mut(&mut self) -> &mut Vec<Software>

Mutably access the list of Software of this data file.

fn samples_mut(&mut self) -> &mut Vec<Sample>

fn source_file_name(&self) -> Option<&str>

Get the name of the primary source file, if available

fn run_description(&self) -> Option<&MassSpectrometryRun>

Access the MassSpectrometryRun metadata record if it is available

fn spectrum_count_hint(&self) -> Option<u64>

A hint about how many spectra are in this data file

fn scan_settings(&self) -> Option<&Vec<ScanSettings>>

A list of scan settings in ScanSettings pre-configured by the instrument operator prior to the start of data acquisition.

fn scan_settings_mut(&mut self) -> Option<&mut Vec<ScanSettings>>

Mutably access the list of ScanSettings for this dataset. Most formats do not possess a related concept and will not carry one.

fn copy_metadata_from(&mut self, source: &impl MSDataFileMetadata)

where Self: Sized,

Copy the metadata from another MSDataFileMetadata implementation into this one.

fn set_spectrum_count_hint(&mut self, _value: Option<u64>)

fn run_description_mut(&mut self) -> Option<&mut MassSpectrometryRun>

Mutably access the MassSpectrometryRun metadata record if it is available