Struct mzdata::io::mzml::AsyncMzMLReaderType

pub struct AsyncMzMLReaderType<R: AsyncReadType + Unpin, C: CentroidPeakAdapting + Send + Sync = CentroidPeak, D: DeconvolutedPeakAdapting + Send + Sync = DeconvolutedPeak> {
    pub state: MzMLParserState,
    pub index: OffsetIndex,
    pub reference_param_groups: HashMap<String, Vec<Param>>,
    pub detail_level: DetailLevel,
    pub run: MassSpectrometryRun,
    /* private fields */
}

An asynchronous version of MzMLReaderType that works with the tokio runtime.

Fields

state: MzMLParserState

The state the parser was in last.

index: OffsetIndex

A spectrum ID to byte offset for fast random access

reference_param_groups: HashMap<String, Vec<Param>>

A cache of repeated paramters

detail_level: DetailLevel

run: MassSpectrometryRun

Implementations

impl<'a, R: AsyncReadType + Unpin + Sync, C: CentroidPeakAdapting + Send + Sync + BuildFromArrayMap, D: DeconvolutedPeakAdapting + Send + Sync + BuildFromArrayMap> MzMLReaderType<R, C, D>

pub async fn new(file: R) -> MzMLReaderType<R, C, D>

Create a new MzMLReaderType instance, wrapping the tokio::io::AsyncRead handle provided with an [io::BufReader] and parses the metadata section of the file.

pub async fn with_buffer_capacity_and_detail_level( file: R, capacity: usize, detail_level: DetailLevel ) -> MzMLReaderType<R, C, D>

pub async fn read_into( &mut self, spectrum: &mut MultiLayerSpectrum<C, D> ) -> Result<usize, MzMLParserError>

Populate a new Spectrum in-place on the next available spectrum data. This allocates memory to build the spectrum’s attributes but then moves it into spectrum rather than copying it.

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

Read the next spectrum directly. Used to implement iteration.

impl<R: AsyncReadType + AsyncSeek + AsyncSeekExt + Unpin + Sync, C: CentroidPeakAdapting + Send + Sync + BuildFromArrayMap, D: DeconvolutedPeakAdapting + Send + Sync + BuildFromArrayMap> MzMLReaderType<R, C, D>

When the underlying stream supports random access, this type can read the index at the end of an indexedmzML document and use the offset map to jump to immediately jump to a specific spectrum.

Note: Because async traits are not yet stable, and this is currently the only asynchronous reader in the library, this also re-creates the SpectrumSource API with asynchronous execution.

pub async fn read_index_from_end(&mut self) -> Result<u64, MzMLIndexingError>

Jump to the end of the document and read the offset indices, if they are available

pub fn len(&self) -> usize

Read the length of the spectrum offset index

pub 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.

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

Retrieve a spectrum by it’s native ID

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

Retrieve a spectrum by it’s integer index

pub async fn reset(&mut self)

Return the data stream to the beginning

pub fn get_index(&self) -> &OffsetIndex

pub fn set_index(&mut self, index: OffsetIndex)

Trait Implementations

impl<R: AsyncReadType + Unpin, C: CentroidPeakAdapting + Send + Sync, D: DeconvolutedPeakAdapting + Send + Sync> MSDataFileMetadata for MzMLReaderType<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 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 run_description(&self) -> Option<&MassSpectrometryRun>

Access the MassSpectrometryRun metadata record if it is available

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

Mutably access the MassSpectrometryRun metadata record if it is available

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

Copy the metadata from another MSDataFileMetadata implementation into this one.

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

A hint about how many spectra are in this data file

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

Get the name of the primary source file, if available