Crate imzml

Expand description

This library provides a means of accessing mass spectrometry and mass spectrometry imaging data stored in either the .mzML or .imzML data formats.

let parser = ImzMLReader::from_path(“/path/to/data.imzML”).unwrap();

for error in parser.errors() { println!(“{:?}”, error); }

let imzml: ImzML<_> = parser.into();

imzml.ion_image(772.573, 100.0);

Re-exports§

pub use self::imzml::ImzML;
pub use self::imzml::ImzMLReader;
pub use mzml::mzml::MzML;
pub use mzml::MzMLReader;
pub use self::mzml::mzml::*;

Modules§

error: Error handling
imzml: ImzML file parsing (relies heavily on mzml)
mzml: MzML file parsing
obo: Parsing ontologies stored in the OBO format
validation: Validating .mzML and .imzML files

Structs§

Activation: Represents an tag.
BinaryDataArray: BinaryDataArray represents the tag and captures information required to read and parse the stored binary data.
BinaryDataArrayList: tag representation. Contains a list of BinaryDataArray
Chromatogram: Represents a tag.
ChromatogramIter: Iterator over a ChromatogramList returning all chromatograms in the list
ChromatogramList: Represents a list of Chromatograms
CompressionReader: Provides a single interface to compressed data, decompressing the data on read() if necessary
Coordinate: Coordinate describes the pixel location of a spectrum/scan
DataAccess: Enables access to data stored in data_location. The data could be compressed and/or encoded and stored with various different types. This information is captured in the data_description
IsolationWindow: Represents a tag.
Precursor: Represents a tag.
PrecursorList: Represents a list of Precursors
Product: Represents a tag.
Scan: Represents a tag.
ScanIter: Iterator over a ScanList returning each Scan in turn.
ScanList: Represents a list of Scans
ScanWindow: Represents a tag.
ScanWindowList: Represents a list of ScanWindows
SelectedIon: Represents a tag.
SelectedIonList: Represents a list of SelectedIons
Spectrum: Spectrum captures both binary data and metadata associated with a mass spectrum.
SpectrumAccess: Provide ability to access a spectrum (contains DataAccess for both m/z and intensity arrays)
SpectrumAccessIterator: SpectrumAccessIterator provides an iterator over a spectrum
SpectrumIter: Iterator over a SpectrumList returning all spectra in the list
SpectrumList: Represents a list of Spectrum
Target: Represents a tag.
WritableSpectrum: WritableSpectrum contains information required to be able to write out a spectrum to imzML.

Enums§

BinaryDataArrayType: The type of data being stored (e.g. m/z values, intensities)
BinaryDataType: The type used to store binary data (e.g. m/zs or intensities)
Compression: Possible means of compressing binary data stored in (i)mzML
Polarity: Polarity used to acquire the spectrum
Representation: Spectrum mode
ScanLocation: ScanLocation describes how ImzMLWriter should deal with a particular scan. Either ignore it, or store it with the specified coordinate.
SpectrumRef: Represents a reference to a Spectrum
SpectrumType: Type of spectrum acquired

Constants§