Module mzdata::io::mzml

Implements a parser for the PSI-MS mzML and indexedmzML XML file formats for representing raw and processed mass spectra, providing a RandomAccessSpectrumIterator interface for reading, and SpectrumWriter interface for writing.

The mzML format is standardized by the Proteomics Standards Initiative (PSI), with a formal schema defined at https://www.psidev.info/mzML.

This crate supports both reading and writing (indexed) mzML documents with spectra of varying degrees of complexity (raw profiles, centroids, processed centroids), though extensive customization of the coercion process relies on the BuildFromArrayMap and BuildArrayMapFrom traits for reading and writing conversion to BinaryArrayMap.

Structs

• AsyncMzMLReaderType
  An asynchronous version of MzMLReaderType that works with the tokio runtime.
• FileMetadataBuilder
  A SAX-style parser for building up the metadata section prior to the <run> element of an mzML file.
• MzMLReaderType
  An mzML parser that supports iteration and random access. The parser produces Spectrum instances, which may be converted to RawSpectrum or CentroidSpectrum as is appropriate to the data.
• MzMLSpectrumBuilder
  An accumulator for the attributes of a spectrum as it is read from an mzML document
• MzMLWriterType
  An indexed mzML writer that writes MultiLayerSpectrum.

Enums

• EntryType
• MzMLParserError
  All the ways that mzML parsing can go wrong
• MzMLParserState
  The different states the MzMLReaderType can enter while parsing different phases of the document. This information is really only needed by the module consumer to determine where in the document an error occurred.
• MzMLWriterError
  All the ways that mzML writing can go wrong
• MzMLWriterState
  The different states that MzMLWriterType can enter while writing an mzML document. This is only necessary for the module consumer when determining where something may have gone wrong.

Traits

• CVParamParse
  Common CVParam parsing behaviors
• MzMLSAX
  SAX-style start/end/text/empty event handlers
• SpectrumBuilding
  Convert mzML spectrum XML into MultiLayerSpectrum
• XMLParseBase
  Common XML error handling behaviors

Type Aliases

• AsyncMzMLReader
  A specialization of AsyncMzMLReaderType for the default peak types, for common use.
• MzMLReader
  A specialization of MzMLReaderType for the default peak types, for common use.
• MzMLWriter
  A specialization of MzMLWriterType for the default peak types, for common use.