Module mzdata::io

Reading and writing mass spectrometry data file formats and abstractions over them.

There are many data file formats for recording mass spectrometry data.

Re-exports

• pub use crate::io::mgf::MGFError;
• pub use crate::io::mgf::MGFReader;
• pub use crate::io::mgf::MGFWriter;
• pub use crate::io::mzml::AsyncMzMLReader;
• pub use crate::io::mzml::MzMLParserError;
• pub use crate::io::mzml::MzMLReader;
• pub use crate::io::mzml::MzMLWriter;
• pub use crate::io::mzmlb::MzMLbError;
• pub use crate::io::mzmlb::MzMLbReader;
• pub use thermo::ThermoRawReader;

Modules

• mgf
  Read and write MGF files. Supports random access when reading from a source that supports io::Seek.
• 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.
• mzmlb
  Implements a parser for the mzMLb file format for representing raw and processed mass spectra, providing a RandomAccessSpectrumIterator interface for reading, and SpectrumWriter interface for writing.
• thermo
  Reader implementation for Thermo RAW files, ThermoRawReaderType.

Structs

• MemorySpectrumSource
  A collection of spectra held in memory but providing an interface identical to a data file. This structure owns its data, so in order to yield ownership for SpectrumSource, they are cloned
• OffsetIndex
  An ordered mapping from entity ID to byte offset into the source file it resides in.
• PreBufferedStream
  A wrapper around an io::Read to provide limited io::Seek access even if the underlying stream does not support it. It pre-buffers the next n bytes of content in memory and permits seek operations within that range, but fails all seeks beyond that range.
• RestartableGzDecoder
  A flate2::bufread::MultiGzDecoder that implements std::io::Seek by by incrementally reading ahead, or rewinding to the beginning of the file and doing the same.
• SpectrumIterator
  A generic iterator over a SpectrumSource implementer that assumes the source has already been indexed. Otherwise, the source’s own iterator behavior should be used.
• SpectrumReceiver
  An in-memory communication, non-rewindable channel carrying spectra with associated metadata.
• StreamingSpectrumIterator
  An alternative implementation of SpectrumSource for non-rewindable underlying streams

Enums

• DetailLevel
  Controls the level of spectral detail read from an MS data file
• MZReaderType
  An explicit file format dispatching ADT that provides the complete SpectrumSource, RandomAccessSpectrumIterator, MZFileReader and MSDataFileMetadata APIs. The preferred means of creating an instance is through the MZReaderType::open_path function.
• MassSpectrometryFormat
  Mass spectrometry file formats that mzdata supports
• Sink
  An abstraction over places to write spectra
• Source
  An abstraction over different ways to get a SpectrumSource from a file path, buffer, or pipe.
• SpectrumAccessError
  Errors that may occur when reading a spectrum from a RandomAccessSpectrumIterator

Traits

• MZFileReader
  A trait defining some helper methods to make efficient use of indices automatic when opening a file from a path-like object.
• MassSpectrometryReadWriteProcess
  Encapsulate the read-transform-write process for mass spectrometry data sources.
• RandomAccessSpectrumGroupingIterator
  Analogous to to RandomAccessSpectrumIterator, but for SpectrumGrouping implementations.
• RandomAccessSpectrumIterator
  An extension of SpectrumSource that supports relocatable iteration relative to a specific spectrum coordinate or identifier.
• RandomAccessSpectrumSource
  A union trait for SpectrumSource and RandomAccessSpectrumIterator
• SpectrumGrouping
  An abstraction over SpectrumGroup’s interface.
• SpectrumSource
  A base trait defining the behaviors of a source of spectra.
• SpectrumSourceWithMetadata
• SpectrumWriter
  Common interface for spectrum writing

Functions

• checksum_file
  Compute a SHA-1 digest of a file path
• infer_format
  Given a path, infer the file format and whether or not the file at that path is GZIP compressed, using both the file name and by trying to open and read the file header
• infer_from_path
  Given a path, infer the file format and whether or not the file at that path is GZIP compressed
• infer_from_stream
  Given a stream of bytes, infer the file format and whether or not the stream is GZIP compressed. This assumes the stream is seekable.

Type Aliases

• MZReader
  A specialization of MZReaderType for the default peak types, for common use. The preferred means of creating an instance is using the MZReader::open_path function.