Crate openmassspec_core 

openmassspec-core is the shared foundation for the open Rust mass-spec parsers (opentfraw, opentimstdf, openwraw, openaraw, opensxraw, openszraw).

It exposes:

• Vendor-neutral spectrum / chromatogram / run records: SpectrumRecord, PrecursorInfo, ChromatogramRecord, RunMetadata, CvTerm. All are #[non_exhaustive] and built with constructors plus with_* setters.
• Shared enums: Polarity, ScanMode, Analyzer, MsPower, Activation, Compression, MobilityArrayKind.
• A trait every vendor parser implements: SpectrumSource. Its iterators yield Result items, so decode errors reach the consumer.
• One canonical mzML 1.1.0 writer: write_mzml and write_indexed_mzml (zlib-compressed binary data arrays, stop at the first record error), with WriteOptions for codec and RecordErrorPolicy control. Each call returns a WriteSummary.
• Typed PSI-MS / UO terms generated from psi-ms.obo: cv.
• A streaming profile-to-centroid transform, Centroided, that wraps any SpectrumSource.
• A conformance harness for parser test suites: conformance.

The Apache Arrow bridge lives in the separate openmassspec-arrow crate.

Each vendor crate is a standalone tool (a user can pull in opentfraw alone and get parsing and mzML export); openmassspec-core is the shared vocabulary that keeps the parsers in lock-step.

Modules

conformance

Conformance checks for any crate::SpectrumSource.

cv

Typed PSI-MS and UO controlled-vocabulary terms used by the mzML writer.

Structs

Centroided

Wraps a SpectrumSource, centroiding every profile-mode spectrum it yields. Spectra already tagged ScanMode::Centroid pass through unchanged (idempotent).

ChromatogramRecord

A chromatogram trace (TIC, BPC, SRM/MRM transition).

CvTerm

A PSI-MS controlled-vocabulary term.

PrecursorInfo

Precursor metadata for an MS2+ spectrum.

RunMetadata

Run-level metadata.

SpectrumRecord

One fully-decoded spectrum.

WriteOptions

Options for write_mzml_with_options and write_indexed_mzml_with_options.

WriteSummary

What a successful write produced.

Enums

Activation

Activation method used for MSn fragmentation.

Analyzer

Detector / mass analyzer family.

Compression

Compression codec applied to a <binaryDataArray>’s <binary> payload by the mzML writer.

Error

Stack-wide error type.

MobilityArrayKind

Unit + meaning of a per-peak ion mobility array.

MsPower

MSn order (MS1, MS2, …).

Polarity

Scan polarity.

RecordErrorPolicy

What the writer does when the source yields an Err record.

ScanMode

Whether a spectrum holds centroided peak picks or the raw profile signal.

Constants

VERSION

Crate version (set from Cargo.toml).

Traits

SpectrumSource

A source of decoded mass spectra.

Functions

write_indexed_mzml

Write the source’s spectra as indexed mzML 1.1.0 (with <indexList> and <fileChecksum> trailer) with default WriteOptions: zlib-compressed arrays, stop at the first record error.

write_indexed_mzml_with_options

Write the source’s spectra as indexed mzML 1.1.0 (with <indexList> and <fileChecksum> trailer) with explicit WriteOptions.

write_mzml

Write the source’s spectra as mzML 1.1.0 (un-indexed) with default WriteOptions: zlib-compressed arrays, stop at the first record error.

write_mzml_with_options

Write the source’s spectra as mzML 1.1.0 (un-indexed) with explicit WriteOptions.

Type Aliases

ChromatogramIter

Boxed, fallible chromatogram iterator returned by SpectrumSource::iter_chromatograms.

Result

Convenience alias.

SpectrumIter

Boxed, fallible spectrum iterator returned by SpectrumSource::iter_spectra.