Node.js API Reference

The TypeScript surface is small and cohesive. For a generated reference matching the published types, run typedoc (see Build from source); for a navigable view, see the source under node-ts/src/.

Module surface

import {
  // Files
  BaseFile,
  MZMLFile,
  MSZFile,

  // Spectra
  Spectrum,
  Spectra,

  // Types
  DataFormat,
  DataPositions,
  Division,
  RuntimeArguments,
  type ExtractOptions,

  // MSZX
  MSZXFile,
  MSZXBuilder,
  MSZXManifest,
  MSZXBatchFile,
  MSZXBatchWriter,
  MSZXBatchManifest,
  compressBatch,
  type AnnotationEntry,
  type MSZXManifestData,
  createMSZX,

  // Module functions
  read,
  getNumThreads,
  getFilesize,
  getVersion,
} from "mscompress";

Files

read(path: string): MZMLFile | MSZFile

Auto-detects the file type and returns the appropriate file object. See read() and file handling.

BaseFile

Common base class. Methods: compress(), decompress(), extract(), close(). Properties: path, filesize, format, spectra, positions, arguments.

MZMLFile extends BaseFile

Handler for uncompressed mzML files.

MSZFile extends BaseFile

Handler for MSZ files. Supports random-access reads.

Spectra

Spectrum

Single mass spectrum. Properties: index, scan, msLevel, retentionTime, size, mz, intensity, xml.

Spectra

Iterable, indexable collection. length, [i], [Symbol.iterator].

Types

DataFormat

Source and target encoding metadata: sourceMzFmt, sourceIntenFmt, sourceCompression, targetXmlFormat, targetMzFormat, targetIntenFormat, mzScaleFactor, intScaleFactor.

DataPositions

Start/end byte positions and spectrum counts for a data block.

Division

Per-worker spectrum partition: spectra, xml, mz, inten (DataPositions), scans, msLevels, retTimes.

RuntimeArguments

Compression configuration. See the compression guide for every field.

ExtractOptions

type ExtractOptions = {
  indices?: number[];
  scanNumbers?: number[];
  msLevel?: number;
};

MSZX

MSZXFile

Reader for .mszx archives. manifest, spectra, openAnnotation(), close().

MSZXBuilder

Fluent builder. setSpectra(), setDescription(), setJoinKey(), addAnnotation(), setExtra(), save().

MSZXManifest

Manifest record for a v1 archive. See the MSZX format spec.

MSZXBatchFile

Reader for a v2 ("batch") archive, as a lazily-opened collection of MSZFile. Also opens a v1 archive as a collection of one.

open(), length, entries, names, get(index | name), has(), decompress(), describe(), close(), iterable, Symbol.dispose.

MSZXBatchWriter

Incremental writer for a v2 archive. Drives the same C writer as the CLI, so output is byte-identical.

add(source, entryName?) (async), addAnnotation(), setJoinKey(), setDescription(), setExtra(), finish(), abort(), entries, length.

compressBatch(inputs, output, options?)

Compress many mzML into one .mszx. Options: recursive, description, extra, onProgress, plus any CompressArgs.

resolveMzmlInputs(inputs, recursive?)

Expand paths and directories into the sorted, deduplicated mzML list compressBatch would use.

MSZXBatchManifest

Manifest record for a v2 archive. spectra_files, description, extra, fromSingleFile().

createMSZX(options)

Convenience function. See the MSZX guide.

Module functions

getNumThreads(): number

Available CPU count.

getFilesize(path: string): number

File size in bytes.

getVersion(): string

Library version (from .cz.toml).

Note

A future revision of these docs will autogen this page with typedoc-plugin-markdown so signatures stay in lock-step with the source. See Build from source for the planned workflow.