MzPeakFile Class Reference

mzPeak file reader and writer (HUPO-PSI mzPeak: Parquet tables in a ZIP archive or a directory). More...

#include <OpenMS/FORMAT/MzPeakFile.h>

Inheritance diagram for MzPeakFile:

Public Member Functions
	MzPeakFile ()
	~MzPeakFile () override
PeakFileOptions &	getOptions ()
	Mutable access to the options for loading/storing.
const PeakFileOptions &	getOptions () const
	Non-mutable access to the options for loading/storing.
void	setOptions (const PeakFileOptions &)
	set options for loading/storing
void	load (const std::string &filename, PeakMap &exp)
	Loads a run from an mzPeak archive or directory into exp.
void	transform (const std::string &filename, Interfaces::IMSDataConsumer *consumer)
	Streams the spectra (and chromatograms) of an mzPeak archive or directory into consumer.
void	store (const std::string &filename, const PeakMap &exp) const
	Stores a run as an mzPeak archive (ZIP) at filename.
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Static Public Member Functions
static bool	isMzPeak (const std::string &path)
	Whether path looks like an mzPeak run: a directory holding 'mzpeak_index.json', or a file that is a ZIP archive (whose members are checked when it is opened). False for anything that does not exist.
static bool	isSupported ()
	Whether OpenMS was built with mzPeak support (OPENMS_ENABLE_MZPEAK)

Private Attributes
PeakFileOptions	options_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
Static Protected Attributes inherited from ProgressLogger
static std::atomic< int >	recursion_depth_

Detailed Description

mzPeak file reader and writer (HUPO-PSI mzPeak: Parquet tables in a ZIP archive or a directory).

Reads an mzPeak run into an MSExperiment or streams it into an Interfaces::IMSDataConsumer (as MzMLFile::transform() does), and writes an MSExperiment as an mzPeak archive. The format is implemented by the vendored mzPeak C++ library (src/openms/thirdparty/mzpeak, see its README.OpenMS.md for the library commit and the format version), which is available when OpenMS is built with OPENMS_ENABLE_MZPEAK (the WITH_MZPEAK define); without it, load(), transform() and store() throw Exception::NotImplemented.

An mzPeak run is a ZIP archive ('.mzpeak' file) with an index ('mzpeak_index.json') and Parquet members, or a directory with the same members; isMzPeak() tells the two from other files and directories.

Reading: spectra (m/z, intensity, per-peak ion mobility arrays), their retention time (in seconds, converted from the minutes the format stores), MS level, native ID, polarity, centroid/profile representation, scan windows, ion mobility (drift time with its unit), precursors (isolation window, selected ion m/z, charge, intensity, ion mobility, activation methods and energy) and chromatograms; run-level metadata (run start time, source files, instrument model). The scan-level PeakFileOptions (MS levels, RT range, precursor m/z range) are applied before the peaks are decoded; the peak-level options (m/z, intensity, ion mobility ranges) after. The spectra are decoded in parallel with the OpenMP threads of the calling thread (one reader per thread, as the library's thread-safety model requires).

Writing: m/z, intensity, representation, MS level, retention time, polarity, native ID, precursors (isolation window, selected ion, charge, intensity) and the spectrum's ion mobility; run-level metadata (run start time, source files with their checksum, file format and native ID format). Not written (yet), with a warning: other data arrays, activation methods and energies, and chromatograms; without one: scan windows and instrument metadata. An experiment with a per-peak ion mobility array is refused (Exception::IllegalArgument), as storing it without one would change what its peaks are.

Constructor & Destructor Documentation

MzPeakFile()

MzPeakFile

(

)

~MzPeakFile()

~MzPeakFile ( )

override

Member Function Documentation

getOptions() [1/2]

PeakFileOptions & getOptions

(

)

Mutable access to the options for loading/storing.

getOptions() [2/2]

const PeakFileOptions & getOptions

(

)

const

Non-mutable access to the options for loading/storing.

isMzPeak()

static bool isMzPeak ( const std::string &  path )

static

Whether path looks like an mzPeak run: a directory holding 'mzpeak_index.json', or a file that is a ZIP archive (whose members are checked when it is opened). False for anything that does not exist.

isSupported()

static bool isSupported ( )

static

Whether OpenMS was built with mzPeak support (OPENMS_ENABLE_MZPEAK)

load()

void load	(	const std::string &	filename,
		PeakMap &	exp
	)

Loads a run from an mzPeak archive or directory into exp.

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing
Exception::NotImplemented	is thrown if OpenMS was built without mzPeak support

setOptions()

void setOptions

(

const PeakFileOptions &

)

set options for loading/storing

store()

void store	(	const std::string &	filename,
		const PeakMap &	exp
	)		const

Stores a run as an mzPeak archive (ZIP) at filename.

Exceptions

Exception::UnableToCreateFile	is thrown if the file could not be created
Exception::NotImplemented	is thrown if OpenMS was built without mzPeak support

transform()

void transform	(	const std::string &	filename,
		Interfaces::IMSDataConsumer *	consumer
	)

Streams the spectra (and chromatograms) of an mzPeak archive or directory into consumer.

The consumer gets the experimental settings and the expected sizes first, then the spectra in file order, decoded in batches with the OpenMP threads of the calling thread, then the chromatograms.

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing
Exception::NotImplemented	is thrown if OpenMS was built without mzPeak support

Member Data Documentation

options_

PeakFileOptions options_

private