An class that uses on-disk caching to read and write spectra and chromatograms. More...

#include <OpenMS/FORMAT/HANDLERS/CachedMzMLHandler.h>

Inheritance diagram for CachedMzMLHandler:

Collaboration diagram for CachedMzMLHandler:

Public Types
typedef PeakMap	MapType

typedef MSSpectrum	SpectrumType

typedef MSChromatogram	ChromatogramType

typedef double	DatumSingleton

typedef std::vector< DatumSingleton >	Datavector

Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Public Member Functions
Constructors and Destructor
	CachedMzMLHandler ()
	Default constructor. More...

	~CachedMzMLHandler () override
	Default destructor. More...

CachedMzMLHandler &	operator= (const CachedMzMLHandler &rhs)
	Assignment operator. More...

Read / Write a complete mass spectrometric experiment (or its meta data)
void	writeMemdump (const MapType &exp, const String &out) const
	Write complete spectra as a dump to the disk. More...

void	writeMetadata (MapType exp, String out_meta, bool addCacheMetaValue=false)
	Write only the meta data of an MSExperiment. More...

void	writeMetadata_x (const MapType &exp, const String &out_meta, bool addCacheMetaValue=false)
	Write only the meta data of an MSExperiment. More...

void	readMemdump (MapType &exp_reading, String filename) const
	Read all spectra from a dump from the disk. More...

Access and creation of the binary indices
void	createMemdumpIndex (String filename)
	Create an index on the location of all the spectra and chromatograms. More...

const std::vector< std::streampos > &	getSpectraIndex () const
	Access to a constant copy of the binary spectra index. More...

const std::vector< std::streampos > &	getChromatogramIndex () const
	Access to a constant copy of the binary chromatogram index. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Types
typedef int	IntType

typedef double	DoubleType

Direct access to a single Spectrum or Chromatogram
std::vector< std::streampos >	spectra_index_
	Members. More...

std::vector< std::streampos >	chrom_index_

static void	readSpectrumFast (OpenSwath::BinaryDataArrayPtr &data1, OpenSwath::BinaryDataArrayPtr &data2, std::ifstream &ifs, int &ms_level, double &rt)
	fast access to a spectrum (a direct copy of the data into the provided arrays) More...

static std::vector< OpenSwath::BinaryDataArrayPtr >	readSpectrumFast (std::ifstream &ifs, int &ms_level, double &rt)
	Fast access to a spectrum. More...

static void	readChromatogramFast (OpenSwath::BinaryDataArrayPtr &data1, OpenSwath::BinaryDataArrayPtr &data2, std::ifstream &ifs)
	Fast access to a chromatogram. More...

static std::vector< OpenSwath::BinaryDataArrayPtr >	readChromatogramFast (std::ifstream &ifs)
	Fast access to a chromatogram. More...

static void	readSpectrum (SpectrumType &spectrum, std::ifstream &ifs)
	Read a single spectrum directly into an OpenMS MSSpectrum (assuming file is already at the correct position) More...

static void	readChromatogram (ChromatogramType &chromatogram, std::ifstream &ifs)
	Read a single chromatogram directly into an OpenMS MSChromatogram (assuming file is already at the correct position) More...

void	writeSpectrum_ (const SpectrumType &spectrum, std::ofstream &ofs) const
	write a single spectrum to filestream More...

void	writeChromatogram_ (const ChromatogramType &chromatogram, std::ofstream &ofs) const
	write a single chromatogram to filestream More...

static void	readDataFast_ (std::ifstream &ifs, std::vector< OpenSwath::BinaryDataArrayPtr > &data, const Size &data_size, const Size &nr_float_arrays)
	helper method for fast reading of spectra and chromatograms More...

Additional Inherited Members
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

An class that uses on-disk caching to read and write spectra and chromatograms.

This class provides functions to read and write spectra and chromatograms to disk using a time-efficient format. Reading the data items from disk can be very fast and done in random order (once the in-memory index is built for the file).

Member Typedef Documentation

◆ ChromatogramType

typedef MSChromatogram ChromatogramType

◆ Datavector

typedef std::vector<DatumSingleton> Datavector

◆ DatumSingleton

typedef double DatumSingleton

◆ DoubleType

typedef double DoubleType

private

◆ IntType

typedef int IntType

private

◆ MapType

typedef PeakMap MapType

◆ SpectrumType

typedef MSSpectrum SpectrumType

Constructor & Destructor Documentation

◆ CachedMzMLHandler()

CachedMzMLHandler ( )

Default constructor.

◆ ~CachedMzMLHandler()

~CachedMzMLHandler ( )

override

Default destructor.

Member Function Documentation

◆ createMemdumpIndex()

void createMemdumpIndex ( String filename )

Create an index on the location of all the spectra and chromatograms.

◆ getChromatogramIndex()

const std::vector<std::streampos>& getChromatogramIndex ( ) const

Access to a constant copy of the binary chromatogram index.

◆ getSpectraIndex()

const std::vector<std::streampos>& getSpectraIndex ( ) const

Access to a constant copy of the binary spectra index.

◆ operator=()

CachedMzMLHandler& operator= ( const CachedMzMLHandler & rhs )

Assignment operator.

◆ readChromatogram()

static void readChromatogram	(	ChromatogramType &	chromatogram,
		std::ifstream &	ifs
	)

static

Read a single chromatogram directly into an OpenMS MSChromatogram (assuming file is already at the correct position)

Parameters

chromatogram	Output chromatogram
ifs	Input file stream (moved to the correct position)

Exceptions

Exception::ParseError is thrown if the chromatogram size cannot be read

◆ readChromatogramFast() [1/2]

static void readChromatogramFast	(	OpenSwath::BinaryDataArrayPtr &	data1,
		OpenSwath::BinaryDataArrayPtr &	data2,
		std::ifstream &	ifs
	)

inlinestatic

Fast access to a chromatogram.

Parameters

data1	First data array (RT)
data2	Second data array (Intensity)

Exceptions

Exception::ParseError is thrown if the chromatogram size cannot be read

◆ readChromatogramFast() [2/2]

static std::vector<OpenSwath::BinaryDataArrayPtr> readChromatogramFast ( std::ifstream & ifs )

static

Fast access to a chromatogram.

Parameters

ifs	Input file stream (moved to the correct position)

Exceptions

Exception::ParseError is thrown if the chromatogram size cannot be read

◆ readDataFast_()

static void readDataFast_	(	std::ifstream &	ifs,
		std::vector< OpenSwath::BinaryDataArrayPtr > &	data,
		const Size &	data_size,
		const Size &	nr_float_arrays
	)

inlinestaticprotected

helper method for fast reading of spectra and chromatograms

◆ readMemdump()

void readMemdump	(	MapType &	exp_reading,
		String	filename
	)		const

Read all spectra from a dump from the disk.

◆ readSpectrum()

static void readSpectrum	(	SpectrumType &	spectrum,
		std::ifstream &	ifs
	)

static

Read a single spectrum directly into an OpenMS MSSpectrum (assuming file is already at the correct position)

Parameters

spectrum	Output spectrum
ifs	Input file stream (moved to the correct position)

Exceptions

Exception::ParseError is thrown if the chromatogram size cannot be read

◆ readSpectrumFast() [1/2]

static void readSpectrumFast	(	OpenSwath::BinaryDataArrayPtr &	data1,
		OpenSwath::BinaryDataArrayPtr &	data2,
		std::ifstream &	ifs,
		int &	ms_level,
		double &	rt
	)

inlinestatic

fast access to a spectrum (a direct copy of the data into the provided arrays)

Parameters

data1	First data array (m/z)
data2	Second data array (Intensity)
ms_level	Output parameter to store the MS level of the spectrum (1, 2, 3 ...)
rt	Output parameter to store the retention time of the spectrum

Exceptions

Exception::ParseError is thrown if the spectrum cannot be read

◆ readSpectrumFast() [2/2]

static std::vector<OpenSwath::BinaryDataArrayPtr> readSpectrumFast	(	std::ifstream &	ifs,
		int &	ms_level,
		double &	rt
	)

static

Fast access to a spectrum.

Parameters

ifs	Input file stream (moved to the correct position)
ms_level	Output parameter to store the MS level of the spectrum (1, 2, 3 ...)
rt	Output parameter to store the retention time of the spectrum

Exceptions

Exception::ParseError is thrown if the spectrum cannot be read

◆ writeChromatogram_()

void writeChromatogram_	(	const ChromatogramType &	chromatogram,
		std::ofstream &	ofs
	)		const

protected

write a single chromatogram to filestream

◆ writeMemdump()

void writeMemdump	(	const MapType &	exp,
		const String &	out
	)		const

Write complete spectra as a dump to the disk.

◆ writeMetadata()

void writeMetadata	(	MapType	exp,
		String	out_meta,
		bool	addCacheMetaValue = `false`
	)

Write only the meta data of an MSExperiment.

Referenced by CachedSwathFileConsumer::ensureMapsAreFilled_().

◆ writeMetadata_x()

void writeMetadata_x	(	const MapType &	exp,
		const String &	out_meta,
		bool	addCacheMetaValue = `false`
	)

Write only the meta data of an MSExperiment.

◆ writeSpectrum_()

void writeSpectrum_	(	const SpectrumType &	spectrum,
		std::ofstream &	ofs
	)		const

protected

write a single spectrum to filestream

Member Data Documentation

◆ chrom_index_

std::vector<std::streampos> chrom_index_

protected

◆ spectra_index_

std::vector<std::streampos> spectra_index_

protected

Members.

Public Types

Public Member Functions

Private Types

Direct access to a single Spectrum or Chromatogram

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ChromatogramType

◆ Datavector

◆ DatumSingleton

◆ DoubleType

◆ IntType

◆ MapType

◆ SpectrumType

Constructor & Destructor Documentation

◆ CachedMzMLHandler()

◆ ~CachedMzMLHandler()

Member Function Documentation

◆ createMemdumpIndex()

◆ getChromatogramIndex()

◆ getSpectraIndex()

◆ operator=()

◆ readChromatogram()

◆ readChromatogramFast() [1/2]

◆ readChromatogramFast() [2/2]

◆ readDataFast_()

◆ readMemdump()

◆ readSpectrum()

◆ readSpectrumFast() [1/2]

◆ readSpectrumFast() [2/2]

◆ writeChromatogram_()

◆ writeMemdump()

◆ writeMetadata()

◆ writeMetadata_x()

◆ writeSpectrum_()

Member Data Documentation

◆ chrom_index_

◆ spectra_index_