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

#include <OpenMS/FORMAT/CachedMzML.h>

Inheritance diagram for CachedmzML:

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
	CachedmzML ()
	Default constructor. More...

	~CachedmzML ()
	Default destructor. More...

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

Read / Write a complete mass spectrometric experiment (or its meta data)
void	writeMemdump (MapType &exp, String out)
	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	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...

	~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...

Static Public Member Functions
Direct access to a single Spectrum or Chromatogram
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 void	readChromatogramFast (OpenSwath::BinaryDataArrayPtr data1, OpenSwath::BinaryDataArrayPtr data2, std::ifstream &ifs)
	fast access to a chromatogram (a direct copy of the data into the provided arrays) More...

Protected Member Functions
void	readSpectrum_ (Datavector &data1, Datavector &data2, std::ifstream &ifs, int &ms_level, double &rt) const
	read a single spectrum directly into a datavector (assuming file is already at the correct position) More...

void	readChromatogram_ (Datavector &data1, Datavector &data2, std::ifstream &ifs) const
	read a single chromatogram directly into a datavector (assuming file is already at the correct position) More...

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

void	readChromatogram_ (ChromatogramType &chromatogram, std::ifstream &ifs) const
	read a single chromatogram directly into an OpenMS MSChromatograms (assuming file is already at the correct position) More...

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

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

Protected Attributes
std::vector< std::streampos >	spectra_index_
	Members. More...

std::vector< std::streampos >	chrom_index_

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Private Attributes
int	int_field_

double	dbl_field_

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...

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

◆ MapType

typedef PeakMap MapType

◆ SpectrumType

typedef MSSpectrum SpectrumType

Constructor & Destructor Documentation

◆ CachedmzML()

CachedmzML ( )

Default constructor.

◆ ~CachedmzML()

~CachedmzML ( )

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=()

CachedmzML& operator= ( const CachedmzML & rhs )

Assignment operator.

◆ readChromatogram_() [1/2]

void readChromatogram_	(	Datavector &	data1,
		Datavector &	data2,
		std::ifstream &	ifs
	)		const

protected

read a single chromatogram directly into a datavector (assuming file is already at the correct position)

◆ readChromatogram_() [2/2]

void readChromatogram_	(	ChromatogramType &	chromatogram,
		std::ifstream &	ifs
	)		const

protected

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

◆ readChromatogramFast()

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

inlinestatic

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

Exceptions

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

◆ readMemdump()

void readMemdump	(	MapType &	exp_reading,
		String	filename
	)		const

Read all spectra from a dump from the disk.

Referenced by extractCachedMetaFilename().

◆ readSpectrum_() [1/2]

void readSpectrum_	(	Datavector &	data1,
		Datavector &	data2,
		std::ifstream &	ifs,
		int &	ms_level,
		double &	rt
	)		const

protected

read a single spectrum directly into a datavector (assuming file is already at the correct position)

◆ readSpectrum_() [2/2]

void readSpectrum_	(	SpectrumType &	spectrum,
		std::ifstream &	ifs
	)		const

protected

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

◆ readSpectrumFast()

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)

Exceptions

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

◆ writeChromatogram_()

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

protected

write a single chromatogram to filestream

◆ writeMemdump()

void writeMemdump	(	MapType &	exp,
		String	out
	)

Write complete spectra as a dump to the disk.

Referenced by extractCachedMetaFilename().

◆ writeMetadata()

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

Write only the meta data of an MSExperiment.

Referenced by SwathFile::doCacheFile_(), CachedSwathFileConsumer::ensureMapsAreFilled_(), and extractCachedMetaFilename().

◆ writeSpectrum_()

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

protected

write a single spectrum to filestream

Member Data Documentation

◆ chrom_index_

std::vector<std::streampos> chrom_index_

protected

◆ dbl_field_

double dbl_field_

private

◆ int_field_

int int_field_

private

◆ spectra_index_

std::vector<std::streampos> spectra_index_

protected

Members.

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ChromatogramType

◆ Datavector

◆ DatumSingleton

◆ MapType

◆ SpectrumType

Constructor & Destructor Documentation

◆ CachedmzML()

◆ ~CachedmzML()

Member Function Documentation

◆ createMemdumpIndex()

◆ getChromatogramIndex()

◆ getSpectraIndex()

◆ operator=()

◆ readChromatogram_() [1/2]

◆ readChromatogram_() [2/2]

◆ readChromatogramFast()

◆ readMemdump()

◆ readSpectrum_() [1/2]

◆ readSpectrum_() [2/2]

◆ readSpectrumFast()

◆ writeChromatogram_()

◆ writeMemdump()

◆ writeMetadata()

◆ writeSpectrum_()

Member Data Documentation

◆ chrom_index_

◆ dbl_field_

◆ int_field_

◆ spectra_index_