Transforming and cached writing consumer of MS data. More...

#include <OpenMS/FORMAT/DATAACCESS/MSDataCachedConsumer.h>

Inheritance diagram for MSDataCachedConsumer:

Collaboration diagram for MSDataCachedConsumer:

Public Member Functions
	MSDataCachedConsumer (const String &filename, bool clearData=true)
	Constructor. More...

	~MSDataCachedConsumer () override
	Destructor. More...

void	consumeSpectrum (SpectrumType &s) override
	Write a spectrum to the output file. More...

void	consumeChromatogram (ChromatogramType &c) override
	Write a chromatogram to the output file. More...

void	setExpectedSize (Size, Size) override
	Set expected size of spectra and chromatograms to be consumed. More...

void	setExperimentalSettings (const ExperimentalSettings &) override
	Set experimental settings (meta-data) of the data to be consumed. More...

Public Member Functions inherited from CachedMzMLHandler
	CachedMzMLHandler ()
	Default constructor. More...

	~CachedMzMLHandler ()
	Default destructor. More...

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

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...

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...

Public Member Functions inherited from IMSDataConsumer
virtual	~IMSDataConsumer ()

Protected Attributes
std::ofstream	ofs_

bool	clearData_

Size	spectra_written_

Size	chromatograms_written_

Protected Attributes inherited from CachedMzMLHandler
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 Types
typedef MSSpectrum	SpectrumType

typedef MSChromatogram	ChromatogramType

Additional Inherited Members
Public Types inherited from CachedMzMLHandler
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 Types inherited from IMSDataConsumer
typedef MSSpectrum	SpectrumType

typedef MSChromatogram	ChromatogramType

Static Public Member Functions inherited from CachedMzMLHandler
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...

Protected Member Functions inherited from CachedMzMLHandler
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 Protected Member Functions inherited from CachedMzMLHandler
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...

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

Transforming and cached writing consumer of MS data.

Is able to transform a spectrum on the fly while it is read using a function pointer that can be set on the object. The spectra is then cached to disk using the functions provided in CachedMzMLHandler.

Member Typedef Documentation

◆ ChromatogramType

typedef MSChromatogram ChromatogramType

private

◆ SpectrumType

typedef MSSpectrum SpectrumType

private

Constructor & Destructor Documentation

◆ MSDataCachedConsumer()

MSDataCachedConsumer	(	const String &	filename,
		bool	clearData = `true`
	)

Constructor.

Opens the output file and writes the header.

Parameters

filename	The output file name to which data is written
clearData	Whether to clear the spectral and chromatogram data after writing (only keep meta-data)

Note: Clearing data from spectra and chromatograms also clears float and integer data arrays associated with the structure as these are written to disk as well.

◆ ~MSDataCachedConsumer()

~MSDataCachedConsumer ( )

override

Destructor.

Closes the output file and writes the footer.

Member Function Documentation

◆ consumeChromatogram()

void consumeChromatogram ( ChromatogramType & c )

overridevirtual

Write a chromatogram to the output file.

Note: May delete data from chromatogram (if clearData is set)

Implements IMSDataConsumer.

◆ consumeSpectrum()

void consumeSpectrum ( SpectrumType & s )

overridevirtual

Write a spectrum to the output file.

Note: May delete data from spectrum (if clearData is set)

Implements IMSDataConsumer.

◆ setExpectedSize()

void setExpectedSize	(	Size	expectedSpectra,
		Size	expectedChromatograms
	)

inlineoverridevirtual

Set expected size of spectra and chromatograms to be consumed.

Some implementations might care about the number of spectra and chromatograms to be consumed and need to be informed about this (usually before consuming starts).

Note: Calling this method is optional but good practice.

Parameters

expectedSpectra	Number of spectra expected
expectedChromatograms	Number of chromatograms expected

Implements IMSDataConsumer.

Referenced by CachedSwathFileConsumer::addNewSwathMap_().

◆ setExperimentalSettings()

void setExperimentalSettings ( const ExperimentalSettings & exp )

inlineoverridevirtual

Set experimental settings (meta-data) of the data to be consumed.

Some implementations might need to know about the meta-data (or the context) of the spectra and chromatograms to be consumed. This method allows them learn this.

Note: Calling this method is optional but good practice.

Parameters

exp	Experimental settings meta data for the data to be consumed

Implements IMSDataConsumer.

Member Data Documentation

◆ chromatograms_written_

Size chromatograms_written_

protected

◆ clearData_

bool clearData_

protected

◆ ofs_

std::ofstream ofs_

protected

◆ spectra_written_

Size spectra_written_

protected

Public Member Functions

Protected Attributes

Private Types

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ChromatogramType

◆ SpectrumType

Constructor & Destructor Documentation

◆ MSDataCachedConsumer()

◆ ~MSDataCachedConsumer()

Member Function Documentation

◆ consumeChromatogram()

◆ consumeSpectrum()

◆ setExpectedSize()

◆ setExperimentalSettings()

Member Data Documentation

◆ chromatograms_written_

◆ clearData_

◆ ofs_

◆ spectra_written_