MSDataCachedConsumer Class Reference

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

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

Inheritance diagram for MSDataCachedConsumer:

Public Member Functions
	MSDataCachedConsumer (String filename, bool clearData=true)
	Constructor. More...
	~MSDataCachedConsumer ()
	Destructor. More...
void	consumeSpectrum (SpectrumType &s)
	Write a spectrum to the output file. More...
void	consumeChromatogram (ChromatogramType &c)
	Write a chromatogram to the output file. More...
void	setExpectedSize (Size, Size)
	Set expected size of spectra and chromatograms to be consumed. More...
void	setExperimentalSettings (const ExperimentalSettings &)
	Set experimental settings (meta-data) of the data to be consumed. More...
Public Member Functions inherited from CachedmzML
	CachedmzML ()
	Default constructor. More...
	~CachedmzML ()
	Default destructor. More...
CachedmzML &	operator= (const CachedmzML &rhs)
	Assignment operator. More...
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...
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...
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 CachedmzML
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 CachedmzML
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 CachedmzML
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 inherited from CachedmzML
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...
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 CachedmzML.

Member Typedef Documentation

ChromatogramType

typedef MSChromatogram ChromatogramType

private

SpectrumType

typedef MSSpectrum SpectrumType

private

Constructor & Destructor Documentation

MSDataCachedConsumer()

MSDataCachedConsumer ( String  filename, bool  clearData = true  )

inline

Constructor.

Opens the output file and writes the header.

References CACHED_MZML_FILE_IDENTIFIER.

~MSDataCachedConsumer()

~MSDataCachedConsumer ( )

inline

Destructor.

Closes the output file and writes the footer.

Member Function Documentation

consumeChromatogram()

void consumeChromatogram ( ChromatogramType &  c )

inlinevirtual

Write a chromatogram to the output file.

Implements IMSDataConsumer.

References MSChromatogram::clear().

consumeSpectrum()

void consumeSpectrum ( SpectrumType &  s )

inlinevirtual

Write a spectrum to the output file.

Implements IMSDataConsumer.

References MSSpectrum::clear().

setExpectedSize()

void setExpectedSize ( Size  expectedSpectra, Size  expectedChromatograms  )

inlinevirtual

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 )

inlinevirtual

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