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

#include <OpenMS/ANALYSIS/OPENSWATH/CachedmzML.h>

Inheritance diagram for CachedmzML:

Public Types
typedef MSExperiment< Peak1D >	MapType
typedef MSSpectrum< Peak1D >	SpectrumType
typedef MSChromatogram < ChromatogramPeak >	ChromatogramType
typedef double	DatumSingleton
typedef std::vector < DatumSingleton >	Datavector
Public Member Functions
void	createMemdumpIndex (String filename)
	Create an index on the location of all the spectra and chromatograms.
void	writeMetadata (MapType exp, String out_meta)
	Write only the meta data of an MSExperiment.
Constructors and Destructor

	CachedmzML ()
	Default constructor.
	~CachedmzML ()
	Default destructor.
CachedmzML &	operator= (const CachedmzML &rhs)
	Assignment operator.
Read / Write an MSExperiment

void	writeMemdump (MapType &exp, String out)
	Write complete spectra as a dump to the disk.
void	readMemdump (MapType &exp_reading, String filename) const
	Read all spectra from a dump from the disk.
Read a single MSSpectrum

void	readSingleSpectrum (MSSpectrum< Peak1D > &spectrum, const String &filename, const Size &idx) const
	Read a single spectrum from the given filename.
void	readSingleSpectrum (MSSpectrum< Peak1D > &spectrum, std::ifstream &ifs, const Size &idx) const
Access to the binary indices

const std::vector< Size > &	getSpectraIndex () const
const std::vector< Size > &	getChromatogramIndex () const
Static Public Member Functions
static void	readSpectrumFast (OpenSwath::BinaryDataArrayPtr data1, OpenSwath::BinaryDataArrayPtr data2, std::ifstream &ifs, int ms_level, double rt)
	fast access without copying
static void	readChromatogramFast (OpenSwath::BinaryDataArrayPtr data1, OpenSwath::BinaryDataArrayPtr data2, std::ifstream &ifs)
	fast access without copying
Private Member Functions
void	readSpectrum_ (Datavector &data1, Datavector &data2, std::ifstream &ifs, int &ms_level, double &rt) const
void	readChromatogram_ (Datavector &data1, Datavector &data2, std::ifstream &ifs) const
void	readSpectrum_ (SpectrumType &spectrum, std::ifstream &ifs) const
void	readChromatogram_ (ChromatogramType &chromatogram, std::ifstream &ifs) const
void	writeSpectrum_ (SpectrumType &spectrum, std::ofstream &ofs)
void	writeChromatogram_ (const ChromatogramType &chromatogram, std::ofstream &ofs)
Private Attributes
int	int_field_
double	dbl_field_
std::vector< Size >	spectra_index_
std::vector< Size >	chrom_index_

Detailed Description

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

This class implements the OpenSWATH Spectrum Access interface (ISpectrumAccess) using the CachedmzML class which is able to read and write a cached mzML file.

Member Typedef Documentation

typedef MSChromatogram<ChromatogramPeak> ChromatogramType

typedef std::vector<DatumSingleton> Datavector

typedef double DatumSingleton

typedef MSExperiment<Peak1D> MapType

typedef MSSpectrum<Peak1D> SpectrumType

Constructor & Destructor Documentation

CachedmzML ( ) [inline]

Default constructor.

~CachedmzML ( ) [inline]

Default destructor.

Member Function Documentation

void createMemdumpIndex ( String filename ) [inline]

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

References MAGIC_NUMBER.

const std::vector<Size>& getChromatogramIndex ( ) const [inline]

const std::vector<Size>& getSpectraIndex ( ) const [inline]

CachedmzML& operator= ( const CachedmzML & rhs ) [inline]

Assignment operator.

References CachedmzML::chrom_index_, and CachedmzML::spectra_index_.

void readChromatogram_	(	Datavector &	data1,
		Datavector &	data2,
		std::ifstream &	ifs
	)			const `[inline, private]`

void readChromatogram_	(	ChromatogramType &	chromatogram,
		std::ifstream &	ifs
	)			const `[inline, private]`

References ChromatogramPeak::setIntensity(), and ChromatogramPeak::setRT().

static void readChromatogramFast	(	OpenSwath::BinaryDataArrayPtr	data1,
		OpenSwath::BinaryDataArrayPtr	data2,
		std::ifstream &	ifs
	)			`[inline, static]`

fast access without copying

void readMemdump	(	MapType &	exp_reading,
		String	filename
	)			const `[inline]`

Read all spectra from a dump from the disk.

References MAGIC_NUMBER, and MSExperiment< PeakT, ChromatogramPeakT >::setChromatograms().

void readSingleSpectrum	(	MSSpectrum< Peak1D > &	spectrum,
		const String &	filename,
		const Size &	idx
	)			const `[inline]`

Read a single spectrum from the given filename.

void readSingleSpectrum	(	MSSpectrum< Peak1D > &	spectrum,
		std::ifstream &	ifs,
		const Size &	idx
	)			const `[inline]`

void readSpectrum_	(	Datavector &	data1,
		Datavector &	data2,
		std::ifstream &	ifs,
		int &	ms_level,
		double &	rt
	)			const `[inline, private]`

void readSpectrum_	(	SpectrumType &	spectrum,
		std::ifstream &	ifs
	)			const `[inline, private]`

References Peak1D::setIntensity(), MSSpectrum< PeakT >::setMSLevel(), Peak1D::setMZ(), and MSSpectrum< PeakT >::setRT().

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