ChromatogramTools Class Reference

Conversion class to convert chromatograms. More...

#include <OpenMS/KERNEL/ChromatogramTools.h>

Public Member Functions
Constructors and destructors
	ChromatogramTools ()
	default constructor More...
	ChromatogramTools (const ChromatogramTools &)
	copy constructor More...
virtual	~ChromatogramTools ()
	destructor More...
Accessors
template<typename ExperimentType >
void	convertChromatogramsToSpectra (ExperimentType &exp)
	converts the chromatogram to a list of spectra with instrument settings More...
template<typename ExperimentType >
void	convertSpectraToChromatograms (ExperimentType &exp, bool remove_spectra=false, bool force_conversion=false)
	converts e.g. SRM spectra to chromatograms More...

Detailed Description

Conversion class to convert chromatograms.

There are basically two methods implemented, conversion of chromatograms into spectra representation and vice versa.

Constructor & Destructor Documentation

ChromatogramTools() [1/2]

ChromatogramTools ( )

inline

default constructor

ChromatogramTools() [2/2]

ChromatogramTools ( const ChromatogramTools &  )

inline

copy constructor

~ChromatogramTools()

virtual ~ChromatogramTools ( )

inlinevirtual

destructor

Member Function Documentation

convertChromatogramsToSpectra()

void convertChromatogramsToSpectra ( ExperimentType &  exp )

inline

converts the chromatogram to a list of spectra with instrument settings

This conversion may be necessary as most of the spectra formats do not support chromatograms, except of mzML. However, most formats support e.g. SRM chromatogram as a list of spectra with instrument settings SRM and a separate spectrum for each data point. The disadvantage of storing chromatograms in spectra is its exhaustive memory consumption.

References SpectrumSettings::getPrecursors(), ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM, ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM, InstrumentSettings::SIM, and InstrumentSettings::SRM.

convertSpectraToChromatograms()

void convertSpectraToChromatograms ( ExperimentType &  exp, bool  remove_spectra = false, bool  force_conversion = false  )

inline

converts e.g. SRM spectra to chromatograms

This conversion is necessary to convert chromatograms, e.g. from SRM or MRM experiments to real chromatograms. mzML 1.1.0 has support for chromatograms which can be stored much more efficiently than spectra based chromatograms. However, most other file formats do not support chromatograms.

Parameters

exp	the experiment to be converted.
remove_spectra	if set to true, the chromatogram spectra are removed from the experiment.
force_conversion	Convert even if ScanMode is not SRM or if there are no precursors (e.g. GC-MS data)

References MSSpectrum::clear(), OPENMS_LOG_WARN, ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM, ChromatogramPeak::setIntensity(), Product::setMZ(), ChromatogramSettings::setPrecursor(), Peak2D::setRT(), ChromatogramPeak::setRT(), and InstrumentSettings::SRM.