| OpenMS 2.5.0

List of all members
ChromatogramTools Class Reference
Kernel

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 SRM 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 | ( |  | ) |

inline virtual

destructor

## Member Function Documentation

## ◆ convertChromatogramsToSpectra()

void convertChromatogramsToSpectra | ( | ExperimentType & | exp | ) |

inline

converts the chromatogram to a list of spectra with instrument settings SRM

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, Peak2D::setMZ(), 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.

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