OpenSwathDataAccessHelper Class Reference

Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.h>

Static Public Member Functions
static void	convertToOpenMSSpectrum (const OpenSwath::SpectrumPtr &sptr, OpenMS::MSSpectrum &spectrum)
	Convert a SpectrumPtr to an OpenMS Spectrum. More...
static OpenSwath::SpectrumPtr	convertToSpectrumPtr (const OpenMS::MSSpectrum &spectrum)
	Convert an OpenMS Spectrum to an SpectrumPtr. More...
static void	convertToOpenMSChromatogram (const OpenSwath::ChromatogramPtr &cptr, OpenMS::MSChromatogram &chromatogram)
	Convert a ChromatogramPtr to an OpenMS Chromatogram. More...
static OpenSwath::ChromatogramPtr	convertToChromatogramPtr (const OpenMS::MSChromatogram &chromatogram)
	Convert an OpenMS Chromatogram to an ChromatogramPtr. More...
static void	convertToOpenMSChromatogramFilter (OpenMS::MSChromatogram &chromatogram, const OpenSwath::ChromatogramPtr &cptr, double rt_min, double rt_max)
static void	convertTargetedExp (const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
	convert from the OpenMS TargetedExperiment to the LightTargetedExperiment More...
static void	convertTargetedCompound (const TargetedExperiment::Peptide &pep, OpenSwath::LightCompound &comp)
	convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide More...
static void	convertTargetedCompound (const TargetedExperiment::Compound &compound, OpenSwath::LightCompound &comp)
	convert from the OpenMS TargetedExperiment Compound to the LightTargetedExperiment Compound More...
static void	convertPeptideToAASequence (const OpenSwath::LightCompound &peptide, AASequence &aa_sequence)
	convert from the LightCompound to an OpenMS AASequence (with correct modifications) More...

Detailed Description

Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interfaces.

Member Function Documentation

convertPeptideToAASequence()

static void convertPeptideToAASequence ( const OpenSwath::LightCompound &  peptide, AASequence &  aa_sequence  )

static

convert from the LightCompound to an OpenMS AASequence (with correct modifications)

convertTargetedCompound() [1/2]

static void convertTargetedCompound ( const TargetedExperiment::Compound &  compound, OpenSwath::LightCompound &  comp  )

static

convert from the OpenMS TargetedExperiment Compound to the LightTargetedExperiment Compound

convertTargetedCompound() [2/2]

static void convertTargetedCompound ( const TargetedExperiment::Peptide &  pep, OpenSwath::LightCompound &  comp  )

static

convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide

convertTargetedExp()

static void convertTargetedExp ( const OpenMS::TargetedExperiment &  transition_exp_, OpenSwath::LightTargetedExperiment &  transition_exp  )

static

convert from the OpenMS TargetedExperiment to the LightTargetedExperiment

Referenced by TOPPOpenSwathBase::loadTransitionList().

convertToChromatogramPtr()

static OpenSwath::ChromatogramPtr convertToChromatogramPtr ( const OpenMS::MSChromatogram &  chromatogram )

static

Convert an OpenMS Chromatogram to an ChromatogramPtr.

convertToOpenMSChromatogram()

static void convertToOpenMSChromatogram ( const OpenSwath::ChromatogramPtr &  cptr, OpenMS::MSChromatogram &  chromatogram  )

static

Convert a ChromatogramPtr to an OpenMS Chromatogram.

Referenced by ChromatogramExtractor::return_chromatogram().

convertToOpenMSChromatogramFilter()

static void convertToOpenMSChromatogramFilter ( OpenMS::MSChromatogram &  chromatogram, const OpenSwath::ChromatogramPtr &  cptr, double  rt_min, double  rt_max  )

static

convertToOpenMSSpectrum()

static void convertToOpenMSSpectrum ( const OpenSwath::SpectrumPtr &  sptr, OpenMS::MSSpectrum &  spectrum  )

static

Convert a SpectrumPtr to an OpenMS Spectrum.

convertToSpectrumPtr()

static OpenSwath::SpectrumPtr convertToSpectrumPtr ( const OpenMS::MSSpectrum &  spectrum )

static

Convert an OpenMS Spectrum to an SpectrumPtr.