OpenMS  2.8.0
Static Public Member Functions | List of all members
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.