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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 (OpenMS::MSChromatogram<> &chromatogram, const OpenSwath::ChromatogramPtr cptr)
 Convert a ChromatogramPtr to an OpenMS Chromatogram. More...
 
static void convertTargetedExp (const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
 convert from the OpenMS TargetedExperiment to the LightTargetedExperiment More...
 
static void convertTargetedPeptide (const TargetedExperiment::Peptide &pep, OpenSwath::LightPeptide &p)
 convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide More...
 
static void convertPeptideToAASequence (const OpenSwath::LightPeptide &peptide, AASequence &aa_sequence)
 convert from the LightPeptide 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

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

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

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

convert from the OpenMS TargetedExperiment to the LightTargetedExperiment

Referenced by OpenSwathWorkflow::RTNormalization().

static void convertTargetedPeptide ( const TargetedExperiment::Peptide pep,
OpenSwath::LightPeptide p 
)
static

convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide

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

Convert a ChromatogramPtr to an OpenMS Chromatogram.

Referenced by ChromatogramExtractor::return_chromatogram(), and OpenSwathWorkflow::scoreAllChromatograms().

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

Convert a SpectrumPtr to an OpenMS Spectrum.

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

Convert an OpenMS Spectrum to an SpectrumPtr.


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:44 using doxygen 1.8.5