OpenMS
DataAccessHelper.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
37 #include <fstream>
38 
39 #include <boost/numeric/conversion/cast.hpp>
40 
46 
47 namespace OpenMS
48 {
53  class OPENMS_DLLAPI OpenSwathDataAccessHelper
54  {
55 public:
58 
61 
64 
67 
69  const OpenSwath::ChromatogramPtr& cptr,
70  double rt_min,
71  double rt_max);
72 
74  static void convertTargetedExp(const OpenMS::TargetedExperiment & transition_exp_, OpenSwath::LightTargetedExperiment & transition_exp);
75 
78 
81 
83  static void convertPeptideToAASequence(const OpenSwath::LightCompound & peptide, AASequence & aa_sequence);
84 
85  };
86 
87 } //end namespace OpenMS
88 
89 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
The representation of a chromatogram.
Definition: MSChromatogram.h:57
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interface...
Definition: DataAccessHelper.h:54
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
static void convertToOpenMSChromatogram(const OpenSwath::ChromatogramPtr &cptr, OpenMS::MSChromatogram &chromatogram)
Convert a ChromatogramPtr to an OpenMS Chromatogram.
static void convertPeptideToAASequence(const OpenSwath::LightCompound &peptide, AASequence &aa_sequence)
convert from the LightCompound to an OpenMS AASequence (with correct modifications)
static OpenSwath::SpectrumPtr convertToSpectrumPtr(const OpenMS::MSSpectrum &spectrum)
Convert an OpenMS Spectrum to an SpectrumPtr.
static void convertToOpenMSChromatogramFilter(OpenMS::MSChromatogram &chromatogram, const OpenSwath::ChromatogramPtr &cptr, double rt_min, double rt_max)
static void convertTargetedCompound(const TargetedExperiment::Compound &compound, OpenSwath::LightCompound &comp)
convert from the OpenMS TargetedExperiment Compound to the LightTargetedExperiment Compound
static void convertTargetedCompound(const TargetedExperiment::Peptide &pep, OpenSwath::LightCompound &comp)
convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide
static OpenSwath::ChromatogramPtr convertToChromatogramPtr(const OpenMS::MSChromatogram &chromatogram)
Convert an OpenMS Chromatogram to an ChromatogramPtr.
static void convertToOpenMSSpectrum(const OpenSwath::SpectrumPtr &sptr, OpenMS::MSSpectrum &spectrum)
Convert a SpectrumPtr to an OpenMS Spectrum.
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:323
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:360
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:65
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:296
Definition: TransitionExperiment.h:161
Definition: TransitionExperiment.h:219