OpenMS  3.0.0
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:
57  static void convertToOpenMSSpectrum(const OpenSwath::SpectrumPtr sptr, OpenMS::MSSpectrum & spectrum);
58 
60  static OpenSwath::SpectrumPtr convertToSpectrumPtr(const OpenMS::MSSpectrum & spectrum);
61 
63  static void convertToOpenMSChromatogram(const OpenSwath::ChromatogramPtr cptr, OpenMS::MSChromatogram & chromatogram);
64 
66  static OpenSwath::ChromatogramPtr convertToChromatogramPtr(const OpenMS::MSChromatogram & chromatogram);
67 
68  static void convertToOpenMSChromatogramFilter(OpenMS::MSChromatogram & chromatogram,
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 
77  static void convertTargetedCompound(const TargetedExperiment::Peptide& pep, OpenSwath::LightCompound& comp);
78 
80  static void convertTargetedCompound(const TargetedExperiment::Compound& compound, OpenSwath::LightCompound& comp);
81 
83  static void convertPeptideToAASequence(const OpenSwath::LightCompound & peptide, AASequence & aa_sequence);
84 
85  };
86 
87 } //end namespace OpenMS
88 
89 
TargetedExperiment.h
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:358
TransitionExperiment.h
ISpectrumAccess.h
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:218
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenSwath::LightCompound
Definition: TransitionExperiment.h:160
OpenMS::TargetedExperimentHelper::Compound
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:321
MSChromatogram.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::OpenSwathDataAccessHelper
Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interface...
Definition: DataAccessHelper.h:53
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:296
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
MSSpectrum.h