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DataAccessHelper.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_DATAACCESSHELPER_H
36 #define OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_DATAACCESSHELPER_H
37 
38 #include <fstream>
39 
40 #include <boost/numeric/conversion/cast.hpp>
41 
47 
48 namespace OpenMS
49 {
54  class OPENMS_DLLAPI OpenSwathDataAccessHelper
55  {
56 public:
58  static void convertToOpenMSSpectrum(const OpenSwath::SpectrumPtr sptr, OpenMS::MSSpectrum & spectrum);
59 
61  static OpenSwath::SpectrumPtr convertToSpectrumPtr(const OpenMS::MSSpectrum & spectrum);
62 
64  static void convertToOpenMSChromatogram(const OpenSwath::ChromatogramPtr cptr, OpenMS::MSChromatogram & chromatogram);
65 
66  static void convertToOpenMSChromatogramFilter(OpenMS::MSChromatogram & chromatogram, const OpenSwath::ChromatogramPtr cptr,
67  double rt_min, double rt_max);
68 
70  static void convertTargetedExp(const OpenMS::TargetedExperiment & transition_exp_, OpenSwath::LightTargetedExperiment & transition_exp);
71 
73  static void convertTargetedCompound(const TargetedExperiment::Peptide& pep, OpenSwath::LightCompound& comp);
74 
76  static void convertTargetedCompound(const TargetedExperiment::Compound& compound, OpenSwath::LightCompound& comp);
77 
79  static void convertPeptideToAASequence(const OpenSwath::LightCompound & peptide, AASequence & aa_sequence);
80 
81  };
82 
83 } //end namespace OpenMS
84 
85 #endif // OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_DATAACCESSHELPER_H
86 
The representation of a chromatogram.
Definition: MSChromatogram.h:55
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:244
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interface...
Definition: DataAccessHelper.h:54
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:156
Definition: TransitionExperiment.h:150
Definition: TargetedExperimentHelper.h:181
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:62
Definition: TransitionExperiment.h:195
Definition: TargetedExperimentHelper.h:266

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:21:59 using doxygen 1.8.13