OpenMS  3.0.0
SpectrumAccessOpenMS.h
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34 
35 #pragma once
36 
41 
43 
44 #include <boost/shared_ptr.hpp>
45 
46 namespace OpenMS
47 {
52  class OPENMS_DLLAPI SpectrumAccessOpenMS :
54  {
55 public:
59 
61  explicit SpectrumAccessOpenMS(boost::shared_ptr<MSExperimentType> ms_experiment);
62 
64  ~SpectrumAccessOpenMS() override;
65 
76 
84  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
85 
86  OpenSwath::SpectrumPtr getSpectrumById(int id) override;
87 
88  OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override;
89 
90  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
91 
92  size_t getNrSpectra() const override;
93 
94  SpectrumSettings getSpectraMetaInfo(int id) const;
95 
96  OpenSwath::ChromatogramPtr getChromatogramById(int id) override;
97 
98  // FEATURE ?
99  // ChromatogramPtr getChromatogramByPrecursorMZ(double mz, double deltaMZ);
100 
101  size_t getNrChromatograms() const override;
102 
103  ChromatogramSettings getChromatogramMetaInfo(int id) const;
104 
105  std::string getChromatogramNativeID(int id) const override;
106 
107 private:
108  boost::shared_ptr<MSExperimentType> ms_experiment_;
109 
110  };
111 } //end namespace OpenMS
112 
OpenMS::SpectrumAccessOpenMS::MSChromatogramType
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessOpenMS.h:58
ISpectrumAccess.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::SpectrumAccessOpenMS
An implementation of the OpenSWATH Spectrum Access interface using OpenMS.
Definition: SpectrumAccessOpenMS.h:52
OpenMS::SpectrumAccessOpenMS::ms_experiment_
boost::shared_ptr< MSExperimentType > ms_experiment_
Definition: SpectrumAccessOpenMS.h:108
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ChromatogramSettings
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
OpenMS::SpectrumAccessOpenMS::MSExperimentType
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMS.h:56
OpenMS::SpectrumAccessOpenMS::MSSpectrumType
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMS.h:57
MSExperiment.h
OpenSwath::OSSpectrumMeta
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:175
OpenSwath::ISpectrumAccess
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:50
MSChromatogram.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:296
OpenMS::SpectrumSettings
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::DIM_UNIT::RT
RT in seconds.
StandardTypes.h
MSSpectrum.h