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SpectrumAccessOpenMS.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/KERNEL/MSSpectrum.h>
39 #include <OpenMS/KERNEL/MSChromatogram.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
43
44 #include <boost/shared_ptr.hpp>
45
46 namespace OpenMS
47 {
52 class OPENMS_DLLAPI SpectrumAccessOpenMS :
53 public OpenSwath::ISpectrumAccess
54 {
55 public:
56 typedef OpenMS::PeakMap MSExperimentType;
57 typedef OpenMS::MSSpectrum MSSpectrumType;
58 typedef OpenMS::MSChromatogram MSChromatogramType;
59
61 explicit SpectrumAccessOpenMS(boost::shared_ptr<MSExperimentType> ms_experiment);
62
64 ~SpectrumAccessOpenMS() override;
65
75 SpectrumAccessOpenMS(const SpectrumAccessOpenMS & rhs);
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
An implementation of the OpenSWATH Spectrum Access interface using OpenMS.
Definition: SpectrumAccessOpenMS.h:52
OpenSwath::OSSpectrumMeta
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:175
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
OpenMS::SpectrumSettings
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::SpectrumAccessOpenMS::MSSpectrumType
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMS.h:57
StandardTypes.h
OpenMS::ChromatogramSettings
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::SpectrumAccessOpenMS::MSChromatogramType
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessOpenMS.h:58
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenSwath::ISpectrumAccess
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:50
MSSpectrum.h
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
MSChromatogram.h
ISpectrumAccess.h
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
OpenMS::SpectrumAccessOpenMS::MSExperimentType
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMS.h:56
OpenMS::SpectrumAccessOpenMS::ms_experiment_
boost::shared_ptr< MSExperimentType > ms_experiment_
Definition: SpectrumAccessOpenMS.h:108