| OpenMS 2.5.0

SpectrumAccessOpenMSCached.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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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/FORMAT/CachedMzML.h>
43
44 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
45
46 #include <fstream>
47
48 namespace OpenMS
49 {
50
64 class OPENMS_DLLAPI SpectrumAccessOpenMSCached :
65 public OpenSwath::ISpectrumAccess,
66 public OpenMS::CachedmzML
67 {
68
69 public:
70 typedef OpenMS::PeakMap MSExperimentType;
71 typedef OpenMS::MSSpectrum MSSpectrumType;
72
82 explicit SpectrumAccessOpenMSCached(const String& filename);
83
87 ~SpectrumAccessOpenMSCached() override;
88
90 SpectrumAccessOpenMSCached(const SpectrumAccessOpenMSCached & rhs);
91
93 boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
94
95 OpenSwath::SpectrumPtr getSpectrumById(int id) override;
96
97 OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override;
98
99 std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
100
101 size_t getNrSpectra() const override;
102
103 SpectrumSettings getSpectraMetaInfo(int id) const;
104
105 OpenSwath::ChromatogramPtr getChromatogramById(int id) override;
106
107 size_t getNrChromatograms() const override;
108
109 ChromatogramSettings getChromatogramMetaInfo(int id) const;
110
111 std::string getChromatogramNativeID(int id) const override;
112 };
113
114 } //end namespace
115
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenSwath::OSSpectrumMeta
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:175
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
StandardTypes.h
OpenMS::SpectrumAccessOpenMSCached::MSSpectrumType
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMSCached.h:71
OpenMS::ChromatogramSettings
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
CachedMzML.h
OpenMS::SpectrumAccessOpenMSCached
An implementation of the Spectrum Access interface using on-disk caching.
Definition: SpectrumAccessOpenMSCached.h:64
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
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
OpenMS::CachedmzML
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzML.h:53
MSSpectrum.h
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
OpenMS::SpectrumAccessOpenMSCached::MSExperimentType
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMSCached.h:70
MSChromatogram.h
ISpectrumAccess.h
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172