| OpenMS 2.5.0

SpectrumAccessSqMass.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/FORMAT/HANDLERS/MzMLSqliteHandler.h>
43
44 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
45
46 #include <boost/shared_ptr.hpp>
47 #include <algorithm> // std::lower_bound, std::upper_bound, std::sort
48
49 namespace OpenMS
50 {
86 class OPENMS_DLLAPI SpectrumAccessSqMass :
87 public OpenSwath::ISpectrumAccess
88 {
89
90 public:
91 typedef OpenMS::MSSpectrum MSSpectrumType;
92 typedef OpenMS::MSChromatogram MSChromatogramType;
93
95 SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler);
96
97 SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler, const std::vector<int> & indices);
98
99 SpectrumAccessSqMass(const SpectrumAccessSqMass& sp, const std::vector<int>& indices);
100
102 ~SpectrumAccessSqMass() override;
103
105 SpectrumAccessSqMass(const SpectrumAccessSqMass & rhs);
106
108 boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
109
110 OpenSwath::SpectrumPtr getSpectrumById(int /* id */) override;
111
112 OpenSwath::SpectrumMeta getSpectrumMetaById(int /* id */) const override;
113
115 void getAllSpectra(std::vector< OpenSwath::SpectrumPtr > & spectra, std::vector< OpenSwath::SpectrumMeta > & spectra_meta) const;
116
117 std::vector<std::size_t> getSpectraByRT(double /* RT */, double /* deltaRT */) const override;
118
119 size_t getNrSpectra() const override;
120
121 OpenSwath::ChromatogramPtr getChromatogramById(int /* id */) override;
122
123 size_t getNrChromatograms() const override;
124
125 std::string getChromatogramNativeID(int /* id */) const override;
126
127 private:
128
130 OpenMS::Internal::MzMLSqliteHandler handler_;
132 std::vector<int> sidx_;
133 };
134 } //end namespace OpenMS
135
136
137
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::SpectrumAccessSqMass::MSSpectrumType
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessSqMass.h:91
StandardTypes.h
OpenMS::SpectrumAccessSqMass
An implementation of the Spectrum Access interface using SQL files.
Definition: SpectrumAccessSqMass.h:86
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SpectrumAccessSqMass::handler_
OpenMS::Internal::MzMLSqliteHandler handler_
Access to underlying sqMass file.
Definition: SpectrumAccessSqMass.h:130
MSExperiment.h
OpenMS::Internal::MzMLSqliteHandler
Sqlite handler for storing spectra and chromatograms in sqMass format.
Definition: MzMLSqliteHandler.h:77
MzMLSqliteHandler.h
OpenSwath::ISpectrumAccess
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:50
OpenMS::SpectrumAccessSqMass::sidx_
std::vector< int > sidx_
Optional subset of spectral indices.
Definition: SpectrumAccessSqMass.h:132
MSSpectrum.h
OpenMS::SpectrumAccessSqMass::MSChromatogramType
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessSqMass.h:92
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