OpenMS  3.0.0
SpectrumAccessSqMass.h
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34 
35 #pragma once
36 
41 
43 
45 
46 #include <boost/shared_ptr.hpp>
47 
48 namespace OpenMS
49 {
85  class OPENMS_DLLAPI SpectrumAccessSqMass :
87  {
88 
89 public:
92 
95 
96  SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler, const std::vector<int> & indices);
97 
98  SpectrumAccessSqMass(const SpectrumAccessSqMass& sp, const std::vector<int>& indices);
99 
101  ~SpectrumAccessSqMass() override;
102 
105 
107  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
108 
109  OpenSwath::SpectrumPtr getSpectrumById(int /* id */) override;
110 
111  OpenSwath::SpectrumMeta getSpectrumMetaById(int /* id */) const override;
112 
114  void getAllSpectra(std::vector< OpenSwath::SpectrumPtr > & spectra, std::vector< OpenSwath::SpectrumMeta > & spectra_meta) const;
115 
116  std::vector<std::size_t> getSpectraByRT(double /* RT */, double /* deltaRT */) const override;
117 
118  size_t getNrSpectra() const override;
119 
120  OpenSwath::ChromatogramPtr getChromatogramById(int /* id */) override;
121 
122  size_t getNrChromatograms() const override;
123 
124  std::string getChromatogramNativeID(int /* id */) const override;
125 
126 private:
127 
131  std::vector<int> sidx_;
132  };
133 } //end namespace OpenMS
134 
135 
136 
OpenMS::SpectrumAccessSqMass::MSChromatogramType
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessSqMass.h:91
OpenMS::Internal::MzMLSqliteHandler
Sqlite handler for storing spectra and chromatograms in sqMass format.
Definition: MzMLSqliteHandler.h:77
OpenMS::SpectrumAccessSqMass
An implementation of the Spectrum Access interface using SQL files.
Definition: SpectrumAccessSqMass.h:85
ISpectrumAccess.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
MzMLSqliteHandler.h
MSExperiment.h
OpenMS::SpectrumAccessSqMass::sidx_
std::vector< int > sidx_
Optional subset of spectral indices.
Definition: SpectrumAccessSqMass.h:131
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::SpectrumAccessSqMass::MSSpectrumType
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessSqMass.h:90
OpenMS::SpectrumAccessSqMass::handler_
OpenMS::Internal::MzMLSqliteHandler handler_
Access to underlying sqMass file.
Definition: SpectrumAccessSqMass.h:129
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
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
StandardTypes.h
MSSpectrum.h