OpenMS
SpectrumAccessSqMass.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hannes Roest $
6 // $Authors: Hannes Roest $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
15 
17 
19 
20 #include <boost/shared_ptr.hpp>
21 
22 namespace OpenMS
23 {
59  class OPENMS_DLLAPI SpectrumAccessSqMass :
61  {
62 
63 public:
66 
69 
70  SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler, const std::vector<int> & indices);
71 
72  SpectrumAccessSqMass(const SpectrumAccessSqMass& sp, const std::vector<int>& indices);
73 
76 
79 
81  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
82 
83  OpenSwath::SpectrumPtr getSpectrumById(int /* id */) override;
84 
85  OpenSwath::SpectrumMeta getSpectrumMetaById(int /* id */) const override;
86 
88  void getAllSpectra(std::vector< OpenSwath::SpectrumPtr > & spectra, std::vector< OpenSwath::SpectrumMeta > & spectra_meta) const;
89 
90  std::vector<std::size_t> getSpectraByRT(double /* RT */, double /* deltaRT */) const override;
91 
92  size_t getNrSpectra() const override;
93 
95 
96  size_t getNrChromatograms() const override;
97 
98  std::string getChromatogramNativeID(int /* id */) const override;
99 
100 private:
101 
105  std::vector<int> sidx_;
106  };
107 } //end namespace OpenMS
108 
109 
110 
Sqlite handler for storing spectra and chromatograms in sqMass format.
Definition: MzMLSqliteHandler.h:52
The representation of a chromatogram.
Definition: MSChromatogram.h:31
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
An implementation of the Spectrum Access interface using SQL files.
Definition: SpectrumAccessSqMass.h:61
size_t getNrSpectra() const override
Returns the number of spectra available.
SpectrumAccessSqMass(const SpectrumAccessSqMass &sp, const std::vector< int > &indices)
OpenSwath::SpectrumMeta getSpectrumMetaById(int) const override
Returns the meta information for a spectrum.
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessSqMass.h:64
SpectrumAccessSqMass(const SpectrumAccessSqMass &rhs)
Copy constructor.
std::vector< std::size_t > getSpectraByRT(double, double) const override
Return a vector of ids of spectra that are within RT +/- deltaRT.
SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler &handler)
Constructor.
OpenMS::Internal::MzMLSqliteHandler handler_
Access to underlying sqMass file.
Definition: SpectrumAccessSqMass.h:103
OpenSwath::SpectrumPtr getSpectrumById(int) override
Return a pointer to a spectrum at the given id.
OpenSwath::ChromatogramPtr getChromatogramById(int) override
Return a pointer to a chromatogram at the given id.
size_t getNrChromatograms() const override
Returns the number of chromatograms available.
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessSqMass.h:65
void getAllSpectra(std::vector< OpenSwath::SpectrumPtr > &spectra, std::vector< OpenSwath::SpectrumMeta > &spectra_meta) const
Load all spectra from the underlying sqMass file into memory.
std::vector< int > sidx_
Optional subset of spectral indices.
Definition: SpectrumAccessSqMass.h:105
SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler &handler, const std::vector< int > &indices)
~SpectrumAccessSqMass() override
Destructor.
boost::shared_ptr< OpenSwath::ISpectrumAccess > lightClone() const override
Light clone operator (actual data will not get copied)
std::string getChromatogramNativeID(int) const override
Returns the native id of the chromatogram at the given id.
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:25
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:146
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:270
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:150