OpenMS
SpectrumAccessOpenMSInMemory.h
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1 // Copyright (c) 2002-present, 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 
18 #include <boost/shared_ptr.hpp>
19 
20 namespace OpenMS
21 {
47  class OPENMS_DLLAPI SpectrumAccessOpenMSInMemory :
49  {
50 public:
54 
57 
60 
63 
65  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
66 
68 
70 
71  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
72 
73  size_t getNrSpectra() const override;
74 
76 
77  size_t getNrChromatograms() const override;
78 
79  std::string getChromatogramNativeID(int id) const override;
80 
81 private:
82 
83  std::vector< OpenSwath::SpectrumPtr > spectra_;
84  std::vector< OpenSwath::SpectrumMeta > spectra_meta_;
85 
86  std::vector< OpenSwath::ChromatogramPtr > chromatograms_;
87  std::vector< std::string > chromatogram_ids_;
88 
89  };
90 
91 } //end namespace OpenMS
92 
The representation of a chromatogram.
Definition: MSChromatogram.h:30
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
An implementation of the OpenSWATH Spectrum Access interface completely in memory.
Definition: SpectrumAccessOpenMSInMemory.h:49
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMSInMemory.h:51
size_t getNrSpectra() const override
Returns the number of spectra available.
~SpectrumAccessOpenMSInMemory() override
Destructor.
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMSInMemory.h:52
SpectrumAccessOpenMSInMemory(const SpectrumAccessOpenMSInMemory &rhs)
Copy constructor.
std::vector< std::size_t > getSpectraByRT(double RT, double deltaRT) const override
Return a vector of ids of spectra that are within RT +/- deltaRT.
size_t getNrChromatograms() const override
Returns the number of chromatograms available.
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessOpenMSInMemory.h:53
std::vector< OpenSwath::ChromatogramPtr > chromatograms_
Definition: SpectrumAccessOpenMSInMemory.h:86
OpenSwath::ChromatogramPtr getChromatogramById(int id) override
Return a pointer to a chromatogram at the given id.
std::vector< std::string > chromatogram_ids_
Definition: SpectrumAccessOpenMSInMemory.h:87
std::vector< OpenSwath::SpectrumPtr > spectra_
Definition: SpectrumAccessOpenMSInMemory.h:83
OpenSwath::SpectrumPtr getSpectrumById(int id) override
Return a pointer to a spectrum at the given id.
std::vector< OpenSwath::SpectrumMeta > spectra_meta_
Definition: SpectrumAccessOpenMSInMemory.h:84
std::string getChromatogramNativeID(int id) const override
Returns the native id of the chromatogram at the given id.
SpectrumAccessOpenMSInMemory(OpenSwath::ISpectrumAccess &origin)
Constructor.
boost::shared_ptr< OpenSwath::ISpectrumAccess > lightClone() const override
Light clone operator (actual data will not get copied)
OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override
Returns the meta information for a spectrum.
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:30
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
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:276
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:150