OpenMS
SpectrumAccessOpenMS.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 
18 #include <boost/shared_ptr.hpp>
19 
20 namespace OpenMS
21 {
26  class OPENMS_DLLAPI SpectrumAccessOpenMS :
28  {
29 public:
33 
35  explicit SpectrumAccessOpenMS(boost::shared_ptr<MSExperimentType> ms_experiment);
36 
39 
50 
58  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
59 
61 
63 
64  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
65 
66  size_t getNrSpectra() const override;
67 
69 
71 
72  // FEATURE ?
73  // ChromatogramPtr getChromatogramByPrecursorMZ(double mz, double deltaMZ);
74 
75  size_t getNrChromatograms() const override;
76 
78 
79  std::string getChromatogramNativeID(int id) const override;
80 
81 private:
82  boost::shared_ptr<MSExperimentType> ms_experiment_;
83 
84  };
85 } //end namespace OpenMS
86 
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:35
The representation of a chromatogram.
Definition: MSChromatogram.h:31
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
An implementation of the OpenSWATH Spectrum Access interface using OpenMS.
Definition: SpectrumAccessOpenMS.h:28
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMS.h:30
size_t getNrSpectra() const override
Returns the number of spectra available.
SpectrumAccessOpenMS(boost::shared_ptr< MSExperimentType > ms_experiment)
Constructor.
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMS.h:31
std::vector< std::size_t > getSpectraByRT(double RT, double deltaRT) const override
Return a vector of ids of spectra that are within RT +/- deltaRT.
~SpectrumAccessOpenMS() override
Destructor.
size_t getNrChromatograms() const override
Returns the number of chromatograms available.
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessOpenMS.h:32
boost::shared_ptr< MSExperimentType > ms_experiment_
Definition: SpectrumAccessOpenMS.h:82
SpectrumSettings getSpectraMetaInfo(int id) const
OpenSwath::ChromatogramPtr getChromatogramById(int id) override
Return a pointer to a chromatogram at the given id.
OpenSwath::SpectrumPtr getSpectrumById(int id) override
Return a pointer to a spectrum at the given id.
ChromatogramSettings getChromatogramMetaInfo(int id) const
std::string getChromatogramNativeID(int id) const override
Returns the native id of the chromatogram at the given id.
boost::shared_ptr< OpenSwath::ISpectrumAccess > lightClone() const override
Light clone operator (actual data will not get copied)
SpectrumAccessOpenMS(const SpectrumAccessOpenMS &rhs)
Copy constructor.
OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override
Returns the meta information for a spectrum.
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:39
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