OpenMS  2.8.0
SpectrumAccessOpenMS.h
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34 
35 #pragma once
36 
41 
43 
44 #include <boost/shared_ptr.hpp>
45 
46 namespace OpenMS
47 {
52  class OPENMS_DLLAPI SpectrumAccessOpenMS :
54  {
55 public:
59 
61  explicit SpectrumAccessOpenMS(boost::shared_ptr<MSExperimentType> ms_experiment);
62 
65 
76 
84  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
85 
87 
89 
90  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
91 
92  size_t getNrSpectra() const override;
93 
95 
97 
98  // FEATURE ?
99  // ChromatogramPtr getChromatogramByPrecursorMZ(double mz, double deltaMZ);
100 
101  size_t getNrChromatograms() const override;
102 
104 
105  std::string getChromatogramNativeID(int id) const override;
106 
107 private:
108  boost::shared_ptr<MSExperimentType> ms_experiment_;
109 
110  };
111 } //end namespace OpenMS
112 
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:61
The representation of a chromatogram.
Definition: MSChromatogram.h:57
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
An implementation of the OpenSWATH Spectrum Access interface using OpenMS.
Definition: SpectrumAccessOpenMS.h:54
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMS.h:56
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:57
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:58
boost::shared_ptr< MSExperimentType > ms_experiment_
Definition: SpectrumAccessOpenMS.h:108
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:65
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:51
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:291
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:176