OpenMS
SpectrumAccessOpenMSCached.h
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31 // $Maintainer: Hannes Roest $
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34 
35 #pragma once
36 
41 
43 
45 
46 #include <fstream>
47 
48 namespace OpenMS
49 {
50 
64  class OPENMS_DLLAPI SpectrumAccessOpenMSCached :
66  public OpenMS::CachedmzML
67  {
68 
69 public:
72 
82  explicit SpectrumAccessOpenMSCached(const String& filename);
83 
88 
91 
93  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
94 
96 
98 
99  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
100 
101  size_t getNrSpectra() const override;
102 
104 
106 
107  size_t getNrChromatograms() const override;
108 
110 
111  std::string getChromatogramNativeID(int id) const override;
112  };
113 
114 } //end namespace
115 
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzML.h:54
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:61
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
An implementation of the Spectrum Access interface using on-disk caching.
Definition: SpectrumAccessOpenMSCached.h:67
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMSCached.h:70
size_t getNrSpectra() const override
Returns the number of spectra available.
SpectrumAccessOpenMSCached(const String &filename)
Constructor, opens the file stream.
SpectrumAccessOpenMSCached(const SpectrumAccessOpenMSCached &rhs)
Copy constructor.
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMSCached.h:71
std::vector< std::size_t > getSpectraByRT(double RT, double deltaRT) const override
Return a vector of ids of spectra that are within RT +/- deltaRT.
~SpectrumAccessOpenMSCached() override
Destructor.
size_t getNrChromatograms() const override
Returns the number of chromatograms available.
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)
OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override
Returns the meta information for a spectrum.
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:65
A more convenient string class.
Definition: String.h:60
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:51
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
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:296
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:176