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SpectrumAccessOpenMSCached.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMSCACHED_H
36 #define OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMSCACHED_H
37 
42 
44 
45 #include <fstream>
46 
47 namespace OpenMS
48 {
49 
63  class OPENMS_DLLAPI SpectrumAccessOpenMSCached :
65  {
66 
67 public:
70 
80  explicit SpectrumAccessOpenMSCached(String filename);
81 
86 
89 
91  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const;
92 
93  OpenSwath::SpectrumPtr getSpectrumById(int id);
94 
95  OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const;
96 
97  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const;
98 
99  size_t getNrSpectra() const;
100 
101  SpectrumSettings getSpectraMetaInfo(int id) const;
102 
103  OpenSwath::ChromatogramPtr getChromatogramById(int id);
104 
105  size_t getNrChromatograms() const;
106 
107  ChromatogramSettings getChromatogramMetaInfo(int id) const;
108 
109  std::string getChromatogramNativeID(int id) const;
110 
111 private:
112 
114  MSExperimentType meta_ms_experiment_;
115 
117  std::ifstream ifs_;
118 
121 
124 
126  std::vector<std::streampos> spectra_index_;
127  std::vector<std::streampos> chrom_index_;
128  };
129 
130 } //end namespace
131 
132 #endif
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMSCached.h:69
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:159
std::vector< std::streampos > spectra_index_
Indices.
Definition: SpectrumAccessOpenMSCached.h:126
MSExperimentType meta_ms_experiment_
Meta data.
Definition: SpectrumAccessOpenMSCached.h:114
A more convenient string class.
Definition: String.h:57
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:244
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:64
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMSCached.h:68
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:156
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
String filename_cached_
Name of the cached mzML file.
Definition: SpectrumAccessOpenMSCached.h:123
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
std::ifstream ifs_
Internal filestream.
Definition: SpectrumAccessOpenMSCached.h:117
An implementation of the Spectrum Access interface using on-disk caching.
Definition: SpectrumAccessOpenMSCached.h:63
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:51
std::vector< std::streampos > chrom_index_
Definition: SpectrumAccessOpenMSCached.h:127
String filename_
Name of the mzML file.
Definition: SpectrumAccessOpenMSCached.h:120

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:04 using doxygen 1.8.13