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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 
41 
43 
44 #include <fstream>
45 
46 namespace OpenMS
47 {
48 
62  class OPENMS_DLLAPI SpectrumAccessOpenMSCached :
64  {
65 
66 public:
69 
79  explicit SpectrumAccessOpenMSCached(String filename);
80 
85 
88 
90  boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const;
91 
92  OpenSwath::SpectrumPtr getSpectrumById(int id);
93 
94  OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const;
95 
96  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const;
97 
98  size_t getNrSpectra() const;
99 
100  SpectrumSettings getSpectraMetaInfo(int id) const;
101 
102  OpenSwath::ChromatogramPtr getChromatogramById(int id);
103 
104  size_t getNrChromatograms() const;
105 
106  ChromatogramSettings getChromatogramMetaInfo(int id) const;
107 
108  std::string getChromatogramNativeID(int id) const;
109 
110 private:
111 
113  MSExperimentType meta_ms_experiment_;
114 
116  std::ifstream ifs_;
117 
120 
123 
125  std::vector<std::streampos> spectra_index_;
126  std::vector<std::streampos> chrom_index_;
127  };
128 
129 } //end namespace
130 
131 #endif
OpenMS::MSExperiment< Peak1D > MSExperimentType
Definition: SpectrumAccessOpenMSCached.h:67
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:157
std::vector< std::streampos > spectra_index_
Indices.
Definition: SpectrumAccessOpenMSCached.h:125
MSExperimentType meta_ms_experiment_
Meta data.
Definition: SpectrumAccessOpenMSCached.h:113
A more convenient string class.
Definition: String.h:57
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:232
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:64
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:154
OpenMS::MSSpectrum< Peak1D > MSSpectrumType
Definition: SpectrumAccessOpenMSCached.h:68
String filename_cached_
Name of the cached mzML file.
Definition: SpectrumAccessOpenMSCached.h:122
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
std::ifstream ifs_
Internal filestream.
Definition: SpectrumAccessOpenMSCached.h:116
An implementation of the Spectrum Access interface using on-disk caching.
Definition: SpectrumAccessOpenMSCached.h:62
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:126
String filename_
Name of the mzML file.
Definition: SpectrumAccessOpenMSCached.h:119

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:25 using doxygen 1.8.11