OpenMS  3.0.0
CachedMzML.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
38 
39 #include <fstream>
40 
41 namespace OpenMS
42 {
43 
53  class OPENMS_DLLAPI CachedmzML
54  {
55 
56 public:
57 
61  CachedmzML();
63 
64  CachedmzML(const String& filename);
65 
67  CachedmzML(const CachedmzML & rhs);
68 
70  ~CachedmzML();
72 
73  MSSpectrum getSpectrum(Size id);
74 
75  MSChromatogram getChromatogram(Size id);
76 
77  size_t getNrSpectra() const;
78 
79  size_t getNrChromatograms() const;
80 
81  const MSExperiment& getMetaData() const
82  {
83  return meta_ms_experiment_;
84  }
85 
94  static void store(const String& filename, const PeakMap& map);
95 
105  static void load(const String& filename, CachedmzML& map);
106 
107 protected:
108 
109  void load_(const String& filename);
110 
113 
115  std::ifstream ifs_;
116 
119 
122 
124  std::vector<std::streampos> spectra_index_;
125  std::vector<std::streampos> chrom_index_;
126 
127  };
128 }
129 
OpenMS::CachedmzML::filename_cached_
String filename_cached_
Name of the cached mzML file.
Definition: CachedMzML.h:121
OpenMS::CachedmzML::meta_ms_experiment_
MSExperiment meta_ms_experiment_
Meta data.
Definition: CachedMzML.h:112
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::CachedmzML
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzML.h:53
OpenMS::CachedmzML::spectra_index_
std::vector< std::streampos > spectra_index_
Indices.
Definition: CachedMzML.h:124
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::CachedmzML::ifs_
std::ifstream ifs_
Internal filestream.
Definition: CachedMzML.h:115
MSExperiment.h
OpenMS::CachedmzML::chrom_index_
std::vector< std::streampos > chrom_index_
Definition: CachedMzML.h:125
OpenMS::CachedmzML::getMetaData
const MSExperiment & getMetaData() const
Definition: CachedMzML.h:81
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::CachedmzML::filename_
String filename_
Name of the mzML file.
Definition: CachedMzML.h:118
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66