| OpenMS 2.5.0

CachedMzML.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/MSExperiment.h>
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
112 MSExperiment meta_ms_experiment_;
113
115 std::ifstream ifs_;
116
118 String filename_;
119
121 String filename_cached_;
122
124 std::vector<std::streampos> spectra_index_;
125 std::vector<std::streampos> chrom_index_;
126
127 };
128 }
129
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::CachedmzML::getMetaData
const MSExperiment & getMetaData() const
Definition: CachedMzML.h:81
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::CachedmzML::spectra_index_
std::vector< std::streampos > spectra_index_
Indices.
Definition: CachedMzML.h:124
OpenMS::CachedmzML::chrom_index_
std::vector< std::streampos > chrom_index_
Definition: CachedMzML.h:125
OpenMS::CachedmzML::filename_
String filename_
Name of the mzML file.
Definition: CachedMzML.h:118
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::CachedmzML::meta_ms_experiment_
MSExperiment meta_ms_experiment_
Meta data.
Definition: CachedMzML.h:112
MSExperiment.h
OpenMS::CachedmzML
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzML.h:53
OpenMS::CachedmzML::filename_cached_
String filename_cached_
Name of the cached mzML file.
Definition: CachedMzML.h:121
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::CachedmzML::ifs_
std::ifstream ifs_
Internal filestream.
Definition: CachedMzML.h:115