| OpenMS 2.5.0

MSDataSqlConsumer.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
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/INTERFACES/IMSDataConsumer.h>
38
39 #include <OpenMS/KERNEL/MSExperiment.h>
40
41 namespace OpenMS
42 {
43
44 namespace Internal
45 {
46 class MzMLSqliteHandler;
47 }
48
60 class OPENMS_DLLAPI MSDataSqlConsumer :
61 public Interfaces::IMSDataConsumer
62 {
63 typedef MSExperiment MapType;
64 typedef MapType::SpectrumType SpectrumType;
65 typedef MapType::ChromatogramType ChromatogramType;
66
67 public:
68
80 MSDataSqlConsumer(String filename, int buffer_size = 500, bool full_meta = true, bool lossy_compression=false, double linear_mass_acc=1e-4);
81
87 ~MSDataSqlConsumer() override;
88
95 void flush();
96
100 void consumeSpectrum(SpectrumType & s) override;
101
105 void consumeChromatogram(ChromatogramType & c) override;
106
107 void setExpectedSize(Size /* expectedSpectra */, Size /* expectedChromatograms */) override;
108
109 void setExperimentalSettings(const ExperimentalSettings& /* exp */) override;
110
111 protected:
112
113 String filename_;
114 OpenMS::Internal::MzMLSqliteHandler * handler_;
115
116 size_t flush_after_;
117 bool full_meta_;
118 std::vector<SpectrumType> spectra_;
119 std::vector<ChromatogramType> chromatograms_;
120
121 MSExperiment peak_meta_;
122 };
123
124 } //end namespace OpenMS
125
126
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
OpenMS::MSDataSqlConsumer::handler_
OpenMS::Internal::MzMLSqliteHandler * handler_
Definition: MSDataSqlConsumer.h:114
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MSDataSqlConsumer::flush_after_
size_t flush_after_
Definition: MSDataSqlConsumer.h:116
OpenMS::MSDataSqlConsumer::MapType
MSExperiment MapType
Definition: MSDataSqlConsumer.h:63
OpenMS::MSDataSqlConsumer
A data consumer that inserts MS data into a SQLite database.
Definition: MSDataSqlConsumer.h:60
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
IMSDataConsumer.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::MSDataSqlConsumer::full_meta_
bool full_meta_
Definition: MSDataSqlConsumer.h:117
OpenMS::Internal::MzMLSqliteHandler
Sqlite handler for storing spectra and chromatograms in sqMass format.
Definition: MzMLSqliteHandler.h:77
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::Constants::c
const double c
OpenMS::MSDataSqlConsumer::spectra_
std::vector< SpectrumType > spectra_
Definition: MSDataSqlConsumer.h:118
OpenMS::MSDataSqlConsumer::peak_meta_
MSExperiment peak_meta_
Definition: MSDataSqlConsumer.h:121
OpenMS::MSDataSqlConsumer::filename_
String filename_
Definition: MSDataSqlConsumer.h:113
OpenMS::MSDataSqlConsumer::ChromatogramType
MapType::ChromatogramType ChromatogramType
Definition: MSDataSqlConsumer.h:65
OpenMS::MSDataSqlConsumer::SpectrumType
MapType::SpectrumType SpectrumType
Definition: MSDataSqlConsumer.h:64
OpenMS::MSDataSqlConsumer::chromatograms_
std::vector< ChromatogramType > chromatograms_
Definition: MSDataSqlConsumer.h:119
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127