OpenMS  3.0.0
SqMassFile.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
38 
40 
41 namespace OpenMS
42 {
43 
56  class OPENMS_DLLAPI SqMassFile
57  {
58 public:
59 
65  struct OPENMS_DLLAPI SqMassConfig
66  {
67  bool write_full_meta{true};
68  bool use_lossy_numpress{false};
69  double linear_fp_mass_acc{-1};
70  };
71 
73 
77  SqMassFile();
79 
81  ~SqMassFile();
83 
87 
88  void load(const String& filename, MapType& map) const;
89 
96  void store(const String& filename, MapType& map) const;
97 
98  void transform(const String& filename_in, Interfaces::IMSDataConsumer* consumer, bool skip_full_count = false, bool skip_first_pass = false) const;
99 
100  void setConfig(const SqMassConfig& config)
101  {
102  config_ = config;
103  }
104 
105  // maybe later ...
106  // static inline void readSpectrumFast(OpenSwath::BinaryDataArrayPtr data1,
107  // OpenSwath::BinaryDataArrayPtr data2, std::ifstream& ifs, int& ms_level,
108  // double& rt)
109 
110  // static inline void readChromatogramFast(OpenSwath::BinaryDataArrayPtr data1,
111  // OpenSwath::BinaryDataArrayPtr data2, std::ifstream& ifs)
112 
113 protected:
115  };
116 }
117 
118 
OpenMS::SqMassFile::MapType
MSExperiment MapType
Definition: SqMassFile.h:72
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
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
IMSDataConsumer.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SqMassFile::setConfig
void setConfig(const SqMassConfig &config)
Definition: SqMassFile.h:100
MSExperiment.h
OpenMS::SqMassFile::config_
SqMassConfig config_
Definition: SqMassFile.h:114
OpenMS::SqMassFile::SqMassConfig
Configuration class for SqMassFile.
Definition: SqMassFile.h:65
OpenMS::SqMassFile
An class that uses on-disk SQLite database to read and write spectra and chromatograms.
Definition: SqMassFile.h:56