OpenMS  3.0.0
MSPGenericFile.h
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31 // $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
32 // $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h> // OPENMS_DLLAPI
41 
42 namespace OpenMS
43 {
67  class OPENMS_DLLAPI MSPGenericFile :
68  public DefaultParamHandler
69  {
70 public:
73 
75  MSPGenericFile(const String& filename, MSExperiment& library);
76 
78  ~MSPGenericFile() override = default;
79 
81  void getDefaultParameters(Param& params);
82 
84  friend class MSPGenericFile_friend;
85 
94  void load(const String& filename, MSExperiment& library);
95 
104  void store(const String& filename, const MSExperiment& library) const;
105 
106  private:
108  void updateMembers_() override;
109 
124  void addSpectrumToLibrary(
125  MSSpectrum& spectrum,
126  MSExperiment& library
127  );
128 
130  std::set<String> loaded_spectra_names_;
131 
132  /*
133  The synonyms of a spectrum are collected into this variable and,
134  when `addSpectrumtoLibrary()` is called, the elements are concatenated
135  and the result is saved as a "Synon" metaValue.
136  The synonyms are separated by `synonyms_separator_`.
137  */
138  std::vector<String> synonyms_;
139 
142  };
143 
145  {
146 public:
147  MSPGenericFile_friend() = default;
148  ~MSPGenericFile_friend() = default;
149 
151  MSSpectrum& spectrum,
152  MSExperiment& library
153  )
154  {
155  return msp_.addSpectrumToLibrary(spectrum, library);
156  }
157 
159  };
160 }
DefaultParamHandler.h
OpenMS::MSPGenericFile::loaded_spectra_names_
std::set< String > loaded_spectra_names_
To keep track of which spectra have already been loaded and avoid duplicates.
Definition: MSPGenericFile.h:130
OpenMS::MSPGenericFile::synonyms_
std::vector< String > synonyms_
Definition: MSPGenericFile.h:138
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::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MSPGenericFile_friend::msp_
MSPGenericFile msp_
Definition: MSPGenericFile.h:158
OpenMS::MSPGenericFile::addSpectrumToLibrary
void addSpectrumToLibrary(MSSpectrum &spectrum, MSExperiment &library)
MSExperiment.h
OpenMS::MSPGenericFile_friend::addSpectrumToLibrary
void addSpectrumToLibrary(MSSpectrum &spectrum, MSExperiment &library)
Definition: MSPGenericFile.h:150
OpenMS::MSPGenericFile
Load MSP text file and save it into an `MSExperiment`.
Definition: MSPGenericFile.h:67
OpenMS::MSPGenericFile_friend::MSPGenericFile_friend
MSPGenericFile_friend()=default
OpenMS::MSPGenericFile_friend
Definition: MSPGenericFile.h:144
String.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::MSPGenericFile_friend::~MSPGenericFile_friend
~MSPGenericFile_friend()=default
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::MSPGenericFile::synonyms_separator_
String synonyms_separator_
The separator to be used in "Synon" metaValue.
Definition: MSPGenericFile.h:141