| OpenMS 2.5.0

MSPGenericFile.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: Douglas McCloskey, Pasquale Domenico Colaianni $
32 // $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/config.h> // OPENMS_DLLAPI
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/DATASTRUCTURES/String.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 namespace OpenMS
43 {
67 class OPENMS_DLLAPI MSPGenericFile :
68 public DefaultParamHandler
69 {
70 public:
72 MSPGenericFile();
73
75 MSPGenericFile(const String& filename, MSExperiment& library);
76
78 ~MSPGenericFile() = default;
79
81 void getDefaultParameters(Param& params);
82
84 friend class MSPGenericFile_friend;
85
94 void load(const String& filename, MSExperiment& library);
95
96 private:
98 void updateMembers_();
99
114 void addSpectrumToLibrary(
115 MSSpectrum& spectrum,
116 MSExperiment& library
117 );
118
120 std::set<String> loaded_spectra_names_;
121
122 /*
123 The synonyms of a spectrum are collected into this variable and,
124 when `addSpectrumtoLibrary()` is called, the elements are concatenated
125 and the result is saved as a "Synon" metaValue.
126 The synonyms are separated by `synonyms_separator_`.
127 */
128 std::vector<String> synonyms_;
129
131 String synonyms_separator_;
132 };
133
134 class MSPGenericFile_friend
135 {
136 public:
137 MSPGenericFile_friend() = default;
138 ~MSPGenericFile_friend() = default;
139
140 void addSpectrumToLibrary(
141 MSSpectrum& spectrum,
142 MSExperiment& library
143 )
144 {
145 return msp_.addSpectrumToLibrary(spectrum, library);
146 }
147
148 MSPGenericFile msp_;
149 };
150 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MSPGenericFile::synonyms_separator_
String synonyms_separator_
The separator to be used in "Synon" metaValue.
Definition: MSPGenericFile.h:131
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::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::MSPGenericFile_friend::msp_
MSPGenericFile msp_
Definition: MSPGenericFile.h:148
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
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:120
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::MSPGenericFile_friend
Definition: MSPGenericFile.h:134
OpenMS::MSPGenericFile_friend::addSpectrumToLibrary
void addSpectrumToLibrary(MSSpectrum &spectrum, MSExperiment &library)
Definition: MSPGenericFile.h:140
OpenMS::MSPGenericFile_friend::MSPGenericFile_friend
MSPGenericFile_friend()=default
OpenMS::MSPGenericFile::addSpectrumToLibrary
void addSpectrumToLibrary(MSSpectrum &spectrum, MSExperiment &library)
OpenMS::MSPGenericFile::synonyms_
std::vector< String > synonyms_
Definition: MSPGenericFile.h:128