| OpenMS 2.5.0

SpectrumSettings.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: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/String.h>
38 #include <OpenMS/METADATA/InstrumentSettings.h>
39 #include <OpenMS/METADATA/AcquisitionInfo.h>
40 #include <OpenMS/METADATA/SourceFile.h>
41 #include <OpenMS/METADATA/Precursor.h>
42 #include <OpenMS/METADATA/Product.h>
43 #include <OpenMS/METADATA/PeptideIdentification.h>
44 #include <OpenMS/METADATA/DataProcessing.h>
45
46 #include <map>
47 #include <vector>
48
49 namespace OpenMS
50 {
63 class OPENMS_DLLAPI SpectrumSettings :
64 public MetaInfoInterface
65 {
66
67 public:
68
70 enum SpectrumType
71 {
72 UNKNOWN,
73 CENTROID,
74 PROFILE,
75 SIZE_OF_SPECTRUMTYPE
76 };
78 static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE];
79
81 SpectrumSettings();
83 SpectrumSettings(const SpectrumSettings &) = default;
85 SpectrumSettings(SpectrumSettings&&) = default;
87 ~SpectrumSettings();
88
89 // Assignment operator
90 SpectrumSettings & operator=(const SpectrumSettings &) = default;
92 SpectrumSettings& operator=(SpectrumSettings&&) & = default;
93
95 bool operator==(const SpectrumSettings & rhs) const;
97 bool operator!=(const SpectrumSettings & rhs) const;
98
100 void unify(const SpectrumSettings & rhs);
101
103 SpectrumType getType() const;
105 void setType(SpectrumType type);
106
108 const String & getNativeID() const;
110 void setNativeID(const String & native_id);
111
113 const String & getComment() const;
115 void setComment(const String & comment);
116
118 const InstrumentSettings & getInstrumentSettings() const;
120 InstrumentSettings & getInstrumentSettings();
122 void setInstrumentSettings(const InstrumentSettings & instrument_settings);
123
125 const AcquisitionInfo & getAcquisitionInfo() const;
127 AcquisitionInfo & getAcquisitionInfo();
129 void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);
130
132 const SourceFile & getSourceFile() const;
134 SourceFile & getSourceFile();
136 void setSourceFile(const SourceFile & source_file);
137
139 const std::vector<Precursor> & getPrecursors() const;
141 std::vector<Precursor> & getPrecursors();
143 void setPrecursors(const std::vector<Precursor> & precursors);
144
146 const std::vector<Product> & getProducts() const;
148 std::vector<Product> & getProducts();
150 void setProducts(const std::vector<Product> & products);
151
153 const std::vector<PeptideIdentification> & getPeptideIdentifications() const;
155 std::vector<PeptideIdentification> & getPeptideIdentifications();
157 void setPeptideIdentifications(const std::vector<PeptideIdentification> & identifications);
158
160 void setDataProcessing(const std::vector< DataProcessingPtr > & data_processing);
161
163 std::vector< DataProcessingPtr > & getDataProcessing();
164
166 const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing() const;
167
168 protected:
169
170 SpectrumType type_;
171 String native_id_;
172 String comment_;
173 InstrumentSettings instrument_settings_;
174 SourceFile source_file_;
175 AcquisitionInfo acquisition_info_;
176 std::vector<Precursor> precursors_;
177 std::vector<Product> products_;
178 std::vector<PeptideIdentification> identification_;
179 std::vector< DataProcessingPtr > data_processing_;
180 };
181
183 OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const SpectrumSettings & spec);
184
185 } // namespace OpenMS
186
OpenMS::SourceFile
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SpectrumSettings
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
OpenMS::InstrumentSettings
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:47
OpenMS::SpectrumSettings::CENTROID
centroid data or stick data
Definition: SpectrumSettings.h:73
Precursor.h
OpenMS::SpectrumSettings::comment_
String comment_
Definition: SpectrumSettings.h:172
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::SpectrumSettings::UNKNOWN
Unknown spectrum type.
Definition: SpectrumSettings.h:72
OpenMS::SpectrumSettings::type_
SpectrumType type_
Definition: SpectrumSettings.h:170
Product.h
DataProcessing.h
OpenMS::SpectrumSettings::instrument_settings_
InstrumentSettings instrument_settings_
Definition: SpectrumSettings.h:173
OpenMS::SpectrumSettings::PROFILE
profile data
Definition: SpectrumSettings.h:74
OpenMS::SpectrumSettings::precursors_
std::vector< Precursor > precursors_
Definition: SpectrumSettings.h:176
OpenMS::SpectrumSettings::products_
std::vector< Product > products_
Definition: SpectrumSettings.h:177
OpenMS::SpectrumSettings::data_processing_
std::vector< DataProcessingPtr > data_processing_
Definition: SpectrumSettings.h:179
String.h
OpenMS::SpectrumSettings::acquisition_info_
AcquisitionInfo acquisition_info_
Definition: SpectrumSettings.h:175
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SpectrumSettings::native_id_
String native_id_
Definition: SpectrumSettings.h:171
AcquisitionInfo.h
SourceFile.h
OpenMS::SpectrumSettings::identification_
std::vector< PeptideIdentification > identification_
Definition: SpectrumSettings.h:178
OpenMS::SpectrumSettings::SpectrumType
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
OpenMS::SpectrumSettings::source_file_
SourceFile source_file_
Definition: SpectrumSettings.h:174
OpenMS::AcquisitionInfo
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:52
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
InstrumentSettings.h