OpenMS  3.0.0
SpectrumSettings.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
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 
71  {
75  SIZE_OF_SPECTRUMTYPE
76  };
78  static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE];
79 
83  SpectrumSettings(const SpectrumSettings &) = default;
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 
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::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
OpenMS::SpectrumSettings::source_file_
SourceFile source_file_
Definition: SpectrumSettings.h:174
OpenMS::SpectrumSettings::data_processing_
std::vector< DataProcessingPtr > data_processing_
Definition: SpectrumSettings.h:179
OpenMS::AcquisitionInfo
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:52
OpenMS::SpectrumSettings::instrument_settings_
InstrumentSettings instrument_settings_
Definition: SpectrumSettings.h:173
OpenMS::String
A more convenient string class.
Definition: String.h:58
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::SpectrumSettings::products_
std::vector< Product > products_
Definition: SpectrumSettings.h:177
OpenMS::SpectrumSettings::native_id_
String native_id_
Definition: SpectrumSettings.h:171
Product.h
OpenMS::SpectrumSettings::PROFILE
profile data
Definition: SpectrumSettings.h:74
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
DataProcessing.h
OpenMS::SpectrumSettings::SpectrumType
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:70
OpenMS::SpectrumSettings::UNKNOWN
Unknown spectrum type.
Definition: SpectrumSettings.h:72
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
AcquisitionInfo.h
OpenMS::SpectrumSettings::comment_
String comment_
Definition: SpectrumSettings.h:172
OpenMS::SpectrumSettings::precursors_
std::vector< Precursor > precursors_
Definition: SpectrumSettings.h:176
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
Precursor.h
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::SpectrumSettings::identification_
std::vector< PeptideIdentification > identification_
Definition: SpectrumSettings.h:178
OpenMS::SourceFile
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
String.h
InstrumentSettings.h
OpenMS::SpectrumSettings
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:63
OpenMS::SpectrumSettings::type_
SpectrumType type_
Definition: SpectrumSettings.h:170
SourceFile.h
PeptideIdentification.h
OpenMS::SpectrumSettings::acquisition_info_
AcquisitionInfo acquisition_info_
Definition: SpectrumSettings.h:175