OpenMS
SpectrumSettings.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Marc Sturm $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
19 
20 #include <map>
21 #include <vector>
22 
23 namespace OpenMS
24 {
37  class OPENMS_DLLAPI SpectrumSettings :
38  public MetaInfoInterface
39  {
40 
41 public:
42 
45  {
49  SIZE_OF_SPECTRUMTYPE
50  };
52  static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE];
53 
57  SpectrumSettings(const SpectrumSettings &) = default;
62 
63  // Assignment operator
67 
69  bool operator==(const SpectrumSettings & rhs) const;
71  bool operator!=(const SpectrumSettings & rhs) const;
72 
74  void unify(const SpectrumSettings & rhs);
75 
79  void setType(SpectrumType type);
80 
82  const String & getNativeID() const;
84  void setNativeID(const String & native_id);
85 
87  const String & getComment() const;
89  void setComment(const String & comment);
90 
96  void setInstrumentSettings(const InstrumentSettings & instrument_settings);
97 
103  void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);
104 
106  const SourceFile & getSourceFile() const;
110  void setSourceFile(const SourceFile & source_file);
111 
113  const std::vector<Precursor> & getPrecursors() const;
115  std::vector<Precursor> & getPrecursors();
117  void setPrecursors(const std::vector<Precursor> & precursors);
118 
120  const std::vector<Product> & getProducts() const;
122  std::vector<Product> & getProducts();
124  void setProducts(const std::vector<Product> & products);
125 
127  const std::vector<PeptideIdentification> & getPeptideIdentifications() const;
129  std::vector<PeptideIdentification> & getPeptideIdentifications();
131  void setPeptideIdentifications(const std::vector<PeptideIdentification> & identifications);
132 
134  void setDataProcessing(const std::vector< DataProcessingPtr > & data_processing);
135 
137  std::vector< DataProcessingPtr > & getDataProcessing();
138 
140  const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing() const;
141 
142 protected:
143 
150  std::vector<Precursor> precursors_;
151  std::vector<Product> products_;
152  std::vector<PeptideIdentification> identification_;
153  std::vector< DataProcessingPtr > data_processing_;
154  };
155 
157  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const SpectrumSettings & spec);
158 
159 } // namespace OpenMS
160 
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:29
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:23
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:35
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:22
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:39
SpectrumSettings & operator=(SpectrumSettings &&) &=default
Move assignment operator.
String comment_
Definition: SpectrumSettings.h:146
SpectrumSettings & operator=(const SpectrumSettings &)=default
AcquisitionInfo acquisition_info_
Definition: SpectrumSettings.h:149
SpectrumSettings()
Constructor.
SourceFile source_file_
Definition: SpectrumSettings.h:148
void setComment(const String &comment)
sets the free-text comment
InstrumentSettings instrument_settings_
Definition: SpectrumSettings.h:147
void unify(const SpectrumSettings &rhs)
merge another spectrum setting into this one (data is usually appended, except for spectrum type whic...
const std::vector< boost::shared_ptr< const DataProcessing > > getDataProcessing() const
returns a const reference to the description of the applied processing
void setProducts(const std::vector< Product > &products)
sets the products
void setInstrumentSettings(const InstrumentSettings &instrument_settings)
sets the instrument settings of the current spectrum
SpectrumType getType() const
returns the spectrum type (centroided (PEAKS) or profile data (RAW))
bool operator!=(const SpectrumSettings &rhs) const
Equality operator.
SpectrumSettings(const SpectrumSettings &)=default
Copy constructor.
std::vector< Precursor > & getPrecursors()
returns a mutable reference to the precursors
const SourceFile & getSourceFile() const
returns a const reference to the source file
AcquisitionInfo & getAcquisitionInfo()
returns a mutable reference to the acquisition info
SpectrumSettings(SpectrumSettings &&)=default
Move constructor.
std::vector< PeptideIdentification > & getPeptideIdentifications()
returns a mutable reference to the PeptideIdentification vector
String native_id_
Definition: SpectrumSettings.h:145
void setType(SpectrumType type)
sets the spectrum type
const AcquisitionInfo & getAcquisitionInfo() const
returns a const reference to the acquisition info
void setSourceFile(const SourceFile &source_file)
sets the source file
std::vector< Product > & getProducts()
returns a mutable reference to the products
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
const InstrumentSettings & getInstrumentSettings() const
returns a const reference to the instrument settings of the current spectrum
std::vector< DataProcessingPtr > data_processing_
Definition: SpectrumSettings.h:153
void setDataProcessing(const std::vector< DataProcessingPtr > &data_processing)
sets the description of the applied processing
SpectrumType type_
Definition: SpectrumSettings.h:144
std::vector< PeptideIdentification > identification_
Definition: SpectrumSettings.h:152
SpectrumType
Spectrum peak type.
Definition: SpectrumSettings.h:45
@ UNKNOWN
Unknown spectrum type.
Definition: SpectrumSettings.h:46
@ PROFILE
profile data
Definition: SpectrumSettings.h:48
@ CENTROID
centroid data or stick data
Definition: SpectrumSettings.h:47
bool operator==(const SpectrumSettings &rhs) const
Equality operator.
std::vector< DataProcessingPtr > & getDataProcessing()
returns a mutable reference to the description of the applied processing
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
SourceFile & getSourceFile()
returns a mutable reference to the source file
std::vector< Precursor > precursors_
Definition: SpectrumSettings.h:150
const std::vector< Product > & getProducts() const
returns a const reference to the products
~SpectrumSettings()
Destructor.
const String & getComment() const
returns the free-text comment
void setPeptideIdentifications(const std::vector< PeptideIdentification > &identifications)
sets the PeptideIdentification vector
void setPrecursors(const std::vector< Precursor > &precursors)
sets the precursors
const String & getNativeID() const
returns the native identifier for the spectrum, used by the acquisition software.
void setAcquisitionInfo(const AcquisitionInfo &acquisition_info)
sets the acquisition info
std::vector< Product > products_
Definition: SpectrumSettings.h:151
InstrumentSettings & getInstrumentSettings()
returns a mutable reference to the instrument settings of the current spectrum
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)