OpenMS
ChromatogramSettings.h
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1 // Copyright (c) 2002-present, 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: Andreas Bertsch $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
18 
19 #include <map>
20 #include <vector>
21 
22 namespace OpenMS
23 {
24 
33  class OPENMS_DLLAPI ChromatogramSettings :
34  public MetaInfoInterface
35  {
36 
37 public:
38 
42  {
43  MASS_CHROMATOGRAM = 0,
52  SIZE_OF_CHROMATOGRAM_TYPE // last entry!
53  };
54 
56  static const char * const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]; // avoid string[], since it gets copied onto heap on initialization
57 
66 
67  // Assignment operator
71 
73  bool operator==(const ChromatogramSettings & rhs) const;
75  bool operator!=(const ChromatogramSettings & rhs) const;
76 
78  const String & getNativeID() const;
80  void setNativeID(const String & native_id);
81 
83  const String & getComment() const;
85  void setComment(const String & comment);
86 
92  void setInstrumentSettings(const InstrumentSettings & instrument_settings);
93 
99  void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);
100 
102  const SourceFile & getSourceFile() const;
106  void setSourceFile(const SourceFile & source_file);
107 
109  const Precursor & getPrecursor() const;
113  void setPrecursor(const Precursor & precursor);
114 
116  const Product & getProduct() const;
120  void setProduct(const Product & product);
121 
124 
127 
129  void setDataProcessing(const std::vector< DataProcessingPtr > & data_processing);
130 
132  std::vector< DataProcessingPtr > & getDataProcessing();
133 
135  const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing() const;
136 
137 protected:
138 
146  std::vector< DataProcessingPtr > data_processing_;
148  };
149 
151  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ChromatogramSettings & spec);
152 
153 } // namespace OpenMS
154 
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:29
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:35
String comment_
Definition: ChromatogramSettings.h:140
void setPrecursor(const Precursor &precursor)
sets the precursors
ChromatogramType type_
Definition: ChromatogramSettings.h:147
AcquisitionInfo acquisition_info_
Definition: ChromatogramSettings.h:143
SourceFile source_file_
Definition: ChromatogramSettings.h:142
void setComment(const String &comment)
sets the free-text comment
ChromatogramSettings & operator=(const ChromatogramSettings &)=default
InstrumentSettings instrument_settings_
Definition: ChromatogramSettings.h:141
void setProduct(const Product &product)
sets the products
const Product & getProduct() const
returns a const reference to the products
const std::vector< boost::shared_ptr< const DataProcessing > > getDataProcessing() const
returns a const reference to the description of the applied processing
void setInstrumentSettings(const InstrumentSettings &instrument_settings)
sets the instrument settings of the current spectrum
Product product_
Definition: ChromatogramSettings.h:145
ChromatogramSettings & operator=(ChromatogramSettings &&) &=default
Move assignment operator.
ChromatogramSettings(ChromatogramSettings &&)=default
Move constructor.
ChromatogramSettings(const ChromatogramSettings &)=default
Copy constructor.
const SourceFile & getSourceFile() const
returns a const reference to the source file
AcquisitionInfo & getAcquisitionInfo()
returns a mutable reference to the acquisition info
ChromatogramType
Definition: ChromatogramSettings.h:42
@ ABSORPTION_CHROMATOGRAM
Definition: ChromatogramSettings.h:50
@ EMISSION_CHROMATOGRAM
Definition: ChromatogramSettings.h:51
@ SELECTED_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:45
@ BASEPEAK_CHROMATOGRAM
Definition: ChromatogramSettings.h:46
@ SELECTED_REACTION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:48
@ TOTAL_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:44
@ ELECTROMAGNETIC_RADIATION_CHROMATOGRAM
Definition: ChromatogramSettings.h:49
@ SELECTED_ION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:47
String native_id_
Definition: ChromatogramSettings.h:139
const AcquisitionInfo & getAcquisitionInfo() const
returns a const reference to the acquisition info
Precursor & getPrecursor()
returns a mutable reference to the precursors
void setSourceFile(const SourceFile &source_file)
sets the source file
ChromatogramSettings()
Constructor.
void setChromatogramType(ChromatogramType type)
sets the chromatogram type
const InstrumentSettings & getInstrumentSettings() const
returns a const reference to the instrument settings of the current spectrum
const Precursor & getPrecursor() const
returns a const reference to the precursors
std::vector< DataProcessingPtr > data_processing_
Definition: ChromatogramSettings.h:146
void setDataProcessing(const std::vector< DataProcessingPtr > &data_processing)
sets the description of the applied processing
Product & getProduct()
returns a mutable reference to the products
std::vector< DataProcessingPtr > & getDataProcessing()
returns a mutable reference to the description of the applied processing
SourceFile & getSourceFile()
returns a mutable reference to the source file
const String & getComment() const
returns the free-text comment
Precursor precursor_
Definition: ChromatogramSettings.h:144
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
bool operator!=(const ChromatogramSettings &rhs) const
Equality operator.
ChromatogramType getChromatogramType() const
returns the chromatogram type, e.g. a SRM chromatogram
virtual ~ChromatogramSettings()
Destructor.
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.
bool operator==(const ChromatogramSettings &rhs) const
Equality operator.
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
Precursor meta information.
Definition: Precursor.h:35
Product meta information.
Definition: Product.h:24
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:22
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)