OpenMS
ChromatogramSettings.h
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32 // $Authors: Andreas Bertsch $
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34 
35 #pragma once
36 
44 
45 #include <map>
46 #include <vector>
47 
48 namespace OpenMS
49 {
50 
59  class OPENMS_DLLAPI ChromatogramSettings :
60  public MetaInfoInterface
61  {
62 
63 public:
64 
68  {
69  MASS_CHROMATOGRAM = 0,
78  SIZE_OF_CHROMATOGRAM_TYPE // last entry!
79  };
80 
82  static const char * const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]; // avoid string[], since it gets copied onto heap on initialization
83 
92 
93  // Assignment operator
97 
99  bool operator==(const ChromatogramSettings & rhs) const;
101  bool operator!=(const ChromatogramSettings & rhs) const;
102 
104  const String & getNativeID() const;
106  void setNativeID(const String & native_id);
107 
109  const String & getComment() const;
111  void setComment(const String & comment);
112 
118  void setInstrumentSettings(const InstrumentSettings & instrument_settings);
119 
125  void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);
126 
128  const SourceFile & getSourceFile() const;
132  void setSourceFile(const SourceFile & source_file);
133 
135  const Precursor & getPrecursor() const;
139  void setPrecursor(const Precursor & precursor);
140 
142  const Product & getProduct() const;
146  void setProduct(const Product & product);
147 
150 
153 
155  void setDataProcessing(const std::vector< DataProcessingPtr > & data_processing);
156 
158  std::vector< DataProcessingPtr > & getDataProcessing();
159 
161  const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing() const;
162 
163 protected:
164 
172  std::vector< DataProcessingPtr > data_processing_;
174  };
175 
177  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ChromatogramSettings & spec);
178 
179 } // namespace OpenMS
180 
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:55
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:61
String comment_
Definition: ChromatogramSettings.h:166
void setPrecursor(const Precursor &precursor)
sets the precursors
ChromatogramType type_
Definition: ChromatogramSettings.h:173
AcquisitionInfo acquisition_info_
Definition: ChromatogramSettings.h:169
SourceFile source_file_
Definition: ChromatogramSettings.h:168
void setComment(const String &comment)
sets the free-text comment
ChromatogramSettings & operator=(const ChromatogramSettings &)=default
InstrumentSettings instrument_settings_
Definition: ChromatogramSettings.h:167
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:171
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:68
@ ABSORPTION_CHROMATOGRAM
Definition: ChromatogramSettings.h:76
@ EMISSION_CHROMATOGRAM
Definition: ChromatogramSettings.h:77
@ SELECTED_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:71
@ BASEPEAK_CHROMATOGRAM
Definition: ChromatogramSettings.h:72
@ SELECTED_REACTION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:74
@ TOTAL_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:70
@ ELECTROMAGNETIC_RADIATION_CHROMATOGRAM
Definition: ChromatogramSettings.h:75
@ SELECTED_ION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:73
String native_id_
Definition: ChromatogramSettings.h:165
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:172
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:170
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:49
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
Precursor meta information.
Definition: Precursor.h:61
Product meta information.
Definition: Product.h:50
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:48
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)