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ChromatogramSettings.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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/DataProcessing.h>
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
67 enum ChromatogramType
68 {
69 MASS_CHROMATOGRAM = 0,
70 TOTAL_ION_CURRENT_CHROMATOGRAM,
71 SELECTED_ION_CURRENT_CHROMATOGRAM,
72 BASEPEAK_CHROMATOGRAM,
73 SELECTED_ION_MONITORING_CHROMATOGRAM,
74 SELECTED_REACTION_MONITORING_CHROMATOGRAM,
75 ELECTROMAGNETIC_RADIATION_CHROMATOGRAM,
76 ABSORPTION_CHROMATOGRAM,
77 EMISSION_CHROMATOGRAM,
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
85 ChromatogramSettings();
87 ChromatogramSettings(const ChromatogramSettings &) = default;
89 ChromatogramSettings(ChromatogramSettings&&) = default;
91 virtual ~ChromatogramSettings();
92
93 // Assignment operator
94 ChromatogramSettings & operator=(const ChromatogramSettings &) = default;
96 ChromatogramSettings& operator=(ChromatogramSettings&&) & = default;
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
114 const InstrumentSettings & getInstrumentSettings() const;
116 InstrumentSettings & getInstrumentSettings();
118 void setInstrumentSettings(const InstrumentSettings & instrument_settings);
119
121 const AcquisitionInfo & getAcquisitionInfo() const;
123 AcquisitionInfo & getAcquisitionInfo();
125 void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);
126
128 const SourceFile & getSourceFile() const;
130 SourceFile & getSourceFile();
132 void setSourceFile(const SourceFile & source_file);
133
135 const Precursor & getPrecursor() const;
137 Precursor & getPrecursor();
139 void setPrecursor(const Precursor & precursor);
140
142 const Product & getProduct() const;
144 Product & getProduct();
146 void setProduct(const Product & product);
147
149 ChromatogramType getChromatogramType() const;
150
152 void setChromatogramType(ChromatogramType type);
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
165 String native_id_;
166 String comment_;
167 InstrumentSettings instrument_settings_;
168 SourceFile source_file_;
169 AcquisitionInfo acquisition_info_;
170 Precursor precursor_;
171 Product product_;
172 std::vector< DataProcessingPtr > data_processing_;
173 ChromatogramType type_;
174 };
175
177 OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ChromatogramSettings & spec);
178
179 } // namespace OpenMS
180
OpenMS::ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:71
OpenMS::ChromatogramSettings::precursor_
Precursor precursor_
Definition: ChromatogramSettings.h:170
OpenMS::Product
Product meta information.
Definition: Product.h:48
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::ChromatogramSettings::type_
ChromatogramType type_
Definition: ChromatogramSettings.h:173
OpenMS::ChromatogramSettings::instrument_settings_
InstrumentSettings instrument_settings_
Definition: ChromatogramSettings.h:167
OpenMS::InstrumentSettings
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:47
OpenMS::Precursor
Precursor meta information.
Definition: Precursor.h:57
Precursor.h
OpenMS::ChromatogramSettings::acquisition_info_
AcquisitionInfo acquisition_info_
Definition: ChromatogramSettings.h:169
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::ChromatogramSettings
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
OpenMS::ChromatogramSettings::BASEPEAK_CHROMATOGRAM
Definition: ChromatogramSettings.h:72
Product.h
OpenMS::ChromatogramSettings::comment_
String comment_
Definition: ChromatogramSettings.h:166
DataProcessing.h
OpenMS::ChromatogramSettings::ELECTROMAGNETIC_RADIATION_CHROMATOGRAM
Definition: ChromatogramSettings.h:75
OpenMS::ChromatogramSettings::source_file_
SourceFile source_file_
Definition: ChromatogramSettings.h:168
OpenMS::ChromatogramSettings::product_
Product product_
Definition: ChromatogramSettings.h:171
String.h
OpenMS::ChromatogramSettings::TOTAL_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:70
OpenMS::ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:74
OpenMS::ChromatogramSettings::native_id_
String native_id_
Definition: ChromatogramSettings.h:165
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
AcquisitionInfo.h
SourceFile.h
OpenMS::ChromatogramSettings::ABSORPTION_CHROMATOGRAM
Definition: ChromatogramSettings.h:76
OpenMS::ChromatogramSettings::ChromatogramType
ChromatogramType
Definition: ChromatogramSettings.h:67
OpenMS::ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:73
OpenMS::ChromatogramSettings::data_processing_
std::vector< DataProcessingPtr > data_processing_
Definition: ChromatogramSettings.h:172
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
OpenMS::ChromatogramSettings::EMISSION_CHROMATOGRAM
Definition: ChromatogramSettings.h:77
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
InstrumentSettings.h