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ReactionMonitoringTransition.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperimentHelper.h>
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <OpenMS/METADATA/CVTermList.h>
40
41 #include <vector>
42 #include <bitset>
43
44 namespace OpenMS
45 {
46
56 class OPENMS_DLLAPI ReactionMonitoringTransition :
57 public CVTermList
58 {
59
60 public:
61
62 typedef TargetedExperimentHelper::Configuration Configuration;
63 typedef TargetedExperimentHelper::RetentionTime RetentionTime;
64 typedef TargetedExperimentHelper::TraMLProduct Product;
65 typedef TargetedExperimentHelper::Prediction Prediction;
66
67 enum DecoyTransitionType
68 {
69 UNKNOWN,
70 TARGET,
71 DECOY
72 };
73
77 ReactionMonitoringTransition();
79
81 ReactionMonitoringTransition(const ReactionMonitoringTransition & rhs);
82
84 ReactionMonitoringTransition(ReactionMonitoringTransition&&) noexcept;
85
87 ~ReactionMonitoringTransition() override;
89
91 ReactionMonitoringTransition & operator=(const ReactionMonitoringTransition & rhs);
92
94 ReactionMonitoringTransition & operator=(ReactionMonitoringTransition && rhs);
95
99 void setName(const String & name);
100
101 const String & getName() const;
102
103 void setNativeID(const String & name);
104
105 const String & getNativeID() const;
106
107 void setPeptideRef(const String & peptide_ref);
108
109 const String & getPeptideRef() const;
110
111 void setCompoundRef(const String & compound_ref);
112
113 const String & getCompoundRef() const;
114
116 void setPrecursorMZ(double mz);
117
119 double getPrecursorMZ() const;
120
122 bool hasPrecursorCVTerms() const;
123
124 void setPrecursorCVTermList(const CVTermList & list);
125
126 void addPrecursorCVTerm(const CVTerm & cv_term);
127
132 const CVTermList & getPrecursorCVTermList() const;
133
134 void setProductMZ(double mz);
135
136 double getProductMZ() const;
137
138 int getProductChargeState() const;
139
140 bool isProductChargeStateSet() const;
141
142 void addProductCVTerm(const CVTerm & cv_term);
143
144 const std::vector<Product> & getIntermediateProducts() const;
145
146 void addIntermediateProduct(Product product);
147
148 void setIntermediateProducts(const std::vector<Product> & products);
149
150 void setProduct(Product product);
151
152 const Product & getProduct() const;
153
155 bool hasPrediction() const;
156
157 void setPrediction(const Prediction & prediction);
158
159 void addPredictionTerm(const CVTerm & prediction);
160
165 const Prediction & getPrediction() const;
166
168 DecoyTransitionType getDecoyTransitionType() const;
169
171 void setDecoyTransitionType(const DecoyTransitionType & d);
172
174 double getLibraryIntensity() const;
175
177 void setLibraryIntensity(double intensity);
178
197 void setRetentionTime(RetentionTime rt);
198
206 const RetentionTime & getRetentionTime() const;
207
209
225 bool isDetectingTransition() const;
226
227 void setDetectingTransition(bool val);
229
243 bool isIdentifyingTransition() const;
244
245 void setIdentifyingTransition(bool val);
247
260 bool isQuantifyingTransition() const;
261
262 void setQuantifyingTransition(bool val);
264
266
270 bool operator==(const ReactionMonitoringTransition & rhs) const;
272
274 bool operator!=(const ReactionMonitoringTransition & rhs) const;
276
282 struct ProductMZLess :
284 std::binary_function<ReactionMonitoringTransition, ReactionMonitoringTransition, bool>
285 {
286 inline bool operator()(ReactionMonitoringTransition const & left, ReactionMonitoringTransition const & right) const
287 {
288 return left.getProductMZ() < right.getProductMZ();
289 }
290
291 };
293
294 protected:
295
296 void updateMembers_();
297
301
302 String name_;
303
304 // attributes to a peptide / compound (optional)
305 String peptide_ref_;
306 String compound_ref_;
307
309 double library_intensity_;
310
312 DecoyTransitionType decoy_type_;
314
318
319 // Precursor
320 // Product
321 // IntermediateProduct
322 // RetentionTime
323 // Prediction
324 // cvparam / userParam
325
327 double precursor_mz_;
328
330 CVTermList* precursor_cv_terms_;
331
333 Product product_;
334
336 std::vector<Product> intermediate_products_;
337
339 RetentionTime rts;
340
342 Prediction* prediction_;
343
346 std::bitset<3> transition_flags_;
348 };
349 }
350
OpenMS::Product
Product meta information.
Definition: Product.h:48
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::ReactionMonitoringTransition::product_
Product product_
Product (Q3) of the transition.
Definition: ReactionMonitoringTransition.h:333
OpenMS::ReactionMonitoringTransition::Prediction
TargetedExperimentHelper::Prediction Prediction
Definition: ReactionMonitoringTransition.h:65
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ReactionMonitoringTransition::rts
RetentionTime rts
Information about predicted or calibrated retention time (optional)
Definition: ReactionMonitoringTransition.h:339
OpenMS::ReactionMonitoringTransition::transition_flags_
std::bitset< 3 > transition_flags_
Definition: ReactionMonitoringTransition.h:346
OpenMS::ReactionMonitoringTransition::compound_ref_
String compound_ref_
Reference to a specific compound.
Definition: ReactionMonitoringTransition.h:306
OpenMS::ReactionMonitoringTransition::precursor_mz_
double precursor_mz_
A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window targe...
Definition: ReactionMonitoringTransition.h:327
OpenMS::TargetedExperimentHelper::RetentionTime
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:127
OpenMS::ReactionMonitoringTransition::name_
String name_
id, required attribute
Definition: ReactionMonitoringTransition.h:302
OpenMS::ReactionMonitoringTransition::Product
TargetedExperimentHelper::TraMLProduct Product
Definition: ReactionMonitoringTransition.h:64
StandardTypes.h
std
STL namespace.
OpenMS::ReactionMonitoringTransition::decoy_type_
DecoyTransitionType decoy_type_
specific properties of a transition (e.g. specific CV terms)
Definition: ReactionMonitoringTransition.h:312
OpenMS::ReactionMonitoringTransition::RetentionTime
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: ReactionMonitoringTransition.h:63
OpenMS::ReactionMonitoringTransition::intermediate_products_
std::vector< Product > intermediate_products_
Intermediate product ion information of the transition when using MS3 or above (optional) ...
Definition: ReactionMonitoringTransition.h:336
OpenMS::TargetedExperimentHelper::Configuration
Definition: TargetedExperimentHelper.h:64
OpenMS::ReactionMonitoringTransition::getProductMZ
double getProductMZ() const
OpenMS::ReactionMonitoringTransition::TARGET
Target transition.
Definition: ReactionMonitoringTransition.h:70
OpenMS::ReactionMonitoringTransition::UNKNOWN
Unknown type.
Definition: ReactionMonitoringTransition.h:69
OpenMS::CVTerm
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
OpenMS::ReactionMonitoringTransition::peptide_ref_
String peptide_ref_
Reference to a specific peptide.
Definition: ReactionMonitoringTransition.h:305
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ReactionMonitoringTransition
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
OpenMS::ReactionMonitoringTransition::prediction_
Prediction * prediction_
Information about a prediction for a suitable transition using some software (optional) ...
Definition: ReactionMonitoringTransition.h:342
CVTermList.h
OpenMS::ReactionMonitoringTransition::ProductMZLess::operator()
bool operator()(ReactionMonitoringTransition const &left, ReactionMonitoringTransition const &right) const
Definition: ReactionMonitoringTransition.h:286
OpenMS::ReactionMonitoringTransition::Configuration
TargetedExperimentHelper::Configuration Configuration
Definition: ReactionMonitoringTransition.h:62
OpenMS::ReactionMonitoringTransition::DecoyTransitionType
DecoyTransitionType
Definition: ReactionMonitoringTransition.h:67
OpenMS::ReactionMonitoringTransition::precursor_cv_terms_
CVTermList * precursor_cv_terms_
(Other) CV Terms of the Precursor (Q1) of the transition or target
Definition: ReactionMonitoringTransition.h:330
OpenMS::TargetedExperimentHelper::Prediction
Definition: TargetedExperimentHelper.h:495
OpenMS::ReactionMonitoringTransition::library_intensity_
double library_intensity_
Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag) ...
Definition: ReactionMonitoringTransition.h:309
TargetedExperimentHelper.h
OpenMS::TargetedExperimentHelper::TraMLProduct
Represents a product ion.
Definition: TargetedExperimentHelper.h:588