OpenMS  3.0.0
ReactionMonitoringTransition.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 
35 #pragma once
36 
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 
66 
68  {
71  DECOY
72  };
73 
79 
82 
85 
87  ~ReactionMonitoringTransition() override;
89 
92 
94  ReactionMonitoringTransition & operator=(ReactionMonitoringTransition && rhs) noexcept ;
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  {
285  inline bool operator()(ReactionMonitoringTransition const & left, ReactionMonitoringTransition const & right) const
286  {
287  return left.getProductMZ() < right.getProductMZ();
288  }
289  };
291 
297  struct NameLess
299  {
300  inline bool operator()(ReactionMonitoringTransition const & left, ReactionMonitoringTransition const & right) const
301  {
302  return left.getName() < right.getName();
303  }
304  };
306 
307 protected:
308 
309  void updateMembers_();
310 
314 
316 
317  // attributes to a peptide / compound (optional)
320 
323 
327 
331 
332  // Precursor
333  // Product
334  // IntermediateProduct
335  // RetentionTime
336  // Prediction
337  // cvparam / userParam
338 
341 
344 
347 
349  std::vector<Product> intermediate_products_;
350 
353 
356 
359  std::bitset<3> transition_flags_;
361  };
362 }
363 
OpenMS::ReactionMonitoringTransition::Product
TargetedExperimentHelper::TraMLProduct Product
Definition: ReactionMonitoringTransition.h:64
OpenMS::ReactionMonitoringTransition::getProductMZ
double getProductMZ() const
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:322
OpenMS::ReactionMonitoringTransition::ProductMZLess::operator()
bool operator()(ReactionMonitoringTransition const &left, ReactionMonitoringTransition const &right) const
Definition: ReactionMonitoringTransition.h:285
OpenMS::ReactionMonitoringTransition::getName
const String & getName() const
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ReactionMonitoringTransition::precursor_cv_terms_
CVTermList * precursor_cv_terms_
(Other) CV Terms of the Precursor (Q1) of the transition or target
Definition: ReactionMonitoringTransition.h:343
OpenMS::ReactionMonitoringTransition::transition_flags_
std::bitset< 3 > transition_flags_
Definition: ReactionMonitoringTransition.h:359
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:349
OpenMS::ReactionMonitoringTransition::product_
Product product_
Product (Q3) of the transition.
Definition: ReactionMonitoringTransition.h:346
OpenMS::ReactionMonitoringTransition::name_
String name_
id, required attribute
Definition: ReactionMonitoringTransition.h:315
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ReactionMonitoringTransition::decoy_type_
DecoyTransitionType decoy_type_
specific properties of a transition (e.g. specific CV terms)
Definition: ReactionMonitoringTransition.h:325
OpenMS::ReactionMonitoringTransition
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
OpenMS::TargetedExperimentHelper::Prediction
Definition: TargetedExperimentHelper.h:478
OpenMS::TargetedExperimentHelper::TraMLProduct
Represents a product ion.
Definition: TargetedExperimentHelper.h:571
OpenMS::ReactionMonitoringTransition::compound_ref_
String compound_ref_
Reference to a specific compound.
Definition: ReactionMonitoringTransition.h:319
OpenMS::ReactionMonitoringTransition::UNKNOWN
Unknown type.
Definition: ReactionMonitoringTransition.h:69
OpenMS::CVTermList
Representation of controlled vocabulary term list.
Definition: CVTermList.h:52
OpenMS::ReactionMonitoringTransition::Configuration
TargetedExperimentHelper::Configuration Configuration
Definition: ReactionMonitoringTransition.h:62
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:340
OpenMS::ReactionMonitoringTransition::peptide_ref_
String peptide_ref_
Reference to a specific peptide.
Definition: ReactionMonitoringTransition.h:318
CVTermList.h
OpenMS::CVTerm
Representation of controlled vocabulary term.
Definition: CVTerm.h:52
OpenMS::TargetedExperimentHelper::Configuration
Definition: TargetedExperimentHelper.h:64
OpenMS::ReactionMonitoringTransition::rts
RetentionTime rts
Information about predicted or calibrated retention time (optional)
Definition: ReactionMonitoringTransition.h:352
OpenMS::TargetedExperimentHelper::RetentionTime
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:124
OpenMS::Product
Product meta information.
Definition: Product.h:48
TargetedExperimentHelper.h
OpenMS::ReactionMonitoringTransition::RetentionTime
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: ReactionMonitoringTransition.h:63
OpenMS::ReactionMonitoringTransition::TARGET
Target transition.
Definition: ReactionMonitoringTransition.h:70
OpenMS::ReactionMonitoringTransition::prediction_
Prediction * prediction_
Information about a prediction for a suitable transition using some software (optional)
Definition: ReactionMonitoringTransition.h:355
OpenMS::ReactionMonitoringTransition::Prediction
TargetedExperimentHelper::Prediction Prediction
Definition: ReactionMonitoringTransition.h:65
OpenMS::ReactionMonitoringTransition::DecoyTransitionType
DecoyTransitionType
Definition: ReactionMonitoringTransition.h:67
StandardTypes.h
OpenMS::ReactionMonitoringTransition::NameLess::operator()
bool operator()(ReactionMonitoringTransition const &left, ReactionMonitoringTransition const &right) const
Definition: ReactionMonitoringTransition.h:300