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ReactionMonitoringTransition.h
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34 
35 #ifndef OPENMS_ANALYSIS_MRM_REACTIONMONITORINGTRANSITION_H
36 #define OPENMS_ANALYSIS_MRM_REACTIONMONITORINGTRANSITION_H
37 
41 
42 #include <vector>
43 #include <bitset>
44 
45 namespace OpenMS
46 {
56  class OPENMS_DLLAPI ReactionMonitoringTransition :
57  public CVTermList
58  {
59 
60 public:
61 
66 
68  {
71  DECOY
72  };
73 
79 
82 
86 
89 
93  void setName(const String & name);
94 
95  const String & getName() const;
96 
97  void setNativeID(const String & name);
98 
99  const String & getNativeID() const;
100 
101  void setPeptideRef(const String & peptide_ref);
102 
103  const String & getPeptideRef() const;
104 
105  void setCompoundRef(const String & compound_ref);
106 
107  const String & getCompoundRef() const;
108 
110  void setPrecursorMZ(double mz);
111 
113  double getPrecursorMZ() const;
114 
116  bool hasPrecursorCVTerms() const;
117 
118  void setPrecursorCVTermList(const CVTermList & list);
119 
120  void addPrecursorCVTerm(const CVTerm & cv_term);
121 
122  /* @brief Obtain the list of CV Terms for the precursor
123  *
124  * @note You first need to check whether they exist using hasPrecursorCVTerms()
125  */
126  const CVTermList & getPrecursorCVTermList() const;
127 
128  void setProductMZ(double mz);
129 
130  double getProductMZ() const;
131 
132  int getProductChargeState() const;
133 
134  bool isProductChargeStateSet() const;
135 
136  void addProductCVTerm(const CVTerm & cv_term);
137 
138  const std::vector<Product> & getIntermediateProducts() const;
139 
140  void addIntermediateProduct(Product product);
141 
142  void setIntermediateProducts(const std::vector<Product> & products);
143 
144  void setProduct(Product product);
145 
146  const Product & getProduct() const;
147 
148  void setRetentionTime(RetentionTime rt);
149 
150  const RetentionTime & getRetentionTime() const;
151 
153  bool hasPrediction() const;
154 
155  void setPrediction(const Prediction & prediction);
156 
157  void addPredictionTerm(const CVTerm & prediction);
158 
159  /* @brief Obtain the Prediction object
160  *
161  * @note You first need to check whether the object is accessible using hasPrediction()
162  */
163  const Prediction & getPrediction() const;
164 
165  DecoyTransitionType getDecoyTransitionType() const;
166 
167  void setDecoyTransitionType(const DecoyTransitionType & d);
168 
169  double getLibraryIntensity() const;
170 
171  void setLibraryIntensity(double intensity);
172 
185  bool isDetectingTransition() const;
186 
187  void setDetectingTransition(bool val);
188 
197  bool isIdentifyingTransition() const;
198 
199  void setIdentifyingTransition(bool val);
200 
210  bool isQuantifyingTransition() const;
211 
212  void setQuantifyingTransition(bool val);
213 
215 
219  bool operator==(const ReactionMonitoringTransition & rhs) const;
221 
223  bool operator!=(const ReactionMonitoringTransition & rhs) const;
225 
231  struct ProductMZLess :
233  std::binary_function<ReactionMonitoringTransition, ReactionMonitoringTransition, bool>
234  {
235  inline bool operator()(ReactionMonitoringTransition const & left, ReactionMonitoringTransition const & right) const
236  {
237  return left.getProductMZ() < right.getProductMZ();
238  }
239 
240  };
242 
243 protected:
244 
245  void updateMembers_();
246 
248 
250  String name_; // id, required attribute
251 
252  // attributes to a peptide / compound (optional)
256 
258 
260  // Precursor
261  // Product
262  // IntermediateProduct
263  // RetentionTime
264  // Prediction
265  // cvparam / userParam
266 
269 
272 
275 
278 
280  Product product_;
281 
283  std::vector<Product> intermediate_products_;
284 
286  RetentionTime rts;
287 
289  Prediction* prediction_;
290 
292  // (currently: detecting, identifying and quantifying)
293  std::bitset<3> transition_flags_;
295  };
296 }
297 
298 #endif // OPENMS_ANALYSIS_MRM_REACTIONMONITORINGTRANSITION_H
DecoyTransitionType decoy_type_
specific properties of a transition (e.g. specific CV terms)
Definition: ReactionMonitoringTransition.h:274
RetentionTime rts
Information about predicted or calibrated retention time (optional)
Definition: ReactionMonitoringTransition.h:286
A more convenient string class.
Definition: String.h:57
TargetedExperimentHelper::Prediction Prediction
Definition: ReactionMonitoringTransition.h:65
Representation of controlled vocabulary term list.
Definition: CVTermList.h:53
Definition: ReactionMonitoringTransition.h:70
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
bool operator()(ReactionMonitoringTransition const &left, ReactionMonitoringTransition const &right) const
Definition: ReactionMonitoringTransition.h:235
DecoyTransitionType
Definition: ReactionMonitoringTransition.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
CVTermList * precursor_cv_terms_
(Other) CV Terms of the Precursor (Q1) of the transition or target
Definition: ReactionMonitoringTransition.h:277
double precursor_mz_
Subelements:
Definition: ReactionMonitoringTransition.h:268
TargetedExperimentHelper::Configuration Configuration
Definition: ReactionMonitoringTransition.h:62
Definition: TargetedExperimentHelper.h:64
Comparator by Product ion MZ.
Definition: ReactionMonitoringTransition.h:232
Definition: TargetedExperimentHelper.h:607
std::bitset< 3 > transition_flags_
A set of flags to store information about the transition at hand.
Definition: ReactionMonitoringTransition.h:293
String peptide_ref_
Definition: ReactionMonitoringTransition.h:253
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: ReactionMonitoringTransition.h:63
Representation of controlled vocabulary term.
Definition: CVTerm.h:51
String name_
Attributes:
Definition: ReactionMonitoringTransition.h:250
Product product_
Product (Q3) of the transition.
Definition: ReactionMonitoringTransition.h:280
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
double library_intensity_
Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag) ...
Definition: ReactionMonitoringTransition.h:271
String compound_ref_
Definition: ReactionMonitoringTransition.h:254
Definition: ReactionMonitoringTransition.h:69
Definition: TargetedExperimentHelper.h:142
Definition: TargetedExperimentHelper.h:493
std::vector< Product > intermediate_products_
Intermediate product ion information of the transition when using MS3 or above (optional) ...
Definition: ReactionMonitoringTransition.h:283
TargetedExperimentHelper::TraMLProduct Product
Definition: ReactionMonitoringTransition.h:64
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:56
Prediction * prediction_
Information about a prediction for a suitable transition using some software (optional) ...
Definition: ReactionMonitoringTransition.h:289

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13