77 void setNativeID(const
String & name);
81 void setPeptideRef(const
String & peptide_ref);
83 const
String & getPeptideRef() const;
85 void setCompoundRef(const
String & compound_ref);
87 const
String & getCompoundRef() const;
90 void setPrecursorMZ(
double mz);
93 double getPrecursorMZ() const;
96 bool hasPrecursorCVTerms() const;
100 void addPrecursorCVTerm(const
CVTerm & cv_term);
108 void setProductMZ(
double mz);
110 double getProductMZ() const;
112 int getProductChargeState() const;
114 bool isProductChargeStateSet() const;
116 void addProductCVTerm(const
CVTerm & cv_term);
118 const std::vector<
Product> & getIntermediateProducts() const;
120 void addIntermediateProduct(const
Product& product);
122 void setIntermediateProducts(const std::vector<
Product> & products);
129 bool hasPrediction() const;
133 void addPredictionTerm(const
CVTerm & prediction);
148 double getLibraryIntensity() const;
151 void setLibraryIntensity(
double intensity);
199 bool isDetectingTransition() const;
201 void setDetectingTransition(
bool val);
217 bool isIdentifyingTransition() const;
219 void setIdentifyingTransition(
bool val);
234 bool isQuantifyingTransition() const;
236 void setQuantifyingTransition(
bool val);
Representation of controlled vocabulary term list.
Definition: CVTermList.h:28
Representation of controlled vocabulary term.
Definition: CVTerm.h:27
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:32
ReactionMonitoringTransition()
default constructor
CVTermList * precursor_cv_terms_
(Other) CV Terms of the Precursor (Q1) of the transition or target
Definition: ReactionMonitoringTransition.h:317
DecoyTransitionType
Definition: ReactionMonitoringTransition.h:42
@ TARGET
Target transition.
Definition: ReactionMonitoringTransition.h:44
@ UNKNOWN
Unknown type.
Definition: ReactionMonitoringTransition.h:43
String name_
id, required attribute
Definition: ReactionMonitoringTransition.h:289
double getProductMZ() const
String peptide_ref_
Reference to a specific peptide.
Definition: ReactionMonitoringTransition.h:292
Product product_
Product (Q3) of the transition.
Definition: ReactionMonitoringTransition.h:320
String compound_ref_
Reference to a specific compound.
Definition: ReactionMonitoringTransition.h:293
ReactionMonitoringTransition(ReactionMonitoringTransition &&) noexcept
Move constructor.
TargetedExperimentHelper::Configuration Configuration
Definition: ReactionMonitoringTransition.h:36
TargetedExperimentHelper::Prediction Prediction
Definition: ReactionMonitoringTransition.h:39
DecoyTransitionType decoy_type_
specific properties of a transition (e.g. specific CV terms)
Definition: ReactionMonitoringTransition.h:299
Prediction * prediction_
Information about a prediction for a suitable transition using some software (optional)
Definition: ReactionMonitoringTransition.h:329
double precursor_mz_
A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window targe...
Definition: ReactionMonitoringTransition.h:314
ReactionMonitoringTransition(const ReactionMonitoringTransition &rhs)
copy constructor
std::bitset< 3 > transition_flags_
Definition: ReactionMonitoringTransition.h:333
const String & getName() const
std::vector< Product > intermediate_products_
Intermediate product ion information of the transition when using MS3 or above (optional)
Definition: ReactionMonitoringTransition.h:323
TargetedExperimentHelper::TraMLProduct Product
Definition: ReactionMonitoringTransition.h:38
double library_intensity_
Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag)
Definition: ReactionMonitoringTransition.h:296
TargetedExperimentHelper::RetentionTime RetentionTime
Definition: ReactionMonitoringTransition.h:37
RetentionTime rts
Information about predicted or calibrated retention time (optional)
Definition: ReactionMonitoringTransition.h:326
A more convenient string class.
Definition: String.h:34
This class stores a retention time structure that is used in TargetedExperiment (representing a TraML...
Definition: TargetedExperimentHelper.h:99
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Comparator by name.
Definition: ReactionMonitoringTransition.h:273
bool operator()(ReactionMonitoringTransition const &left, ReactionMonitoringTransition const &right) const
Definition: ReactionMonitoringTransition.h:274
Comparator by Product ion MZ.
Definition: ReactionMonitoringTransition.h:258
bool operator()(ReactionMonitoringTransition const &left, ReactionMonitoringTransition const &right) const
Definition: ReactionMonitoringTransition.h:259
Definition: TargetedExperimentHelper.h:39
Definition: TargetedExperimentHelper.h:453
Represents a product ion.
Definition: TargetedExperimentHelper.h:546