This class stores a SRM/MRM transition. More...
#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>
 
  
 | Classes | |
| struct | ProductMZLess | 
| Comparator by Product ion MZ.  More... | |
| Public Types | |
| enum | DecoyTransitionType { UNKNOWN, TARGET, DECOY } | 
| typedef TargetedExperimentHelper::Configuration | Configuration | 
| typedef TargetedExperimentHelper::RetentionTime | RetentionTime | 
| typedef TargetedExperimentHelper::TraMLProduct | Product | 
| typedef TargetedExperimentHelper::Prediction | Prediction | 
| Public Member Functions | |
| ReactionMonitoringTransition & | operator= (const ReactionMonitoringTransition &rhs) | 
| assignment operator  More... | |
| Constructors and destructors | |
| ReactionMonitoringTransition () | |
| default constructor  More... | |
| ReactionMonitoringTransition (const ReactionMonitoringTransition &rhs) | |
| copy constructor  More... | |
| virtual | ~ReactionMonitoringTransition () | 
| destructor  More... | |
| Accessors | |
| void | setName (const String &name) | 
| const String & | getName () const | 
| void | setNativeID (const String &name) | 
| const String & | getNativeID () const | 
| void | setPeptideRef (const String &peptide_ref) | 
| const String & | getPeptideRef () const | 
| void | setCompoundRef (const String &compound_ref) | 
| const String & | getCompoundRef () const | 
| void | setPrecursorMZ (DoubleReal mz) | 
| sets the precursor mz (Q1 value)  More... | |
| DoubleReal | getPrecursorMZ () const | 
| void | setPrecursorCVTermList (const CVTermList &list) | 
| void | addPrecursorCVTerm (const CVTerm &cv_term) | 
| const CVTermList & | getPrecursorCVTermList () const | 
| void | setProductMZ (DoubleReal mz) | 
| DoubleReal | getProductMZ () const | 
| void | addProductCVTerm (const CVTerm &cv_term) | 
| const std::vector< Product > & | getIntermediateProducts () const | 
| void | addIntermediateProduct (Product product) | 
| void | setIntermediateProducts (const std::vector< Product > &products) | 
| void | setProduct (Product product) | 
| const Product & | getProduct () const | 
| void | setRetentionTime (RetentionTime rt) | 
| const RetentionTime & | getRetentionTime () const | 
| void | setPrediction (const Prediction &prediction) | 
| void | addPredictionTerm (const CVTerm &prediction) | 
| const Prediction & | getPrediction () const | 
| DecoyTransitionType | getDecoyTransitionType () const | 
| void | setDecoyTransitionType (const DecoyTransitionType &d) | 
| DoubleReal | getLibraryIntensity () const | 
| void | setLibraryIntensity (DoubleReal intensity) | 
| Predicates | |
| bool | operator== (const ReactionMonitoringTransition &rhs) const | 
| equality operator  More... | |
| bool | operator!= (const ReactionMonitoringTransition &rhs) const | 
| inequality operator  More... | |
|  Public Member Functions inherited from CVTermList | |
| CVTermList () | |
| Defaults constructor.  More... | |
| CVTermList (const CVTermList &rhs) | |
| Copy constructor.  More... | |
| virtual | ~CVTermList () | 
| Destructor.  More... | |
| CVTermList & | operator= (const CVTermList &rhs) | 
| Assignment operator.  More... | |
| void | setCVTerms (const std::vector< CVTerm > &terms) | 
| sets the CV terms  More... | |
| void | replaceCVTerm (const CVTerm &cv_term) | 
| replaces the specified CV term  More... | |
| void | replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession) | 
| replaces the specified CV terms using the given accession number  More... | |
| void | replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map) | 
| replaces all cv terms with a map (can be obtained via getCVTerms)  More... | |
| const Map< String, std::vector < CVTerm > > & | getCVTerms () const | 
| returns the accession string of the term  More... | |
| void | addCVTerm (const CVTerm &term) | 
| adds a CV term  More... | |
| bool | operator== (const CVTermList &cv_term_list) const | 
| equality operator  More... | |
| bool | operator!= (const CVTermList &cv_term_list) const | 
| inequality operator  More... | |
| bool | hasCVTerm (const String &accession) const | 
| checks whether the term has a value  More... | |
| bool | empty () const | 
| return true if no terms are available  More... | |
|  Public Member Functions inherited from MetaInfoInterface | |
| MetaInfoInterface () | |
| constructor  More... | |
| MetaInfoInterface (const MetaInfoInterface &rhs) | |
| copy constructor  More... | |
| ~MetaInfoInterface () | |
| destructor  More... | |
| MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) | 
| assignment operator  More... | |
| bool | operator== (const MetaInfoInterface &rhs) const | 
| Equality operator.  More... | |
| bool | operator!= (const MetaInfoInterface &rhs) const | 
| Equality operator.  More... | |
| const DataValue & | getMetaValue (const String &name) const | 
| returns the value corresponding to a string  More... | |
| const DataValue & | getMetaValue (UInt index) const | 
| returns the value corresponding to an index  More... | |
| bool | metaValueExists (const String &name) const | 
| returns if this MetaInfo is set  More... | |
| bool | metaValueExists (UInt index) const | 
| returns if this MetaInfo is set  More... | |
| void | setMetaValue (const String &name, const DataValue &value) | 
| sets the DataValue corresponding to a name  More... | |
| void | setMetaValue (UInt index, const DataValue &value) | 
| sets the DataValue corresponding to an index  More... | |
| void | removeMetaValue (const String &name) | 
| Removes the DataValue corresponding to nameif it exists.  More... | |
| void | removeMetaValue (UInt index) | 
| Removes the DataValue corresponding to indexif it exists.  More... | |
| void | getKeys (std::vector< String > &keys) const | 
| fills the given vector with a list of all keys for which a value is set  More... | |
| void | getKeys (std::vector< UInt > &keys) const | 
| fills the given vector with a list of all keys for which a value is set  More... | |
| bool | isMetaEmpty () const | 
| returns if the MetaInfo is empty  More... | |
| void | clearMetaInfo () | 
| removes all meta values  More... | |
| Protected Member Functions | |
| void | updateMembers_ () | 
|  Protected Member Functions inherited from MetaInfoInterface | |
| void | createIfNotExists_ () | 
| creates the MetaInfo object if it does not exist  More... | |
| Protected Attributes | |
| DecoyTransitionType | decoy_type_ | 
| specific properties of a transition (e.g. specific CV terms)  More... | |
| DoubleReal | library_intensity_ | 
| String | name_ | 
| Attributes:  More... | |
| String | peptide_ref_ | 
| String | compound_ref_ | 
| DoubleReal | precursor_mz_ | 
| Subelements:  More... | |
| CVTermList | precursor_cv_terms_ | 
| Product | product_ | 
| std::vector< Product > | intermediate_products_ | 
| RetentionTime | rts | 
| Prediction | prediction_ | 
|  Protected Attributes inherited from CVTermList | |
| Map< String, std::vector < CVTerm > > | cv_terms_ | 
|  Protected Attributes inherited from MetaInfoInterface | |
| MetaInfo * | meta_ | 
| pointer to the MetaInfo object. 0 by default  More... | |
| Additional Inherited Members | |
|  Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () | 
| retuns a reference to the MetaInfoRegistry  More... | |
This class stores a SRM/MRM transition.
The default values for precursor and product m/z values are set to numeric_limits<DoubleReal>::max(). Default values for precursor an product charge is set to numeric_limits<Int>::max().
| enum DecoyTransitionType | 
default constructor
| ReactionMonitoringTransition | ( | const ReactionMonitoringTransition & | rhs | ) | 
copy constructor
| 
 | virtual | 
destructor
| void addIntermediateProduct | ( | Product | product | ) | 
| void addPrecursorCVTerm | ( | const CVTerm & | cv_term | ) | 
| void addPredictionTerm | ( | const CVTerm & | prediction | ) | 
| void addProductCVTerm | ( | const CVTerm & | cv_term | ) | 
| const String& getCompoundRef | ( | ) | const | 
| DecoyTransitionType getDecoyTransitionType | ( | ) | const | 
| const std::vector<Product>& getIntermediateProducts | ( | ) | const | 
| DoubleReal getLibraryIntensity | ( | ) | const | 
| const String& getName | ( | ) | const | 
| const String& getNativeID | ( | ) | const | 
Referenced by ChromatogramExtractor::prepareSpectra_().
| const String& getPeptideRef | ( | ) | const | 
| const CVTermList& getPrecursorCVTermList | ( | ) | const | 
| DoubleReal getPrecursorMZ | ( | ) | const | 
Referenced by ChromatogramExtractor::prepareSpectra_().
| const Prediction& getPrediction | ( | ) | const | 
| const Product& getProduct | ( | ) | const | 
| DoubleReal getProductMZ | ( | ) | const | 
| const RetentionTime& getRetentionTime | ( | ) | const | 
| bool operator!= | ( | const ReactionMonitoringTransition & | rhs | ) | const | 
inequality operator
| ReactionMonitoringTransition& operator= | ( | const ReactionMonitoringTransition & | rhs | ) | 
assignment operator
| bool operator== | ( | const ReactionMonitoringTransition & | rhs | ) | const | 
equality operator
| void setCompoundRef | ( | const String & | compound_ref | ) | 
| void setDecoyTransitionType | ( | const DecoyTransitionType & | d | ) | 
| void setIntermediateProducts | ( | const std::vector< Product > & | products | ) | 
| void setLibraryIntensity | ( | DoubleReal | intensity | ) | 
| void setName | ( | const String & | name | ) | 
| void setNativeID | ( | const String & | name | ) | 
| void setPeptideRef | ( | const String & | peptide_ref | ) | 
| void setPrecursorCVTermList | ( | const CVTermList & | list | ) | 
| void setPrecursorMZ | ( | DoubleReal | mz | ) | 
sets the precursor mz (Q1 value)
| void setPrediction | ( | const Prediction & | prediction | ) | 
| void setProduct | ( | Product | product | ) | 
| void setProductMZ | ( | DoubleReal | mz | ) | 
| void setRetentionTime | ( | RetentionTime | rt | ) | 
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 | protected | 
specific properties of a transition (e.g. specific CV terms)
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 | protected | 
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 | protected | 
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 | protected | 
Attributes:
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 | protected | 
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 | protected | 
Subelements:
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 | protected | 
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 | protected | 
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 | protected | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |