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ReactionMonitoringTransition Class Reference

This class stores a SRM/MRM transition. More...

#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>

Inheritance diagram for ReactionMonitoringTransition:
CVTermList MetaInfoInterface

List of all members.

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

ReactionMonitoringTransitionoperator= (const ReactionMonitoringTransition &rhs)
 assignment operator
Constructors and destructors

 ReactionMonitoringTransition ()
 default constructor
 ReactionMonitoringTransition (const ReactionMonitoringTransition &rhs)
 copy constructor
virtual ~ReactionMonitoringTransition ()
 destructor
Accessors

void setName (const String &name)
const StringgetName () const
void setNativeID (const String &name)
const StringgetNativeID () const
void setPeptideRef (const String &peptide_ref)
const StringgetPeptideRef () const
void setCompoundRef (const String &compound_ref)
const StringgetCompoundRef () const
void setPrecursorMZ (DoubleReal mz)
 sets the precursor mz (Q1 value)
DoubleReal getPrecursorMZ () const
void setPrecursorCVTermList (const CVTermList &list)
void addPrecursorCVTerm (const CVTerm &cv_term)
const CVTermListgetPrecursorCVTermList () 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 ProductgetProduct () const
void setRetentionTime (RetentionTime rt)
const RetentionTimegetRetentionTime () const
void setPrediction (const Prediction &prediction)
void addPredictionTerm (const CVTerm &prediction)
const PredictiongetPrediction () 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
bool operator!= (const ReactionMonitoringTransition &rhs) const
 inequality operator

Protected Member Functions

void updateMembers_ ()

Protected Attributes

DecoyTransitionType decoy_type_
 specific properties of a transition (e.g. specific CV terms)
DoubleReal library_intensity_

String name_
 Attributes:
String peptide_ref_
String compound_ref_

DoubleReal precursor_mz_
 Subelements:
CVTermList precursor_cv_terms_
Product product_
std::vector< Productintermediate_products_
RetentionTime rts
Prediction prediction_

Detailed Description

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().


Member Typedef Documentation


Member Enumeration Documentation

Enumerator:
UNKNOWN 
TARGET 
DECOY 

Constructor & Destructor Documentation

default constructor

copy constructor

virtual ~ReactionMonitoringTransition (  )  [virtual]

destructor


Member Function Documentation

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
const CVTermList& getPrecursorCVTermList (  )  const
DoubleReal getPrecursorMZ (  )  const
const Prediction& getPrediction (  )  const
const Product& getProduct (  )  const
const RetentionTime& getRetentionTime (  )  const
bool operator!= ( const ReactionMonitoringTransition rhs  )  const

inequality operator

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  ) 
void updateMembers_ (  )  [protected]

Member Data Documentation

String compound_ref_ [protected]

specific properties of a transition (e.g. specific CV terms)

std::vector<Product> intermediate_products_ [protected]
String name_ [protected]

Attributes:

String peptide_ref_ [protected]

Subelements:

Prediction prediction_ [protected]
Product product_ [protected]
RetentionTime rts [protected]

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1