Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Classes | Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
ReactionMonitoringTransition Class Reference

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

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

Inheritance diagram for ReactionMonitoringTransition:
CVTermList MetaInfoInterface

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 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 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 (double mz)
 sets the precursor mz (Q1 value) More...
 
double getPrecursorMZ () const
 
void setPrecursorCVTermList (const CVTermList &list)
 
void addPrecursorCVTerm (const CVTerm &cv_term)
 
const CVTermListgetPrecursorCVTermList () const
 
void setProductMZ (double mz)
 
double 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)
 
double getLibraryIntensity () const
 
void setLibraryIntensity (double 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...
 
CVTermListoperator= (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...
 
void consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
 merges the given map into the member map, no duplicate checking 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...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (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 name if it exists. More...
 
void removeMetaValue (UInt index)
 Removes the DataValue corresponding to index if 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...
 
double library_intensity_
 
String name_
 Attributes: More...
 
String peptide_ref_
 
String compound_ref_
 
double precursor_mz_
 Subelements: More...
 
CVTermList precursor_cv_terms_
 
Product product_
 
std::vector< Productintermediate_products_
 
RetentionTime rts
 
Prediction prediction_
 
- Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > > cv_terms_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 pointer to the MetaInfo object. 0 by default More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 returns a reference to the MetaInfoRegistry More...
 

Detailed Description

This class stores a SRM/MRM transition.

This class is capable of representing a <Transition> tag in a TraML document completely and contains all associated information.

The default values for precursor m/z is 0.0 which indicates that it is uninitialized.

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
double getLibraryIntensity ( ) const
const String& getName ( ) const
const String& getNativeID ( ) const
const String& getPeptideRef ( ) const
const CVTermList& getPrecursorCVTermList ( ) const
double getPrecursorMZ ( ) const
const Prediction& getPrediction ( ) const
const Product& getProduct ( ) const
double getProductMZ ( ) 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 ( double  intensity)
void setName ( const String name)
void setNativeID ( const String name)
void setPeptideRef ( const String peptide_ref)
void setPrecursorCVTermList ( const CVTermList list)
void setPrecursorMZ ( double  mz)

sets the precursor mz (Q1 value)

void setPrediction ( const Prediction prediction)
void setProduct ( Product  product)
void setProductMZ ( double  mz)
void setRetentionTime ( RetentionTime  rt)
void updateMembers_ ( )
protected

Member Data Documentation

String compound_ref_
protected
DecoyTransitionType decoy_type_
protected

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

std::vector<Product> intermediate_products_
protected
double library_intensity_
protected
String name_
protected

Attributes:

String peptide_ref_
protected
CVTermList precursor_cv_terms_
protected
double precursor_mz_
protected

Subelements:

Prediction prediction_
protected
Product product_
protected
RetentionTime rts
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:14:03 using doxygen 1.8.9.1