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... | |
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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... | |
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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 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_ () |
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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_ |
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Map< String, std::vector < CVTerm > > | cv_terms_ |
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MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default More... | |
Additional Inherited Members | |
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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
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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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specific properties of a transition (e.g. specific CV terms)
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Attributes:
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Subelements:
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OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |