OpenMS  2.6.0
Public Types | List of all members
IncludeExcludeTarget Class Reference

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

#include <OpenMS/ANALYSIS/TARGETED/IncludeExcludeTarget.h>

Inheritance diagram for IncludeExcludeTarget:
Collaboration diagram for IncludeExcludeTarget:

Public Types

typedef TargetedExperimentHelper::Configuration Configuration
typedef TargetedExperimentHelper::RetentionTime RetentionTime

Public Member Functions

Constructors and destructors
 IncludeExcludeTarget ()
 default constructor More...
 IncludeExcludeTarget (const IncludeExcludeTarget &rhs)
 copy constructor More...
 ~IncludeExcludeTarget () override
 destructor More...
IncludeExcludeTargetoperator= (const IncludeExcludeTarget &rhs)
 assignment operator More...
void setName (const String &name)
const StringgetName () 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 setProductCVTermList (const CVTermList &list)
void addProductCVTerm (const CVTerm &cv_term)
const CVTermListgetProductCVTermList () const
void setInterpretations (const std::vector< CVTermList > &interpretations)
const std::vector< CVTermList > & getInterpretations () const
void addInterpretation (const CVTermList &interpretation)
void setConfigurations (const std::vector< Configuration > &configuration)
const std::vector< Configuration > & getConfigurations () const
void addConfiguration (const Configuration &configuration)
void setPrediction (const CVTermList &prediction)
void addPredictionTerm (const CVTerm &prediction)
const CVTermListgetPrediction () const
void setRetentionTime (RetentionTime rt)
const RetentionTimegetRetentionTime () const
- Public Member Functions inherited from CVTermList
 CVTermList ()=default
 Defaults constructor. More...
 CVTermList (const CVTermList &)=default
 Copy constructor. More...
 CVTermList (CVTermList &&) noexcept
 Move constructor. More...
virtual ~CVTermList ()
 Destructor. More...
CVTermListoperator= (const CVTermList &rhs) &=default
 Assignment operator. More...
CVTermListoperator= (CVTermList &&) &=default
 Move 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 (MetaInfoInterface &&) noexcept
 Move constructor. More...
 ~MetaInfoInterface ()
 Destructor. More...
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move 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 DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValuegetMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...
bool metaValueExists (const String &name) const
 Returns whether an entry with the given name exists. More...
bool metaValueExists (UInt index) const
 Returns whether an entry with the given index exists. 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 addMetaValues (const MetaInfoInterface &from)
 function to copy all meta values from one object to this one 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...


String name_
double precursor_mz_
CVTermList precursor_cv_terms_
double product_mz_
CVTermList product_cv_terms_
std::vector< CVTermListinterpretation_list_
String peptide_ref_
String compound_ref_
std::vector< Configurationconfigurations_
CVTermList prediction_
RetentionTime rts_
bool operator== (const IncludeExcludeTarget &rhs) const
 equality operator More...
bool operator!= (const IncludeExcludeTarget &rhs) const
 inequality operator More...
void updateMembers_ ()

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 Returns a reference to the MetaInfoRegistry. More...
- Protected Member Functions inherited from MetaInfoInterface
void createIfNotExists_ ()
 Creates the MetaInfo object if it does not exist. More...
- Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > > cv_terms_
- Protected Attributes inherited from MetaInfoInterface
 Pointer to the MetaInfo object (0 by default) More...

Detailed Description

This class stores a SRM/MRM transition.

The default values for precursor and product m/z values are set to numeric_limits<double>::max(). Default values for precursor an product charge is set to numeric_limits<Int>::max().

Member Typedef Documentation

◆ Configuration

◆ RetentionTime

Constructor & Destructor Documentation

◆ IncludeExcludeTarget() [1/2]

default constructor

◆ IncludeExcludeTarget() [2/2]

copy constructor

◆ ~IncludeExcludeTarget()

~IncludeExcludeTarget ( )


Member Function Documentation

◆ addConfiguration()

void addConfiguration ( const Configuration configuration)

◆ addInterpretation()

void addInterpretation ( const CVTermList interpretation)

◆ addPrecursorCVTerm()

void addPrecursorCVTerm ( const CVTerm cv_term)

◆ addPredictionTerm()

void addPredictionTerm ( const CVTerm prediction)

◆ addProductCVTerm()

void addProductCVTerm ( const CVTerm cv_term)

◆ getCompoundRef()

const String& getCompoundRef ( ) const

◆ getConfigurations()

const std::vector<Configuration>& getConfigurations ( ) const

◆ getInterpretations()

const std::vector<CVTermList>& getInterpretations ( ) const

◆ getName()

const String& getName ( ) const

◆ getPeptideRef()

const String& getPeptideRef ( ) const

◆ getPrecursorCVTermList()

const CVTermList& getPrecursorCVTermList ( ) const

◆ getPrecursorMZ()

double getPrecursorMZ ( ) const

◆ getPrediction()

const CVTermList& getPrediction ( ) const

◆ getProductCVTermList()

const CVTermList& getProductCVTermList ( ) const

◆ getProductMZ()

double getProductMZ ( ) const

◆ getRetentionTime()

const RetentionTime& getRetentionTime ( ) const

◆ operator!=()

bool operator!= ( const IncludeExcludeTarget rhs) const

inequality operator

◆ operator=()

IncludeExcludeTarget& operator= ( const IncludeExcludeTarget rhs)

assignment operator

◆ operator==()

bool operator== ( const IncludeExcludeTarget rhs) const

equality operator

◆ setCompoundRef()

void setCompoundRef ( const String compound_ref)

◆ setConfigurations()

void setConfigurations ( const std::vector< Configuration > &  configuration)

◆ setInterpretations()

void setInterpretations ( const std::vector< CVTermList > &  interpretations)

◆ setName()

void setName ( const String name)

◆ setPeptideRef()

void setPeptideRef ( const String peptide_ref)

◆ setPrecursorCVTermList()

void setPrecursorCVTermList ( const CVTermList list)

◆ setPrecursorMZ()

void setPrecursorMZ ( double  mz)

sets the precursor mz (Q1 value)

◆ setPrediction()

void setPrediction ( const CVTermList prediction)

◆ setProductCVTermList()

void setProductCVTermList ( const CVTermList list)

◆ setProductMZ()

void setProductMZ ( double  mz)

◆ setRetentionTime()

void setRetentionTime ( RetentionTime  rt)

◆ updateMembers_()

void updateMembers_ ( )

Member Data Documentation

◆ compound_ref_

String compound_ref_

◆ configurations_

std::vector<Configuration> configurations_

◆ interpretation_list_

std::vector<CVTermList> interpretation_list_

◆ name_

String name_

◆ peptide_ref_

String peptide_ref_

◆ precursor_cv_terms_

CVTermList precursor_cv_terms_

◆ precursor_mz_

double precursor_mz_

◆ prediction_

CVTermList prediction_

◆ product_cv_terms_

CVTermList product_cv_terms_

◆ product_mz_

double product_mz_

◆ rts_

RetentionTime rts_