OpenMS
IncludeExcludeTarget Class Reference

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

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

Inheritance diagram for IncludeExcludeTarget:
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Collaboration diagram for IncludeExcludeTarget:
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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...
 
Accessors
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 std::map< String, std::vector< CVTerm > > &cv_term_map)
 replaces all cv terms with a map (can be obtained via getCVTerms) More...
 
void consumeCVTerms (const std::map< String, std::vector< CVTerm > > &cv_term_map)
 merges the given map into the member map, no duplicate checking More...
 
const std::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...
 
void swap (MetaInfoInterface &rhs)
 Swap contents. 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, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (const String &name, const DataValue &default_value) const
 Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found
More...
 
const DataValuegetMetaValue (UInt index) const
 Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (UInt index, const DataValue &default_value) const
 Returns the value corresponding to the index, or a default value (e.g.: 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...
 

Predicates

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
std::map< String, std::vector< CVTerm > > cv_terms_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 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 ( )
override

destructor

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_ ( )
protected

Member Data Documentation

◆ compound_ref_

String compound_ref_
protected

◆ configurations_

std::vector<Configuration> configurations_
protected

◆ interpretation_list_

std::vector<CVTermList> interpretation_list_
protected

◆ name_

String name_
protected

◆ peptide_ref_

String peptide_ref_
protected

◆ precursor_cv_terms_

CVTermList precursor_cv_terms_
protected

◆ precursor_mz_

double precursor_mz_
protected

◆ prediction_

CVTermList prediction_
protected

◆ product_cv_terms_

CVTermList product_cv_terms_
protected

◆ product_mz_

double product_mz_
protected

◆ rts_

RetentionTime rts_
protected