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...
IncludeExcludeTarget &	operator= (const IncludeExcludeTarget &rhs)
	assignment operator More...
Accessors
void	setName (const String &name)
const String &	getName () const
void	setPeptideRef (const String &peptide_ref)
const String &	getPeptideRef () const
void	setCompoundRef (const String &compound_ref)
const String &	getCompoundRef () 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 CVTermList &	getPrecursorCVTermList () const
void	setProductMZ (double mz)
double	getProductMZ () const
void	setProductCVTermList (const CVTermList &list)
void	addProductCVTerm (const CVTerm &cv_term)
const CVTermList &	getProductCVTermList () 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 CVTermList &	getPrediction () const
void	setRetentionTime (RetentionTime rt)
const RetentionTime &	getRetentionTime () 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...
CVTermList &	operator= (const CVTermList &rhs) &=default
	Assignment operator. More...
CVTermList &	operator= (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...
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...
MetaInfoInterface &	operator= (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 DataValue &	getMetaValue (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 DataValue &	getMetaValue (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< CVTermList >	interpretation_list_
String	peptide_ref_
String	compound_ref_
std::vector< Configuration >	configurations_
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 MetaInfoRegistry &	metaRegistry ()
	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
MetaInfo *	meta_
	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

typedef TargetedExperimentHelper::Configuration Configuration

RetentionTime

typedef TargetedExperimentHelper::RetentionTime RetentionTime

Constructor & Destructor Documentation

IncludeExcludeTarget() [1/2]

IncludeExcludeTarget

(

)

default constructor

IncludeExcludeTarget() [2/2]

IncludeExcludeTarget

(

const IncludeExcludeTarget &

rhs

)

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