Base class to represent either a peptide or a compound. More...

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

Inheritance diagram for PeptideCompound:

Collaboration diagram for PeptideCompound:

Public Member Functions
	PeptideCompound ()=default

	PeptideCompound (const PeptideCompound &)=default

	PeptideCompound (PeptideCompound &&) noexcept=default

PeptideCompound &	operator= (const PeptideCompound &) &=default

PeptideCompound &	operator= (PeptideCompound &&) &=default

bool	operator== (const PeptideCompound &rhs) const

void	setChargeState (int charge)
	Set the peptide or compound charge state. More...

bool	hasCharge () const
	Whether peptide or compound has set charge state. More...

int	getChargeState () const
	Return the peptide or compound charge state. More...

void	setDriftTime (double dt)
	Set the peptide or compound ion mobility drift time. More...

double	getDriftTime () const
	Return the peptide or compound ion mobility drift time. More...

bool	hasRetentionTime () const
	Check whether compound or peptide has an annotated retention time. More...

double	getRetentionTime () const
	Gets compound or peptide retention time. More...

RetentionTime::RTType	getRetentionTimeType () const
	Get compound or peptide retentiontime type. More...

RetentionTime::RTUnit	getRetentionTimeUnit () const
	Get compound or peptide retentiontime unit (minute/seconds) More...

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...

Public Attributes
String	id

std::vector< RetentionTime >	rts

Protected Attributes
int	charge_ {0}

bool	charge_set_ {false}

double	drift_time_ {-1}

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...

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...

Detailed Description

Base class to represent either a peptide or a compound.

Stores retention time, identifiers, charge and precursor ion mobility drift time.

Constructor & Destructor Documentation

◆ PeptideCompound() [1/3]

PeptideCompound ( )

default

◆ PeptideCompound() [2/3]

PeptideCompound ( const PeptideCompound & )

default

◆ PeptideCompound() [3/3]

PeptideCompound ( PeptideCompound && )

defaultnoexcept

Member Function Documentation

◆ getChargeState()

int getChargeState ( ) const

inline

Return the peptide or compound charge state.

References OPENMS_PRECONDITION.

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >().

◆ getDriftTime()

double getDriftTime ( ) const

inline

Return the peptide or compound ion mobility drift time.

◆ getRetentionTime()

double getRetentionTime ( ) const

inline

Gets compound or peptide retention time.

Note: Ensure that retention time is present by calling hasRetentionTime()

◆ getRetentionTimeType()

RetentionTime::RTType getRetentionTimeType ( ) const

inline

Get compound or peptide retentiontime type.

◆ getRetentionTimeUnit()

RetentionTime::RTUnit getRetentionTimeUnit ( ) const

inline

Get compound or peptide retentiontime unit (minute/seconds)

◆ hasCharge()

bool hasCharge ( ) const

inline

Whether peptide or compound has set charge state.

Referenced by OpenMS::ChromatogramExtractor::extract_id_< OpenMS::TargetedExperiment >().

◆ hasRetentionTime()

bool hasRetentionTime ( ) const

inline

Check whether compound or peptide has an annotated retention time.

◆ operator=() [1/2]

PeptideCompound& operator= ( const PeptideCompound & ) &

default

◆ operator=() [2/2]

PeptideCompound& operator= ( PeptideCompound && ) &

default

◆ operator==()

bool operator== ( const PeptideCompound & rhs ) const

inline

References CVTermList::operator==().

Referenced by Compound::operator==(), and Peptide::operator==().

◆ setChargeState()

void setChargeState ( int charge )

inline

Set the peptide or compound charge state.

◆ setDriftTime()

void setDriftTime ( double dt )

inline

Set the peptide or compound ion mobility drift time.

Member Data Documentation

◆ charge_

int charge_ {0}

protected

◆ charge_set_

bool charge_set_ {false}

protected

◆ drift_time_

double drift_time_ {-1}

protected

◆ id

String id

Referenced by ChromatogramExtractor::prepareSpectra_().

◆ rts

std::vector<RetentionTime> rts

Public Member Functions

Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PeptideCompound() [1/3]

◆ PeptideCompound() [2/3]

◆ PeptideCompound() [3/3]

Member Function Documentation

◆ getChargeState()

◆ getDriftTime()

◆ getRetentionTime()

◆ getRetentionTimeType()

◆ getRetentionTimeUnit()

◆ hasCharge()

◆ hasRetentionTime()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setChargeState()

◆ setDriftTime()

Member Data Documentation

◆ charge_

◆ charge_set_

◆ drift_time_

◆ id

◆ rts