PeptideCompound Class Reference

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

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

Inheritance diagram for PeptideCompound:

Public Member Functions
	PeptideCompound ()
	PeptideCompound (const PeptideCompound &rhs)
PeptideCompound &	operator= (const PeptideCompound &rhs)
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 ()
	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...
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 ()
	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 (or DataValue::EMPTY if not found) More...
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or 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	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_
bool	charge_set_
double	drift_time_
Protected Attributes inherited from CVTermList
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() [1/2]

PeptideCompound ( )

inline

PeptideCompound() [2/2]

PeptideCompound ( const PeptideCompound &  rhs )

inline

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=()

PeptideCompound& operator= ( const PeptideCompound &  rhs )

inline

References PeptideCompound::charge_, PeptideCompound::charge_set_, PeptideCompound::drift_time_, PeptideCompound::id, CVTermList::operator=(), and PeptideCompound::rts.

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

operator==()

bool operator== ( const PeptideCompound &  rhs ) const

inline

References PeptideCompound::charge_, PeptideCompound::charge_set_, PeptideCompound::id, CVTermList::operator==(), and PeptideCompound::rts.

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_

protected

Referenced by PeptideCompound::operator=(), and PeptideCompound::operator==().

charge_set_

bool charge_set_

protected

Referenced by PeptideCompound::operator=(), and PeptideCompound::operator==().

drift_time_

double drift_time_

protected

Referenced by PeptideCompound::operator=().

id

String id

Referenced by PeptideCompound::operator=(), PeptideCompound::operator==(), and ChromatogramExtractor::prepareSpectra_().

rts

std::vector<RetentionTime> rts

Referenced by PeptideCompound::operator=(), and PeptideCompound::operator==().