Peptide Class Reference

Represents a peptide (amino acid sequence) More...

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

Inheritance diagram for Peptide:

Collaboration diagram for Peptide:

Classes
struct	Modification

Public Member Functions
	Peptide ()=default
	Peptide (const Peptide &)=default
	Peptide (Peptide &&) noexcept=default
Peptide &	operator= (const Peptide &) &=default
Peptide &	operator= (Peptide &&) &=default
bool	operator== (const Peptide &rhs) const
Public Member Functions inherited from PeptideCompound
	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 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...
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...
MetaInfoInterface &	operator= (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 DataValue &	getMetaValue (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 DataValue &	getMetaValue (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...

The peptide group label specifies to non-labeled peptide group to which the peptide belongs
MS:1000893: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS]
std::vector< String >	protein_refs
CVTermList	evidence
String	sequence
std::vector< Modification >	mods
String	peptide_group_label_
void	setPeptideGroupLabel (const String &label)
	Set the peptide group label. More...
String	getPeptideGroupLabel () const
	Get the peptide group label. More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...
Public Attributes inherited from PeptideCompound
String	id
std::vector< RetentionTime >	rts
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...
Protected Attributes inherited from PeptideCompound
int	charge_ {0}
bool	charge_set_ {false}
double	drift_time_ {-1}
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...

Detailed Description

Represents a peptide (amino acid sequence)

Also stores information about the sequence, a linked protein and modified amino acids.

Constructor & Destructor Documentation

Peptide() [1/3]

Peptide ( )

default

Peptide() [2/3]

Peptide ( const Peptide &  )

default

Peptide() [3/3]

Peptide ( Peptide &&  )

defaultnoexcept

Member Function Documentation

getPeptideGroupLabel()

String getPeptideGroupLabel ( ) const

inline

Get the peptide group label.

operator=() [1/2]

Peptide& operator= ( const Peptide &  ) &

default

operator=() [2/2]

Peptide& operator= ( Peptide &&  ) &

default

operator==()

bool operator== ( const Peptide &  rhs ) const

inline

References PeptideCompound::operator==().

setPeptideGroupLabel()

void setPeptideGroupLabel ( const String &  label )

inline

Set the peptide group label.

Member Data Documentation

evidence

CVTermList evidence

mods

std::vector<Modification> mods

peptide_group_label_

String peptide_group_label_

protected

protein_refs

std::vector<String> protein_refs

sequence

String sequence

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