RetentionTime Class Reference

This class stores a retention time structure that is used in TargetedExperiment (representing a TraML file) More...

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

Inheritance diagram for RetentionTime:

Collaboration diagram for RetentionTime:

Public Types
enum class	RTUnit : std::int8_t { SECOND = 0 , MINUTE , UNKNOWN , SIZE_OF_RTUNIT }
enum class	RTType : std::int8_t {   LOCAL = 0 , NORMALIZED , PREDICTED , HPINS ,   IRT , UNKNOWN , SIZE_OF_RTTYPE }

Public Member Functions
	RetentionTime ()
	RetentionTime (const RetentionTime &)=default
	RetentionTime (RetentionTime &&) noexcept=default
virtual	~RetentionTime ()=default
RetentionTime &	operator= (const RetentionTime &) &=default
RetentionTime &	operator= (RetentionTime &&) &=default
bool	operator== (const RetentionTime &rhs) const
bool	isRTset () const
void	setRT (double rt)
double	getRT () const
Public Member Functions inherited from CVTermListInterface
	CVTermListInterface ()
	CVTermListInterface (const CVTermListInterface &rhs)
	Copy constructor. More...
	CVTermListInterface (CVTermListInterface &&) noexcept
	Move constructor. More...
	~CVTermListInterface ()
CVTermListInterface &	operator= (const CVTermListInterface &rhs)
	Assignment operator. More...
CVTermListInterface &	operator= (CVTermListInterface &&) noexcept
	Move assignment operator. More...
bool	operator== (const CVTermListInterface &rhs) const
	equality operator More...
bool	operator!= (const CVTermListInterface &rhs) const
	inequality operator More...
void	replaceCVTerms (Map< String, std::vector< CVTerm > > &cv_terms)
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	hasCVTerm (const String &accession) const
	checks whether the term has a value More...
bool	empty () const
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 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...

Public Attributes
String	software_ref
RTUnit	retention_time_unit
RTType	retention_time_type

Private Attributes
bool	retention_time_set_
double	retention_time_

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 MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Detailed Description

This class stores a retention time structure that is used in TargetedExperiment (representing a TraML file)

According to the standard, each retention time tag can have one or more CV terms describing the retention time in question. The unit and type of retention time are stored using the RTUnit and RTType structure while the actual value is stored in retention_time_ and can be accessed by getRT / setRT. Currently support for RT windows or lower/upper limits is not implemented but is available via CV terms.

Member Enumeration Documentation

RTType

enum RTType : std::int8_t

strong

Enumerator
LOCAL	undefined local chromatography
NORMALIZED	standardized reference chromatography
PREDICTED	predicted by referenced software
HPINS	H-PINS "The de facto standard providing the retention times".
IRT	iRT retention time standard
UNKNOWN	no stored annotation
SIZE_OF_RTTYPE

RTUnit

enum RTUnit : std::int8_t

strong

Enumerator
SECOND	RT stored in seconds.
MINUTE	RT stored in minutes.
UNKNOWN	no stored annotation
SIZE_OF_RTUNIT

Constructor & Destructor Documentation

RetentionTime() [1/3]

RetentionTime ( )

inline

RetentionTime() [2/3]

RetentionTime ( const RetentionTime &  )

default

RetentionTime() [3/3]

RetentionTime ( RetentionTime &&  )

defaultnoexcept

~RetentionTime()

virtual ~RetentionTime ( )

virtualdefault

Member Function Documentation

getRT()

double getRT ( ) const

inline

References OPENMS_PRECONDITION.

isRTset()

bool isRTset ( ) const

inline

operator=() [1/2]

RetentionTime& operator= ( const RetentionTime &  ) &

default

operator=() [2/2]

RetentionTime& operator= ( RetentionTime &&  ) &

default

operator==()

bool operator== ( const RetentionTime &  rhs ) const

inline

References CVTermListInterface::operator==().

setRT()

void setRT ( double  rt )

inline

Member Data Documentation

retention_time_

double retention_time_

private

retention_time_set_

bool retention_time_set_

private

retention_time_type

RTType retention_time_type

retention_time_unit

RTUnit retention_time_unit

software_ref

String software_ref