OpenMS
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:
[legend]
Collaboration diagram for RetentionTime:
[legend]

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
 
RetentionTimeoperator= (const RetentionTime &) &=default
 
RetentionTimeoperator= (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 ()
 
CVTermListInterfaceoperator= (const CVTermListInterface &rhs)
 Assignment operator. More...
 
CVTermListInterfaceoperator= (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 (std::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 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 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...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (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 DataValuegetMetaValue (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 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 MetaInfoRegistrymetaRegistry ()
 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
MetaInfometa_
 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

◆ 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