| OpenMS 2.5.0

Public Types | Public Member Functions | Public Attributes | Private Attributes | List of all members
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:

## Public Types

enum | RTUnit : std::int8_t { SECOND = 0, MINUTE, UNKNOWN, SIZE_OF_RTUNIT }
enum | 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
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
| 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...
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 | 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 && |  | ) |

default noexcept

## ◆ ~RetentionTime()

virtual ~RetentionTime | ( |  | ) |

virtual default

## 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