| OpenMS 2.5.0

Public Member Functions | Public Attributes | Protected Attributes | List of all members
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 &)=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 | 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() [1/3]

PeptideCompound | ( |  | ) |

inline

## ◆ PeptideCompound() [2/3]

PeptideCompound | ( | const PeptideCompound & |  | ) |

default

## ◆ PeptideCompound() [3/3]

PeptideCompound | ( | PeptideCompound && |  | ) |

default noexcept

## 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=() [1/2]

PeptideCompound& operator= | ( | const PeptideCompound & |  | ) | &

default

## ◆ operator=() [2/2]

PeptideCompound& operator= | ( | PeptideCompound && |  | ) | &

default

## ◆ operator==()

bool operator== | ( | const PeptideCompound & | rhs | ) | const

inline

References CVTermList::operator==().

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

## ◆ charge_set_

bool charge_set_

protected

## ◆ drift_time_

double drift_time_

protected

## ◆ id

String id

Referenced by ChromatogramExtractor::prepareSpectra_().

## ◆ rts

std::vector<RetentionTime> rts