OpenMS: Peptide Class Reference

| OpenMS 2.5.0

Classes | Public Member Functions | Public Attributes | Protected Attributes | List of all members
Peptide Class Reference

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

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

Inheritance diagram for Peptide:

## Classes

struct | Modification

## Public Member Functions

| Peptide ()
| Peptide (const Peptide &)=default
| Peptide (Peptide &&) noexcept=default
Peptide & | operator= (const Peptide &) &=default
Peptide & | operator= (Peptide &&) &=default
bool | operator== (const Peptide &rhs) const
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]
void | setPeptideGroupLabel (const String &label)
| Set the peptide group label. More...
String | getPeptideGroupLabel () const
| Get the peptide group label. More...
Public Member Functions inherited from PeptideCompound
| 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

std::vector< String > | protein_refs
CVTermList | evidence
String | sequence
std::vector< Modification > | mods
Public Attributes inherited from PeptideCompound
String | id
std::vector< RetentionTime > | rts

## Protected Attributes

String | peptide_group_label_
Protected Attributes inherited from PeptideCompound
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

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 | ( |  | ) |

inline

## ◆ 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_().