OpenMS  2.5.0
Classes | Public Member Functions | List of all members
Peptide Class Reference

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

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

Inheritance diagram for Peptide:
PeptideCompound CVTermList MetaInfoInterface

Classes

struct  Modification
 

Public Member Functions

 Peptide ()
 
 Peptide (const Peptide &)=default
 
 Peptide (Peptide &&) noexcept=default
 
Peptideoperator= (const Peptide &) &=default
 
Peptideoperator= (Peptide &&) &=default
 
bool operator== (const Peptide &rhs) const
 
- Public Member Functions inherited from PeptideCompound
 PeptideCompound ()
 
 PeptideCompound (const PeptideCompound &)=default
 
 PeptideCompound (PeptideCompound &&) noexcept=default
 
PeptideCompoundoperator= (const PeptideCompound &) &=default
 
PeptideCompoundoperator= (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...
 
CVTermListoperator= (const CVTermList &rhs) &=default
 Assignment operator. More...
 
CVTermListoperator= (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...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (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 DataValuegetMetaValue (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...
 

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]

std::vector< Stringprotein_refs
 
CVTermList evidence
 
String sequence
 
std::vector< Modificationmods
 
String peptide_group_label_
 
void setPeptideGroupLabel (const String &label)
 Set the peptide group label. More...
 
String getPeptideGroupLabel () const
 Get the peptide group label. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 Returns a reference to the MetaInfoRegistry. More...
 
- Public Attributes inherited from PeptideCompound
String id
 
std::vector< RetentionTimerts
 
- Protected Member Functions inherited from MetaInfoInterface
void createIfNotExists_ ()
 Creates the MetaInfo object if it does not exist. More...
 
- 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
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) 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

◆ 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