OpenMS
PeptideCompound Class Reference

Base class to represent either a peptide or a compound. More...

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

Inheritance diagram for PeptideCompound:
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Collaboration diagram for PeptideCompound:
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Public Member Functions

 PeptideCompound ()=default
 
 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 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 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...
 
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 id
 
std::vector< RetentionTimerts
 

Protected Attributes

int charge_ {0}
 
bool charge_set_ {false}
 
double drift_time_ {-1}
 
- Protected Attributes inherited from CVTermList
std::map< String, std::vector< CVTerm > > cv_terms_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

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...
 

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 ( )
default

◆ PeptideCompound() [2/3]

PeptideCompound ( const PeptideCompound )
default

◆ PeptideCompound() [3/3]

PeptideCompound ( PeptideCompound &&  )
defaultnoexcept

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

◆ 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_ {0}
protected

◆ charge_set_

bool charge_set_ {false}
protected

◆ drift_time_

double drift_time_ {-1}
protected

◆ id

◆ rts

std::vector<RetentionTime> rts