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Peptide Class Reference

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

Inheritance diagram for Peptide:
CVTermList MetaInfoInterface

Classes

struct  Modification
 

Public Member Functions

 Peptide ()
 
 Peptide (const Peptide &rhs)
 
Peptideoperator= (const Peptide &rhs)
 
bool operator== (const Peptide &rhs) const
 
void setChargeState (int charge)
 Set the peptide charge state. More...
 
int getChargeState () const
 Return the peptide charge state. More...
 
double getRetentionTime () 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 CVTermList
 CVTermList ()
 Defaults constructor. More...
 
 CVTermList (const CVTermList &rhs)
 Copy constructor. More...
 
virtual ~CVTermList ()
 Destructor. More...
 
CVTermListoperator= (const CVTermList &rhs)
 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 ()
 destructor More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 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
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (UInt index) const
 returns the value corresponding to an index More...
 
bool metaValueExists (const String &name) const
 returns if this MetaInfo is set More...
 
bool metaValueExists (UInt index) const
 returns if this MetaInfo is set 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< RetentionTimerts
 
String id
 
std::vector< Stringprotein_refs
 
CVTermList evidence
 
String sequence
 
std::vector< Modificationmods
 

Protected Attributes

int charge_
 
String peptide_group_label_
 
- 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...
 

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...
 

Constructor & Destructor Documentation

Peptide ( )
inline
Peptide ( const Peptide rhs)
inline

Member Function Documentation

int getChargeState ( ) const
inline

Return the peptide charge state.

String getPeptideGroupLabel ( ) const
inline

Get the peptide group label.

double getRetentionTime ( ) const
inline
Peptide& operator= ( const Peptide rhs)
inline
bool operator== ( const Peptide rhs) const
inline
void setChargeState ( int  charge)
inline

Set the peptide charge state.

void setPeptideGroupLabel ( const String label)
inline

Set the peptide group label.

Member Data Documentation

int charge_
protected
CVTermList evidence
String id
std::vector<Modification> mods
String peptide_group_label_
protected
std::vector<String> protein_refs
std::vector<RetentionTime> rts
String sequence

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:48 using doxygen 1.8.9.1