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PeptideHit Class Reference

Representation of a peptide hit. More...

#include <OpenMS/METADATA/PeptideHit.h>

Inheritance diagram for PeptideHit:
MetaInfoInterface

Classes

class  ScoreLess
 Lesser predicate for scores of hits. More...
 
class  ScoreMore
 Greater predicate for scores of hits. More...
 

Public Member Functions

PeptideHitoperator= (const PeptideHit &source)
 assignment operator More...
 
bool operator== (const PeptideHit &rhs) const
 Equality operator. More...
 
bool operator!= (const PeptideHit &rhs) const
 Inequality operator. More...
 
std::set< StringextractProteinAccessions () const
 extracts the set of non-empty protein accessions from peptide evidences More...
 
Constructors and Destructor
 PeptideHit ()
 default constructor More...
 
 PeptideHit (double score, UInt rank, Int charge, const AASequence &sequence)
 values constructor More...
 
 PeptideHit (const PeptideHit &source)
 copy constructor More...
 
virtual ~PeptideHit ()
 destructor More...
 
Accessors
const AASequencegetSequence () const
 returns the peptide sequence without trailing or following spaces More...
 
void setSequence (const AASequence &sequence)
 sets the peptide sequence More...
 
Int getCharge () const
 returns the charge of the peptide More...
 
void setCharge (Int charge)
 sets the charge of the peptide More...
 
const std::vector< PeptideEvidence > & getPeptideEvidences () const
 returns information on peptides (potentially) identified by this PSM More...
 
void setPeptideEvidences (const std::vector< PeptideEvidence > &peptide_evidences)
 set information on peptides (potentially) identified by this PSM More...
 
void addPeptideEvidence (const PeptideEvidence &peptide_evidence)
 adds information on a peptide that is (potentially) identified by this PSM More...
 
double getScore () const
 returns the PSM score More...
 
void setScore (double score)
 sets the PSM score More...
 
UInt getRank () const
 returns the PSM rank More...
 
void setRank (UInt newrank)
 sets the PSM rank 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...
 

Protected Attributes

AASequence sequence_
 
double score_
 the score of the peptide hit More...
 
UInt rank_
 the position(rank) where the hit appeared in the hit list More...
 
Int charge_
 the charge of the peptide More...
 
std::vector< PeptideEvidencepeptide_evidences_
 information on the potential peptides observed through this PSM. More...
 
- 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

Representation of a peptide hit.

It contains the fields score, score_type, rank, and sequence.

Constructor & Destructor Documentation

default constructor

PeptideHit ( double  score,
UInt  rank,
Int  charge,
const AASequence sequence 
)

values constructor

PeptideHit ( const PeptideHit source)

copy constructor

virtual ~PeptideHit ( )
virtual

destructor

Member Function Documentation

void addPeptideEvidence ( const PeptideEvidence peptide_evidence)

adds information on a peptide that is (potentially) identified by this PSM

std::set<String> extractProteinAccessions ( ) const

extracts the set of non-empty protein accessions from peptide evidences

Referenced by TOPPMetaProSIP::main_().

Int getCharge ( ) const

returns the charge of the peptide

Referenced by TOPPMetaProSIP::main_().

const std::vector<PeptideEvidence>& getPeptideEvidences ( ) const

returns information on peptides (potentially) identified by this PSM

UInt getRank ( ) const

returns the PSM rank

double getScore ( ) const

returns the PSM score

Referenced by TOPPMetaProSIP::main_().

const AASequence& getSequence ( ) const

returns the peptide sequence without trailing or following spaces

Referenced by TOPPMetaProSIP::main_().

bool operator!= ( const PeptideHit rhs) const

Inequality operator.

PeptideHit& operator= ( const PeptideHit source)

assignment operator

bool operator== ( const PeptideHit rhs) const

Equality operator.

void setCharge ( Int  charge)

sets the charge of the peptide

Referenced by SimpleSearchEngine::main_(), and TOPPMetaProSIP::main_().

void setPeptideEvidences ( const std::vector< PeptideEvidence > &  peptide_evidences)

set information on peptides (potentially) identified by this PSM

void setRank ( UInt  newrank)

sets the PSM rank

void setScore ( double  score)

sets the PSM score

Referenced by SimpleSearchEngine::main_().

void setSequence ( const AASequence sequence)

sets the peptide sequence

Referenced by SimpleSearchEngine::main_(), and TOPPMetaProSIP::main_().

Member Data Documentation

Int charge_
protected

the charge of the peptide

std::vector<PeptideEvidence> peptide_evidences_
protected

information on the potential peptides observed through this PSM.

UInt rank_
protected

the position(rank) where the hit appeared in the hit list

double score_
protected

the score of the peptide hit

AASequence sequence_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:05 using doxygen 1.8.9.1