OpenMS
PeptideHit Class Reference

Representation of a peptide hit. More...

#include <OpenMS/METADATA/PeptideHit.h>

Inheritance diagram for PeptideHit:
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Collaboration diagram for PeptideHit:
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Classes

struct  PeakAnnotation
 Contains annotations of a peak. More...
 
class  PepXMLAnalysisResult
 Analysis Result (containing search engine / prophet results) More...
 
class  RankLess
 Lesser predicate for scores of hits. More...
 
class  ScoreLess
 Lesser predicate for scores of hits. More...
 
class  ScoreMore
 Greater predicate for scores of hits. More...
 
class  SequenceLessComparator
 Lesser predicate for (modified) sequence of hits. More...
 

Public Member Functions

Constructors and Assignment
 PeptideHit ()
 Default constructor. More...
 
 PeptideHit (double score, UInt rank, Int charge, const AASequence &sequence)
 Values constructor that copies sequence. More...
 
 PeptideHit (double score, UInt rank, Int charge, AASequence &&sequence)
 Values constructor that moves sequence R-value. More...
 
 PeptideHit (const PeptideHit &source)
 Copy constructor. More...
 
 PeptideHit (PeptideHit &&) noexcept
 Move constructor. More...
 
virtual ~PeptideHit ()
 Destructor. More...
 
PeptideHitoperator= (const PeptideHit &source)
 Assignment operator. More...
 
PeptideHitoperator= (PeptideHit &&) noexcept
 Move assignment operator. More...
 
bool operator== (const PeptideHit &rhs) const
 Equality operator. More...
 
bool operator!= (const PeptideHit &rhs) const
 Inequality operator. 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...
 

Accessors

AASequence sequence_
 
double score_ {}
 the score of the peptide hit More...
 
std::vector< PepXMLAnalysisResult > * analysis_results_
 additional scores attached to the original, aggregated score 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...
 
std::vector< PeptideHit::PeakAnnotationfragment_annotations_
 annotations of fragments in the corresponding spectrum More...
 
const AASequencegetSequence () const
 returns the peptide sequence More...
 
AASequencegetSequence ()
 returns the mutable peptide sequence More...
 
void setSequence (const AASequence &sequence)
 sets the peptide sequence More...
 
void setSequence (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 setPeptideEvidences (std::vector< PeptideEvidence > &&peptide_evidences)
 
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...
 
void setAnalysisResults (std::vector< PepXMLAnalysisResult > aresult)
 set information on (search engine) sub scores associated with this PSM More...
 
void addAnalysisResults (const PepXMLAnalysisResult &aresult)
 add information on (search engine) sub scores associated with this PSM More...
 
const std::vector< PepXMLAnalysisResult > & getAnalysisResults () const
 returns information on (search engine) sub scores associated with this PSM More...
 
UInt getRank () const
 returns the PSM rank More...
 
void setRank (UInt newrank)
 sets the PSM rank More...
 
std::vector< PeptideHit::PeakAnnotation > & getPeakAnnotations ()
 returns the fragment annotations More...
 
const std::vector< PeptideHit::PeakAnnotation > & getPeakAnnotations () const
 
void setPeakAnnotations (std::vector< PeptideHit::PeakAnnotation > frag_annotations)
 sets the fragment annotations More...
 
std::set< StringextractProteinAccessionsSet () const
 extracts the set of non-empty protein accessions from peptide evidences 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...
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Detailed Description

Representation of a peptide hit.

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

Constructor & Destructor Documentation

◆ PeptideHit() [1/5]

Default constructor.

◆ PeptideHit() [2/5]

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

Values constructor that copies sequence.

◆ PeptideHit() [3/5]

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

Values constructor that moves sequence R-value.

◆ PeptideHit() [4/5]

PeptideHit ( const PeptideHit source)

Copy constructor.

◆ PeptideHit() [5/5]

PeptideHit ( PeptideHit &&  )
noexcept

Move constructor.

◆ ~PeptideHit()

virtual ~PeptideHit ( )
virtual

Destructor.

Member Function Documentation

◆ addAnalysisResults()

void addAnalysisResults ( const PepXMLAnalysisResult aresult)

add information on (search engine) sub scores associated with this PSM

◆ addPeptideEvidence()

void addPeptideEvidence ( const PeptideEvidence peptide_evidence)

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

◆ extractProteinAccessionsSet()

std::set<String> extractProteinAccessionsSet ( ) const

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

Referenced by IDFilter::HasMatchingAccessionUnordered< HitType >::operator()(), and IDFilter::HasMatchingAccession< HitType >::operator()().

◆ getAnalysisResults()

const std::vector<PepXMLAnalysisResult>& getAnalysisResults ( ) const

returns information on (search engine) sub scores associated with this PSM

◆ getCharge()

◆ getPeakAnnotations() [1/2]

std::vector<PeptideHit::PeakAnnotation>& getPeakAnnotations ( )

returns the fragment annotations

◆ getPeakAnnotations() [2/2]

const std::vector<PeptideHit::PeakAnnotation>& getPeakAnnotations ( ) const

◆ getPeptideEvidences()

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

returns information on peptides (potentially) identified by this PSM

◆ getRank()

UInt getRank ( ) const

returns the PSM rank

◆ getScore()

◆ getSequence() [1/2]

AASequence& getSequence ( )

returns the mutable peptide sequence

◆ getSequence() [2/2]

◆ operator!=()

bool operator!= ( const PeptideHit rhs) const

Inequality operator.

◆ operator=() [1/2]

PeptideHit& operator= ( const PeptideHit source)

Assignment operator.

◆ operator=() [2/2]

PeptideHit& operator= ( PeptideHit &&  )
noexcept

Move assignment operator.

◆ operator==()

bool operator== ( const PeptideHit rhs) const

Equality operator.

◆ setAnalysisResults()

void setAnalysisResults ( std::vector< PepXMLAnalysisResult aresult)

set information on (search engine) sub scores associated with this PSM

◆ setCharge()

void setCharge ( Int  charge)

sets the charge of the peptide

◆ setPeakAnnotations()

void setPeakAnnotations ( std::vector< PeptideHit::PeakAnnotation frag_annotations)

sets the fragment annotations

◆ setPeptideEvidences() [1/2]

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

set information on peptides (potentially) identified by this PSM

◆ setPeptideEvidences() [2/2]

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

◆ setRank()

void setRank ( UInt  newrank)

sets the PSM rank

◆ setScore()

void setScore ( double  score)

◆ setSequence() [1/2]

void setSequence ( AASequence &&  sequence)

sets the peptide sequence

◆ setSequence() [2/2]

void setSequence ( const AASequence sequence)

sets the peptide sequence

Member Data Documentation

◆ analysis_results_

std::vector<PepXMLAnalysisResult>* analysis_results_
protected

additional scores attached to the original, aggregated score

◆ charge_

Int charge_ {}
protected

the charge of the peptide

◆ fragment_annotations_

std::vector<PeptideHit::PeakAnnotation> fragment_annotations_
protected

annotations of fragments in the corresponding spectrum

◆ peptide_evidences_

std::vector<PeptideEvidence> peptide_evidences_
protected

information on the potential peptides observed through this PSM.

◆ rank_

UInt rank_ {}
protected

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

◆ score_

double score_ {}
protected

the score of the peptide hit

◆ sequence_

AASequence sequence_
protected