| OpenMS 2.5.0

Classes | Public Member Functions | Protected Attributes | List of all members
PeptideHit Class Reference
Metadata

Representation of a peptide hit. More...

`#include <OpenMS/METADATA/PeptideHit.h>`

Inheritance diagram for PeptideHit:

## 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

bool | operator== (const PeptideHit &rhs) const
| Equality operator. More...
bool | operator!= (const PeptideHit &rhs) const
| Inequality operator. More...
std::set< String > | extractProteinAccessionsSet () const
| extracts the set of non-empty protein accessions from peptide evidences More...
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...
PeptideHit & | operator= (const PeptideHit &source)
| Assignment operator. More...
PeptideHit & | operator= (PeptideHit &&) noexcept
| Move assignment operator. More...
Accessors
const AASequence & | getSequence () const
| returns the peptide sequence without trailing or following spaces 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 (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 () const
| returns the fragment annotations More...
void | setPeakAnnotations (std::vector< PeptideHit::PeakAnnotation > frag_annotations)
| sets the fragment annotations 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...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (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 DataValue & | getMetaValue (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 DataValue & | getMetaValue (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...

## Protected Attributes

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< PeptideEvidence > | peptide_evidences_
| information on the potential peptides observed through this PSM. More...
std::vector< PeptideHit::PeakAnnotation > | fragment_annotations_
| annotations of fragments in the corresponding spectrum More...
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...

## Additional Inherited Members

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry & | metaRegistry ()
| 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

## ◆ PeptideHit() [1/5]

PeptideHit | ( |  | ) |

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 | ( | 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()

Int getCharge | ( |  | ) | const

returns the charge of the peptide

Referenced by IDFilter::annotateBestPerPeptideWithData(), IDScoreGetterSetter::getScores_(), IDBoostGraph::LabelVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().

## ◆ getPeakAnnotations()

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

returns the fragment annotations

## ◆ 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()

double getScore | ( |  | ) | const

returns the PSM score

Referenced by IDFilter::annotateBestPerPeptideWithData(), IDScoreGetterSetter::getScores_(), IDBoostGraph::GetPosteriorVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().

## ◆ getSequence()

const AASequence& getSequence | ( |  | ) | const

returns the peptide sequence without trailing or following spaces

Referenced by IDFilter::annotateBestPerPeptideWithData(), IDBoostGraph::LabelVisitor::operator()(), IDBoostGraph::PrintAddressVisitor< CharT >::operator()(), IDFilter::PeptideDigestionFilter::operator()(), and IDConflictResolverAlgorithm::resolveBetweenFeatures_().

## ◆ 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 | ) |

sets the PSM score

Referenced by IDBoostGraph::SetPosteriorVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().

## ◆ setSequence() [1/2]

void setSequence | ( | const AASequence & | sequence | ) |

sets the peptide sequence

## ◆ setSequence() [2/2]

void setSequence | ( | 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