OpenMS
2.5.0
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Representation of a peptide hit. More...
#include <OpenMS/METADATA/PeptideHit.h>
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... | |
PeptideHit & | operator= (const PeptideHit &source) |
Assignment operator. More... | |
PeptideHit & | operator= (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... | |
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... | |
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< 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... | |
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... | |
std::set< String > | extractProteinAccessionsSet () const |
extracts the set of non-empty protein accessions from peptide evidences 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... | |
Protected Attributes inherited from MetaInfoInterface | |
MetaInfo * | meta_ |
Pointer to the MetaInfo object (0 by default) More... | |
Representation of a peptide hit.
It contains the fields score, score_type, rank, and sequence.
PeptideHit | ( | ) |
Default constructor.
PeptideHit | ( | double | score, |
UInt | rank, | ||
Int | charge, | ||
const AASequence & | sequence | ||
) |
Values constructor that copies sequence.
PeptideHit | ( | double | score, |
UInt | rank, | ||
Int | charge, | ||
AASequence && | sequence | ||
) |
Values constructor that moves sequence R-value.
PeptideHit | ( | const PeptideHit & | source | ) |
Copy constructor.
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noexcept |
Move constructor.
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virtual |
Destructor.
void addAnalysisResults | ( | PepXMLAnalysisResult | aresult | ) |
add information on (search engine) sub scores associated with this PSM
void addPeptideEvidence | ( | const PeptideEvidence & | peptide_evidence | ) |
adds information on a peptide that is (potentially) identified by this PSM
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()().
const std::vector<PepXMLAnalysisResult>& getAnalysisResults | ( | ) | const |
returns information on (search engine) sub scores associated with this PSM
Int getCharge | ( | ) | const |
returns the charge of the peptide
Referenced by IDFilter::annotateBestPerPeptideWithData(), IDScoreGetterSetter::getScores_(), IDBoostGraph::LabelVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().
std::vector<PeptideHit::PeakAnnotation> getPeakAnnotations | ( | ) | const |
returns the fragment annotations
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 IDFilter::annotateBestPerPeptideWithData(), IDScoreGetterSetter::getScores_(), IDBoostGraph::GetPosteriorVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().
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_().
bool operator!= | ( | const PeptideHit & | rhs | ) | const |
Inequality operator.
PeptideHit& operator= | ( | const PeptideHit & | source | ) |
Assignment operator.
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noexcept |
Move assignment operator.
bool operator== | ( | const PeptideHit & | rhs | ) | const |
Equality operator.
void setAnalysisResults | ( | std::vector< PepXMLAnalysisResult > | aresult | ) |
set information on (search engine) sub scores associated with this PSM
void setCharge | ( | Int | charge | ) |
sets the charge of the peptide
void setPeakAnnotations | ( | std::vector< PeptideHit::PeakAnnotation > | frag_annotations | ) |
sets the fragment annotations
void setPeptideEvidences | ( | const std::vector< PeptideEvidence > & | peptide_evidences | ) |
set information on peptides (potentially) identified by this PSM
void setPeptideEvidences | ( | std::vector< PeptideEvidence > && | peptide_evidences | ) |
void setRank | ( | UInt | newrank | ) |
sets the PSM rank
void setScore | ( | double | score | ) |
sets the PSM score
Referenced by IDBoostGraph::SetPosteriorVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().
void setSequence | ( | AASequence && | sequence | ) |
sets the peptide sequence
void setSequence | ( | const AASequence & | sequence | ) |
sets the peptide sequence
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protected |
additional scores attached to the original, aggregated score
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the charge of the peptide
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annotations of fragments in the corresponding spectrum
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protected |
information on the potential peptides observed through this PSM.
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protected |
the position(rank) where the hit appeared in the hit list
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protected |
the score of the peptide hit
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protected |