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PeptideIdentification Class Reference

Represents the peptide hits for a spectrum. More...

#include <OpenMS/METADATA/PeptideIdentification.h>

Inheritance diagram for PeptideIdentification:
MetaInfoInterface

Public Types

typedef PeptideHit HitType
 Hit type definition. More...
 

Public Member Functions

const std::vector< PeptideHit > & getHits () const
 returns the peptide hits More...
 
void insertHit (const PeptideHit &hit)
 Appends a peptide hit. More...
 
void setHits (const std::vector< PeptideHit > &hits)
 Sets the peptide hits. More...
 
DoubleReal getSignificanceThreshold () const
 returns the peptide significance threshold value More...
 
void setSignificanceThreshold (DoubleReal value)
 setting of the peptide significance threshold value More...
 
String getScoreType () const
 returns the peptide score type More...
 
void setScoreType (const String &type)
 sets the peptide score type More...
 
bool isHigherScoreBetter () const
 returns the peptide score orientation More...
 
void setHigherScoreBetter (bool value)
 sets the peptide score orientation More...
 
const StringgetIdentifier () const
 returns the identifier More...
 
void setIdentifier (const String &id)
 sets the indentifier More...
 
void assignRanks ()
 Sorts the hits by score and assigns ranks coording to the scores. More...
 
void sort ()
 Sorts the hits by score. More...
 
bool empty () const
 Returns if this PeptideIdentification result is empty. More...
 
constructors,destructors,assignment operator
 PeptideIdentification ()
 default constructor More...
 
virtual ~PeptideIdentification ()
 destructor More...
 
 PeptideIdentification (const PeptideIdentification &source)
 copy constructor More...
 
PeptideIdentificationoperator= (const PeptideIdentification &source)
 assignment operator More...
 
bool operator== (const PeptideIdentification &rhs) const
 Equality operator. More...
 
bool operator!= (const PeptideIdentification &rhs) const
 Inequality operator. More...
 
Methods for linking peptide and protein hits
void getReferencingHits (const String &protein_accession, std::vector< PeptideHit > &peptide_hits) const
 finds and inserts all peptide hits which reference to a given protein accession More...
 
void getReferencingHits (const std::vector< String > &accessions, std::vector< PeptideHit > &peptide_hits) const
 finds and inserts all peptide hits which reference to a given list of protein accessions More...
 
void getReferencingHits (const std::vector< ProteinHit > &protein_hits, std::vector< PeptideHit > &peptide_hits) const
 finds and inserts all peptide hits which reference to a given list of proteins (via their accessions) More...
 
void getNonReferencingHits (const String &protein_accession, std::vector< PeptideHit > &peptide_hits) const
 the complement of the above More...
 
void getNonReferencingHits (const std::vector< String > &accessions, std::vector< PeptideHit > &peptide_hits) const
 
void getNonReferencingHits (const std::vector< ProteinHit > &protein_hits, std::vector< PeptideHit > &peptide_hits) const
 
- 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

String id_
 Identifier by which ProteinIdentification and PeptideIdentification are matched. More...
 
std::vector< PeptideHithits_
 A list containing the peptide hits. More...
 
DoubleReal significance_threshold_
 the peptide significance threshold More...
 
String score_type_
 The score type (Mascot, Sequest, e-value, p-value) More...
 
bool higher_score_better_
 The score orientation. 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 ()
 retuns 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

Represents the peptide hits for a spectrum.

This class is closely related to ProteinIdentification, which stores the protein hits and the general information about the identification run. More than one PeptideIdentification can belong to one ProteinIdentification. The general information about a PeptideIdentification has to be looked up in the correpsonding ProteinIndentification, using the unique identifier that links the two.

When loading PeptideHit instances from a File, the retention time and mass-to-charge ratio of the precursor spectrum is stored in the MetaInfoInterface using the names 'MZ' and 'RT'. This information can be used to map the peptide hits to an MSExperiment, a FeatureMap or a ConsensusMap using the IDMapper class.

Member Typedef Documentation

Hit type definition.

Constructor & Destructor Documentation

default constructor

virtual ~PeptideIdentification ( )
virtual

destructor

copy constructor

Member Function Documentation

void assignRanks ( )

Sorts the hits by score and assigns ranks coording to the scores.

Referenced by TOPPRNPxl::main_().

bool empty ( ) const

Returns if this PeptideIdentification result is empty.

const std::vector<PeptideHit>& getHits ( ) const
const String& getIdentifier ( ) const

returns the identifier

void getNonReferencingHits ( const String protein_accession,
std::vector< PeptideHit > &  peptide_hits 
) const

the complement of the above

void getNonReferencingHits ( const std::vector< String > &  accessions,
std::vector< PeptideHit > &  peptide_hits 
) const
void getNonReferencingHits ( const std::vector< ProteinHit > &  protein_hits,
std::vector< PeptideHit > &  peptide_hits 
) const
void getReferencingHits ( const String protein_accession,
std::vector< PeptideHit > &  peptide_hits 
) const

finds and inserts all peptide hits which reference to a given protein accession

void getReferencingHits ( const std::vector< String > &  accessions,
std::vector< PeptideHit > &  peptide_hits 
) const

finds and inserts all peptide hits which reference to a given list of protein accessions

void getReferencingHits ( const std::vector< ProteinHit > &  protein_hits,
std::vector< PeptideHit > &  peptide_hits 
) const

finds and inserts all peptide hits which reference to a given list of proteins (via their accessions)

String getScoreType ( ) const

returns the peptide score type

DoubleReal getSignificanceThreshold ( ) const

returns the peptide significance threshold value

void insertHit ( const PeptideHit hit)

Appends a peptide hit.

Referenced by MRMFeatureFinderScoring::scorePeakgroups_().

bool isHigherScoreBetter ( ) const

returns the peptide score orientation

bool operator!= ( const PeptideIdentification rhs) const

Inequality operator.

PeptideIdentification& operator= ( const PeptideIdentification source)

assignment operator

bool operator== ( const PeptideIdentification rhs) const

Equality operator.

void setHigherScoreBetter ( bool  value)

sets the peptide score orientation

Referenced by DBAdapter::loadSpectrum(), and TOPPRNPxl::main_().

void setHits ( const std::vector< PeptideHit > &  hits)

Sets the peptide hits.

Referenced by DBAdapter::loadSpectrum(), and TOPPRNPxl::main_().

void setIdentifier ( const String id)

sets the indentifier

Referenced by MRMFeatureFinderScoring::scorePeakgroups_().

void setScoreType ( const String type)

sets the peptide score type

Referenced by DBAdapter::loadSpectrum().

void setSignificanceThreshold ( DoubleReal  value)

setting of the peptide significance threshold value

Referenced by DBAdapter::loadSpectrum().

void sort ( )

Sorts the hits by score.

Sorting takes the score orientation (higher_score_better_) into account, i.e. after sorting, the best-scoring hit is the first.

Member Data Documentation

bool higher_score_better_
protected

The score orientation.

std::vector<PeptideHit> hits_
protected

A list containing the peptide hits.

String id_
protected

Identifier by which ProteinIdentification and PeptideIdentification are matched.

String score_type_
protected

The score type (Mascot, Sequest, e-value, p-value)

DoubleReal significance_threshold_
protected

the peptide significance threshold


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5