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

#include <OpenMS/METADATA/PeptideIdentification.h>

Inheritance diagram for PeptideIdentification:

Public Types
typedef PeptideHit	HitType
	Hit type definition. More...

Public Member Functions
double	getRT () const
	returns the RT of the MS2 spectrum where the identification occurred More...

void	setRT (double rt)
	sets the RT of the MS2 spectrum where the identification occurred More...

bool	hasRT () const
	shortcut for isnan(getRT()) More...

double	getMZ () const
	returns the MZ of the MS2 spectrum More...

void	setMZ (double mz)
	sets the MZ of the MS2 spectrum More...

bool	hasMZ () const
	shortcut for isnan(getRT()) More...

const std::vector< PeptideHit > &	getHits () const
	returns the peptide hits as const More...

std::vector< PeptideHit > &	getHits ()
	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...

double	getSignificanceThreshold () const
	returns the peptide significance threshold value More...

void	setSignificanceThreshold (double value)
	setting of the peptide significance threshold value More...

const 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 String &	getIdentifier () const
	returns the identifier More...

void	setIdentifier (const String &id)
	sets the identifier More...

const String &	getBaseName () const
	returns the base name which links to underlying peak map More...

void	setBaseName (const String &base_name)
	sets the base name which links to underlying peak map More...

const String	getExperimentLabel () const
	returns the experiment label for this identification More...

void	setExperimentLabel (const String &type)
	sets the experiment label for this identification More...

void	assignRanks ()
	Sorts the hits by score and assigns ranks according to the scores. More...

void	sort ()
	Sorts the hits by score. More...

void	sortByRank ()
	Sorts the hits by rank. More...

bool	empty () const
	Returns if this PeptideIdentification result is empty. More...

const DataValue &	getMetaValue (const String &name) const

void	setMetaValue (const String &name, const DataValue &value)
	re-implemented from MetaValueInterface as a precaution against deprecated usage of "RT" and "MZ" values More...

Constructors, destructor, operators
	PeptideIdentification ()
	default constructor More...

virtual	~PeptideIdentification ()
	destructor More...

	PeptideIdentification (const PeptideIdentification &source)
	copy constructor More...

PeptideIdentification &	operator= (const PeptideIdentification &source)
	assignment operator More...

bool	operator== (const PeptideIdentification &rhs) const
	Equality operator. More...

bool	operator!= (const PeptideIdentification &rhs) const
	Inequality operator. More...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (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 DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or 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...

Static Public Member Functions
static std::vector< PeptideHit >	getReferencingHits (const std::vector< PeptideHit > &, const std::set< String > &accession)
	returns all peptide hits which reference to a given protein accession (i.e. filter by protein accession) More...

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Protected Attributes
String	id_
	Identifier by which ProteinIdentification and PeptideIdentification are matched. More...

std::vector< PeptideHit >	hits_
	A list containing the peptide hits. More...

double	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...

String	base_name_

double	mz_

double	rt_

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
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 corresponding 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 can be accessed using getRT() and getMZ(). 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

◆ HitType

typedef PeptideHit HitType

Hit type definition.

Constructor & Destructor Documentation

◆ PeptideIdentification() [1/2]

PeptideIdentification ( )

default constructor

◆ ~PeptideIdentification()

virtual ~PeptideIdentification ( )

virtual

destructor

◆ PeptideIdentification() [2/2]

PeptideIdentification ( const PeptideIdentification & source )

copy constructor

Member Function Documentation

◆ assignRanks()

void assignRanks ( )

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

Referenced by TOPPRNPxl::main_(), TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

◆ empty()

bool empty ( ) const

Returns if this PeptideIdentification result is empty.

◆ getBaseName()

const String& getBaseName ( ) const

returns the base name which links to underlying peak map

◆ getExperimentLabel()

const String getExperimentLabel ( ) const

returns the experiment label for this identification

◆ getHits() [1/2]

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

returns the peptide hits as const

Referenced by TOPPRNPxl::main_(), TOPPMetaProSIP::main_(), and IDMapper::mapPrecursorsToIdentifications().

◆ getHits() [2/2]

std::vector<PeptideHit>& getHits ( )

returns the peptide hits

◆ getIdentifier()

const String& getIdentifier ( ) const

returns the identifier

◆ getMetaValue()

const DataValue& getMetaValue ( const String & name ) const

remove the two helper functions below a some point, when we are sure that we did not miss or merge in deprecated code! re-implemented from MetaValueInterface as a precaution against deprecated usage of "RT" and "MZ" values

Referenced by TOPPOpenPepXL::main_().

◆ getMZ()

double getMZ ( ) const

returns the MZ of the MS2 spectrum

Referenced by IDMapper::mapPrecursorsToIdentifications().

◆ getReferencingHits()

static std::vector<PeptideHit> getReferencingHits	(	const std::vector< PeptideHit > &	,
		const std::set< String > &	accession
	)

static

returns all peptide hits which reference to a given protein accession (i.e. filter by protein accession)

◆ getRT()

double getRT ( ) const

returns the RT of the MS2 spectrum where the identification occurred

Referenced by IDMapper::mapPrecursorsToIdentifications().

◆ getScoreType()

const String& getScoreType ( ) const

returns the peptide score type

◆ getSignificanceThreshold()

double getSignificanceThreshold ( ) const

returns the peptide significance threshold value

◆ hasMZ()

bool hasMZ ( ) const

shortcut for isnan(getRT())

◆ hasRT()

bool hasRT ( ) const

shortcut for isnan(getRT())

◆ insertHit()

void insertHit ( const PeptideHit & hit )

Appends a peptide hit.

Referenced by TOPPMetaProSIP::main_().

◆ isHigherScoreBetter()

bool isHigherScoreBetter ( ) const

returns the peptide score orientation

◆ operator!=()

bool operator!= ( const PeptideIdentification & rhs ) const

Inequality operator.

◆ operator=()

PeptideIdentification& operator= ( const PeptideIdentification & source )

assignment operator

◆ operator==()

bool operator== ( const PeptideIdentification & rhs ) const

Equality operator.

◆ setBaseName()

void setBaseName ( const String & base_name )

sets the base name which links to underlying peak map

◆ setExperimentLabel()

void setExperimentLabel ( const String & type )

sets the experiment label for this identification

◆ setHigherScoreBetter()

void setHigherScoreBetter ( bool value )

sets the peptide score orientation

Referenced by TOPPRNPxl::main_(), TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

◆ setHits()

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

Sets the peptide hits.

Referenced by TOPPRNPxl::main_(), TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

◆ setIdentifier()

void setIdentifier ( const String & id )

sets the identifier

◆ setMetaValue()

void setMetaValue	(	const String &	name,
		const DataValue &	value
	)

re-implemented from MetaValueInterface as a precaution against deprecated usage of "RT" and "MZ" values

Referenced by RNPxlSearch::postProcessHits_().

◆ setMZ()

void setMZ ( double mz )

sets the MZ of the MS2 spectrum

Referenced by TOPPRNPxl::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

◆ setRT()

void setRT ( double rt )

sets the RT of the MS2 spectrum where the identification occurred

Referenced by TOPPRNPxl::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

◆ setScoreType()

void setScoreType ( const String & type )

sets the peptide score type

Referenced by SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

◆ setSignificanceThreshold()

void setSignificanceThreshold ( double value )

setting of the peptide significance threshold value

◆ sort()

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.

◆ sortByRank()

void sortByRank ( )

Sorts the hits by rank.

Sorting hits by rank attribute, i.e. after sorting, the hits will be in ascending order of rank.

Member Data Documentation

◆ base_name_

String base_name_

protected

◆ higher_score_better_

bool higher_score_better_

protected

The score orientation.

◆ hits_

std::vector<PeptideHit> hits_

protected

A list containing the peptide hits.

◆ id_

String id_

protected

Identifier by which ProteinIdentification and PeptideIdentification are matched.

◆ mz_

double mz_

protected

◆ rt_

double rt_

protected

◆ score_type_

String score_type_

protected

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

◆ significance_threshold_

double significance_threshold_

protected

the peptide significance threshold

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ HitType

Constructor & Destructor Documentation

◆ PeptideIdentification() [1/2]

◆ ~PeptideIdentification()

◆ PeptideIdentification() [2/2]

Member Function Documentation

◆ assignRanks()

◆ empty()

◆ getBaseName()

◆ getExperimentLabel()

◆ getHits() [1/2]

◆ getHits() [2/2]

◆ getIdentifier()

◆ getMetaValue()

◆ getMZ()

◆ getReferencingHits()

◆ getRT()

◆ getScoreType()

◆ getSignificanceThreshold()

◆ hasMZ()

◆ hasRT()

◆ insertHit()

◆ isHigherScoreBetter()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ setBaseName()

◆ setExperimentLabel()

◆ setHigherScoreBetter()

◆ setHits()

◆ setIdentifier()

◆ setMetaValue()

◆ setMZ()

◆ setRT()

◆ setScoreType()

◆ setSignificanceThreshold()

◆ sort()

◆ sortByRank()

Member Data Documentation

◆ base_name_

◆ higher_score_better_

◆ hits_

◆ id_

◆ mz_

◆ rt_

◆ score_type_

◆ significance_threshold_