Representation of a protein identification run. More...

#include <OpenMS/METADATA/ProteinIdentification.h>

Inheritance diagram for ProteinIdentification:

Collaboration diagram for ProteinIdentification:

Classes
struct	Mapping
	two way mapping from ms-run-path to protID\|pepID-identifier More...

class	ProteinGroup
	Bundles multiple (e.g. indistinguishable) proteins in a group. More...

struct	SearchParameters
	Search parameters of the DB search. More...

Public Types
enum	PeakMassType { MONOISOTOPIC , AVERAGE , SIZE_OF_PEAKMASSTYPE }
	Peak mass type. More...

typedef ProteinHit	HitType
	Hit type definition. More...

Public Member Functions
Constructors, destructors, assignment operator <br>
	ProteinIdentification ()
	Default constructor. More...

	ProteinIdentification (const ProteinIdentification &)=default
	Copy constructor. More...

	ProteinIdentification (ProteinIdentification &&)=default
	Move constructor. More...

virtual	~ProteinIdentification ()
	Destructor. More...

ProteinIdentification &	operator= (const ProteinIdentification &)=default
	Assignment operator. More...

ProteinIdentification &	operator= (ProteinIdentification &&)=default
	Move assignment operator. More...

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

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

Protein hit information (public members)
const std::vector< ProteinHit > &	getHits () const
	Returns the protein hits. More...

std::vector< ProteinHit > &	getHits ()
	Returns the protein hits (mutable) More...

void	insertHit (const ProteinHit &input)
	Appends a protein hit. More...

void	insertHit (ProteinHit &&input)
	Appends a protein hit. More...

void	setHits (const std::vector< ProteinHit > &hits)
	Sets the protein hits. More...

std::vector< ProteinHit >::iterator	findHit (const String &accession)
	Finds a protein hit by accession (returns past-the-end iterator if not found) More...

const std::vector< ProteinGroup > &	getProteinGroups () const
	Returns the protein groups. More...

std::vector< ProteinGroup > &	getProteinGroups ()
	Returns the protein groups (mutable) More...

void	insertProteinGroup (const ProteinGroup &group)
	Appends a new protein group. More...

const std::vector< ProteinGroup > &	getIndistinguishableProteins () const
	Returns the indistinguishable proteins. More...

std::vector< ProteinGroup > &	getIndistinguishableProteins ()
	Returns the indistinguishable proteins (mutable) More...

void	insertIndistinguishableProteins (const ProteinGroup &group)
	Appends new indistinguishable proteins. More...

void	fillIndistinguishableGroupsWithSingletons ()
	Appends singleton groups (with the current score) for every yet ungrouped protein hit. More...

double	getSignificanceThreshold () const
	Returns the protein significance threshold value. More...

void	setSignificanceThreshold (double value)
	Sets the protein significance threshold value. More...

const String &	getScoreType () const
	Returns the protein score type. More...

void	setScoreType (const String &type)
	Sets the protein score type. More...

bool	isHigherScoreBetter () const
	Returns true if a higher score represents a better score. More...

void	setHigherScoreBetter (bool higher_is_better)
	Sets the orientation of the score (is higher better?) More...

void	sort ()
	Sorts the protein hits according to their score. More...

void	assignRanks ()
	Sorts the protein hits by score and assigns ranks (best score has rank 1) More...

void	computeCoverage (const std::vector< PeptideIdentification > &pep_ids)
	Compute the coverage (in percent) of all ProteinHits given PeptideHits. More...

void	computeCoverage (const ConsensusMap &cmap, bool use_unassigned_ids)

void	computeModifications (const std::vector< PeptideIdentification > &pep_ids, const StringList &skip_modifications)
	Compute the modifications of all ProteinHits given PeptideHits. More...

void	computeModifications (const ConsensusMap &cmap, const StringList &skip_modifications, bool use_unassigned_ids)

General information
const DateTime &	getDateTime () const
	Returns the date of the protein identification run. More...

void	setDateTime (const DateTime &date)
	Sets the date of the protein identification run. More...

void	setSearchEngine (const String &search_engine)
	Sets the search engine type. More...

const String &	getSearchEngine () const
	Returns the type of search engine used. More...

const String	getOriginalSearchEngineName () const
	Return the type of search engine that was first applied (e.g., before percolator or consensusID) or "Unknown". More...

void	setSearchEngineVersion (const String &search_engine_version)
	Sets the search engine version. More...

const String &	getSearchEngineVersion () const
	Returns the search engine version. More...

void	setInferenceEngine (const String &search_engine)
	Sets the inference engine type. More...

const String	getInferenceEngine () const
	Returns the type of search engine used. More...

void	setInferenceEngineVersion (const String &inference_engine_version)
	Sets the search engine version. More...

const String	getInferenceEngineVersion () const
	Returns the search engine version. More...

void	setSearchParameters (const SearchParameters &search_parameters)
	Sets the search parameters. More...

void	setSearchParameters (SearchParameters &&search_parameters)
	Sets the search parameters (move) More...

const SearchParameters &	getSearchParameters () const
	Returns the search parameters. More...

SearchParameters &	getSearchParameters ()
	Returns the search parameters (mutable) More...

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

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

void	setPrimaryMSRunPath (const StringList &s, bool raw=false)

void	setPrimaryMSRunPath (const StringList &s, MSExperiment &e)
	set the file path to the primary MS run but try to use the mzML annotated in the MSExperiment. More...

void	addPrimaryMSRunPath (const String &s, bool raw=false)

void	addPrimaryMSRunPath (const StringList &s, bool raw=false)

void	getPrimaryMSRunPath (StringList &output, bool raw=false) const

Size	nrPrimaryMSRunPaths (bool raw=false) const
	get the number of primary MS runs involve in this ID run More...

bool	hasInferenceData () const

bool	hasInferenceEngineAsSearchEngine () const
	Checks if the search engine name matches an inference engine known to OpenMS. More...

bool	peptideIDsMergeable (const ProteinIdentification &id_run, const String &experiment_type) const

std::vector< std::pair< String, String > >	getSearchEngineSettingsAsPairs (const String &se="") const

void	copyMetaDataOnly (const ProteinIdentification &)
	Copies only metadata (no protein hits or protein groups) 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...

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 DataValue &	getMetaValue (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 DataValue &	getMetaValue (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...

Static Public Attributes
static const std::string	NamesOfPeakMassType [SIZE_OF_PEAKMASSTYPE]
	Names corresponding to peak mass types. More...

Protected Attributes
General information (search engine, parameters and database)
String	id_

String	search_engine_

String	search_engine_version_

SearchParameters	search_parameters_

DateTime	date_

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

Protein hit information (protected members)
String	protein_score_type_

bool	higher_score_better_

std::vector< ProteinHit >	protein_hits_

std::vector< ProteinGroup >	protein_groups_

std::vector< ProteinGroup >	indistinguishable_proteins_
	Indistinguishable proteins: `accessions`[0] is "group leader", `probability` is meaningless. More...

double	protein_significance_threshold_

void	computeCoverageFromEvidenceMapping_ (const std::unordered_map< String, std::set< PeptideEvidence >> &map)

void	fillEvidenceMapping_ (std::unordered_map< String, std::set< PeptideEvidence > > &map_acc_2_evidence, const std::vector< PeptideIdentification > &pep_ids) const

void	fillModMapping_ (const std::vector< PeptideIdentification > &pep_ids, const StringList &skip_modifications, std::unordered_map< String, std::set< std::pair< Size, ResidueModification >>> &prot2mod) const

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 protein identification run.

This class stores the general information and the protein hits of a protein identification run.

The actual peptide hits are stored in PeptideIdentification instances that are part of spectra or features.

In order to be able to connect the ProteinIdentification and the corresponding peptide identifications, both classes have a string identifier. We recommend using the search engine name and the date as identifier. Setting this identifier is especially important when there are several protein identification runs for a map, i.e. several ProteinIdentification instances.

Todo:: Add MetaInfoInterface to modifications => update IdXMLFile and ProteinIdentificationVisualizer (Andreas)

Member Typedef Documentation

◆ HitType

typedef ProteinHit HitType

Hit type definition.

Member Enumeration Documentation

◆ PeakMassType

enum PeakMassType

Peak mass type.

Enumerator
MONOISOTOPIC
AVERAGE
SIZE_OF_PEAKMASSTYPE

Constructor & Destructor Documentation

◆ ProteinIdentification() [1/3]

ProteinIdentification ( )

Default constructor.

◆ ProteinIdentification() [2/3]

ProteinIdentification ( const ProteinIdentification & )

default

Copy constructor.

◆ ProteinIdentification() [3/3]

ProteinIdentification ( ProteinIdentification && )

default

Move constructor.

◆ ~ProteinIdentification()

virtual ~ProteinIdentification ( )

virtual

Destructor.

Member Function Documentation

◆ addPrimaryMSRunPath() [1/2]

void addPrimaryMSRunPath	(	const String &	s,
		bool	raw = `false`
	)

◆ addPrimaryMSRunPath() [2/2]

void addPrimaryMSRunPath	(	const StringList &	s,
		bool	raw = `false`
	)

◆ assignRanks()

void assignRanks ( )

Sorts the protein hits by score and assigns ranks (best score has rank 1)

◆ computeCoverage() [1/2]

void computeCoverage	(	const ConsensusMap &	cmap,
		bool	use_unassigned_ids
	)

◆ computeCoverage() [2/2]

void computeCoverage ( const std::vector< PeptideIdentification > & pep_ids )

Compute the coverage (in percent) of all ProteinHits given PeptideHits.

Exceptions

Exception::MissingInformation if ProteinsHits do not have sequence information

Does not return anything but stores the coverage inside the ProteinHit objects

◆ computeCoverageFromEvidenceMapping_()

void computeCoverageFromEvidenceMapping_ ( const std::unordered_map< String, std::set< PeptideEvidence >> & map )

private

◆ computeModifications() [1/2]

void computeModifications	(	const ConsensusMap &	cmap,
		const StringList &	skip_modifications,
		bool	use_unassigned_ids
	)

◆ computeModifications() [2/2]

void computeModifications	(	const std::vector< PeptideIdentification > &	pep_ids,
		const StringList &	skip_modifications
	)

Compute the modifications of all ProteinHits given PeptideHits.

For every protein accession, the pair of position and modification is returned. Because fixed modifications might not be of interest, a list can be provided to skip those.

◆ copyMetaDataOnly()

void copyMetaDataOnly ( const ProteinIdentification & )

Copies only metadata (no protein hits or protein groups)

◆ fillEvidenceMapping_()

void fillEvidenceMapping_	(	std::unordered_map< String, std::set< PeptideEvidence > > &	map_acc_2_evidence,
		const std::vector< PeptideIdentification > &	pep_ids
	)		const

private

◆ fillIndistinguishableGroupsWithSingletons()

void fillIndistinguishableGroupsWithSingletons ( )

Appends singleton groups (with the current score) for every yet ungrouped protein hit.

◆ fillModMapping_()

void fillModMapping_	(	const std::vector< PeptideIdentification > &	pep_ids,
		const StringList &	skip_modifications,
		std::unordered_map< String, std::set< std::pair< Size, ResidueModification >>> &	prot2mod
	)		const

private

◆ findHit()

std::vector<ProteinHit>::iterator findHit ( const String & accession )

Finds a protein hit by accession (returns past-the-end iterator if not found)

◆ getDateTime()

const DateTime& getDateTime ( ) const

Returns the date of the protein identification run.

◆ getHits() [1/2]

std::vector<ProteinHit>& getHits ( )

Returns the protein hits (mutable)

◆ getHits() [2/2]

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

Returns the protein hits.

◆ getIdentifier()

const String& getIdentifier ( ) const

Returns the identifier.

◆ getIndistinguishableProteins() [1/2]

std::vector<ProteinGroup>& getIndistinguishableProteins ( )

Returns the indistinguishable proteins (mutable)

◆ getIndistinguishableProteins() [2/2]

const std::vector<ProteinGroup>& getIndistinguishableProteins ( ) const

Returns the indistinguishable proteins.

◆ getInferenceEngine()

const String getInferenceEngine ( ) const

Returns the type of search engine used.

◆ getInferenceEngineVersion()

const String getInferenceEngineVersion ( ) const

Returns the search engine version.

◆ getOriginalSearchEngineName()

const String getOriginalSearchEngineName ( ) const

Return the type of search engine that was first applied (e.g., before percolator or consensusID) or "Unknown".

◆ getPrimaryMSRunPath()

void getPrimaryMSRunPath	(	StringList &	output,
		bool	raw = `false`
	)		const

Get the file paths to the primary MS runs

Parameters

[out]	output	The file paths
	raw	Get raw files (or equivalent) instead of mzMLs

◆ getProteinGroups() [1/2]

std::vector<ProteinGroup>& getProteinGroups ( )

Returns the protein groups (mutable)

◆ getProteinGroups() [2/2]

const std::vector<ProteinGroup>& getProteinGroups ( ) const

Returns the protein groups.

◆ getScoreType()

const String& getScoreType ( ) const

Returns the protein score type.

◆ getSearchEngine()

const String& getSearchEngine ( ) const

Returns the type of search engine used.

◆ getSearchEngineSettingsAsPairs()

std::vector<std::pair<String,String> > getSearchEngineSettingsAsPairs ( const String & se = "" ) const

Collects all search engine settings registered for the given search engine se. If se is empty, the main search engine is used, otherwise it will also search the metavalues.

◆ getSearchEngineVersion()

const String& getSearchEngineVersion ( ) const

Returns the search engine version.

◆ getSearchParameters() [1/2]

SearchParameters& getSearchParameters ( )

Returns the search parameters (mutable)

◆ getSearchParameters() [2/2]

const SearchParameters& getSearchParameters ( ) const

Returns the search parameters.

◆ getSignificanceThreshold()

double getSignificanceThreshold ( ) const

Returns the protein significance threshold value.

◆ hasInferenceData()

bool hasInferenceData ( ) const

Checks if this object has inference data. Looks for "InferenceEngine" metavalue. If not, falls back to old behaviour of reading the search engine name.

◆ hasInferenceEngineAsSearchEngine()

bool hasInferenceEngineAsSearchEngine ( ) const

Checks if the search engine name matches an inference engine known to OpenMS.

◆ insertHit() [1/2]

void insertHit ( const ProteinHit & input )

Appends a protein hit.

◆ insertHit() [2/2]

void insertHit ( ProteinHit && input )

Appends a protein hit.

◆ insertIndistinguishableProteins()

void insertIndistinguishableProteins ( const ProteinGroup & group )

Appends new indistinguishable proteins.

◆ insertProteinGroup()

void insertProteinGroup ( const ProteinGroup & group )

Appends a new protein group.

◆ isHigherScoreBetter()

bool isHigherScoreBetter ( ) const

Returns true if a higher score represents a better score.

◆ nrPrimaryMSRunPaths()

Size nrPrimaryMSRunPaths ( bool raw = false ) const

get the number of primary MS runs involve in this ID run

◆ operator!=()

bool operator!= ( const ProteinIdentification & rhs ) const

Inequality operator.

◆ operator=() [1/2]

ProteinIdentification& operator= ( const ProteinIdentification & )

default

Assignment operator.

◆ operator=() [2/2]

ProteinIdentification& operator= ( ProteinIdentification && )

default

Move assignment operator.

◆ operator==()

bool operator== ( const ProteinIdentification & rhs ) const

Equality operator.

◆ peptideIDsMergeable()

bool peptideIDsMergeable	(	const ProteinIdentification &	id_run,
		const String &	experiment_type
	)		const

Checks if the peptide IDs of this IDRun are mergeable with another id_run given an experiment_type . Checks search engine and search engine settings.

◆ setDateTime()

void setDateTime ( const DateTime & date )

Sets the date of the protein identification run.

◆ setHigherScoreBetter()

void setHigherScoreBetter ( bool higher_is_better )

Sets the orientation of the score (is higher better?)

◆ setHits()

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

Sets the protein hits.

Note: This may invalidate (indistinguishable) protein groups! If necessary, use e.g. IDFilter::updateProteinGroups to update the groupings.

◆ setIdentifier()

void setIdentifier ( const String & id )

Sets the identifier.

◆ setInferenceEngine()

void setInferenceEngine ( const String & search_engine )

Sets the inference engine type.

◆ setInferenceEngineVersion()

void setInferenceEngineVersion ( const String & inference_engine_version )

Sets the search engine version.

◆ setPrimaryMSRunPath() [1/2]

void setPrimaryMSRunPath	(	const StringList &	s,
		bool	raw = `false`
	)

Set the file paths to the primary MS runs (usually the mzML files obtained after data conversion from raw files)

Parameters

s	The file paths
raw	Store paths to the raw files (or equivalent) rather than mzMLs

◆ setPrimaryMSRunPath() [2/2]

void setPrimaryMSRunPath	(	const StringList &	s,
		MSExperiment &	e
	)

set the file path to the primary MS run but try to use the mzML annotated in the MSExperiment.

◆ setScoreType()

void setScoreType ( const String & type )

Sets the protein score type.

◆ setSearchEngine()

void setSearchEngine ( const String & search_engine )

Sets the search engine type.

◆ setSearchEngineVersion()

void setSearchEngineVersion ( const String & search_engine_version )

Sets the search engine version.

◆ setSearchParameters() [1/2]

void setSearchParameters ( const SearchParameters & search_parameters )

Sets the search parameters.

◆ setSearchParameters() [2/2]

void setSearchParameters ( SearchParameters && search_parameters )

Sets the search parameters (move)

◆ setSignificanceThreshold()

void setSignificanceThreshold ( double value )

Sets the protein significance threshold value.

◆ sort()

void sort ( )

Sorts the protein hits according to their score.

Member Data Documentation

◆ date_

DateTime date_

protected

◆ higher_score_better_

bool higher_score_better_

protected

◆ id_

String id_

protected

◆ indistinguishable_proteins_

std::vector<ProteinGroup> indistinguishable_proteins_

protected

Indistinguishable proteins: accessions[0] is "group leader", probability is meaningless.

◆ NamesOfPeakMassType

const std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE]

static

Names corresponding to peak mass types.

◆ protein_groups_

std::vector<ProteinGroup> protein_groups_

protected

◆ protein_hits_

std::vector<ProteinHit> protein_hits_

protected

◆ protein_score_type_

String protein_score_type_

protected

◆ protein_significance_threshold_

double protein_significance_threshold_

protected

◆ search_engine_

String search_engine_

protected

◆ search_engine_version_

String search_engine_version_

protected

◆ search_parameters_

SearchParameters search_parameters_

protected

Classes

Public Types

Public Member Functions

Static Public Attributes

Protected Attributes

Protein hit information (protected members)

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ HitType

Member Enumeration Documentation

◆ PeakMassType

Constructor & Destructor Documentation

◆ ProteinIdentification() [1/3]

◆ ProteinIdentification() [2/3]

◆ ProteinIdentification() [3/3]

◆ ~ProteinIdentification()

Member Function Documentation

◆ addPrimaryMSRunPath() [1/2]

◆ addPrimaryMSRunPath() [2/2]

◆ assignRanks()

◆ computeCoverage() [1/2]

◆ computeCoverage() [2/2]

◆ computeCoverageFromEvidenceMapping_()

◆ computeModifications() [1/2]

◆ computeModifications() [2/2]

◆ copyMetaDataOnly()

◆ fillEvidenceMapping_()

◆ fillIndistinguishableGroupsWithSingletons()

◆ fillModMapping_()

◆ findHit()

◆ getDateTime()

◆ getHits() [1/2]

◆ getHits() [2/2]

◆ getIdentifier()

◆ getIndistinguishableProteins() [1/2]

◆ getIndistinguishableProteins() [2/2]

◆ getInferenceEngine()

◆ getInferenceEngineVersion()

◆ getOriginalSearchEngineName()

◆ getPrimaryMSRunPath()

◆ getProteinGroups() [1/2]

◆ getProteinGroups() [2/2]

◆ getScoreType()

◆ getSearchEngine()

◆ getSearchEngineSettingsAsPairs()

◆ getSearchEngineVersion()

◆ getSearchParameters() [1/2]

◆ getSearchParameters() [2/2]

◆ getSignificanceThreshold()

◆ hasInferenceData()

◆ hasInferenceEngineAsSearchEngine()

◆ insertHit() [1/2]

◆ insertHit() [2/2]

◆ insertIndistinguishableProteins()

◆ insertProteinGroup()

◆ isHigherScoreBetter()

◆ nrPrimaryMSRunPaths()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ peptideIDsMergeable()

◆ setDateTime()

◆ setHigherScoreBetter()

◆ setHits()

◆ setIdentifier()

◆ setInferenceEngine()

◆ setInferenceEngineVersion()

◆ setPrimaryMSRunPath() [1/2]

◆ setPrimaryMSRunPath() [2/2]

◆ setScoreType()

◆ setSearchEngine()

◆ setSearchEngineVersion()

◆ setSearchParameters() [1/2]

◆ setSearchParameters() [2/2]

◆ setSignificanceThreshold()

◆ sort()

Member Data Documentation

◆ date_