ProteinIdentification Class Reference

Representation of a protein identification run. More...

#include <OpenMS/METADATA/ProteinIdentification.h>

Inheritance diagram for ProteinIdentification:

Classes
struct	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...
virtual	~ProteinIdentification ()
	Destructor. More...
	ProteinIdentification (const ProteinIdentification &source)
	Copy constructor. More...
ProteinIdentification &	operator= (const ProteinIdentification &source)
	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	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...
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...
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...
void	setSearchEngineVersion (const String &search_engine_version)
	Sets the search engine version. More...
const String &	getSearchEngineVersion () const
	Returns the search engine version. More...
void	setSearchParameters (const SearchParameters &search_parameters)
	Sets the search parameters. More...
const SearchParameters &	getSearchParameters () const
	Returns the search parameters. More...
const String &	getIdentifier () const
	Returns the identifier. More...
void	setIdentifier (const String &id)
	Sets the identifier. More...
void	setPrimaryMSRunPath (const StringList &s)
	set the file path to the primary MS run (usually the mzML file obtained after data conversion from raw files) More...
void	getPrimaryMSRunPath (StringList &toFill) const
	get the file path to the first MS run 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 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_
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_
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 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() [1/2]

ProteinIdentification

(

)

Default constructor.

~ProteinIdentification()

virtual ~ProteinIdentification ( )

virtual

Destructor.

ProteinIdentification() [2/2]

ProteinIdentification

(

const ProteinIdentification &

source

)

Copy constructor.

Member Function Documentation

assignRanks()

void assignRanks

(

)

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

computeCoverage()

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

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]

const std::vector<ProteinHit>& getHits

(

)

const

Returns the protein hits.

getHits() [2/2]

std::vector<ProteinHit>& getHits

(

)

Returns the protein hits (mutable)

getIdentifier()

const String& getIdentifier

(

)

const

Returns the identifier.

getIndistinguishableProteins() [1/2]

const std::vector<ProteinGroup>& getIndistinguishableProteins

(

)

const

Returns the indistinguishable proteins.

getIndistinguishableProteins() [2/2]

std::vector<ProteinGroup>& getIndistinguishableProteins

(

)

Returns the indistinguishable proteins (mutable)

getPrimaryMSRunPath()

void getPrimaryMSRunPath

(

StringList &

toFill

)

const

get the file path to the first MS run

getProteinGroups() [1/2]

const std::vector<ProteinGroup>& getProteinGroups

(

)

const

Returns the protein groups.

getProteinGroups() [2/2]

std::vector<ProteinGroup>& getProteinGroups

(

)

Returns the protein groups (mutable)

getScoreType()

const String& getScoreType

(

)

const

Returns the protein score type.

getSearchEngine()

const String& getSearchEngine

(

)

const

Returns the type of search engine used.

getSearchEngineVersion()

const String& getSearchEngineVersion

(

)

const

Returns the search engine version.

getSearchParameters()

const SearchParameters& getSearchParameters

(

)

const

Returns the search parameters.

getSignificanceThreshold()

double getSignificanceThreshold

(

)

const

Returns the protein significance threshold value.

insertHit()

void insertHit

(

const 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.

operator!=()

bool operator!=

(

const ProteinIdentification &

rhs

)

const

Inequality operator.

operator=()

ProteinIdentification& operator=

(

const ProteinIdentification &

source

)

Assignment operator.

operator==()

bool operator==

(

const ProteinIdentification &

rhs

)

const

Equality operator.

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.

setPrimaryMSRunPath()

void setPrimaryMSRunPath

(

const StringList &

s

)

set the file path to the primary MS run (usually the mzML file obtained after data conversion from raw files)

Referenced by TOPPRNPxl::main_().

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()

void setSearchParameters

(

const SearchParameters &

search_parameters

)

Sets the search parameters.

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