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...
enum	DigestionEnzyme { TRYPSIN, PEPSIN_A, PROTEASE_K, CHYMOTRYPSIN, NO_ENZYME, UNKNOWN_ENZYME, SIZE_OF_DIGESTIONENZYME }
typedef ProteinHit	HitType
	Hit type definition.
Public Member Functions
Constructors, destructors, assignment operator <br>

	ProteinIdentification ()
	Default constructor.
virtual	~ProteinIdentification ()
	Destructor.
	ProteinIdentification (const ProteinIdentification &source)
	Copy constructor.
ProteinIdentification &	operator= (const ProteinIdentification &source)
	Assignment operator.
bool	operator== (const ProteinIdentification &rhs) const
	Equality operator.
bool	operator!= (const ProteinIdentification &rhs) const
	Inequality operator.
Protein hit information (public members)

const std::vector< ProteinHit > &	getHits () const
	Returns the protein hits.
std::vector< ProteinHit > &	getHits ()
	Returns the protein hits (mutable).
void	insertHit (const ProteinHit &input)
	Appends a protein hit.
void	setHits (const std::vector< ProteinHit > &hits)
	Sets the protein hits.
std::vector< ProteinHit >::iterator	findHit (const String &accession)
	Finds a protein hit by accession (returns past-the-end iterator if not found).
const std::vector< ProteinGroup > &	getProteinGroups () const
	Returns the protein groups.
std::vector< ProteinGroup > &	getProteinGroups ()
	Returns the protein groups (mutable).
void	insertProteinGroup (const ProteinGroup &group)
	Appends a new protein group.
const std::vector< ProteinGroup > &	getIndistinguishableProteins () const
	Returns the indistinguishable proteins.
std::vector< ProteinGroup > &	getIndistinguishableProteins ()
	Returns the indistinguishable proteins (mutable).
void	insertIndistinguishableProteins (const ProteinGroup &group)
	Appends new indistinguishable proteins.
DoubleReal	getSignificanceThreshold () const
	Returns the protein significance threshold value.
void	setSignificanceThreshold (DoubleReal value)
	Sets the protein significance threshold value.
const String &	getScoreType () const
	Returns the protein score type.
void	setScoreType (const String &type)
	Sets the protein score type.
bool	isHigherScoreBetter () const
	Returns true if a higher score represents a better score.
void	setHigherScoreBetter (bool higher_is_better)
	Sets the orientation of the score (is higher better?).
void	sort ()
	Sorts the protein hits according to their score.
void	assignRanks ()
	Sorts the protein hits by score and assigns ranks (best score has rank 1).
Size	computeCoverage (const std::vector< PeptideIdentification > &pep_ids)
	Compute the coverage (in percent) of all ProteinHits given PeptideHits.
General information

const DateTime &	getDateTime () const
	Returns the date of the protein identification run.
void	setDateTime (const DateTime &date)
	Sets the date of the protein identification run.
void	setSearchEngine (const String &search_engine)
	Sets the search engine type.
const String &	getSearchEngine () const
	Returns the type of search engine used.
void	setSearchEngineVersion (const String &search_engine_version)
	Sets the search engine version.
const String &	getSearchEngineVersion () const
	Returns the search engine version.
void	setSearchParameters (const SearchParameters &search_parameters)
	Sets the search parameters.
const SearchParameters &	getSearchParameters () const
	Returns the search parameters.
const String &	getIdentifier () const
	Returns the identifier.
void	setIdentifier (const String &id)
	Sets the identifier.
Static Public Attributes
static const std::string	NamesOfPeakMassType [SIZE_OF_PEAKMASSTYPE]
	Names corresponding to peak mass types.
static const std::string	NamesOfDigestionEnzyme [SIZE_OF_DIGESTIONENZYME]
	Names corresponding to digestion enzymes.
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.
DoubleReal	protein_significance_threshold_

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

typedef ProteinHit HitType

Hit type definition.

Member Enumeration Documentation

enum DigestionEnzyme

Enumerator:

TRYPSIN
PEPSIN_A
PROTEASE_K
CHYMOTRYPSIN
NO_ENZYME
UNKNOWN_ENZYME
SIZE_OF_DIGESTIONENZYME

enum PeakMassType

Peak mass type.

Enumerator:

MONOISOTOPIC
AVERAGE
SIZE_OF_PEAKMASSTYPE

Constructor & Destructor Documentation

ProteinIdentification ( )

Default constructor.

virtual ~ProteinIdentification ( ) [virtual]

Destructor.

ProteinIdentification ( const ProteinIdentification & source )

Copy constructor.

Member Function Documentation

void assignRanks ( )

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

Size 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

Returns:: The number of Proteins referenced by the pep_ids that are not contained in this ProteinIdentification set (should be 0)

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

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

const DateTime& getDateTime ( ) const

Returns the date of the protein identification run.

std::vector<ProteinHit>& getHits ( )

Returns the protein hits (mutable).

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

Returns the protein hits.

Referenced by IDFilter::filterIdentificationsByBestNHits(), IDFilter::filterIdentificationsByScores(), and IDFilter::filterIdentificationsByThresholds().

const String& getIdentifier ( ) const

Returns the identifier.

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

Returns the indistinguishable proteins.

std::vector<ProteinGroup>& getIndistinguishableProteins ( )

Returns the indistinguishable proteins (mutable).

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

Returns the protein groups.

std::vector<ProteinGroup>& getProteinGroups ( )

Returns the protein groups (mutable).

const String& getScoreType ( ) const

Returns the protein score type.

const String& getSearchEngine ( ) const

Returns the type of search engine used.

const String& getSearchEngineVersion ( ) const

Returns the search engine version.

const SearchParameters& getSearchParameters ( ) const

Returns the search parameters.

Referenced by DBAdapter::loadExperiment().

DoubleReal getSignificanceThreshold ( ) const

Returns the protein significance threshold value.

void insertHit ( const ProteinHit & input )

Appends a protein hit.

void insertIndistinguishableProteins ( const ProteinGroup & group )

Appends new indistinguishable proteins.

void insertProteinGroup ( const ProteinGroup & group )

Appends a new protein group.

bool isHigherScoreBetter ( ) const

Returns true if a higher score represents a better score.

bool operator!= ( const ProteinIdentification & rhs ) const

Inequality operator.

ProteinIdentification& operator= ( const ProteinIdentification & source )

Assignment operator.

bool operator== ( const ProteinIdentification & rhs ) const

Equality operator.

void setDateTime ( const DateTime & date )

Sets the date of the protein identification run.

Referenced by DBAdapter::loadExperiment().

void setHigherScoreBetter ( bool higher_is_better )

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

Referenced by DBAdapter::loadExperiment().

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

Sets the protein hits.

Referenced by DBAdapter::loadExperiment(), and MRMFeatureFinderScoring::pickExperiment().

void setIdentifier ( const String & id )

Sets the identifier.

Referenced by MRMFeatureFinderScoring::pickExperiment().

void setScoreType ( const String & type )

Sets the protein score type.

Referenced by DBAdapter::loadExperiment().

void setSearchEngine ( const String & search_engine )

Sets the search engine type.

Referenced by DBAdapter::loadExperiment().

void setSearchEngineVersion ( const String & search_engine_version )

Sets the search engine version.

Referenced by DBAdapter::loadExperiment().

void setSearchParameters ( const SearchParameters & search_parameters )

Sets the search parameters.

Referenced by DBAdapter::loadExperiment().

void setSignificanceThreshold ( DoubleReal value )

Sets the protein significance threshold value.

Referenced by DBAdapter::loadExperiment().

void sort ( )

Sorts the protein hits according to their score.

Member Data Documentation

DateTime date_ [protected]

bool higher_score_better_ [protected]

String id_ [protected]

std::vector<ProteinGroup> indistinguishable_proteins_ [protected]

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

const std::string NamesOfDigestionEnzyme[SIZE_OF_DIGESTIONENZYME] [static]

Names corresponding to digestion enzymes.

const std::string NamesOfPeakMassType[SIZE_OF_PEAKMASSTYPE] [static]

Names corresponding to peak mass types.

std::vector<ProteinGroup> protein_groups_ [protected]

std::vector<ProteinHit> protein_hits_ [protected]

String protein_score_type_ [protected]

DoubleReal protein_significance_threshold_ [protected]

String search_engine_ [protected]

String search_engine_version_ [protected]

SearchParameters search_parameters_ [protected]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1

ProteinIdentification Class Reference [Metadata]

Classes

Public Types

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

ProteinIdentification Class Reference
[Metadata]