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ProteinIdentification Class Reference

Representation of a protein identification run. More...

#include <OpenMS/METADATA/ProteinIdentification.h>

Inheritance diagram for ProteinIdentification:
MetaInfoInterface

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. More...
 

Public Member Functions

Constructors, destructors, assignment operator <br>
 ProteinIdentification ()
 Default constructor. More...
 
virtual ~ProteinIdentification ()
 Destructor. More...
 
 ProteinIdentification (const ProteinIdentification &source)
 Copy constructor. More...
 
ProteinIdentificationoperator= (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 StringgetScoreType () 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...
 
Size computeCoverage (const std::vector< PeptideIdentification > &pep_ids)
 Compute the coverage (in percent) of all ProteinHits given PeptideHits. More...
 
General information
const DateTimegetDateTime () 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 StringgetSearchEngine () const
 Returns the type of search engine used. More...
 
void setSearchEngineVersion (const String &search_engine_version)
 Sets the search engine version. More...
 
const StringgetSearchEngineVersion () const
 Returns the search engine version. More...
 
void setSearchParameters (const SearchParameters &search_parameters)
 Sets the search parameters. More...
 
const SearchParametersgetSearchParameters () const
 Returns the search parameters. More...
 
const StringgetIdentifier () const
 Returns the identifier. More...
 
void setIdentifier (const String &id)
 Sets the identifier. More...
 
- 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...
 

Static Public Attributes

static const std::string NamesOfPeakMassType [SIZE_OF_PEAKMASSTYPE]
 Names corresponding to peak mass types. More...
 
static const std::string NamesOfDigestionEnzyme [SIZE_OF_DIGESTIONENZYME]
 Names corresponding to digestion enzymes. 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< ProteinHitprotein_hits_
 
std::vector< ProteinGroupprotein_groups_
 
std::vector< ProteinGroupindistinguishable_proteins_
 Indistinguishable proteins: accessions[0] is "group leader", probability is meaningless. More...
 
double protein_significance_threshold_
 
- 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 ()
 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

Hit type definition.

Constructor & Destructor Documentation

Default constructor.

virtual ~ProteinIdentification ( )
virtual

Destructor.

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::MissingInformationif 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.

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

Returns the protein hits (mutable)

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.

double 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.

void setHigherScoreBetter ( bool  higher_is_better)

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

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.
void setIdentifier ( const String id)

Sets the identifier.

void setScoreType ( const String type)

Sets the protein score type.

void setSearchEngine ( const String search_engine)

Sets the search engine type.

void setSearchEngineVersion ( const String search_engine_version)

Sets the search engine version.

void setSearchParameters ( const SearchParameters search_parameters)

Sets the search parameters.

void setSignificanceThreshold ( double  value)

Sets the protein significance threshold value.

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
double protein_significance_threshold_
protected
String search_engine_
protected
String search_engine_version_
protected
SearchParameters search_parameters_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:06 using doxygen 1.8.9.1