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ProteinIdentification Class Reference
[Metadata]

#include <OpenMS/METADATA/ProteinIdentification.h>

Inheritance diagram for ProteinIdentification:

MetaInfoInterface

List of all members.


Detailed Description

Representation of a peptide/protein ProteinIdentification.

This class stores the general information and the protein hits of an ProteinIdentification 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 ProteinIdentification runs for a map i.e. several ProteinIdentification instances.

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
ProteinIdentificationoperator= (const ProteinIdentification &source)
 assignment operator
bool operator== (const ProteinIdentification &rhs) const
 Equality operator.
bool operator!= (const ProteinIdentification &rhs) const
 Inequality operator.
Protein hit information
const std::vector< ProteinHit > & getHits () const
 returns the protein hits
void insertHit (const ProteinHit &input)
 Appends a protein hit.
void setHits (const std::vector< ProteinHit > &hits)
 Sets the peptide and protein hits.
Real getSignificanceThreshold () const
 returns the peptide significance threshold value
void setSignificanceThreshold (Real value)
 setting of the peptide significance threshold value
const StringgetScoreType () 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 (higher is better?)
void sort ()
 sorts the peptide and protein hits according to their score
void assignRanks ()
 sorts the peptide hits and assigns ranks according to the sorting
General information
const DateTimegetDateTime () const
 returns the date of the ProteinIdentification
void setDateTime (const DateTime &date)
 sets the date of the ProteinIdentification
void setSearchEngine (const String &search_engine)
 sets the search engine type
const StringgetSearchEngine () const
 returns the type of search engine used
void setSearchEngineVersion (const String &search_engine_version)
 sets the search engine version
const StringgetSearchEngineVersion () const
 returns the search engine version
void setSearchParameters (const SearchParameters &search_parameters)
 sets the search parameters
const SearchParametersgetSearchParameters () const
 returns the search parameters
const StringgetIdentifier () const
 returns the identifier
void setIdentifier (const String &id)
 sets the indentifier

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 DB)
String id_
String search_engine_
String search_engine_version_
SearchParameters search_parameters_
DateTime date_
Protein hit information
String protein_score_type_
bool higher_score_better_
std::vector< ProteinHitprotein_hits_
Real protein_significance_threshold_

Classes

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


Member Typedef Documentation

typedef ProteinHit HitType

Hit type definition.


Member Enumeration Documentation

enum PeakMassType

Peak mass type.

Enumerator:
MONOISOTOPIC 
AVERAGE 
SIZE_OF_PEAKMASSTYPE 

enum DigestionEnzyme

Enumerator:
TRYPSIN 
PEPSIN_A 
PROTEASE_K 
CHYMOTRYPSIN 
NO_ENZYME 
UNKNOWN_ENZYME 
SIZE_OF_DIGESTIONENZYME 


Constructor & Destructor Documentation

ProteinIdentification (  ) 

default constructor

virtual ~ProteinIdentification (  )  [virtual]

destructor

ProteinIdentification ( const ProteinIdentification source  ) 

copy constructor


Member Function Documentation

ProteinIdentification& operator= ( const ProteinIdentification source  ) 

assignment operator

bool operator== ( const ProteinIdentification rhs  )  const

Equality operator.

bool operator!= ( const ProteinIdentification rhs  )  const

Inequality operator.

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

returns the protein hits

void insertHit ( const ProteinHit input  ) 

Appends a protein hit.

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

Sets the peptide and protein hits.

Real getSignificanceThreshold (  )  const

returns the peptide significance threshold value

void setSignificanceThreshold ( Real  value  ) 

setting of the peptide 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 (higher is better?)

void sort (  ) 

sorts the peptide and protein hits according to their score

void assignRanks (  ) 

sorts the peptide hits and assigns ranks according to the sorting

const DateTime& getDateTime (  )  const

returns the date of the ProteinIdentification

void setDateTime ( const DateTime date  ) 

sets the date of the ProteinIdentification

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 indentifier


Member Data Documentation

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

Names corresponding to peak mass types.

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

Names corresponding to digestion enzymes.

String id_ [protected]

String search_engine_ [protected]

String search_engine_version_ [protected]

SearchParameters search_parameters_ [protected]

DateTime date_ [protected]

String protein_score_type_ [protected]

bool higher_score_better_ [protected]

std::vector<ProteinHit> protein_hits_ [protected]

Real protein_significance_threshold_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:47 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1