#include <OpenMS/METADATA/ProteinIdentification.h>
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 | |
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 | |
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 | |
General information | |
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 | |
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< ProteinHit > | protein_hits_ |
Real | protein_significance_threshold_ |
Classes | |
struct | SearchParameters |
Search parameters of the DB search. More... |
typedef ProteinHit HitType |
Hit type definition.
enum PeakMassType |
enum DigestionEnzyme |
default constructor
virtual ~ProteinIdentification | ( | ) | [virtual] |
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.
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
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 search_engine_ [protected] |
String search_engine_version_ [protected] |
SearchParameters search_parameters_ [protected] |
String protein_score_type_ [protected] |
bool higher_score_better_ [protected] |
std::vector<ProteinHit> protein_hits_ [protected] |
Real protein_significance_threshold_ [protected] |
Generated Tue Apr 1 15:36:47 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |