#include <OpenMS/METADATA/PeptideIdentification.h>
This class is closely related to Identification, which stores the protein hits and the general information about the ProteinIdentification run.
When loading PeptideHit instances from a File, the retention time and mass-to-charge ratio of the precursor spectrum is stored in the MetaInfoInterface using the names 'MZ' and 'RT'. This information can be used to map the PeptideHits to a MSExperiment or a FeatureMap using IDSpectrumMapper or IDFeatureMapper.
Public Types | |
typedef PeptideHit | HitType |
Hit type definition. | |
Public Member Functions | |
const std::vector< PeptideHit > & | getHits () const |
returns the peptide hits | |
void | insertHit (const PeptideHit &hit) |
Appends a peptide hit. | |
void | setHits (const std::vector< PeptideHit > &hits) |
Sets the peptide hits. | |
Real | getSignificanceThreshold () const |
returns the peptide significance threshold value | |
void | setSignificanceThreshold (Real value) |
setting of the peptide significance threshold value | |
String | getScoreType () const |
returns the peptide score type | |
void | setScoreType (const String &type) |
sets the peptide score type | |
bool | isHigherScoreBetter () const |
returns the peptide score orientation | |
void | setHigherScoreBetter (bool value) |
sets the peptide score orientation | |
const String & | getIdentifier () const |
returns the identifier | |
void | setIdentifier (const String &id) |
sets the indentifier | |
void | assignRanks () |
Sorts the hits by score and assigns ranks coording to the scores. | |
void | sort () |
Sorts the hits by score. | |
bool | empty () const |
Returns if this ProteinIdentification result is empty. | |
constructors,destructors,assignment operator | |
PeptideIdentification () | |
default constructor | |
virtual | ~PeptideIdentification () |
destructor | |
PeptideIdentification (const PeptideIdentification &source) | |
copy constructor | |
PeptideIdentification & | operator= (const PeptideIdentification &source) |
assignment operator | |
bool | operator== (const PeptideIdentification &rhs) const |
Equality operator. | |
bool | operator!= (const PeptideIdentification &rhs) const |
Inequality operator. | |
Methods for linking peptide and protein hits | |
void | getReferencingHits (const String &protein_accession, std::vector< PeptideHit > &peptide_hits) const |
void | getReferencingHits (const std::vector< String > &accessions, std::vector< PeptideHit > &peptide_hits) const |
void | getReferencingHits (const std::vector< ProteinHit > &protein_hits, std::vector< PeptideHit > &peptide_hits) const |
void | getNonReferencingHits (const String &protein_accession, std::vector< PeptideHit > &peptide_hits) const |
void | getNonReferencingHits (const std::vector< String > &accessions, std::vector< PeptideHit > &peptide_hits) const |
void | getNonReferencingHits (const std::vector< ProteinHit > &protein_hits, std::vector< PeptideHit > &peptide_hits) const |
Protected Attributes | |
String | id_ |
Identifier by which ProteinIdentification and PeptideIdentification are matched. | |
std::vector< PeptideHit > | hits_ |
A list containing the peptide hits. | |
Real | significance_threshold_ |
the peptide significance threshold | |
String | score_type_ |
The score type (Mascot, Sequest, e-value, p-value). | |
bool | higher_score_better_ |
The score orientation. |
typedef PeptideHit HitType |
Hit type definition.
default constructor
virtual ~PeptideIdentification | ( | ) | [virtual] |
destructor
PeptideIdentification | ( | const PeptideIdentification & | source | ) |
copy constructor
PeptideIdentification& operator= | ( | const PeptideIdentification & | source | ) |
assignment operator
bool operator== | ( | const PeptideIdentification & | rhs | ) | const |
Equality operator.
bool operator!= | ( | const PeptideIdentification & | rhs | ) | const |
Inequality operator.
const std::vector<PeptideHit>& getHits | ( | ) | const |
returns the peptide hits
void insertHit | ( | const PeptideHit & | hit | ) |
Appends a peptide hit.
void setHits | ( | const std::vector< PeptideHit > & | hits | ) |
Sets the peptide hits.
Real getSignificanceThreshold | ( | ) | const |
returns the peptide significance threshold value
void setSignificanceThreshold | ( | Real | value | ) |
setting of the peptide significance threshold value
String getScoreType | ( | ) | const |
returns the peptide score type
void setScoreType | ( | const String & | type | ) |
sets the peptide score type
bool isHigherScoreBetter | ( | ) | const |
returns the peptide score orientation
void setHigherScoreBetter | ( | bool | value | ) |
sets the peptide score orientation
const String& getIdentifier | ( | ) | const |
returns the identifier
void setIdentifier | ( | const String & | id | ) |
sets the indentifier
void assignRanks | ( | ) |
Sorts the hits by score and assigns ranks coording to the scores.
void sort | ( | ) |
Sorts the hits by score.
bool empty | ( | ) | const |
Returns if this ProteinIdentification result is empty.
void getReferencingHits | ( | const String & | protein_accession, | |
std::vector< PeptideHit > & | peptide_hits | |||
) | const |
void getReferencingHits | ( | const std::vector< String > & | accessions, | |
std::vector< PeptideHit > & | peptide_hits | |||
) | const |
void getReferencingHits | ( | const std::vector< ProteinHit > & | protein_hits, | |
std::vector< PeptideHit > & | peptide_hits | |||
) | const |
void getNonReferencingHits | ( | const String & | protein_accession, | |
std::vector< PeptideHit > & | peptide_hits | |||
) | const |
void getNonReferencingHits | ( | const std::vector< String > & | accessions, | |
std::vector< PeptideHit > & | peptide_hits | |||
) | const |
void getNonReferencingHits | ( | const std::vector< ProteinHit > & | protein_hits, | |
std::vector< PeptideHit > & | peptide_hits | |||
) | const |
Identifier by which ProteinIdentification and PeptideIdentification are matched.
std::vector<PeptideHit> hits_ [protected] |
A list containing the peptide hits.
Real significance_threshold_ [protected] |
the peptide significance threshold
String score_type_ [protected] |
The score type (Mascot, Sequest, e-value, p-value).
bool higher_score_better_ [protected] |
The score orientation.
Generated Tue Apr 1 15:36:46 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |