Represents the peptide hits for a spectrum. More...
#include <OpenMS/METADATA/PeptideIdentification.h>
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. | |
| DoubleReal | getSignificanceThreshold () const |
| returns the peptide significance threshold value | |
| void | setSignificanceThreshold (DoubleReal 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 PeptideIdentification 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 |
| finds and inserts all peptide hits which reference to a given protein accession | |
| void | getReferencingHits (const std::vector< String > &accessions, std::vector< PeptideHit > &peptide_hits) const |
| finds and inserts all peptide hits which reference to a given list of protein accessions | |
| void | getReferencingHits (const std::vector< ProteinHit > &protein_hits, std::vector< PeptideHit > &peptide_hits) const |
| finds and inserts all peptide hits which reference to a given list of proteins (via their accessions) | |
| void | getNonReferencingHits (const String &protein_accession, std::vector< PeptideHit > &peptide_hits) const |
| the complement of the above | |
| 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. | |
| DoubleReal | 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. | |
Detailed Description
Represents the peptide hits for a spectrum.
This class is closely related to ProteinIdentification, which stores the protein hits and the general information about the identification run. More than one PeptideIdentification can belong to one ProteinIdentification. The general information about a PeptideIdentification has to be looked up in the correpsonding ProteinIndentification, using the unique identifier that links the two.
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 peptide hits to an MSExperiment, a FeatureMap or a ConsensusMap using the IDMapper class.
Member Typedef Documentation
| typedef PeptideHit HitType |
Hit type definition.
Constructor & Destructor Documentation
default constructor
| virtual ~PeptideIdentification | ( | ) | [virtual] |
destructor
| PeptideIdentification | ( | const PeptideIdentification & | source | ) |
copy constructor
Member Function Documentation
| void assignRanks | ( | ) |
Sorts the hits by score and assigns ranks coording to the scores.
Referenced by TOPPRNPxl::main_().
| bool empty | ( | ) | const |
Returns if this PeptideIdentification result is empty.
| const std::vector<PeptideHit>& getHits | ( | ) | const |
returns the peptide hits
Referenced by IDFilter::filterIdentificationsByBestNHits(), IDFilter::filterIdentificationsByProteins(), IDFilter::filterIdentificationsByScores(), IDFilter::filterIdentificationsByThresholds(), and TOPPRNPxl::main_().
| const String& getIdentifier | ( | ) | const |
returns the identifier
| void getNonReferencingHits | ( | const std::vector< ProteinHit > & | protein_hits, | |
| std::vector< PeptideHit > & | peptide_hits | |||
| ) | const |
| void getNonReferencingHits | ( | const String & | protein_accession, | |
| std::vector< PeptideHit > & | peptide_hits | |||
| ) | const |
the complement of the above
| void getNonReferencingHits | ( | const std::vector< String > & | accessions, | |
| std::vector< PeptideHit > & | peptide_hits | |||
| ) | const |
| void getReferencingHits | ( | const String & | protein_accession, | |
| std::vector< PeptideHit > & | peptide_hits | |||
| ) | const |
finds and inserts all peptide hits which reference to a given protein accession
| void getReferencingHits | ( | const std::vector< String > & | accessions, | |
| std::vector< PeptideHit > & | peptide_hits | |||
| ) | const |
finds and inserts all peptide hits which reference to a given list of protein accessions
| void getReferencingHits | ( | const std::vector< ProteinHit > & | protein_hits, | |
| std::vector< PeptideHit > & | peptide_hits | |||
| ) | const |
finds and inserts all peptide hits which reference to a given list of proteins (via their accessions)
| String getScoreType | ( | ) | const |
returns the peptide score type
| DoubleReal getSignificanceThreshold | ( | ) | const |
returns the peptide significance threshold value
| void insertHit | ( | const PeptideHit & | hit | ) |
Appends a peptide hit.
Referenced by MRMFeatureFinderScoring::scorePeakgroups_().
| bool isHigherScoreBetter | ( | ) | const |
returns the peptide score orientation
| bool operator!= | ( | const PeptideIdentification & | rhs | ) | const |
Inequality operator.
| PeptideIdentification& operator= | ( | const PeptideIdentification & | source | ) |
assignment operator
| bool operator== | ( | const PeptideIdentification & | rhs | ) | const |
Equality operator.
| void setHigherScoreBetter | ( | bool | value | ) |
sets the peptide score orientation
Referenced by DBAdapter::loadSpectrum(), and TOPPRNPxl::main_().
| void setHits | ( | const std::vector< PeptideHit > & | hits | ) |
Sets the peptide hits.
Referenced by DBAdapter::loadSpectrum(), and TOPPRNPxl::main_().
| void setIdentifier | ( | const String & | id | ) |
sets the indentifier
Referenced by MRMFeatureFinderScoring::scorePeakgroups_().
| void setScoreType | ( | const String & | type | ) |
sets the peptide score type
Referenced by DBAdapter::loadSpectrum().
| void setSignificanceThreshold | ( | DoubleReal | value | ) |
setting of the peptide significance threshold value
Referenced by DBAdapter::loadSpectrum().
| void sort | ( | ) |
Sorts the hits by score.
Sorting takes the score orientation (higher_score_better_) into account, i.e. after sorting, the best-scoring hit is the first.
Member Data Documentation
bool higher_score_better_ [protected] |
The score orientation.
std::vector<PeptideHit> hits_ [protected] |
A list containing the peptide hits.
Identifier by which ProteinIdentification and PeptideIdentification are matched.
String score_type_ [protected] |
The score type (Mascot, Sequest, e-value, p-value).
DoubleReal significance_threshold_ [protected] |
the peptide significance threshold
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |