Represents the peptide hits for a spectrum. More...
#include <OpenMS/METADATA/PeptideIdentification.h>
Public Types | |
typedef PeptideHit | HitType |
Hit type definition. More... | |
Public Member Functions | |
const std::vector< PeptideHit > & | getHits () const |
returns the peptide hits More... | |
void | insertHit (const PeptideHit &hit) |
Appends a peptide hit. More... | |
void | setHits (const std::vector< PeptideHit > &hits) |
Sets the peptide hits. More... | |
DoubleReal | getSignificanceThreshold () const |
returns the peptide significance threshold value More... | |
void | setSignificanceThreshold (DoubleReal value) |
setting of the peptide significance threshold value More... | |
String | getScoreType () const |
returns the peptide score type More... | |
void | setScoreType (const String &type) |
sets the peptide score type More... | |
bool | isHigherScoreBetter () const |
returns the peptide score orientation More... | |
void | setHigherScoreBetter (bool value) |
sets the peptide score orientation More... | |
const String & | getIdentifier () const |
returns the identifier More... | |
void | setIdentifier (const String &id) |
sets the indentifier More... | |
void | assignRanks () |
Sorts the hits by score and assigns ranks coording to the scores. More... | |
void | sort () |
Sorts the hits by score. More... | |
bool | empty () const |
Returns if this PeptideIdentification result is empty. More... | |
constructors,destructors,assignment operator | |
PeptideIdentification () | |
default constructor More... | |
virtual | ~PeptideIdentification () |
destructor More... | |
PeptideIdentification (const PeptideIdentification &source) | |
copy constructor More... | |
PeptideIdentification & | operator= (const PeptideIdentification &source) |
assignment operator More... | |
bool | operator== (const PeptideIdentification &rhs) const |
Equality operator. More... | |
bool | operator!= (const PeptideIdentification &rhs) const |
Inequality operator. More... | |
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 More... | |
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 More... | |
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) More... | |
void | getNonReferencingHits (const String &protein_accession, std::vector< PeptideHit > &peptide_hits) const |
the complement of the above More... | |
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 |
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MetaInfoInterface () | |
constructor More... | |
MetaInfoInterface (const MetaInfoInterface &rhs) | |
copy constructor More... | |
~MetaInfoInterface () | |
destructor More... | |
MetaInfoInterface & | operator= (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 DataValue & | getMetaValue (const String &name) const |
returns the value corresponding to a string More... | |
const DataValue & | getMetaValue (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... | |
Protected Attributes | |
String | id_ |
Identifier by which ProteinIdentification and PeptideIdentification are matched. More... | |
std::vector< PeptideHit > | hits_ |
A list containing the peptide hits. More... | |
DoubleReal | significance_threshold_ |
the peptide significance threshold More... | |
String | score_type_ |
The score type (Mascot, Sequest, e-value, p-value) More... | |
bool | higher_score_better_ |
The score orientation. More... | |
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MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default More... | |
Additional Inherited Members | |
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static MetaInfoRegistry & | metaRegistry () |
retuns a reference to the MetaInfoRegistry More... | |
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void | createIfNotExists_ () |
creates the MetaInfo object if it does not exist More... | |
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.
typedef PeptideHit HitType |
Hit type definition.
default constructor
|
virtual |
destructor
PeptideIdentification | ( | const PeptideIdentification & | source | ) |
copy constructor
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 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 |
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.
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protected |
The score orientation.
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protected |
A list containing the peptide hits.
|
protected |
Identifier by which ProteinIdentification and PeptideIdentification are matched.
|
protected |
The score type (Mascot, Sequest, e-value, p-value)
|
protected |
the peptide significance threshold
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |