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 | |
double | getRT () const |
returns the RT of the MS2 spectrum More... | |
void | setRT (double rt) |
sets the RT of the MS2 spectrum More... | |
bool | hasRT () const |
shortcut for isnan(getRT()) More... | |
double | getMZ () const |
returns the MZ of the MS2 spectrum More... | |
void | setMZ (double mz) |
sets the MZ of the MS2 spectrum More... | |
bool | hasMZ () const |
shortcut for isnan(getRT()) More... | |
const std::vector< PeptideHit > & | getHits () const |
returns the peptide hits as const More... | |
std::vector< PeptideHit > & | getHits () |
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... | |
double | getSignificanceThreshold () const |
returns the peptide significance threshold value More... | |
void | setSignificanceThreshold (double value) |
setting of the peptide significance threshold value More... | |
const 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 identifier More... | |
const String & | getBaseName () const |
returns the base name which links to underlying peak map More... | |
void | setBaseName (const String &base_name) |
sets the base name which links to underlying peak map More... | |
void | assignRanks () |
Sorts the hits by score and assigns ranks according 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... | |
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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... | |
Helper methods for linking peptide and protein hits | |
String | id_ |
Identifier by which ProteinIdentification and PeptideIdentification are matched. More... | |
std::vector< PeptideHit > | hits_ |
A list containing the peptide hits. More... | |
double | 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... | |
String | base_name_ |
double | mz_ |
double | rt_ |
const DataValue & | getMetaValue (const String &name) const |
void | setMetaValue (const String &name, const DataValue &value) |
re-implemented from MetaValueInterface as a precaution against deprecated usage of "RT" and "MZ" values More... | |
static std::vector< PeptideHit > | getReferencingHits (const std::vector< PeptideHit > &, const std::set< String > &accession) |
returns all peptide hits which reference to a given protein accession (aka filter by protein accession) More... | |
Additional Inherited Members | |
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static MetaInfoRegistry & | metaRegistry () |
returns a reference to the MetaInfoRegistry More... | |
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void | createIfNotExists_ () |
creates the MetaInfo object if it does not exist More... | |
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MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default 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 corresponding 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 can be accessed using getRT() and getMZ(). 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
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virtual |
destructor
PeptideIdentification | ( | const PeptideIdentification & | source | ) |
copy constructor
void assignRanks | ( | ) |
Sorts the hits by score and assigns ranks according to the scores.
Referenced by TOPPRNPxl::main_(), and SimpleSearchEngine::postProcessHits_().
bool empty | ( | ) | const |
Returns if this PeptideIdentification result is empty.
const String& getBaseName | ( | ) | const |
returns the base name which links to underlying peak map
const std::vector<PeptideHit>& getHits | ( | ) | const |
returns the peptide hits as const
Referenced by IDFilter::filterIdentificationsByBestNHits(), IDFilter::filterIdentificationsByProteins(), IDFilter::filterIdentificationsByScores(), IDFilter::filterIdentificationsByThresholds(), and TOPPRNPxl::main_().
std::vector<PeptideHit>& getHits | ( | ) |
returns the peptide hits
const String& getIdentifier | ( | ) | const |
returns the identifier
remove the two helper functions below a some point, when we are sure that we did not miss or merge in deprecated code! re-implemented from MetaValueInterface as a precaution against deprecated usage of "RT" and "MZ" values
double getMZ | ( | ) | const |
returns the MZ of the MS2 spectrum
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static |
returns all peptide hits which reference to a given protein accession (aka filter by protein accession)
double getRT | ( | ) | const |
returns the RT of the MS2 spectrum
const String& getScoreType | ( | ) | const |
returns the peptide score type
double getSignificanceThreshold | ( | ) | const |
returns the peptide significance threshold value
void insertHit | ( | const PeptideHit & | hit | ) |
Appends a peptide hit.
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 setBaseName | ( | const String & | base_name | ) |
sets the base name which links to underlying peak map
void setHigherScoreBetter | ( | bool | value | ) |
sets the peptide score orientation
Referenced by TOPPRNPxl::main_(), and SimpleSearchEngine::postProcessHits_().
void setHits | ( | const std::vector< PeptideHit > & | hits | ) |
Sets the peptide hits.
Referenced by TOPPRNPxl::main_(), and SimpleSearchEngine::postProcessHits_().
void setIdentifier | ( | const String & | id | ) |
sets the identifier
re-implemented from MetaValueInterface as a precaution against deprecated usage of "RT" and "MZ" values
void setMZ | ( | double | mz | ) |
sets the MZ of the MS2 spectrum
Referenced by TOPPRNPxl::main_(), and SimpleSearchEngine::postProcessHits_().
void setRT | ( | double | rt | ) |
sets the RT of the MS2 spectrum
Referenced by TOPPRNPxl::main_(), and SimpleSearchEngine::postProcessHits_().
void setScoreType | ( | const String & | type | ) |
sets the peptide score type
Referenced by SimpleSearchEngine::postProcessHits_().
void setSignificanceThreshold | ( | double | value | ) |
setting of the peptide significance threshold value
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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The score orientation.
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A list containing the peptide hits.
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Identifier by which ProteinIdentification and PeptideIdentification are matched.
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The score type (Mascot, Sequest, e-value, p-value)
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the peptide significance threshold
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:48 using doxygen 1.8.5 |