OpenMS
2.4.0
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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 where the identification occurred More... | |
void | setRT (double rt) |
sets the RT of the MS2 spectrum where the identification occurred 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... | |
const String | getExperimentLabel () const |
returns the experiment label for this identification More... | |
void | setExperimentLabel (const String &type) |
sets the experiment label for this identification More... | |
void | assignRanks () |
Sorts the hits by score and assigns ranks according to the scores. More... | |
void | sort () |
Sorts the hits by score. More... | |
void | sortByRank () |
Sorts the hits by rank. More... | |
bool | empty () const |
Returns if this PeptideIdentification result is empty. More... | |
Constructors, destructor, operators | |
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... | |
Public Member Functions inherited from MetaInfoInterface | |
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 (or DataValue::EMPTY if not found) More... | |
const DataValue & | getMetaValue (UInt index) const |
Returns the value corresponding to an index (or DataValue::EMPTY if not found) More... | |
bool | metaValueExists (const String &name) const |
Returns whether an entry with the given name exists. More... | |
bool | metaValueExists (UInt index) const |
Returns whether an entry with the given index exists. 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... | |
Static Public Member Functions | |
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 (i.e. filter by protein accession) More... | |
Static Public Member Functions inherited from MetaInfoInterface | |
static MetaInfoRegistry & | metaRegistry () |
Returns a reference to the MetaInfoRegistry. 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... | |
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_ |
Protected Attributes inherited from MetaInfoInterface | |
MetaInfo * | meta_ |
Pointer to the MetaInfo object (0 by default) More... | |
Additional Inherited Members | |
Protected Member Functions inherited from MetaInfoInterface | |
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 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 TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::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 String getExperimentLabel | ( | ) | const |
returns the experiment label for this identification
const std::vector<PeptideHit>& getHits | ( | ) | const |
returns the peptide hits as const
Referenced by TOPPMetaProSIP::main_(), IDMapper::mapPrecursorsToIdentifications(), and FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()().
std::vector<PeptideHit>& getHits | ( | ) |
returns the peptide hits
const String& getIdentifier | ( | ) | const |
returns the identifier
double getMZ | ( | ) | const |
returns the MZ of the MS2 spectrum
Referenced by IDMapper::mapPrecursorsToIdentifications().
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returns all peptide hits which reference to a given protein accession (i.e. filter by protein accession)
double getRT | ( | ) | const |
returns the RT of the MS2 spectrum where the identification occurred
Referenced by IDMapper::mapPrecursorsToIdentifications(), and FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()().
const String& getScoreType | ( | ) | const |
returns the peptide score type
double getSignificanceThreshold | ( | ) | const |
returns the peptide significance threshold value
bool hasMZ | ( | ) | const |
shortcut for isnan(getRT())
bool hasRT | ( | ) | const |
shortcut for isnan(getRT())
void insertHit | ( | const PeptideHit & | hit | ) |
Appends a peptide hit.
Referenced by TOPPMetaProSIP::main_().
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 setExperimentLabel | ( | const String & | type | ) |
sets the experiment label for this identification
void setHigherScoreBetter | ( | bool | value | ) |
sets the peptide score orientation
Referenced by TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().
void setHits | ( | const std::vector< PeptideHit > & | hits | ) |
Sets the peptide hits.
Referenced by TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().
void setIdentifier | ( | const String & | id | ) |
sets the identifier
void setMZ | ( | double | mz | ) |
sets the MZ of the MS2 spectrum
Referenced by SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().
void setRT | ( | double | rt | ) |
sets the RT of the MS2 spectrum where the identification occurred
Referenced by SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().
void setScoreType | ( | const String & | type | ) |
sets the peptide score type
Referenced by SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::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.
void sortByRank | ( | ) |
Sorts the hits by rank.
Sorting hits by rank attribute, i.e. after sorting, the hits will be in ascending order of rank.
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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