run with CompNovoIonScoring More...
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoring.h>
Inheritance diagram for CompNovoIonScoring:
Public Types | |
| typedef CompNovoIonScoringBase::IsotopeType | IsotopeType |
| typedef CompNovoIonScoringBase::IonScore | IonScore |
 Public Types inherited from CompNovoIonScoringBase | |
| enum | IsotopeType { PARENT = 0, CHILD = 1, LONE = 2 } |
Public Member Functions | |
| CompNovoIonScoring & | operator= (const CompNovoIonScoring &source) |
| assignment operator More... | |
constructors and destructors | |
| CompNovoIonScoring () | |
| default constructor More... | |
| CompNovoIonScoring (const CompNovoIonScoring &source) | |
| copy constructor More... | |
| virtual | ~CompNovoIonScoring () |
| destructor More... | |
Accessors | |
| void | scoreSpectra (Map< double, IonScore > &CID_ion_scores, PeakSpectrum &CID_spec, PeakSpectrum &ETD_spec, double precursor_weight, Size charge) |
| Public Member Functions inherited from CompNovoIonScoringBase | |
| CompNovoIonScoringBase & | operator= (const CompNovoIonScoringBase &source) |
| CompNovoIonScoringBase () | |
| default constructor More... | |
| CompNovoIonScoringBase (const CompNovoIonScoringBase &source) | |
| copy constructor More... | |
| virtual | ~CompNovoIonScoringBase () |
| destructor More... | |
| double | scoreIsotopes (const PeakSpectrum &CID_spec, PeakSpectrum::ConstIterator it, Size charge) |
| Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages. More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor. More... | |
| virtual | ~DefaultParamHandler () |
| Destructor. More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More... | |
| void | setParameters (const Param ¶m) |
| Sets the parameters. More... | |
| const Param & | getParameters () const |
| Non-mutable access to the parameters. More... | |
| const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More... | |
| const String & | getName () const |
| Non-mutable access to the name. More... | |
| void | setName (const String &name) |
| Mutable access to the name. More... | |
| const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More... | |
Protected Member Functions | |
| void | scoreETDFeatures_ (Size charge, double precursor_weight, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, const PeakSpectrum &ETD_orig_spec) |
| void | scoreWitnessSet_ (Size charge, double precursor_weight, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec) |
| Protected Member Functions inherited from CompNovoIonScoringBase | |
| void | updateMembers_ () |
| update members method from DefaultParamHandler to update the members More... | |
| IsotopeType | classifyIsotopes_ (const PeakSpectrum &spec, PeakSpectrum::ConstIterator it) |
| double | scoreIsotopes_ (const PeakSpectrum &spec, PeakSpectrum::ConstIterator it, Map< double, IonScore > &CID_nodes, Size charge=1) |
| void | addSingleChargedIons_ (Map< double, IonScore > &ion_scores, PeakSpectrum &CID_spec) |
| void | initIsotopeDistributions_ () |
| Protected Member Functions inherited from DefaultParamHandler | |
| void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More... | |
Additional Inherited Members | |
| Protected Attributes inherited from CompNovoIonScoringBase | |
| Map< Size, std::vector< double > > | isotope_distributions_ |
| double | fragment_mass_tolerance_ |
| Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ |
| Container for current parameters. More... | |
| Param | defaults_ |
| Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
| std::vector< String > | subsections_ |
| Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
| String | error_name_ |
| Name that is displayed in error messages during the parameter checking. More... | |
| bool | check_defaults_ |
| If this member is set to false no checking if parameters in done;. More... | |
| bool | warn_empty_defaults_ |
| If this member is set to false no warning is emitted when defaults are empty;. More... | |
Detailed Description
run with CompNovoIonScoring
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| fragment_mass_tolerance | float | 0.4 | fragment mass tolerance | |
| decomp_weights_precision | float | 0.01 | precision used to calculate the decompositions, this only affects cache usage! | |
| double_charged_iso_threshold | float | 0.9 | minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions | |
| double_charged_iso_threshold_single | float | 0.99 | Isotope scoring threshold used for doubly charged ions to infer singly charged variants | |
| max_isotope_to_score | int | 3 | max isotope peak to be considered in the scoring | |
| max_decomp_weight | int | 600 | maximal m/z difference used to calculate the decompositions | |
| max_isotope | int | 3 | max isotope used in the theoretical spectra to score | |
| max_mz | float | 2000 | maximal m/z value used to calculate isotope distributions |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Member Typedef Documentation
◆ IonScore
◆ IsotopeType
Constructor & Destructor Documentation
◆ CompNovoIonScoring() [1/2]
default constructor
◆ CompNovoIonScoring() [2/2]
| CompNovoIonScoring | ( | const CompNovoIonScoring & | source | ) |
copy constructor
◆ ~CompNovoIonScoring()
|
virtual |
destructor
Member Function Documentation
◆ operator=()
| CompNovoIonScoring& operator= | ( | const CompNovoIonScoring & | source | ) |
assignment operator
◆ scoreETDFeatures_()
|
protected |
◆ scoreSpectra()
| void scoreSpectra | ( | Map< double, IonScore > & | CID_ion_scores, |
| PeakSpectrum & | CID_spec, | ||
| PeakSpectrum & | ETD_spec, | ||
| double | precursor_weight, | ||
| Size | charge | ||
| ) |
◆ scoreWitnessSet_()
|
protectedvirtual |
Implements CompNovoIonScoringBase.