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 Member Functions | |
| CompNovoIonScoring & | operator= (const CompNovoIonScoring &source) |
| assignment operator | |
constructors and destructors | |
| CompNovoIonScoring () | |
| default constructor | |
| CompNovoIonScoring (const CompNovoIonScoring &source) | |
| copy constructor | |
| virtual | ~CompNovoIonScoring () |
| destructor | |
Accessors | |
| void | scoreSpectra (Map< DoubleReal, IonScore > &CID_ion_scores, PeakSpectrum &CID_spec, PeakSpectrum &ETD_spec, DoubleReal precursor_weight, Size charge) |
Protected Member Functions | |
| void | scoreETDFeatures_ (Size charge, DoubleReal precursor_weight, Map< DoubleReal, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, const PeakSpectrum &ETD_orig_spec) |
| void | scoreWitnessSet_ (Size charge, DoubleReal precursor_weight, Map< DoubleReal, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec) |
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
Reimplemented from CompNovoIonScoringBase.
Constructor & Destructor Documentation
default constructor
| CompNovoIonScoring | ( | const CompNovoIonScoring & | source | ) |
copy constructor
| virtual ~CompNovoIonScoring | ( | ) | [virtual] |
destructor
Member Function Documentation
| CompNovoIonScoring& operator= | ( | const CompNovoIonScoring & | source | ) |
assignment operator
| void scoreETDFeatures_ | ( | Size | charge, | |
| DoubleReal | precursor_weight, | |||
| Map< DoubleReal, IonScore > & | CID_nodes, | |||
| const PeakSpectrum & | CID_orig_spec, | |||
| const PeakSpectrum & | ETD_orig_spec | |||
| ) | [protected] |
| void scoreSpectra | ( | Map< DoubleReal, IonScore > & | CID_ion_scores, | |
| PeakSpectrum & | CID_spec, | |||
| PeakSpectrum & | ETD_spec, | |||
| DoubleReal | precursor_weight, | |||
| Size | charge | |||
| ) |
| void scoreWitnessSet_ | ( | Size | charge, | |
| DoubleReal | precursor_weight, | |||
| Map< DoubleReal, IonScore > & | CID_nodes, | |||
| const PeakSpectrum & | CID_orig_spec | |||
| ) | [protected, virtual] |
Implements CompNovoIonScoringBase.
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |