run with CompNovoIonScoring More...
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoring.h>
 
  
 | 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< DoubleReal, IonScore > &CID_ion_scores, PeakSpectrum &CID_spec, PeakSpectrum &ETD_spec, DoubleReal 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... | |
| DoubleReal | 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, 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) | 
|  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) | 
| DoubleReal | scoreIsotopes_ (const PeakSpectrum &spec, PeakSpectrum::ConstIterator it, Map< DoubleReal, IonScore > &CID_nodes, Size charge=1) | 
| void | addSingleChargedIons_ (Map< DoubleReal, 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 < DoubleReal > > | isotope_distributions_ | 
| DoubleReal | 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... | |
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 | 
default constructor
| CompNovoIonScoring | ( | const CompNovoIonScoring & | source | ) | 
copy constructor
| 
 | virtual | 
destructor
| CompNovoIonScoring& operator= | ( | const CompNovoIonScoring & | source | ) | 
assignment operator
| 
 | protected | 
| void scoreSpectra | ( | Map< DoubleReal, IonScore > & | CID_ion_scores, | 
| PeakSpectrum & | CID_spec, | ||
| PeakSpectrum & | ETD_spec, | ||
| DoubleReal | precursor_weight, | ||
| Size | charge | ||
| ) | 
| 
 | protectedvirtual | 
Implements CompNovoIonScoringBase.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5 |