OpenMS
CompNovoIonScoring Class Reference

run with CompNovoIonScoring More...

#include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoring.h>

Inheritance diagram for CompNovoIonScoring:
[legend]
Collaboration diagram for CompNovoIonScoring:
[legend]

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

constructors and destructors
 CompNovoIonScoring ()
 default constructor More...
 
 CompNovoIonScoring (const CompNovoIonScoring &source)
 copy constructor More...
 
 ~CompNovoIonScoring () override
 destructor More...
 
CompNovoIonScoringoperator= (const CompNovoIonScoring &source)
 assignment operator More...
 
- Public Member Functions inherited from CompNovoIonScoringBase
 CompNovoIonScoringBase ()
 default constructor More...
 
 CompNovoIonScoringBase (const CompNovoIonScoringBase &source)
 copy constructor More...
 
 ~CompNovoIonScoringBase () override
 destructor More...
 
CompNovoIonScoringBaseoperator= (const CompNovoIonScoringBase &source)
 
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...
 
DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 

Accessors

void scoreSpectra (std::map< double, IonScore > &CID_ion_scores, PeakSpectrum &CID_spec, PeakSpectrum &ETD_spec, double precursor_weight, Size charge)
 
void scoreETDFeatures_ (Size charge, double precursor_weight, std::map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, const PeakSpectrum &ETD_orig_spec)
 
void scoreWitnessSet_ (Size charge, double precursor_weight, std::map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec) override
 

Additional Inherited Members

- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- Protected Member Functions inherited from CompNovoIonScoringBase
void updateMembers_ () override
 update members method from DefaultParamHandler to update the members More...
 
IsotopeType classifyIsotopes_ (const PeakSpectrum &spec, PeakSpectrum::ConstIterator it) const
 
double scoreIsotopes_ (const PeakSpectrum &spec, PeakSpectrum::ConstIterator it, std::map< double, IonScore > &CID_nodes, Size charge=1)
 
void addSingleChargedIons_ (std::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...
 
- Protected Attributes inherited from CompNovoIonScoringBase
std::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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
fragment_mass_tolerance float0.4  fragment mass tolerance
decomp_weights_precision float0.01  precision used to calculate the decompositions, this only affects cache usage!
double_charged_iso_threshold float0.9  minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions
double_charged_iso_threshold_single float0.99  Isotope scoring threshold used for doubly charged ions to infer singly charged variants
max_isotope_to_score int3  max isotope peak to be considered in the scoring
max_decomp_weight int600  maximal m/z difference used to calculate the decompositions
max_isotope int3  max isotope used in the theoretical spectra to score
max_mz float2000.0  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]

copy constructor

◆ ~CompNovoIonScoring()

~CompNovoIonScoring ( )
override

destructor

Member Function Documentation

◆ operator=()

CompNovoIonScoring& operator= ( const CompNovoIonScoring source)

assignment operator

◆ scoreETDFeatures_()

void scoreETDFeatures_ ( Size  charge,
double  precursor_weight,
std::map< double, IonScore > &  CID_nodes,
const PeakSpectrum CID_orig_spec,
const PeakSpectrum ETD_orig_spec 
)
protected

◆ scoreSpectra()

void scoreSpectra ( std::map< double, IonScore > &  CID_ion_scores,
PeakSpectrum CID_spec,
PeakSpectrum ETD_spec,
double  precursor_weight,
Size  charge 
)

◆ scoreWitnessSet_()

void scoreWitnessSet_ ( Size  charge,
double  precursor_weight,
std::map< double, IonScore > &  CID_nodes,
const PeakSpectrum CID_orig_spec 
)
overrideprotectedvirtual