OpenMS  2.8.0
Public Types | List of all members
CompNovoIonScoringCID Class Reference

run with CompNovoIonScoringCID More...

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

Inheritance diagram for CompNovoIonScoringCID:
Collaboration diagram for CompNovoIonScoringCID:

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
 CompNovoIonScoringCID ()
 default constructor More...
 CompNovoIonScoringCID (const CompNovoIonScoringCID &source)
 copy constructor More...
 ~CompNovoIonScoringCID () override
 destructor More...
CompNovoIonScoringCIDoperator= (const CompNovoIonScoringCID &source)
- 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...
virtual 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...


void scoreSpectrum (Map< double, IonScore > &CID_ion_scores, PeakSpectrum &CID_spec, double precursor_weight, Size charge)
void scoreWitnessSet_ (Size charge, double precursor_weight, 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, 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...
- 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< 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 CompNovoIonScoringCID

Parameters of this class are:

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
precursor_mass_tolerance float1.5  precursor mass tolerance


Member Typedef Documentation

◆ IonScore

◆ IsotopeType

Constructor & Destructor Documentation

◆ CompNovoIonScoringCID() [1/2]

default constructor

◆ CompNovoIonScoringCID() [2/2]

copy constructor

◆ ~CompNovoIonScoringCID()

~CompNovoIonScoringCID ( )


Member Function Documentation

◆ operator=()

CompNovoIonScoringCID& operator= ( const CompNovoIonScoringCID source)

◆ scoreSpectrum()

void scoreSpectrum ( Map< double, IonScore > &  CID_ion_scores,
PeakSpectrum CID_spec,
double  precursor_weight,
Size  charge 

◆ scoreWitnessSet_()

void scoreWitnessSet_ ( Size  charge,
double  precursor_weight,
Map< double, IonScore > &  CID_nodes,
const PeakSpectrum CID_orig_spec