OpenMS  2.8.0
Classes | Public Types | List of all members
CompNovoIonScoringBase Class Referenceabstract

run with CompNovoIonScoringBase More...

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

Inheritance diagram for CompNovoIonScoringBase:
Collaboration diagram for CompNovoIonScoringBase:


struct  IonScore

Public Types

enum  IsotopeType { PARENT = 0 , CHILD = 1 , LONE = 2 }

Public Member Functions

constructors and destructors
 CompNovoIonScoringBase ()
 default constructor More...
 CompNovoIonScoringBase (const CompNovoIonScoringBase &source)
 copy constructor More...
 ~CompNovoIonScoringBase () override
 destructor More...
CompNovoIonScoringBaseoperator= (const CompNovoIonScoringBase &source)
- 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...


Map< Size, std::vector< double > > isotope_distributions_
double fragment_mass_tolerance_
double scoreIsotopes (const PeakSpectrum &CID_spec, PeakSpectrum::ConstIterator it, Size charge)
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)
virtual void scoreWitnessSet_ (Size charge, double precursor_weight, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec)=0
void addSingleChargedIons_ (Map< double, IonScore > &ion_scores, PeakSpectrum &CID_spec)
void initIsotopeDistributions_ ()

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 DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
- 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 CompNovoIonScoringBase

Member Enumeration Documentation

◆ IsotopeType


Constructor & Destructor Documentation

◆ CompNovoIonScoringBase() [1/2]

default constructor

◆ CompNovoIonScoringBase() [2/2]

copy constructor

◆ ~CompNovoIonScoringBase()

~CompNovoIonScoringBase ( )


Member Function Documentation

◆ addSingleChargedIons_()

void addSingleChargedIons_ ( Map< double, IonScore > &  ion_scores,
PeakSpectrum CID_spec 

◆ classifyIsotopes_()

IsotopeType classifyIsotopes_ ( const PeakSpectrum spec,
PeakSpectrum::ConstIterator  it 
) const

◆ initIsotopeDistributions_()

void initIsotopeDistributions_ ( )

◆ operator=()

CompNovoIonScoringBase& operator= ( const CompNovoIonScoringBase source)

◆ scoreIsotopes()

double scoreIsotopes ( const PeakSpectrum CID_spec,
PeakSpectrum::ConstIterator  it,
Size  charge 

◆ scoreIsotopes_()

double scoreIsotopes_ ( const PeakSpectrum spec,
PeakSpectrum::ConstIterator  it,
Map< double, IonScore > &  CID_nodes,
Size  charge = 1 

◆ scoreWitnessSet_()

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

◆ updateMembers_()

void updateMembers_ ( )

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

◆ isotope_distributions_

Map<Size, std::vector<double> > isotope_distributions_