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

Inheritance diagram for CompNovoIonScoring:

Collaboration diagram for CompNovoIonScoring:

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...

CompNovoIonScoring &	operator= (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...

CompNovoIonScoringBase &	operator= (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 DefaultParamHandler &	operator= (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 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...

Accessors
void	scoreSpectra (Map< double, IonScore > &CID_ion_scores, PeakSpectrum &CID_spec, PeakSpectrum &ETD_spec, double precursor_weight, Size charge)

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

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 &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)

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< 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...

Detailed Description

run with CompNovoIonScoring

Parameters of this class are:

Name	Type	Default	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	2000.0	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

typedef CompNovoIonScoringBase::IonScore IonScore

◆ IsotopeType

typedef CompNovoIonScoringBase::IsotopeType IsotopeType

Constructor & Destructor Documentation

◆ CompNovoIonScoring() [1/2]

CompNovoIonScoring ( )

default constructor

◆ CompNovoIonScoring() [2/2]

CompNovoIonScoring ( const CompNovoIonScoring & source )

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,
		Map< double, IonScore > &	CID_nodes,
		const PeakSpectrum &	CID_orig_spec,
		const PeakSpectrum &	ETD_orig_spec
	)

protected

◆ scoreSpectra()

void scoreSpectra	(	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,
		Map< double, IonScore > &	CID_nodes,
		const PeakSpectrum &	CID_orig_spec
	)

overrideprotectedvirtual

Implements CompNovoIonScoringBase.

Public Types

Public Member Functions

Accessors

Additional Inherited Members