CompNovoIonScoringBase Class Reference

run with CompNovoIonScoringBase More...

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

Inheritance diagram for CompNovoIonScoringBase:

Collaboration diagram for CompNovoIonScoringBase:

Classes
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...
CompNovoIonScoringBase &	operator= (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...
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
std::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, std::map< double, IonScore > &CID_nodes, Size charge=1)
virtual void	scoreWitnessSet_ (Size charge, double precursor_weight, std::map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec)=0
void	addSingleChargedIons_ (std::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< 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 CompNovoIonScoringBase

Member Enumeration Documentation

IsotopeType

enum IsotopeType

Enumerator
PARENT
CHILD
LONE

Constructor & Destructor Documentation

CompNovoIonScoringBase() [1/2]

CompNovoIonScoringBase

(

)

default constructor

CompNovoIonScoringBase() [2/2]

CompNovoIonScoringBase

(

const CompNovoIonScoringBase &

source

)

copy constructor

~CompNovoIonScoringBase()

~CompNovoIonScoringBase ( )

override

destructor

Member Function Documentation

addSingleChargedIons_()

void addSingleChargedIons_ ( std::map< double, IonScore > &  ion_scores, PeakSpectrum &  CID_spec  )

protected

classifyIsotopes_()

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

protected

initIsotopeDistributions_()

void initIsotopeDistributions_ ( )

protected

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, std::map< double, IonScore > &  CID_nodes, Size  charge = 1  )

protected

scoreWitnessSet_()

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

protectedpure virtual

Implemented in CompNovoIonScoringCID, and CompNovoIonScoring.

updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Member Data Documentation

fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

isotope_distributions_

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

protected