Base class for ion scoring implementation for de novo algorithms. More...

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

Inheritance diagram for DeNovoAlgorithm:

Public Member Functions
Constructors and destructors
	DeNovoAlgorithm ()
	default constructor More...

	~DeNovoAlgorithm () override
	destructor More...

	DeNovoAlgorithm (const DeNovoAlgorithm &rhs)
	copy constructor More...

DeNovoAlgorithm &	operator= (const DeNovoAlgorithm &rhs)
	assignment operator More...

virtual void	generateCandidates (std::vector< PeptideIdentification > &candidates, const std::vector< std::vector< DeNovoIonScoring::IonScore > > &ion_scores, const PeakMap &exp)=0

virtual void	generateCandidates (PeptideIdentification &candidates, std::vector< DeNovoIonScoring::IonScore > &ion_scores, const PeakSpectrum &spec)=0

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...

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

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

Base class for ion scoring implementation for de novo algorithms.

Constructor & Destructor Documentation

◆ DeNovoAlgorithm() [1/2]

DeNovoAlgorithm ( )

default constructor

◆ ~DeNovoAlgorithm()

~DeNovoAlgorithm ( )

override

destructor

◆ DeNovoAlgorithm() [2/2]

DeNovoAlgorithm ( const DeNovoAlgorithm & rhs )

copy constructor

Member Function Documentation

◆ generateCandidates() [1/2]

virtual void generateCandidates	(	PeptideIdentification &	candidates,
		std::vector< DeNovoIonScoring::IonScore > &	ion_scores,
		const PeakSpectrum &	spec
	)

pure virtual

◆ generateCandidates() [2/2]

virtual void generateCandidates	(	std::vector< PeptideIdentification > &	candidates,
		const std::vector< std::vector< DeNovoIonScoring::IonScore > > &	ion_scores,
		const PeakMap &	exp
	)

pure virtual

◆ operator=()

DeNovoAlgorithm& operator= ( const DeNovoAlgorithm & rhs )

assignment operator

Public Member Functions

Additional Inherited Members