IsotopeMarker marks peak pairs which could represent an ion and its isotope. More...

#include <OpenMS/FILTERING/TRANSFORMERS/IsotopeMarker.h>

Inheritance diagram for IsotopeMarker:

Collaboration diagram for IsotopeMarker:

Public Member Functions
	IsotopeMarker ()
	default constructor More...

	IsotopeMarker (const IsotopeMarker &source)
	copy constructor More...

	~IsotopeMarker () override
	destructor More...

IsotopeMarker &	operator= (const IsotopeMarker &source)
	assignment operator More...

template<typename SpectrumType >
void	apply (std::map< double, bool > &marked, SpectrumType &spectrum)

Public Member Functions inherited from PeakMarker
	PeakMarker ()
	default constructor More...

	PeakMarker (const PeakMarker &source)
	copy constructor More...

	~PeakMarker () override
	destructor More...

PeakMarker &	operator= (const PeakMarker &source)
	assignment operator More...

template<typename SpectrumType >
void	apply (std::map< double, bool > &, SpectrumType &)
	method to mark peaks More...

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...

Static Public Member Functions
static PeakMarker *	create ()

static const String	getProductName ()

Static Public Member Functions inherited from PeakMarker
static const String	getProductName ()

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...

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

IsotopeMarker marks peak pairs which could represent an ion and its isotope.

Todo:: implement a real isotope marking here with isotopedistributions and fitting (Andreas)

Parameters of this class are:

Name	Type	Default	Description
marks	int	1	How often a peak must be marked to be reported
mz_variation	float	0.1	variation in m/z direction
in_variation	float	0.5	variation in intensity

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ IsotopeMarker() [1/2]

IsotopeMarker ( )

default constructor

◆ IsotopeMarker() [2/2]

IsotopeMarker ( const IsotopeMarker & source )

copy constructor

◆ ~IsotopeMarker()

~IsotopeMarker ( )

override

destructor

Member Function Documentation

◆ apply()

void apply	(	std::map< double, bool > &	marked,
		SpectrumType &	spectrum
	)

inline

References CoarseIsotopePatternGenerator::estimateFromPeptideWeight(), and MSSpectrum::sortByPosition().

◆ create()

static PeakMarker* create ( )

inlinestatic

◆ getProductName()

static const String getProductName ( )

inlinestatic

◆ operator=()

IsotopeMarker& operator= ( const IsotopeMarker & source )

assignment operator

Public Member Functions

Static Public Member Functions

Additional Inherited Members