FeatureFinderAlgorithm Class Reference

Abstract base class for FeatureFinder algorithms. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>

Inheritance diagram for FeatureFinderAlgorithm:

Public Types
typedef PeakMap	MapType
	Input map type. More...
typedef MapType::CoordinateType	CoordinateType
	Coordinate/Position type of peaks. More...
typedef MapType::IntensityType	IntensityType
	Intensity type of peaks. More...

Public Member Functions
	FeatureFinderAlgorithm ()
	default constructor More...
	~FeatureFinderAlgorithm () override
	destructor More...
virtual void	run ()=0
	Main method that implements the actual algorithm. More...
virtual Param	getDefaultParameters () const
	Returns the default parameters. Reimplement. More...
void	setData (const MapType &map, FeatureMap &features, FeatureFinder &ff)
	Sets a reference to the calling FeatureFinder. More...
virtual void	setSeeds (const FeatureMap &seeds)
	Sets a reference to the calling FeatureFinder. 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 void	registerChildren ()
	register all derived classes here (see FeatureFinderAlgorithm_impl.h) More...

Protected Attributes
const MapType *	map_
	Input data pointer. More...
FeatureMap *	features_
	Output data pointer. More...
FeatureFinder *	ff_
	Pointer to the calling FeatureFinder that is used to access the feature flags. 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...

Private Member Functions
FeatureFinderAlgorithm &	operator= (const FeatureFinderAlgorithm &)
	Not implemented. More...
	FeatureFinderAlgorithm (const FeatureFinderAlgorithm &)
	Not implemented. 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...

Detailed Description

Abstract base class for FeatureFinder algorithms.

Member Typedef Documentation

CoordinateType

typedef MapType::CoordinateType CoordinateType

Coordinate/Position type of peaks.

IntensityType

typedef MapType::IntensityType IntensityType

Intensity type of peaks.

MapType

typedef PeakMap MapType

Input map type.

Constructor & Destructor Documentation

FeatureFinderAlgorithm() [1/2]

FeatureFinderAlgorithm ( )

inline

default constructor

~FeatureFinderAlgorithm()

~FeatureFinderAlgorithm ( )

inlineoverride

destructor

FeatureFinderAlgorithm() [2/2]

FeatureFinderAlgorithm ( const FeatureFinderAlgorithm &  )

private

Not implemented.

Member Function Documentation

getDefaultParameters()

virtual Param getDefaultParameters ( ) const

inlinevirtual

Returns the default parameters. Reimplement.

Reimplement if you derive a class and have to incorporate sub-algorithm default parameters.

References DefaultParamHandler::defaults_.

operator=()

FeatureFinderAlgorithm& operator= ( const FeatureFinderAlgorithm &  )

private

Not implemented.

registerChildren()

static void registerChildren ( )

static

register all derived classes here (see FeatureFinderAlgorithm_impl.h)

run()

virtual void run ( )

pure virtual

Main method that implements the actual algorithm.

Implemented in FeatureFinderAlgorithmSH, FeatureFinderAlgorithmPicked, FeatureFinderAlgorithmMRM, and FeatureFinderAlgorithmIsotopeWavelet.

setData()

void setData ( const MapType &  map, FeatureMap &  features, FeatureFinder &  ff  )

inline

Sets a reference to the calling FeatureFinder.

References FeatureFinderAlgorithm::features_, FeatureFinderAlgorithm::ff_, and FeatureFinderAlgorithm::map_.

setSeeds()

virtual void setSeeds ( const FeatureMap &  seeds )

inlinevirtual

Sets a reference to the calling FeatureFinder.

Exceptions

Exception::IllegalArgument

is thrown if the algorithm does not support user-specified seed lists

Reimplemented in FeatureFinderAlgorithmPicked.

Member Data Documentation

features_

FeatureMap* features_

protected

Output data pointer.

Referenced by FeatureFinderAlgorithm::setData().

ff_

FeatureFinder* ff_

protected

Pointer to the calling FeatureFinder that is used to access the feature flags.

Referenced by FeatureFinderAlgorithm::setData().

map_

const MapType* map_

protected

Input data pointer.

Referenced by FeatureFinderAlgorithm::setData().