Abstract base class for FeatureFinder algorithms. More...

#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithm.h>

Inheritance diagram for FeatureFinderAlgorithm:

Collaboration 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 Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

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

	~FeatureFinderAlgorithm () override
	destructor More...

virtual void	run ()=0
	register all derived classes here (see FeatureFinderAlgorithm_impl.h) More...

virtual Param	getDefaultParameters () const
	Returns the default parameters. Reimplement. More...

void	setData (const MapType &map, FeatureMap &features)
	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...

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Attributes
const MapType *	map_
	Input data pointer. More...

FeatureMap *	features_
	Output data pointer. 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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

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

	FeatureFinderAlgorithm (const FeatureFinderAlgorithm &)
	Not implemented. More...

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
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...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

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.

◆ run()

virtual void run ( )

pure virtual

register all derived classes here (see FeatureFinderAlgorithm_impl.h)

Main method that implements the actual algorithm

◆ setData()

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

inline

Sets a reference to the calling FeatureFinder.

References FeatureFinderAlgorithm::features_, 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

References ExposedVector< VectorElement >::empty().

Member Data Documentation

◆ features_

FeatureMap* features_

protected

Output data pointer.

Referenced by FeatureFinderAlgorithm::setData().

◆ map_

const MapType* map_