Implements a module of the FeatureFinder algorithm. More...

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

Inheritance diagram for FeaFiModule< PeakType >:

Public Types
typedef PeakMap	MapType
	Input map type. More...

typedef MapType::SpectrumType	SpectrumType
	Input spectrum type. More...

typedef PeakType::IntensityType	IntensityType
	Input intensity type. More...

typedef PeakType::CoordinateType	CoordinateType
	Input coordinate type. More...

Public Member Functions
	FeaFiModule (const PeakMap map, FeatureMap features, FeatureFinder *ff)
	Constructor. More...

virtual	~FeaFiModule ()
	destructor More...

IntensityType	getPeakIntensity (const FeatureFinderDefs::IndexPair &index) const
	Returns the intensity of a peak. More...

CoordinateType	getPeakMz (const FeatureFinderDefs::IndexPair &index) const
	Returns the m/z of a peak. More...

CoordinateType	getPeakRt (const FeatureFinderDefs::IndexPair &index) const
	Returns the retention time of a peak. More...

void	getNextMz (FeatureFinderDefs::IndexPair &index) const
	fills `index` with the index of next peak in m/z dimension More...

void	getPrevMz (FeatureFinderDefs::IndexPair &index) const
	fills `index` with the index of previous peak in m/z dimension More...

void	getNextRt (FeatureFinderDefs::IndexPair &index)
	fills `index` with the index of the nearest peak in the next scan More...

void	getPrevRt (FeatureFinderDefs::IndexPair &index)
	fills `index` with the index of the nearest peak in the previous scan More...

void	addConvexHull (const FeatureFinderDefs::IndexSet &set, Feature &feature) const
	Calculates the convex hull of a index `set` and adds it to the `feature`. 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...

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 and report progress. 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
	FeaFiModule ()
	Not implemented. More...

FeaFiModule &	operator= (const FeaFiModule &)
	Not implemented. More...

	FeaFiModule (const FeaFiModule &)
	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

template<class PeakType>
class OpenMS::FeaFiModule< PeakType >

Implements a module of the FeatureFinder algorithm.

Member Typedef Documentation

◆ CoordinateType

typedef PeakType::CoordinateType CoordinateType

Input coordinate type.

◆ IntensityType

typedef PeakType::IntensityType IntensityType

Input intensity type.

◆ MapType

typedef PeakMap MapType

Input map type.

◆ SpectrumType

typedef MapType::SpectrumType SpectrumType

Input spectrum type.

Constructor & Destructor Documentation

◆ FeaFiModule() [1/3]

FeaFiModule	(	const PeakMap *	map,
		FeatureMap *	features,
		FeatureFinder *	ff
	)

inline

Constructor.

◆ ~FeaFiModule()

virtual ~FeaFiModule ( )

inlinevirtual

destructor

◆ FeaFiModule() [2/3]

FeaFiModule ( )

private

Not implemented.

◆ FeaFiModule() [3/3]

FeaFiModule ( const FeaFiModule< PeakType > & )

private

Not implemented.

Member Function Documentation

◆ addConvexHull()

void addConvexHull	(	const FeatureFinderDefs::IndexSet &	set,
		Feature &	feature
	)		const

inline

Calculates the convex hull of a index set and adds it to the feature.

References Feature::getConvexHulls(), Peak2D::MZ, and Peak2D::RT.

◆ getNextMz()

void getNextMz ( FeatureFinderDefs::IndexPair & index ) const

inline

fills index with the index of next peak in m/z dimension

Exceptions

FeatureFinderDefs::NoSuccessor	is thrown if there is no next peak
Exception::Precondition	is thrown if an invalid index is given

References OPENMS_PRECONDITION.

◆ getNextRt()

void getNextRt ( FeatureFinderDefs::IndexPair & index )

inline

fills index with the index of the nearest peak in the next scan

Exceptions

FeatureFinderDefs::NoSuccessor	is thrown if there is no next spectrum
Exception::Precondition	is thrown if an invalid index is given

References OPENMS_PRECONDITION.

◆ getPeakIntensity()

IntensityType getPeakIntensity ( const FeatureFinderDefs::IndexPair & index ) const

inline

Returns the intensity of a peak.

References OPENMS_PRECONDITION.

◆ getPeakMz()

CoordinateType getPeakMz ( const FeatureFinderDefs::IndexPair & index ) const

inline

Returns the m/z of a peak.

References OPENMS_PRECONDITION.

◆ getPeakRt()

CoordinateType getPeakRt ( const FeatureFinderDefs::IndexPair & index ) const

inline

Returns the retention time of a peak.

References OPENMS_PRECONDITION.

◆ getPrevMz()

void getPrevMz ( FeatureFinderDefs::IndexPair & index ) const

inline

fills index with the index of previous peak in m/z dimension

Exceptions

FeatureFinderDefs::NoSuccessor	is thrown if there is no previous peak
Exception::Precondition	is thrown if an invalid index is given

References OPENMS_PRECONDITION.

◆ getPrevRt()

void getPrevRt ( FeatureFinderDefs::IndexPair & index )

inline

fills index with the index of the nearest peak in the previous scan

Exceptions

FeatureFinderDefs::NoSuccessor	is thrown if there is no previous spectrum
Exception::Precondition	is thrown if an invalid index is given

References OPENMS_PRECONDITION.

◆ operator=()

FeaFiModule& operator= ( const FeaFiModule< PeakType > & )

private

Not implemented.

Member Data Documentation

◆ features_

FeatureMap* features_

protected

Output data pointer.

◆ ff_

FeatureFinder* ff_

protected

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

◆ map_

const MapType* map_

protected

Input data pointer.

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

template<class PeakType> class OpenMS::FeaFiModule< PeakType >

Member Typedef Documentation

◆ CoordinateType

◆ IntensityType

◆ MapType

◆ SpectrumType

Constructor & Destructor Documentation

◆ FeaFiModule() [1/3]

◆ ~FeaFiModule()

◆ FeaFiModule() [2/3]

◆ FeaFiModule() [3/3]

Member Function Documentation

◆ addConvexHull()

◆ getNextMz()

◆ getNextRt()

◆ getPeakIntensity()

◆ getPeakMz()

◆ getPeakRt()

◆ getPrevMz()

◆ getPrevRt()

◆ operator=()

Member Data Documentation

◆ features_

◆ ff_

◆ map_

template<class PeakType>
class OpenMS::FeaFiModule< PeakType >