OpenMS
FeatureFinderAlgorithm Class Referenceabstract

Abstract base class for FeatureFinder algorithms. More...

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

Inheritance diagram for FeatureFinderAlgorithm:
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Collaboration diagram for FeatureFinderAlgorithm:
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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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 
- 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 Attributes

const MapTypemap_
 Input data pointer. More...
 
FeatureMapfeatures_
 Output data pointer. More...
 
FeatureFinderff_
 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< Stringsubsections_
 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

FeatureFinderAlgorithmoperator= (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

Coordinate/Position type of peaks.

◆ IntensityType

Intensity type of peaks.

◆ MapType

typedef PeakMap MapType

Input map type.

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithm() [1/2]

default constructor

◆ ~FeatureFinderAlgorithm()

~FeatureFinderAlgorithm ( )
inlineoverride

destructor

◆ FeatureFinderAlgorithm() [2/2]

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 FeatureFinderAlgorithmPicked, FeatureFinderAlgorithmMRM, and FeatureFinderAlgorithmIsotopeWavelet.

◆ setData()

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

◆ setSeeds()

virtual void setSeeds ( const FeatureMap seeds)
inlinevirtual

Sets a reference to the calling FeatureFinder.

Exceptions
Exception::IllegalArgumentis thrown if the algorithm does not support user-specified seed lists

Reimplemented in FeatureFinderAlgorithmPicked.

References ExposedVector< VectorElement >::empty().

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().