| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Member Functions | Protected Attributes | Private Member Functions | List of all members
FeatureFinderAlgorithm Class Referenceabstract

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 | ( |  | ) |

inline override

destructor

## ◆ FeatureFinderAlgorithm() [2/2]

FeatureFinderAlgorithm | ( | const FeatureFinderAlgorithm & |  | ) |

private

Not implemented.

## Member Function Documentation

## ◆ getDefaultParameters()

virtual Param getDefaultParameters | ( |  | ) | const

inline virtual

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 | ) |

inline virtual

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().