Abstract base class for FeatureFinder algorithms. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
Public Types | |
| typedef MSExperiment< PeakType > | MapType |
| Input map type. | |
| typedef MapType::CoordinateType | CoordinateType |
| Coordinate/Position type of peaks. | |
| typedef MapType::IntensityType | IntensityType |
| Intensity type of peaks. | |
| typedef FeatureMap< FeatureType > | FeatureMapType |
| Output feature type. | |
Public Member Functions | |
| FeatureFinderAlgorithm () | |
| default constructor | |
| virtual | ~FeatureFinderAlgorithm () |
| destructor | |
| virtual void | run ()=0 |
| Main method that implements the actual algorithm. | |
| virtual Param | getDefaultParameters () const |
| Returns the default parameters. Reimplment. | |
| void | setData (const MapType &map, FeatureMapType &features, FeatureFinder &ff) |
| Sets a reference to the calling FeatureFinder. | |
| virtual void | setSeeds (const FeatureMapType &seeds) |
| Sets a reference to the calling FeatureFinder. | |
Static Public Member Functions | |
| static void | registerChildren () |
| register all derived classes here (see FeatureFinderAlgorithm_impl.h) | |
Protected Attributes | |
| const MapType * | map_ |
| Input data pointer. | |
| FeatureMapType * | features_ |
| Output data pointer. | |
| FeatureFinder * | ff_ |
| Pointer to the calling FeatureFinder that is used to access the feature flags. | |
Private Member Functions | |
| FeatureFinderAlgorithm & | operator= (const FeatureFinderAlgorithm &) |
| Not implemented. | |
| FeatureFinderAlgorithm (const FeatureFinderAlgorithm &) | |
| Not implemented. | |
Detailed Description
template<class PeakType, class FeatureType>
class OpenMS::FeatureFinderAlgorithm< PeakType, FeatureType >
Abstract base class for FeatureFinder algorithms.
Member Typedef Documentation
Coordinate/Position type of peaks.
| typedef FeatureMap<FeatureType> FeatureMapType |
Output feature type.
| typedef MapType::IntensityType IntensityType |
Intensity type of peaks.
| typedef MSExperiment<PeakType> MapType |
Input map type.
Constructor & Destructor Documentation
| FeatureFinderAlgorithm | ( | ) | [inline] |
default constructor
| virtual ~FeatureFinderAlgorithm | ( | ) | [inline, virtual] |
destructor
| FeatureFinderAlgorithm | ( | const FeatureFinderAlgorithm< PeakType, FeatureType > & | ) | [private] |
Not implemented.
Member Function Documentation
| virtual Param getDefaultParameters | ( | ) | const [inline, virtual] |
Returns the default parameters. Reimplment.
Reimplment if you derive a class and have to incoopreate sub-algorithm default parameters.
References DefaultParamHandler::defaults_.
| FeatureFinderAlgorithm& operator= | ( | const FeatureFinderAlgorithm< PeakType, FeatureType > & | ) | [private] |
Not implemented.
| void registerChildren | ( | ) | [static] |
register all derived classes here (see FeatureFinderAlgorithm_impl.h)
| virtual void run | ( | ) | [pure virtual] |
Main method that implements the actual algorithm.
Implemented in FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >.
Referenced by FeatureFinder::run().
| void setData | ( | const MapType & | map, | |
| FeatureMapType & | features, | |||
| FeatureFinder & | ff | |||
| ) | [inline] |
Sets a reference to the calling FeatureFinder.
References FeatureFinderAlgorithm< PeakType, FeatureType >::features_, FeatureFinderAlgorithm< PeakType, FeatureType >::ff_, and FeatureFinderAlgorithm< PeakType, FeatureType >::map_.
Referenced by FeatureFinder::run().
| virtual void setSeeds | ( | const FeatureMapType & | 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
Referenced by FeatureFinder::run().
Member Data Documentation
FeatureMapType* features_ [protected] |
Output data pointer.
Referenced by FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSH< PeakType, FeatureType >::run(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run(), FeatureFinderAlgorithm< PeakType, FeatureType >::setData(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::writeFeatureDebugInfo_().
FeatureFinder* ff_ [protected] |
Pointer to the calling FeatureFinder that is used to access the feature flags.
Referenced by FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run(), and FeatureFinderAlgorithm< PeakType, FeatureType >::setData().
Input data pointer.
Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::createHRData(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run(), and FeatureFinderAlgorithm< PeakType, FeatureType >::setData().
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1 |