Abstract base class for FeatureFinder algorithms. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
 
  
 | Public Types | |
| typedef MSExperiment< PeakType > | MapType | 
| Input map type.  More... | |
| typedef MapType::CoordinateType | CoordinateType | 
| Coordinate/Position type of peaks.  More... | |
| typedef MapType::IntensityType | IntensityType | 
| Intensity type of peaks.  More... | |
| typedef FeatureMap< FeatureType > | FeatureMapType | 
| Output feature type.  More... | |
| Public Member Functions | |
| FeatureFinderAlgorithm () | |
| default constructor  More... | |
| virtual | ~FeatureFinderAlgorithm () | 
| destructor  More... | |
| virtual void | run ()=0 | 
| Main method that implements the actual algorithm.  More... | |
| virtual Param | getDefaultParameters () const | 
| Returns the default parameters. Reimplment.  More... | |
| void | setData (const MapType &map, FeatureMapType &features, FeatureFinder &ff) | 
| Sets a reference to the calling FeatureFinder.  More... | |
| virtual void | setSeeds (const FeatureMapType &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 ¶m) | 
| 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... | |
| FeatureMapType * | 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... | |
Abstract base class for FeatureFinder algorithms.
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.
| 
 | inline | 
default constructor
| 
 | inlinevirtual | 
destructor
| 
 | private | 
Not implemented.
| 
 | inlinevirtual | 
Returns the default parameters. Reimplment.
Reimplment if you derive a class and have to incoopreate sub-algorithm default parameters.
Reimplemented in FeatureFinderAlgorithmSimple< PeakType, FeatureType >, and FeatureFinderAlgorithmSimplest< PeakType, FeatureType >.
References DefaultParamHandler::defaults_.
| 
 | private | 
Not implemented.
| 
 | static | 
register all derived classes here (see FeatureFinderAlgorithm_impl.h)
| 
 | pure virtual | 
Main method that implements the actual algorithm.
Implemented in FeatureFinderAlgorithmSH< PeakType, FeatureType >, FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >, FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >, FeatureFinderAlgorithmPicked< PeakType, FeatureType >, FeatureFinderAlgorithmMRM< PeakType, FeatureType >, FeatureFinderAlgorithmSimple< PeakType, FeatureType >, and FeatureFinderAlgorithmSimplest< PeakType, FeatureType >.
Referenced by FeatureFinder::run().
| 
 | 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().
| 
 | inlinevirtual | 
Sets a reference to the calling FeatureFinder.
| Exception::IllegalArgument | is thrown if the algorithm does not support user-specified seed lists | 
Reimplemented in FeatureFinderAlgorithmPicked< PeakType, FeatureType >.
Referenced by FeatureFinder::run().
| 
 | protected | 
Output data pointer.
Referenced by FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run(), FeatureFinderAlgorithmSH< PeakType, FeatureType >::run(), FeatureFinderAlgorithm< PeakType, FeatureType >::setData(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::writeFeatureDebugInfo_().
| 
 | 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(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run(), and FeatureFinderAlgorithm< PeakType, FeatureType >::setData().
| 
 | protected | 
Input data pointer.
Referenced by FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::createHRData(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::getDefaultParameters(), FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run(), and FeatureFinderAlgorithm< PeakType, FeatureType >::setData().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |