 |
OpenMS
|
Abstract base class for FeatureFinder algorithms. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
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... | |
| 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... | |
| 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 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... | |
Abstract base class for FeatureFinder algorithms.
Coordinate/Position type of peaks.
| typedef MapType::IntensityType IntensityType |
Intensity type of peaks.
|
inline |
default constructor
|
inlineoverride |
destructor
|
private |
Not implemented.
|
inlinevirtual |
Returns the default parameters. Reimplement.
Reimplement if you derive a class and have to incorporate sub-algorithm default parameters.
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 FeatureFinderAlgorithmPicked, FeatureFinderAlgorithmMRM, and FeatureFinderAlgorithmIsotopeWavelet.
|
inline |
Sets a reference to the calling FeatureFinder.
References FeatureFinderAlgorithm::features_, FeatureFinderAlgorithm::ff_, and FeatureFinderAlgorithm::map_.
|
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.
References ExposedVector< VectorElement >::empty().
|
protected |
Output data pointer.
Referenced by FeatureFinderAlgorithm::setData().
|
protected |
Pointer to the calling FeatureFinder that is used to access the feature flags.
Referenced by FeatureFinderAlgorithm::setData().
|
protected |
Input data pointer.
Referenced by FeatureFinderAlgorithm::setData().
1.9.1 
