OpenMS
2.6.0
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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... | |
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... | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &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.
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inline |
default constructor
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inlineoverride |
destructor
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private |
Not implemented.
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inlinevirtual |
Returns the default parameters. Reimplement.
Reimplement if you derive a class and have to incorporate sub-algorithm default parameters.
References DefaultParamHandler::defaults_.
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private |
Not implemented.
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static |
register all derived classes here (see FeatureFinderAlgorithm_impl.h)
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pure virtual |
Main method that implements the actual algorithm.
Implemented in FeatureFinderAlgorithmSH, FeatureFinderAlgorithmPicked, FeatureFinderAlgorithmMRM, and FeatureFinderAlgorithmIsotopeWavelet.
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inline |
Sets a reference to the calling FeatureFinder.
References FeatureFinderAlgorithm::features_, FeatureFinderAlgorithm::ff_, and FeatureFinderAlgorithm::map_.
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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.
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protected |
Output data pointer.
Referenced by FeatureFinderAlgorithm::setData().
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protected |
Pointer to the calling FeatureFinder that is used to access the feature flags.
Referenced by FeatureFinderAlgorithm::setData().
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protected |
Input data pointer.
Referenced by FeatureFinderAlgorithm::setData().