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FeaFiModule< PeakType > Class Template Reference

Implements a module of the FeatureFinder algorithm. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeaFiModule.h>

Inheritance diagram for FeaFiModule< PeakType >:
DefaultParamHandler

Public Types

typedef MSExperiment< PeakTypeMapType
 Input map type. More...
 
typedef MapType::SpectrumType SpectrumType
 Input spectrum type. More...
 
typedef PeakType::IntensityType IntensityType
 Input intensity type. More...
 
typedef PeakType::CoordinateType CoordinateType
 Input coordinate type. More...
 

Public Member Functions

 FeaFiModule (const MSExperiment< PeakType > *map, FeatureMap *features, FeatureFinder *ff)
 Constructor. More...
 
virtual ~FeaFiModule ()
 destructor More...
 
IntensityType getPeakIntensity (const FeatureFinderDefs::IndexPair &index) const
 Returns the intensity of a peak. More...
 
CoordinateType getPeakMz (const FeatureFinderDefs::IndexPair &index) const
 Returns the m/z of a peak. More...
 
CoordinateType getPeakRt (const FeatureFinderDefs::IndexPair &index) const
 Returns the retention time of a peak. More...
 
void getNextMz (FeatureFinderDefs::IndexPair &index) const
 fills index with the index of next peak in m/z dimension More...
 
void getPrevMz (FeatureFinderDefs::IndexPair &index) const
 fills index with the index of previous peak in m/z dimension More...
 
void getNextRt (FeatureFinderDefs::IndexPair &index)
 fills index with the index of the nearest peak in the next scan More...
 
void getPrevRt (FeatureFinderDefs::IndexPair &index)
 fills index with the index of the nearest peak in the previous scan More...
 
void addConvexHull (const FeatureFinderDefs::IndexSet &set, Feature &feature) const
 Calculates the convex hull of a index set and adds it to the feature. 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 DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 

Protected Attributes

const MapTypemap_
 Input data pointer. More...
 
FeatureMapfeatures_
 Output data pointer. More...
 
FeatureFinderff_
 Pointer to the calling FeatureFinder that is used to access the feature flags and report progress. 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< Stringsubsections_
 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

 FeaFiModule ()
 Not implemented. More...
 
FeaFiModuleoperator= (const FeaFiModule &)
 Not implemented. More...
 
 FeaFiModule (const FeaFiModule &)
 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

template<class PeakType>
class OpenMS::FeaFiModule< PeakType >

Implements a module of the FeatureFinder algorithm.

Member Typedef Documentation

Input coordinate type.

Input intensity type.

Input map type.

Input spectrum type.

Constructor & Destructor Documentation

FeaFiModule ( const MSExperiment< PeakType > *  map,
FeatureMap features,
FeatureFinder ff 
)
inline
virtual ~FeaFiModule ( )
inlinevirtual

destructor

FeaFiModule ( )
private

Not implemented.

FeaFiModule ( const FeaFiModule< PeakType > &  )
private

Not implemented.

Member Function Documentation

void addConvexHull ( const FeatureFinderDefs::IndexSet set,
Feature feature 
) const
inline

Calculates the convex hull of a index set and adds it to the feature.

References Feature::getConvexHulls(), Peak2D::MZ, and Peak2D::RT.

void getNextMz ( FeatureFinderDefs::IndexPair index) const
inline

fills index with the index of next peak in m/z dimension

Exceptions
FeatureFinderDefs::NoSuccessoris thrown if there is no next peak
Exception::Preconditionis thrown if an invalid index is given

References FeaFiModule< PeakType >::map_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().

void getNextRt ( FeatureFinderDefs::IndexPair index)
inline

fills index with the index of the nearest peak in the next scan

Exceptions
FeatureFinderDefs::NoSuccessoris thrown if there is no next spectrum
Exception::Preconditionis thrown if an invalid index is given

References FeaFiModule< PeakType >::map_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().

IntensityType getPeakIntensity ( const FeatureFinderDefs::IndexPair index) const
inline
CoordinateType getPeakMz ( const FeatureFinderDefs::IndexPair index) const
inline
CoordinateType getPeakRt ( const FeatureFinderDefs::IndexPair index) const
inline
void getPrevMz ( FeatureFinderDefs::IndexPair index) const
inline

fills index with the index of previous peak in m/z dimension

Exceptions
FeatureFinderDefs::NoSuccessoris thrown if there is no previous peak
Exception::Preconditionis thrown if an invalid index is given

References FeaFiModule< PeakType >::map_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().

void getPrevRt ( FeatureFinderDefs::IndexPair index)
inline

fills index with the index of the nearest peak in the previous scan

Exceptions
FeatureFinderDefs::NoSuccessoris thrown if there is no previous spectrum
Exception::Preconditionis thrown if an invalid index is given

References FeaFiModule< PeakType >::map_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().

FeaFiModule& operator= ( const FeaFiModule< PeakType > &  )
private

Not implemented.

Member Data Documentation

FeatureMap* features_
protected

Output data pointer.

Referenced by FeaFiModule< PeakType >::FeaFiModule().

FeatureFinder* ff_
protected

Pointer to the calling FeatureFinder that is used to access the feature flags and report progress.

Referenced by FeaFiModule< PeakType >::FeaFiModule().

const MapType* map_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:00 using doxygen 1.8.9.1