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FeaFiModule Class Template Reference
[FeatureFinder]

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

Inheritance diagram for FeaFiModule:

DefaultParamHandler ModelFitter SimpleExtender SimpleSeeder

List of all members.


Detailed Description

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

Implements a module of the FeatureFinder algorithm.

Public Types

typedef FeatureMap< FeatureType > FeatureMapType
 Output feature map type.
typedef MSExperiment< PeakType > MapType
 Input map type.
typedef MapType::SpectrumType SpectrumType
 Input spectrum type.
typedef PeakType::IntensityType IntensityType
 Input intensity type.
typedef PeakType::CoordinateType CoordinateType
 Input coordinate type.

Public Member Functions

 FeaFiModule (const MSExperiment< PeakType > *map, FeatureMap< FeatureType > *features, FeatureFinder *ff)
 Constructor.
virtual ~FeaFiModule ()
 destructor
IntensityType getPeakIntensity (const FeatureFinderDefs::IndexPair &index) const
 Returns the intensity of a peak.
CoordinateType getPeakMz (const FeatureFinderDefs::IndexPair &index) const
 Returns the m/z of a peak.
CoordinateType getPeakRt (const FeatureFinderDefs::IndexPair &index) const
 Returns the retention time of a peak.
void getNextMz (FeatureFinderDefs::IndexPair &index) const throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition)
 fills index with the index of next peak in m/z dimension
void getPrevMz (FeatureFinderDefs::IndexPair &index) const throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition)
 fills index with the index of previous peak in m/z dimension
void getNextRt (FeatureFinderDefs::IndexPair &index) throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition)
 fills index with the index of the nearest peak in the next scan
void getPrevRt (FeatureFinderDefs::IndexPair &index) throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition)
 fills index with the index of the nearest peak in the previous scan
void addConvexHull (const FeatureFinderDefs::IndexSet &set, Feature &feature) const
 Calculates the convex hull of a index set and adds it to the feature.

Protected Attributes

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

Private Member Functions

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

Member Typedef Documentation

typedef FeatureMap<FeatureType> FeatureMapType

Output feature map type.

typedef MSExperiment<PeakType> MapType

Input map type.

typedef MapType::SpectrumType SpectrumType

Input spectrum type.

typedef PeakType::IntensityType IntensityType

Input intensity type.

Reimplemented in ModelFitter, and SimpleExtender.

typedef PeakType::CoordinateType CoordinateType

Input coordinate type.

Reimplemented in ModelFitter, and SimpleExtender.


Constructor & Destructor Documentation

FeaFiModule ( const MSExperiment< PeakType > *  map,
FeatureMap< FeatureType > *  features,
FeatureFinder ff 
) [inline]

Constructor.

virtual ~FeaFiModule (  )  [inline, virtual]

destructor

FeaFiModule (  )  [private]

Not implemented.

FeaFiModule ( const FeaFiModule< PeakType, FeatureType > &   )  [private]

Not implemented.


Member Function Documentation

IntensityType getPeakIntensity ( const FeatureFinderDefs::IndexPair index  )  const [inline]

Returns the intensity of a peak.

CoordinateType getPeakMz ( const FeatureFinderDefs::IndexPair index  )  const [inline]

Returns the m/z of a peak.

CoordinateType getPeakRt ( const FeatureFinderDefs::IndexPair index  )  const [inline]

Returns the retention time of a peak.

void getNextMz ( FeatureFinderDefs::IndexPair index  )  const throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition) [inline]

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

void getPrevMz ( FeatureFinderDefs::IndexPair index  )  const throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition) [inline]

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

void getNextRt ( FeatureFinderDefs::IndexPair index  )  throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition) [inline]

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

void getPrevRt ( FeatureFinderDefs::IndexPair index  )  throw (FeatureFinderDefs::NoSuccessor, Exception::Precondition) [inline]

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

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

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

FeaFiModule& operator= ( const FeaFiModule< PeakType, FeatureType > &   )  [private]

Not implemented.


Member Data Documentation

const MapType* map_ [protected]

Input data pointer.

FeatureMapType* features_ [protected]

Output data pointer.

FeatureFinder* ff_ [protected]

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


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:47 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1