Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Types | Public Member Functions | Protected Attributes | Private Member Functions

FeaFiModule< PeakType, FeatureType > Class Template Reference

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

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

Inheritance diagram for FeaFiModule< PeakType, FeatureType >:
DefaultParamHandler ModelFitter< PeakType, FeatureType > SimpleExtender< PeakType, FeatureType > SimpleSeeder< PeakType, FeatureType >

List of all members.

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
 fills index with the index of next peak in m/z dimension
void getPrevMz (FeatureFinderDefs::IndexPair &index) const
 fills index with the index of previous peak in m/z dimension
void getNextRt (FeatureFinderDefs::IndexPair &index)
 fills index with the index of the nearest peak in the next scan
void getPrevRt (FeatureFinderDefs::IndexPair &index)
 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 MapType * map_
 Input data pointer.
FeatureMapType * features_
 Output data pointer.
FeatureFinder * ff_
 Pointer to the calling FeatureFinder that is used to access the feature flags and report progress.

Private Member Functions

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

Detailed Description

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

Implements a module of the FeatureFinder algorithm.

Member Typedef Documentation

typedef PeakType::CoordinateType CoordinateType

Input coordinate type.

typedef FeatureMap<FeatureType> FeatureMapType

Output feature map type.

typedef PeakType::IntensityType IntensityType

Input intensity type.

typedef MSExperiment<PeakType> MapType

Input map type.

typedef MapType::SpectrumType SpectrumType

Input spectrum type.

Constructor & Destructor Documentation

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

Constructor.

References FeaFiModule< PeakType, FeatureType >::features_, FeaFiModule< PeakType, FeatureType >::ff_, and FeaFiModule< PeakType, FeatureType >::map_.

virtual ~FeaFiModule (  )  [inline, virtual]

destructor

FeaFiModule (  )  [private]

Not implemented.

FeaFiModule ( const FeaFiModule< PeakType, FeatureType > &   )  [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().

Referenced by ModelFitter< PeakType, FeatureType >::fit().

void getNextMz ( FeatureFinderDefs::IndexPair &  index  )  const [inline]

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

Exceptions:
FeatureFinderDefs::NoSuccessor is thrown if there is no next peak
Exception::Precondition is thrown if an invalid index is given

References FeaFiModule< PeakType, FeatureType >::map_, and OPENMS_PRECONDITION.

Referenced by SimpleExtender< PeakType, FeatureType >::moveMzUp_().

void getNextRt ( FeatureFinderDefs::IndexPair &  index  )  [inline]

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

Exceptions:
FeatureFinderDefs::NoSuccessor is thrown if there is no next spectrum
Exception::Precondition is thrown if an invalid index is given

References FeaFiModule< PeakType, FeatureType >::map_, and OPENMS_PRECONDITION.

Referenced by SimpleExtender< PeakType, FeatureType >::moveRtUp_().

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

Returns the intensity of a peak.

References FeaFiModule< PeakType, FeatureType >::map_, and OPENMS_PRECONDITION.

Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), ModelFitter< PeakType, FeatureType >::doProjectionDim_(), ModelFitter< PeakType, FeatureType >::evaluate_(), SimpleExtender< PeakType, FeatureType >::extend(), ModelFitter< PeakType, FeatureType >::fit(), and SimpleSeeder< PeakType, FeatureType >::initialize_().

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

Returns the m/z of a peak.

References FeaFiModule< PeakType, FeatureType >::map_, and OPENMS_PRECONDITION.

Referenced by ModelFitter< PeakType, FeatureType >::doProjectionDim_(), ModelFitter< PeakType, FeatureType >::evaluate_(), SimpleExtender< PeakType, FeatureType >::extend(), ModelFitter< PeakType, FeatureType >::fit(), SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_(), and SimpleExtender< PeakType, FeatureType >::writeDebugFile_().

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

Returns the retention time of a peak.

References FeaFiModule< PeakType, FeatureType >::map_, and OPENMS_PRECONDITION.

Referenced by ModelFitter< PeakType, FeatureType >::doProjectionDim_(), SimpleExtender< PeakType, FeatureType >::extend(), ModelFitter< PeakType, FeatureType >::fit(), SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_(), and SimpleExtender< PeakType, FeatureType >::writeDebugFile_().

void getPrevMz ( FeatureFinderDefs::IndexPair &  index  )  const [inline]

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

Exceptions:
FeatureFinderDefs::NoSuccessor is thrown if there is no previous peak
Exception::Precondition is thrown if an invalid index is given

References FeaFiModule< PeakType, FeatureType >::map_, and OPENMS_PRECONDITION.

Referenced by SimpleExtender< PeakType, FeatureType >::moveMzDown_().

void getPrevRt ( FeatureFinderDefs::IndexPair &  index  )  [inline]

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

Exceptions:
FeatureFinderDefs::NoSuccessor is thrown if there is no previous spectrum
Exception::Precondition is thrown if an invalid index is given

References FeaFiModule< PeakType, FeatureType >::map_, and OPENMS_PRECONDITION.

Referenced by SimpleExtender< PeakType, FeatureType >::moveRtDown_().

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

Not implemented.

Member Data Documentation

FeatureMapType* features_ [protected]

Output data pointer.

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

FeatureFinder* ff_ [protected]

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

Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), SimpleExtender< PeakType, FeatureType >::extend(), FeaFiModule< PeakType, FeatureType >::FeaFiModule(), ModelFitter< PeakType, FeatureType >::fit(), SimpleSeeder< PeakType, FeatureType >::initialize_(), and SimpleSeeder< PeakType, FeatureType >::nextSeed().

const MapType* map_ [protected]

Input data pointer.

Referenced by SimpleExtender< PeakType, FeatureType >::computePeakPriority_(), FeaFiModule< PeakType, FeatureType >::FeaFiModule(), FeaFiModule< PeakType, FeatureType >::getNextMz(), FeaFiModule< PeakType, FeatureType >::getNextRt(), FeaFiModule< PeakType, FeatureType >::getPeakIntensity(), FeaFiModule< PeakType, FeatureType >::getPeakMz(), FeaFiModule< PeakType, FeatureType >::getPeakRt(), FeaFiModule< PeakType, FeatureType >::getPrevMz(), FeaFiModule< PeakType, FeatureType >::getPrevRt(), and SimpleSeeder< PeakType, FeatureType >::initialize_().

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1