Implements a module of the FeatureFinder algorithm. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeaFiModule.h>
 
  
 | Public Types | |
| typedef FeatureMap< FeatureType > | FeatureMapType | 
| Output feature map type.  More... | |
| typedef MSExperiment< PeakType > | MapType | 
| 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< FeatureType > *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 indexwith the index of next peak in m/z dimension  More... | |
| void | getPrevMz (FeatureFinderDefs::IndexPair &index) const | 
| fills indexwith the index of previous peak in m/z dimension  More... | |
| void | getNextRt (FeatureFinderDefs::IndexPair &index) | 
| fills indexwith the index of the nearest peak in the next scan  More... | |
| void | getPrevRt (FeatureFinderDefs::IndexPair &index) | 
| fills indexwith 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 setand adds it to thefeature.  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... | |
| Protected Attributes | |
| const MapType * | map_ | 
| Input data pointer.  More... | |
| FeatureMapType * | features_ | 
| Output data pointer.  More... | |
| FeatureFinder * | ff_ | 
| 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< 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 | |
| FeaFiModule () | |
| Not implemented.  More... | |
| FeaFiModule & | operator= (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... | |
Implements a module of the FeatureFinder algorithm.
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.
| 
 | inline | 
Constructor.
References FeaFiModule< PeakType, FeatureType >::features_, FeaFiModule< PeakType, FeatureType >::ff_, and FeaFiModule< PeakType, FeatureType >::map_.
| 
 | inlinevirtual | 
destructor
| 
 | private | 
Not implemented.
| 
 | private | 
Not implemented.
| 
 | inline | 
Calculates the convex hull of a index set and adds it to the feature. 
References Feature::getConvexHulls(), Peak2D::MZ, and Peak2D::RT.
Referenced by ModelFitter< PeakType, FeatureType >::fit().
| 
 | inline | 
fills index with the index of next peak in m/z dimension 
| 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_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by SimpleExtender< PeakType, FeatureType >::moveMzUp_().
| 
 | inline | 
fills index with the index of the nearest peak in the next scan 
| 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_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by SimpleExtender< PeakType, FeatureType >::moveRtUp_().
| 
 | inline | 
Returns the intensity of a peak.
References FeaFiModule< PeakType, FeatureType >::map_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().
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_().
| 
 | inline | 
Returns the m/z of a peak.
References FeaFiModule< PeakType, FeatureType >::map_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().
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_().
| 
 | inline | 
Returns the retention time of a peak.
References FeaFiModule< PeakType, FeatureType >::map_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by ModelFitter< PeakType, FeatureType >::doProjectionDim_(), SimpleExtender< PeakType, FeatureType >::extend(), ModelFitter< PeakType, FeatureType >::fit(), SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_(), and SimpleExtender< PeakType, FeatureType >::writeDebugFile_().
| 
 | inline | 
fills index with the index of previous peak in m/z dimension 
| 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_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by SimpleExtender< PeakType, FeatureType >::moveMzDown_().
| 
 | inline | 
fills index with the index of the nearest peak in the previous scan 
| 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_, OPENMS_PRECONDITION, and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by SimpleExtender< PeakType, FeatureType >::moveRtDown_().
| 
 | private | 
Not implemented.
| 
 | protected | 
Output data pointer.
Referenced by FeaFiModule< PeakType, FeatureType >::FeaFiModule().
| 
 | 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().
| 
 | 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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |