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 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 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_.
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inlinevirtual |
destructor
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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_().
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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_().
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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_().
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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_().
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private |
Not implemented.
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protected |
Output data pointer.
Referenced by FeaFiModule< PeakType, FeatureType >::FeaFiModule().
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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().
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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 |