OpenMS
MapAlignmentAlgorithmPoseClustering.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Eva Lange, Clemens Groepl $
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34 
35 #pragma once
36 
43 
45 
46 namespace OpenMS
47 {
71  public DefaultParamHandler,
72  public ProgressLogger
73  {
74 public:
77 
80 
81  void align(const FeatureMap& map, TransformationDescription& trafo);
82  void align(const PeakMap& map, TransformationDescription& trafo);
83  void align(const ConsensusMap& map, TransformationDescription& trafo);
84 
86  template <typename MapType>
87  void setReference(const MapType& map)
88  {
89  MapType map2 = map; // todo: avoid copy (MSExperiment version of convert() demands non-const version)
90  MapConversion::convert(0, map2, reference_, max_num_peaks_considered_);
91  }
92 
93 protected:
94 
95  void updateMembers_() override;
96 
98 
100 
102 
104 
105 private:
106 
111  };
112 } // namespace OpenMS
113 
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
A container for features.
Definition: FeatureMap.h:106
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
A map alignment algorithm based on pose clustering.
Definition: MapAlignmentAlgorithmPoseClustering.h:73
Int max_num_peaks_considered_
Definition: MapAlignmentAlgorithmPoseClustering.h:103
ConsensusMap reference_
Definition: MapAlignmentAlgorithmPoseClustering.h:101
MapAlignmentAlgorithmPoseClustering()
Default constructor.
PoseClusteringAffineSuperimposer superimposer_
Definition: MapAlignmentAlgorithmPoseClustering.h:97
void setReference(const MapType &map)
Sets the reference for the alignment.
Definition: MapAlignmentAlgorithmPoseClustering.h:87
void align(const FeatureMap &map, TransformationDescription &trafo)
void align(const ConsensusMap &map, TransformationDescription &trafo)
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
~MapAlignmentAlgorithmPoseClustering() override
Destructor.
void align(const PeakMap &map, TransformationDescription &trafo)
MapAlignmentAlgorithmPoseClustering(const MapAlignmentAlgorithmPoseClustering &)
Copy constructor intentionally not implemented -> private.
StablePairFinder pairfinder_
Definition: MapAlignmentAlgorithmPoseClustering.h:99
MapAlignmentAlgorithmPoseClustering & operator=(const MapAlignmentAlgorithmPoseClustering &)
Assignment operator intentionally not implemented -> private.
static void convert(UInt64 const input_map_index, PeakMap &input_map, ConsensusMap &output_map, Size n=-1)
Similar to convert for FeatureMaps.
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transf...
Definition: PoseClusteringAffineSuperimposer.h:68
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:111
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:63
int Int
Signed integer type.
Definition: Types.h:102
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48