OpenMS  3.0.0
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 
DefaultParamHandler.h
ConversionHelper.h
OpenMS::MapConversion::convert
static void convert(UInt64 const input_map_index, PeakMap &input_map, ConsensusMap &output_map, Size n=-1)
Similar to convert for FeatureMaps.
OpenMS::PoseClusteringAffineSuperimposer
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transf...
Definition: PoseClusteringAffineSuperimposer.h:66
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
PoseClusteringAffineSuperimposer.h
TransformationDescription.h
OpenMS::MapAlignmentAlgorithmPoseClustering::max_num_peaks_considered_
Int max_num_peaks_considered_
Definition: MapAlignmentAlgorithmPoseClustering.h:103
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
StablePairFinder.h
OpenMS::StablePairFinder
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:109
OpenMS::MapAlignmentAlgorithmPoseClustering
A map alignment algorithm based on pose clustering.
Definition: MapAlignmentAlgorithmPoseClustering.h:70
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::MapAlignmentAlgorithmPoseClustering::reference_
ConsensusMap reference_
Definition: MapAlignmentAlgorithmPoseClustering.h:101
OpenMS::MapAlignmentAlgorithmPoseClustering::superimposer_
PoseClusteringAffineSuperimposer superimposer_
Definition: MapAlignmentAlgorithmPoseClustering.h:97
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:62
OpenMS::MapAlignmentAlgorithmPoseClustering::setReference
void setReference(const MapType &map)
Sets the reference for the alignment.
Definition: MapAlignmentAlgorithmPoseClustering.h:87
OpenMS::MapAlignmentAlgorithmPoseClustering::pairfinder_
StablePairFinder pairfinder_
Definition: MapAlignmentAlgorithmPoseClustering.h:99