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MapAlignmentAlgorithmPoseClustering.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Eva Lange, Clemens Groepl $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
38 #include <OpenMS/ANALYSIS/MAPMATCHING/StablePairFinder.h>
39 #include <OpenMS/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
42 #include <OpenMS/KERNEL/ConsensusMap.h>
43
44 #include <OpenMS/KERNEL/ConversionHelper.h>
45
46 namespace OpenMS
47 {
70 class OPENMS_DLLAPI MapAlignmentAlgorithmPoseClustering :
71 public DefaultParamHandler,
72 public ProgressLogger
73 {
74 public:
76 MapAlignmentAlgorithmPoseClustering();
77
79 ~MapAlignmentAlgorithmPoseClustering() override;
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
97 PoseClusteringAffineSuperimposer superimposer_;
98
99 StablePairFinder pairfinder_;
100
101 ConsensusMap reference_;
102
103 Int max_num_peaks_considered_;
104
105 private:
106
108 MapAlignmentAlgorithmPoseClustering(const MapAlignmentAlgorithmPoseClustering&);
110 MapAlignmentAlgorithmPoseClustering& operator=(const MapAlignmentAlgorithmPoseClustering&);
111 };
112 } // namespace OpenMS
113
PoseClusteringAffineSuperimposer.h
OpenMS::StablePairFinder
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:109
OpenMS::MapAlignmentAlgorithmPoseClustering::max_num_peaks_considered_
Int max_num_peaks_considered_
Definition: MapAlignmentAlgorithmPoseClustering.h:103
OpenMS::MapAlignmentAlgorithmPoseClustering::pairfinder_
StablePairFinder pairfinder_
Definition: MapAlignmentAlgorithmPoseClustering.h:99
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::PoseClusteringAffineSuperimposer
A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transf...
Definition: PoseClusteringAffineSuperimposer.h:66
OpenMS::MapAlignmentAlgorithmPoseClustering::reference_
ConsensusMap reference_
Definition: MapAlignmentAlgorithmPoseClustering.h:101
ConsensusMap.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
OpenMS::MapAlignmentAlgorithmPoseClustering::setReference
void setReference(const MapType &map)
Sets the reference for the alignment.
Definition: MapAlignmentAlgorithmPoseClustering.h:87
ConversionHelper.h
ProgressLogger.h
StablePairFinder.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
TransformationDescription.h
DefaultParamHandler.h
int
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
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::MapAlignmentAlgorithmPoseClustering
A map alignment algorithm based on pose clustering.
Definition: MapAlignmentAlgorithmPoseClustering.h:70
OpenMS::MapAlignmentAlgorithmPoseClustering::superimposer_
PoseClusteringAffineSuperimposer superimposer_
Definition: MapAlignmentAlgorithmPoseClustering.h:97