OpenMS
MapAlignmentAlgorithmPoseClustering.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Eva Lange, Clemens Groepl $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
17 
19 
20 namespace OpenMS
21 {
45  public DefaultParamHandler,
46  public ProgressLogger
47  {
48 public:
51 
54 
55  void align(const FeatureMap& map, TransformationDescription& trafo);
56  void align(const PeakMap& map, TransformationDescription& trafo);
57  void align(const ConsensusMap& map, TransformationDescription& trafo);
58 
60  template <typename MapType>
61  void setReference(const MapType& map)
62  {
63  MapType map2 = map; // todo: avoid copy (MSExperiment version of convert() demands non-const version)
64  MapConversion::convert(0, map2, reference_, max_num_peaks_considered_);
65  }
66 
67 protected:
68 
69  void updateMembers_() override;
70 
72 
74 
76 
78 
79 private:
80 
85  };
86 } // namespace OpenMS
87 
A container for consensus elements.
Definition: ConsensusMap.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
A container for features.
Definition: FeatureMap.h:80
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:46
A map alignment algorithm based on pose clustering.
Definition: MapAlignmentAlgorithmPoseClustering.h:47
Int max_num_peaks_considered_
Definition: MapAlignmentAlgorithmPoseClustering.h:77
ConsensusMap reference_
Definition: MapAlignmentAlgorithmPoseClustering.h:75
MapAlignmentAlgorithmPoseClustering()
Default constructor.
PoseClusteringAffineSuperimposer superimposer_
Definition: MapAlignmentAlgorithmPoseClustering.h:71
void setReference(const MapType &map)
Sets the reference for the alignment.
Definition: MapAlignmentAlgorithmPoseClustering.h:61
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:73
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:42
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
This class implements a pair finding algorithm for consensus features.
Definition: StablePairFinder.h:85
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:37
int Int
Signed integer type.
Definition: Types.h:76
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22