MapAlignmentAlgorithmPoseClustering.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Eva Lange, Clemens Groepl $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/StablePairFinder.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MapAlignmentAlgorithmPoseClustering :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    MapAlignmentAlgorithmPoseClustering();
 
    ~MapAlignmentAlgorithmPoseClustering() override;
 
    void align(const FeatureMap& map, TransformationDescription& trafo);
    void align(const PeakMap& map, TransformationDescription& trafo);
    void align(const ConsensusMap& map, TransformationDescription& trafo);
 
    void setReference(const FeatureMap& map);
 
    void setReference(const PeakMap& map);
 
protected:
 
    void updateMembers_() override;
 
    static void selectPeaks_(UInt64 map_index, const PeakMap& map, ConsensusMap& output, Size n);
 
    static void selectSpreadPeaks_(UInt64 map_index, const PeakMap& map, ConsensusMap& output, Size n,
                                   double rt_window, double mz_tolerance_ppm, Size max_charge, Size rt_bins, Size mz_bins);
 
    void selectPeakLandmarks_(UInt64 map_index, const PeakMap& map, ConsensusMap& output) const;
 
    static void selectFeatures_(UInt64 map_index, const FeatureMap& map, ConsensusMap& output, Size n);
 
    PoseClusteringAffineSuperimposer superimposer_;
 
    StablePairFinder pairfinder_;
 
    ConsensusMap reference_;
 
    Int max_num_peaks_considered_;
 
    bool spread_peaks_ = true;
    double spread_rt_window_ = 20.0;
    double spread_mz_tolerance_ppm_ = 10.0;
    Size spread_max_charge_ = 4;
    Size spread_rt_bins_ = 10;
    Size spread_mz_bins_ = 10;
 
private:
 
    MapAlignmentAlgorithmPoseClustering(const MapAlignmentAlgorithmPoseClustering&);
    MapAlignmentAlgorithmPoseClustering& operator=(const MapAlignmentAlgorithmPoseClustering&);
  };
} // namespace OpenMS