MapAlignmentAlgorithmPoseClustering.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Clemens Groepl $
// $Authors: Eva Lange, Clemens Groepl $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_H
#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_H

#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/StablePairFinder.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/PoseClusteringAffineSuperimposer.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MapAlignmentAlgorithmPoseClustering :
    public MapAlignmentAlgorithm
  {
public:
    MapAlignmentAlgorithmPoseClustering();

    virtual ~MapAlignmentAlgorithmPoseClustering();

    void align(const FeatureMap<> & map, TransformationDescription & trafo);
    void align(const MSExperiment<> & map, TransformationDescription & trafo);
    void align(const ConsensusMap & map, TransformationDescription & trafo);

    template <typename MapType>
    void setReference(const MapType & map)
    {
      MapType map2 = map; // todo: avoid copy (MSExperiment version of convert() demands non-const version)
      ConsensusMap::convert(0, map2, reference_, max_num_peaks_considered_);
    }

    static MapAlignmentAlgorithm * create()
    {
      return new MapAlignmentAlgorithmPoseClustering();
    }

    static String getProductName()
    {
      return "pose_clustering";
    }

protected:

    virtual void updateMembers_();

    PoseClusteringAffineSuperimposer superimposer_;

    StablePairFinder pairfinder_;

    ConsensusMap reference_;

    Int max_num_peaks_considered_;

private:

    MapAlignmentAlgorithmPoseClustering(const MapAlignmentAlgorithmPoseClustering &);
    MapAlignmentAlgorithmPoseClustering & operator=(const MapAlignmentAlgorithmPoseClustering &);
  };
} // namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_H