MapAlignmentAlgorithmPoseClustering.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg $
// $Authors: Eva Lange, Clemens Groepl $
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#ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_H
#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMPOSECLUSTERING_H

#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/ConversionHelper.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MapAlignmentAlgorithmPoseClustering :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    MapAlignmentAlgorithmPoseClustering();

    virtual ~MapAlignmentAlgorithmPoseClustering();

    void align(const FeatureMap& map, TransformationDescription& trafo);
    void align(const PeakMap& 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)
      MapConversion::convert(0, map2, reference_, max_num_peaks_considered_);
    }

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