MapAlignmentAlgorithm.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: Marc Sturm, Clemens Groepl $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHM_H
#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHM_H

#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>

namespace OpenMS
{

  class OPENMS_DLLAPI MapAlignmentAlgorithm :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    MapAlignmentAlgorithm();

    virtual ~MapAlignmentAlgorithm();

    virtual void alignPeakMaps(std::vector<MSExperiment<> > &, std::vector<TransformationDescription> &);

    virtual void alignCompactFeatureMaps(std::vector<std::vector<Peak2D> > &, std::vector<TransformationDescription> &);

    virtual void alignFeatureMaps(std::vector<FeatureMap<> > &, std::vector<TransformationDescription> &);

    virtual void alignConsensusMaps(std::vector<ConsensusMap> &, std::vector<TransformationDescription> &);

    virtual void alignPeptideIdentifications(std::vector<std::vector<PeptideIdentification> > &, std::vector<TransformationDescription> &);

    virtual void setReference(Size reference_index = 0, const String & reference_file = "");

    static void fitModel(const String & model_type, const Param & params, std::vector<TransformationDescription> & trafos);

    static void registerChildren();

private:
    MapAlignmentAlgorithm(const MapAlignmentAlgorithm &);
    MapAlignmentAlgorithm & operator=(const MapAlignmentAlgorithm &);

  };

} // namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHM_H