SONARScoring.h

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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#ifndef OPENMS_ANALYSIS_OPENSWATH_SONARSCORING_H
#define OPENMS_ANALYSIS_OPENSWATH_SONARSCORING_H

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ITransition.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>

namespace OpenMS
{
  class OPENMS_DLLAPI SONARScoring :
    public DefaultParamHandler
  {
public:


    SONARScoring();

    virtual ~SONARScoring() {}
    //

    void computeSonarScores(OpenSwath::IMRMFeature* imrmfeature,
                      const std::vector<OpenSwath::LightTransition> & transitions,
                      std::vector<OpenSwath::SwathMap>& swath_maps,
                      OpenSwath_Scores & scores);

private:

    void computeXCorr_(std::vector<std::vector<double> >& sonar_profiles,
                       double& xcorr_coelution_score, double& xcorr_shape_score);

    SONARScoring(const SONARScoring& rhs);

    SONARScoring& operator=(const SONARScoring& rhs);

    void updateMembers_();

    double dia_extract_window_;
    bool dia_centroided_;

  };
}

#endif // OPENMS_ANALYSIS_OPENSWATH_SONARSCORING_H