SpectraSTSimilarityScore.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: David Wojnar $
// $Authors: David Wojnar $
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#ifndef OPENMS_COMPARISON_SPECTRA_SPECTRASTSIMILARITYSCORE_H
#define OPENMS_COMPARISON_SPECTRA_SPECTRASTSIMILARITYSCORE_H

#include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>

namespace OpenMS
{

  class OPENMS_DLLAPI SpectraSTSimilarityScore :
    public PeakSpectrumCompareFunctor
  {
public:

    // @name Constructors and Destructors
    // @{
    SpectraSTSimilarityScore();

    SpectraSTSimilarityScore(const SpectraSTSimilarityScore & source);

    virtual ~SpectraSTSimilarityScore();
    // @}

    SpectraSTSimilarityScore & operator=(const SpectraSTSimilarityScore & source);

    DoubleReal operator()(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const;
    DoubleReal operator()(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2)   const;
    DoubleReal operator()(const PeakSpectrum & spec) const;

    bool preprocess(PeakSpectrum & spec, Real remove_peak_intensity_threshold = 2.01, UInt cut_peaks_below = 1000, Size min_peak_number = 5, Size max_peak_number = 150);


    BinnedSpectrum transform(const PeakSpectrum & spec);

    DoubleReal dot_bias(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2, DoubleReal dot_product = -1) const;

    DoubleReal delta_D(DoubleReal top_hit, DoubleReal runner_up);

    DoubleReal compute_F(DoubleReal dot_product, DoubleReal delta_D, DoubleReal dot_bias);



    static PeakSpectrumCompareFunctor * create() { return new SpectraSTSimilarityScore(); }

    static const String getProductName()
    {
      return "SpectraSTSimilarityScore";
    }

protected:


  };

}
#endif //OPENMS_COMPARISON_SPECTRA_SPECTRASTSIMILARTIYSCORE_H