AScore.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: David Wojnar $
// $Authors: David Wojnar $
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#ifndef  OPENMS_ANALYSIS_ID_ASCORE_H
#define  OPENMS_ANALYSIS_ID_ASCORE_H

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <vector>

namespace OpenMS
{
  class PeptideHit;
  class AASequence;
  struct ProbablePhosphoSites
  {
    Size first;
    Size second;
    Size seq_1;
    Size seq_2;
    Size peak_depth;
    Size AScore;
  };
  class OPENMS_DLLAPI AScore
  {
public:
    AScore();
    ~AScore();

    PeptideHit compute(PeptideHit & hit, RichPeakSpectrum & real_spectrum, DoubleReal fmt, Int number_of_phospho_sites);

    DoubleReal computeCumulativeScore(UInt N, UInt n, DoubleReal p);

    void computeHighestPeptides(std::vector<std::vector<DoubleReal> > & peptide_site_scores, std::vector<ProbablePhosphoSites> & sites, std::vector<std::vector<Size> > & permutations);
    void compute_site_determining_ions(std::vector<RichPeakSpectrum> & th_spectra, ProbablePhosphoSites & candidates, Int charge, std::vector<RichPeakSpectrum> & site_determining_ions);
private:
    Int numberOfMatchedIons_(const RichPeakSpectrum & th, const RichPeakSpectrum & windows, Size depth, DoubleReal fmt);
    DoubleReal peptideScore_(std::vector<DoubleReal> & scores);
public:
    std::vector<Size> computeTupel_(AASequence & without_phospho);
    std::vector<std::vector<Size> > computePermutations_(std::vector<Size> tupel, Int number_of_phospho_sites);
  };

} // namespace OpenMS

#endif // OPENMS_ANALYSIS_ID_ASCORE_H