AScore.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 2002-2017.
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// $Maintainer: Petra Gutenbrunner $
// $Authors: David Wojnar, Timo Sachsenberg, Petra Gutenbrunner $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_ID_ASCORE_H
#define OPENMS_ANALYSIS_ID_ASCORE_H

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/ANALYSIS/RNPXL/PScore.h>

#include <limits>
#include <vector>

namespace OpenMS
{
class PeptideHit;
class AASequence;
struct ProbablePhosphoSites
{
    Size first;
    Size second;
    Size seq_1; // index of best permutation with site in phosphorylated state
    Size seq_2; // index of permutation with site in unphosphorylated state
    Size peak_depth; // filtering level that gave rise to maximum discriminatory score
    Size AScore;
};
class OPENMS_DLLAPI AScore
{
  friend struct PScore;
  public:
    AScore();

    ~AScore();

    PeptideHit compute(const PeptideHit & hit, PeakSpectrum &real_spectrum, double fragment_mass_tolerance, bool fragment_mass_unit_ppm, Size max_peptide_len = 60, Size max_num_perm = 16384);

  protected:
    int compareMZ_(double mz1, double mz2, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const;
    
    template <class InputIterator1, class InputIterator2, class OutputIterator>
    OutputIterator getSpectrumDifference_(InputIterator1 first1, InputIterator1 last1,
      InputIterator2 first2, InputIterator2 last2, OutputIterator result, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const
    {
      while (first1 != last1 && first2 != last2)
      {
        double mz1 = first1->getMZ();
        double mz2 = first2->getMZ();
        int val = compareMZ_(mz1, mz2, fragment_mass_tolerance, fragment_mass_unit_ppm);
        
        if (val == -1)
        { 
          *result = *first1; 
          ++result; 
          ++first1; 
        }
        else if (val == 1)
        {
          ++first2;
        }
        else // check if more ions are within the same tolerance. If so, these can not be site determining ions
        {
          //check mz2 until no match
          ++first2;
          if (first2 != last2)
          {
            int ret = compareMZ_(mz1, first2->getMZ(), fragment_mass_tolerance, fragment_mass_unit_ppm);
            while (ret == 0 && first2 != last2)
            {
              ++first2;
              ret = compareMZ_(mz1, first2->getMZ(), fragment_mass_tolerance, fragment_mass_unit_ppm);
            }
          }
          
          //check mz1 until no match
          ++first1;
          if (first1 != last1)
          {
            int ret = compareMZ_(first1->getMZ(), mz2, fragment_mass_tolerance, fragment_mass_unit_ppm);
            while (ret == 0 && first1 != last1)
            {
              ++first1;
              ret = compareMZ_(first1->getMZ(), mz2, fragment_mass_tolerance, fragment_mass_unit_ppm);
            }
          }
        }
      }
      return std::copy(first1, last1, result);
    }
    
    void computeSiteDeterminingIons_(const std::vector<PeakSpectrum> & th_spectra, const ProbablePhosphoSites & candidates, std::vector<PeakSpectrum> & site_determining_ions, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const;

    std::vector<Size> getSites_(const AASequence & without_phospho) const;

    std::vector<std::vector<Size> > computePermutations_(const std::vector<Size> & sites, Int n_phosphorylation_events) const;

    Size numberOfMatchedIons_(const PeakSpectrum & th, const PeakSpectrum & windows, Size depth, double fragment_mass_tolerance, bool fragment_mass_tolerance_ppm = false) const;

    double peptideScore_(const std::vector<double> & scores) const;

    void determineHighestScoringPermutations_(const std::vector<std::vector<double> > & peptide_site_scores, std::vector<ProbablePhosphoSites> & sites, const std::vector<std::vector<Size> > & permutations, std::multimap<double, Size>& ranking) const;

    double computeCumulativeScore_(Size N, Size n, double p) const;
    
    Size numberOfPhosphoEvents_(const String sequence) const;
    
    AASequence removePhosphositesFromSequence_(const String sequence) const;
    
    std::vector<PeakSpectrum> createTheoreticalSpectra_(const std::vector<std::vector<Size> > & permutations, const AASequence & seq_without_phospho) const;
    
    std::vector<PeakSpectrum> peakPickingPerWindowsInSpectrum_(PeakSpectrum & real_spectrum) const;
    
    std::vector<std::vector<double> > calculatePermutationPeptideScores_(std::vector<PeakSpectrum> & th_spectra, const std::vector<PeakSpectrum> & windows_top10, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const;
    
    std::multimap<double, Size> rankWeightedPermutationPeptideScores_(const std::vector<std::vector<double> > & peptide_site_scores) const;
};

} // namespace OpenMS

#endif // OPENMS_ANALYSIS_ID_ASCORE_H