AScore.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Petra Gutenbrunner $
// $Authors: David Wojnar, Timo Sachsenberg, Petra Gutenbrunner $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.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: public DefaultParamHandler
  {
    friend struct PScore;
    
  public:
    AScore();

    ~AScore() override;

    PeptideHit compute(const PeptideHit& hit, PeakSpectrum& real_spectrum);

  protected:
    int compareMZ_(double mz1, double mz2) const;
    
    template <class InputIterator1, class InputIterator2, class OutputIterator>
    OutputIterator getSpectrumDifference_(InputIterator1 first1, InputIterator1 last1,
      InputIterator2 first2, InputIterator2 last2, OutputIterator result) const
    {
      while (first1 != last1 && first2 != last2)
      {
        double mz1 = first1->getMZ();
        double mz2 = first2->getMZ();
        int val = compareMZ_(mz1, mz2);
        
        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());
            while (ret == 0 && first2 != last2)
            {
              ++first2;
              ret = compareMZ_(mz1, first2->getMZ());
            }
          }
          
          //check mz1 until no match
          ++first1;
          if (first1 != last1)
          {
            int ret = compareMZ_(first1->getMZ(), mz2);
            while (ret == 0 && first1 != last1)
            {
              ++first1;
              ret = compareMZ_(first1->getMZ(), mz2);
            }
          }
        }
      }
      return std::copy(first1, last1, result);
    }
    
    void computeSiteDeterminingIons_(const std::vector<PeakSpectrum>& th_spectra, const ProbablePhosphoSites& candidates, std::vector<PeakSpectrum>& site_determining_ions) 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) 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) const;
    
    std::multimap<double, Size> rankWeightedPermutationPeptideScores_(const std::vector<std::vector<double>>& peptide_site_scores) const;

    void updateMembers_() override;

    // variables:
    double fragment_mass_tolerance_; 
    bool fragment_tolerance_ppm_; 
    Size max_peptide_length_; 
    Size max_permutations_; 
    double unambiguous_score_; 
    
  };

} // namespace OpenMS