MapAlignmentAlgorithmSpectrumAlignment.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Vipul Patel $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MapAlignmentAlgorithmSpectrumAlignment :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    MapAlignmentAlgorithmSpectrumAlignment();
 
    ~MapAlignmentAlgorithmSpectrumAlignment() override;
 
    virtual void align(std::vector<PeakMap >&, std::vector<TransformationDescription>&);
 
private:
    MapAlignmentAlgorithmSpectrumAlignment(const MapAlignmentAlgorithmSpectrumAlignment&);
    MapAlignmentAlgorithmSpectrumAlignment & operator=(const MapAlignmentAlgorithmSpectrumAlignment &);
 
    class OPENMS_DLLAPI Compare
    {
    protected:
      bool flag;
 
    public:
 
      explicit Compare(bool b = false) :
        flag(b)
      {
      }
 
      inline bool operator()(const std::pair<std::pair<Int, float>, float>& c1, const std::pair<std::pair<Int, float>, float>& c2) const
      {
        if (!flag)
        {
          return c1.second > c2.second;
        }
        else
        {
          return (c1.first).first < (c2.first).first;
        }
      }
 
      inline bool operator()(const std::pair<float, float>& c1, const std::pair<float, float>& c2) const
      {
        if (!flag)
        {
          return c1.first > c2.first;
        }
        else
        {
          return c1.first < c2.first;
        }
      }
 
    };
 
    void prepareAlign_(const std::vector<MSSpectrum*>& pattern, PeakMap& aligned, std::vector<TransformationDescription>& transformation);
 
    void msFilter_(PeakMap& peakmap, std::vector<MSSpectrum*>& spectrum_pointer_container);
 
    bool insideBand_(Size i, Size j, Size n, Size m, Int k_);
 
    Int bestk_(const std::vector<MSSpectrum*>& pattern,
              std::vector<MSSpectrum*>& aligned, std::map<Size, std::map<Size, float> >& buffer,
              bool column_row_orientation, Size xbegin, Size xend, Size ybegin, Size yend);
 
    float scoreCalculation_(Size i, Size j, Size patternbegin, Size alignbegin,
                            const std::vector<MSSpectrum*>& pattern, std::vector<MSSpectrum*>& aligned,
                            std::map<Size, std::map<Size, float> >& buffer, bool column_row_orientation);
 
    float scoring_(const MSSpectrum& a, MSSpectrum& b);
 
    void affineGapalign_(Size xbegin, Size ybegin, Size xend, Size yend,
                        const std::vector<MSSpectrum*>& pattern,
                        std::vector<MSSpectrum*>& aligned,
                        std::vector<int>& xcoordinate, std::vector<float>& ycoordinate, 
                        std::vector<int>& xcoordinatepattern);
 
    void bucketFilter_(const std::vector<MSSpectrum*>& pattern,
                       std::vector<MSSpectrum*>& aligned, std::vector<Int>& xcoordinate,
                       std::vector<float>& ycoordinate, std::vector<Int>& xcoordinatepattern);
 
    void debugFileCreator_(const std::vector<MSSpectrum*>& pattern, std::vector<MSSpectrum*>& aligned);
 
    void debugscoreDistributionCalculation_(float score);
 
    float gap_;
    float e_;
    PeakSpectrumCompareFunctor* c1_;
    float cutoffScore_;
    Size bucketsize_;
    Size anchorPoints_;
    bool debug_;
    float mismatchscore_;
    float threshold_;
    std::vector<std::vector<float> > debugmatrix_;
    std::vector<std::vector<float> > debugscorematrix_;
    std::vector<std::pair<float, float> > debugtraceback_;
    std::vector<float> scoredistribution_; //save the cell i, j , matchscore, insertscore, traceback
    //docu in base class
    void updateMembers_() override;
  };
 
} // namespace OpenMS