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 2002-2012.
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// $Maintainer: Erhan Kenar $
// $Authors: Vipul Patel $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H
#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H

#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.h>
#include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <iostream>
#include <fstream>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_spline.h>
#include <gsl/gsl_fft_real.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MapAlignmentAlgorithmSpectrumAlignment :
    public MapAlignmentAlgorithm
  {
public:
    MapAlignmentAlgorithmSpectrumAlignment();

    virtual ~MapAlignmentAlgorithmSpectrumAlignment();

    //Docu in base class
    virtual void alignPeakMaps(std::vector<MSExperiment<> > &, std::vector<TransformationDescription> &);

    static MapAlignmentAlgorithm * create()
    {
      return new MapAlignmentAlgorithmSpectrumAlignment();
    }

    static String getProductName()
    {
      return "spectrum_alignment";
    }

private:
    MapAlignmentAlgorithmSpectrumAlignment(const MapAlignmentAlgorithmSpectrumAlignment &);
    MapAlignmentAlgorithmSpectrumAlignment & operator=(const MapAlignmentAlgorithmSpectrumAlignment &);

    class OPENMS_DLLAPI Compare
    {
protected:
      bool flag;

public:

      Compare(bool b = false) :
        flag(b)
      {
      }

      inline bool operator()(const std::pair<std::pair<Int, Real>, Real> & c1, const std::pair<std::pair<Int, Real>, Real> & c2)
      {
        if (!flag)
        {
          return c1.second > c2.second;
        }
        else
        {
          return (c1.first).first < (c2.first).first;
        }
      }

      inline bool operator()(const std::pair<Real, Real> & c1, const std::pair<Real, Real> & c2)
      {
        if (!flag)
        {
          return c1.first > c2.first;
        }
        else
        {
          return c1.first < c2.first;
        }
      }

    };

    void prepareAlign_(const std::vector<MSSpectrum<> *> & pattern, MSExperiment<> & aligned, std::vector<TransformationDescription> & transformation);

    void msFilter_(MSExperiment<> & peakmap, std::vector<MSSpectrum<> *> & spectrum_pointer_container);

    void fourierActivation_(std::vector<MSSpectrum<> *> & spectrum_pointer_container);

    void transform_(MSSpectrum<> & spec);

    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, Real> > & buffer, bool column_row_orientation, Size xbegin, Size xend, Size ybegin, Size yend);

    Real scoreCalculation_(Size i, Size j, Size patternbegin, Size alignbegin, const std::vector<MSSpectrum<> *> & pattern, std::vector<MSSpectrum<> *> & aligned, std::map<Size, std::map<Size, Real> > & buffer, bool column_row_orientation);

    Real 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<Real> & ycoordinate, std::vector<int> & xcoordinatepattern);

    void bucketFilter_(const std::vector<MSSpectrum<> *> & pattern, std::vector<MSSpectrum<> *> & aligned, std::vector<Int> & xcoordinate, std::vector<Real> & ycoordinate, std::vector<Int> & xcoordinatepattern);

    void debugFileCreator_(const std::vector<MSSpectrum<> *> & pattern, std::vector<MSSpectrum<> *> & aligned);

    void eraseFloatDataArrayEntry_(std::vector<MSSpectrum<> *> & spectrum_pointer_container);

    void debugscoreDistributionCalculation_(Real score);
    Real gap_;
    Real e_;
    PeakSpectrumCompareFunctor * c1_;
    Real cutoffScore_;
    Size bucketsize_;
    Size anchorPoints_;
    bool debug_;
    Real mismatchscore_;
    Real threshold_;
    std::vector<std::vector<Real> > debugmatrix_;
    std::vector<std::vector<Real> > debugscorematrix_;
    std::vector<std::pair<Real, Real> > debugtraceback_;
    std::vector<Real> scoredistribution_;        //save the cell i, j , matchscore, insertscore, traceback
    //docu in base class
    void updateMembers_();
  };



} // namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H