MRMRTNormalizer.h

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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger, Hannes Roest $
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#ifndef OPENMS_ANALYSIS_OPENSWATH_MRMRTNORMALIZER_H
#define OPENMS_ANALYSIS_OPENSWATH_MRMRTNORMALIZER_H

#include <OpenMS/config.h>

#include <cstddef> // for size_t & ptrdiff_t
#include <vector>
#include <string>

namespace OpenMS
{

  class OPENMS_DLLAPI MRMRTNormalizer
  {

protected:
  
    static int jackknifeOutlierCandidate_(std::vector<double>& x, std::vector<double>& y);

    static int residualOutlierCandidate_(std::vector<double>& x, std::vector<double>& y);

public:
 
    static std::vector<std::pair<double, double> > removeOutliersRANSAC(std::vector<std::pair<double, double> >& pairs,
        double rsq_limit,
        double coverage_limit,
        size_t max_iterations,
        double max_rt_threshold,
        size_t sampling_size);

    static std::vector<std::pair<double, double> > removeOutliersIterative(std::vector<std::pair<double, double> >& pairs,
                                                               double rsq_limit, 
                                                               double coverage_limit, 
                                                               bool use_chauvenet,
                                                               std::string method);

    static double chauvenet_probability(std::vector<double>& residuals, int pos);

    static bool chauvenet(std::vector<double>& residuals, int pos);

    static bool computeBinnedCoverage(const std::pair<double,double> & rtRange, 
                                      const std::vector<std::pair<double, double> > & pairs,
                                      int nrBins, 
                                      int minPeptidesPerBin,
                                      int minBinsFilled);

  };

}
#endif // OPENMS_ANALYSIS_OPENSWATH_MRMRTNORMALIZER_H