chromSimMatrix.h

#ifndef CHROMSIMMATRIX_H
#define CHROMSIMMATRIX_H

#include <vector>
#include <numeric>
#include "utils.h"
#include "similarityMatrix.h"

namespace DIAlign
{

namespace SimilarityMatrix
{
  template<typename T>
  struct square
  {
    T operator()(const T& Left, const T& Right) const
    {
      // We use this struct as binary operation function object. It should take current accumulation value (Left) and value of current element (Right).
      return (Left + Right*Right);
    }
  };

  double meanVecOfVec(const std::vector<std::vector<double>>& vov);

  double eucLenVecOfVec(const std::vector<std::vector<double>>& vov);

  std::vector<double> perSampleEucLenVecOfVec(const std::vector<std::vector<double>>& vec);

  std::vector<double> perSampleSqrSumVecOfVec(const std::vector<std::vector<double>>& vec);

  std::vector<double> perSampleMeanVecOfVec(const std::vector<std::vector<double>>& vec);

  std::vector<double> perSampleSumVecOfVec(const std::vector<std::vector<double>>& vec);

  void distToSim(SimMatrix& s, double offset, double Numerator);

  void clamp(std::vector<double>& vec, double minValue, double maxValue);

    std::vector<std::vector<double>> meanNormalizeVecOfVec(const std::vector<std::vector<double>>& d);

  std::vector<std::vector<double>> L2NormalizeVecOfVec(const std::vector<std::vector<double>>& d);

  std::vector<std::vector<double>> divideVecOfVec(const std::vector<std::vector<double>>& vov, double num);

  void ElemWiseSumOuterProd(const std::vector<double>& d1, const std::vector<double>& d2, SimMatrix& s);

  void ElemWiseSumOuterProdMeanSub(const std::vector<double>& d1, const std::vector<double>& d2, SimMatrix& s, const std::vector<double>& mean1, const std::vector<double>& mean2);

  void ElemWiseSumOuterEucl(const std::vector<double>& d1, const std::vector<double>& d2, SimMatrix& s);

  void ElemWiseOuterCosine(const std::vector<double>& d1, const std::vector<double>& d2, const std::vector<double>& d1_mag, const std::vector<double>& d2_mag, SimMatrix& s);

  void SumOuterProd(const std::vector<std::vector<double>>& d1, const std::vector<std::vector<double>>& d2, const std::string Normalization, SimMatrix& s);

  void SumOuterCov(const std::vector<std::vector<double>>& d1, const std::vector<std::vector<double>>& d2, const std::string Normalization, SimMatrix& s);

  void SumOuterCorr(const std::vector<std::vector<double>>& d1, const std::vector<std::vector<double>>& d2, const std::string Normalization, SimMatrix& s);

  void SumOuterEucl(const std::vector<std::vector<double>>& d1, const std::vector<std::vector<double>>& d2, const std::string Normalization, SimMatrix& s);

  void SumOuterCosine(const std::vector<std::vector<double>>& d1, const std::vector<std::vector<double>>& d2, const std::string Normalization, SimMatrix& s);

  SimMatrix getSimilarityMatrix(const std::vector<std::vector<double>>& d1, const std::vector<std::vector<double>>& d2,
                                const std::string Normalization, const std::string SimType, double cosAngleThresh,
                                double dotProdThresh);

} // namespace SimilarityMatrix
} // namespace DIAlign

#endif // CHROMSIMMATRIX_H