LocalLinearMap.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Alexandra Scherbart $
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#ifndef OPENMS_ANALYSIS_PIP_LOCALLINEARMAP_H
#define OPENMS_ANALYSIS_PIP_LOCALLINEARMAP_H

#include <OpenMS/DATASTRUCTURES/Matrix.h>

namespace OpenMS
{

  class OPENMS_DLLAPI LocalLinearMap
  {

public:

    struct OPENMS_DLLAPI LLMParam
    {
      UInt xdim;           
      UInt ydim;           
      DoubleReal radius;           
    };

    LocalLinearMap();
    virtual ~LocalLinearMap();

    const LLMParam & getLLMParam() const;
    const Matrix<DoubleReal> & getCodebooks() const;
    const Matrix<DoubleReal> & getMatrixA() const;
    const std::vector<DoubleReal> & getVectorWout() const;
    const Matrix<UInt> & getCord() const;
    void normalizeVector(std::vector<DoubleReal> & aaIndexVariables);
    std::vector<DoubleReal> neigh(const Matrix<UInt> & cord, Size win, DoubleReal radius);

private:

    LLMParam param_;                                            
    Matrix<DoubleReal> code_;                           
    Matrix<DoubleReal> A_;                              
    std::vector<DoubleReal> wout_;              
    Matrix<UInt> cord_;                                     

    Matrix<UInt> genCord_(Size xdim, Size ydim);
    DoubleReal dist_(const Matrix<UInt> & u, const Matrix<UInt> & v, Size a, Size b);

    LocalLinearMap(LocalLinearMap & rhs);
    LocalLinearMap & operator=(const LocalLinearMap & llm);

  };


}
#endif