LocalLinearMap.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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#pragma once

#include <OpenMS/DATASTRUCTURES/Matrix.h>

namespace OpenMS
{

  class OPENMS_DLLAPI LocalLinearMap
  {

public:

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

    LocalLinearMap();
    virtual ~LocalLinearMap();

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

private:

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

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

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

  };


}