LocalLinearMap.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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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);
 
  };
 
 
}