CoalaCore.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_PROTEIN_COALACORE_H
#define BPP_PHYL_MODEL_PROTEIN_COALACORE_H
 
 
// From bpp-core:
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/Numeric/ParameterList.h>
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
#include <Bpp/Seq/Container/SequenceData.h>
 
 
namespace bpp
{
class CoalaCore
{
protected:
  bool init_;
  size_t nbrOfAxes_;
  RowMatrix<double> P_;
  RowMatrix<double> R_;
  std::vector<double> colWeights_;
  ParameterList paramValues_;
 
public:
  CoalaCore(size_t nbAxes = 0);
 
  virtual ~CoalaCore() {}
 
  CoalaCore* clone() const { return new CoalaCore(*this); }
 
public:
  size_t getNbrOfAxes() const { return nbrOfAxes_; }
  const RowMatrix<double>& getTppalAxesMatrix() const { return P_; }
  const RowMatrix<double>& getRowCoordinates() const { return R_; }
  const std::vector<double>& getColumnWeights() const { return colWeights_; }
 
protected:
  ParameterList computeCOA(const SequenceDataInterface& data, double pseudoCount = 0, bool param = true);
 
  std::vector<double> prodMatrixVector(RowMatrix<double>& P, std::vector<double>& V);
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_PROTEIN_COALACORE_H