NumericAlphabet.h

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//
// File: NumericAlphabet.h
// Created by: Laurent Gueguen
// Created on: March 2010
//

/*
  Copyright or Copr. Bio++ Development Team, (November 17, 2004)

  This software is a computer program whose purpose is to provide classes
  for sequences analysis.

  This software is governed by the CeCILL license under French law and
  abiding by the rules of distribution of free software. You can use,
  modify and/ or redistribute the software under the terms of the CeCILL
  license as circulated by CEA, CNRS and INRIA at the following URL
  "http://www.cecill.info".

  As a counterpart to the access to the source code and rights to copy,
  modify and redistribute granted by the license, users are provided
  only with a limited warranty and the software's author, the holder of
  the economic rights, and the successive licensors have only limited
  liability.

  In this respect, the user's attention is drawn to the risks associated
  with loading, using, modifying and/or developing or reproducing the
  software by the user in light of its specific status of free software,
  that may mean that it is complicated to manipulate, and that also
  therefore means that it is reserved for developers and experienced
  professionals having in-depth computer knowledge. Users are therefore
  encouraged to load and test the software's suitability as regards
  their requirements in conditions enabling the security of their
  systems and/or data to be ensured and, more generally, to use and
  operate it in the same conditions as regards security.

  The fact that you are presently reading this means that you have had
  knowledge of the CeCILL license and that you accept its terms.
*/


#ifndef _NUMERICALPHABET_H_
#define _NUMERICALPHABET_H_

#include "AbstractAlphabet.h"
#include "AlphabetNumericState.h"

#include <Bpp/Numeric/Prob/UniformDiscreteDistribution.h>

#include <string>

namespace bpp
{
  class NumericAlphabet : public AbstractAlphabet
  {
  private:
    const UniformDiscreteDistribution* pdd_;

    std::map<double, size_t> values_;
  
  public:

    NumericAlphabet(const UniformDiscreteDistribution&);

    virtual ~NumericAlphabet() { delete pdd_;}

    NumericAlphabet(const NumericAlphabet&);

    NumericAlphabet& operator=(const NumericAlphabet&);

    NumericAlphabet* clone() const
    {
      return new NumericAlphabet(*this);
    }
  
  public:
    void setState(size_t pos, AlphabetState* st) throw (Exception);
    void registerState(AlphabetState* st) throw (Exception);
  
    bool containsGap(const std::string& state) const throw (BadCharException);

    unsigned int getSize() const;
    unsigned int getNumberOfTypes() const;
    int getUnknownCharacterCode() const { return -1; }
    bool isGap(int state) const;
    std::vector<int> getAlias(int state) const throw (BadIntException);
    std::vector<std::string> getAlias(const std::string& state) const throw (BadCharException);
    bool isUnresolved(int state) const;
    bool isUnresolved(const std::string& state) const;

    std::string getAlphabetType() const { return "Numeric alphabet"; }

    AlphabetNumericState& getStateAt(size_t stateIndex)  throw (IndexOutOfBoundsException);
    const AlphabetNumericState& getStateAt(size_t stateIndex) const throw (IndexOutOfBoundsException);
    
    double getDelta() const;

    double intToValue(int state) const throw (BadIntException);

    size_t getValueIndex(double value) const;

    void remap();
  
  };
}
#endif // _NUMERICALPHABET_H_