ProbabilisticSequence.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_PROBABILISTICSEQUENCE_H
#define BPP_SEQ_PROBABILISTICSEQUENCE_H
 
 
#include "CoreSequence.h"
#include "ProbabilisticSymbolList.h"
#include <Bpp/Numeric/Table.h>
 
// From the STL :
#include <string>
 
namespace bpp
{
class ProbabilisticSequenceInterface :
  public virtual CoreSequenceInterface,
  public virtual ProbabilisticSymbolListInterface
{
public:
  typedef std::vector<double> ElementType;
 
public:
  virtual ~ProbabilisticSequenceInterface() {}
 
public:
  virtual ProbabilisticSequenceInterface* clone() const = 0;
};
 
class ProbabilisticSequence :
  public virtual ProbabilisticSequenceInterface,
  public AbstractCoreSequence,
  public virtual ProbabilisticSymbolList // Diamond inheritance
{
public:
  ProbabilisticSequence(std::shared_ptr<const Alphabet>& alphabet) :
    ProbabilisticSymbolList(alphabet), AbstractCoreSequence()
  {}
 
  ProbabilisticSequence(
      const std::string& name,
      const std::vector<ProbabilisticSequence::SymbolType>& sequence,
      std::shared_ptr<const Alphabet>& alphabet) :
    ProbabilisticSymbolList(sequence, alphabet), AbstractCoreSequence(name)
  {}
 
  ProbabilisticSequence(
      const std::string& name,
      const DTable& sequence,
      std::shared_ptr<const Alphabet>& alphabet) :
    ProbabilisticSymbolList(sequence, alphabet),
    AbstractCoreSequence(name)
  {}
 
  ProbabilisticSequence(
      const std::string& name,
      const std::vector<ProbabilisticSequence::SymbolType>& sequence,
      const Comments& comments,
      std::shared_ptr<const Alphabet>& alphabet) :
    ProbabilisticSymbolList(sequence, alphabet),
    AbstractCoreSequence(name, comments)
  {}
 
  ProbabilisticSequence(
      const std::string& name,
      const DTable& sequence,
      const Comments& comments,
      std::shared_ptr<const Alphabet>& alphabet) :
    ProbabilisticSymbolList(sequence, alphabet),
    AbstractCoreSequence(name, comments)
  {}
 
  ProbabilisticSequence(const ProbabilisticSequence& sequence) :
    ProbabilisticSymbolList(sequence),
    AbstractCoreSequence(sequence)
  {}
 
 
  ProbabilisticSequence& operator=(const ProbabilisticSequence& sequence)
  {
    ProbabilisticSymbolList::operator=(sequence);
    AbstractCoreSequence::operator=(sequence);
    return *this;
  }
 
 
  ProbabilisticSequence* clone() const override
  {
    return new ProbabilisticSequence(*this);
  }
 
  // class destructor
  virtual ~ProbabilisticSequence() {}
 
public:
  /*
   * @brief append or remove lines at the bottom (ie end of the
   * sequence) to fit newSize.
   *
   * Additional characters are gaps, ie vectors of 0
   */
 
  void setToSizeR(size_t newSize) override;
 
  /*
   * @brief append or remove lines at the top (ie start of the
   * sequence) to fit newSize.
   *
   * Additional characters are gaps, ie vectors of 0
   */
 
  void setToSizeL(size_t newSize) override;
 
  double getStateValueAt(size_t sitePosition, int state) const override
  {
    if (sitePosition  >= size()) throw IndexOutOfBoundsException("ProbabilisticSequence::getStateValueAt.", sitePosition, 0, size() - 1);
    return (*this)[sitePosition][static_cast<size_t>(state)];
  }
};
} // end of namespace bpp
#endif // BPP_SEQ_PROBABILISTICSEQUENCE_H