CodonFrequenciesSet.h

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//
// File: CodonFrequenciesSet.h
// Created by: laurent Gueguen
// Created on: lundi 2 avril 2012, à 14h 03
//

/*
   Copyright or (c) or Copr. Bio++ Development Team, (November 16, 2004)

   This software is a computer program whose purpose is to provide classes
   for phylogenetic data 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 _CODONFREQUENCIESSET_H_
#define _CODONFREQUENCIESSET_H_

#include "WordFrequenciesSet.h"
#include "FrequenciesSet.h"
#include "ProteinFrequenciesSet.h"

#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include <Bpp/Numeric/Prob/Simplex.h>

namespace bpp
{
class CodonFrequenciesSet :
  public virtual FrequenciesSet
{
public:
#ifndef NO_VIRTUAL_COV
  CodonFrequenciesSet* clone() const = 0;

  const CodonAlphabet* getAlphabet() const = 0;
#endif

public:
  virtual const GeneticCode* getGeneticCode() const = 0;

  static FrequenciesSet* getFrequenciesSetForCodons(short option, const GeneticCode* gCode, const std::string& mgmtStopFreq = "quadratic", unsigned short method = 1);

  static const short F0;
  static const short F1X4;
  static const short F3X4;
  static const short F61;
};


class FullCodonFrequenciesSet :
  public virtual CodonFrequenciesSet,
  public AbstractFrequenciesSet
{
protected:
  const GeneticCode* pgc_;

private:
  Simplex sFreq_;

public:
  FullCodonFrequenciesSet(const GeneticCode* gCode, bool allowNullFreqs = false, unsigned short method = 1, const std::string& name = "Full");
  FullCodonFrequenciesSet(const GeneticCode* gCode, const std::vector<double>& initFreqs, bool allowNullFreqs = false, unsigned short method = 1, const std::string& name = "Full");

  FullCodonFrequenciesSet(const FullCodonFrequenciesSet& fcfs);
  FullCodonFrequenciesSet& operator=(const FullCodonFrequenciesSet& fcfs);

#ifndef NO_VIRTUAL_COV
  FullCodonFrequenciesSet*
#else
  Clonable*
#endif
  clone() const { return new FullCodonFrequenciesSet(*this); }

public:
  const GeneticCode* getGeneticCode() const { return pgc_; }

  void setFrequencies(const std::vector<double>& frequencies);

#ifndef NO_VIRTUAL_COV
  const CodonAlphabet* getAlphabet() const
  {
    return dynamic_cast<const CodonAlphabet*>(AbstractFrequenciesSet::getAlphabet());
  }
#endif

  void setNamespace(const std::string& nameSpace);

  unsigned short getMethod() const
  {
    return sFreq_.getMethod();
  }

protected:
  void fireParameterChanged(const ParameterList& parameters);

  void updateFreq_();
};


class FixedCodonFrequenciesSet :
  public virtual CodonFrequenciesSet,
  public AbstractFrequenciesSet
{
protected:
  const GeneticCode* pgc_;

public:
  FixedCodonFrequenciesSet(const GeneticCode* gCode, const std::vector<double>& initFreqs, const std::string& name = "Fixed");

  FixedCodonFrequenciesSet(const GeneticCode* gCode, const std::string& name = "Fixed");

  FixedCodonFrequenciesSet(const FixedCodonFrequenciesSet& fcfs) :
    AbstractFrequenciesSet(fcfs),
    pgc_(fcfs.pgc_)
  {}

  FixedCodonFrequenciesSet& operator=(const FixedCodonFrequenciesSet& fcfs)
  {
    AbstractFrequenciesSet::operator=(fcfs);
    pgc_ = fcfs.pgc_;
    return *this;
  }

#ifndef NO_VIRTUAL_COV
  FixedCodonFrequenciesSet*
#else
  Clonable*
#endif
  clone() const { return new FixedCodonFrequenciesSet(*this); }

public:
  const GeneticCode* getGeneticCode() const { return pgc_; }

#ifndef NO_VIRTUAL_COV
  const CodonAlphabet* getAlphabet() const
  {
    return dynamic_cast<const CodonAlphabet*>(AbstractFrequenciesSet::getAlphabet());
  }
#endif

  void setFrequencies(const std::vector<double>& frequencies);

protected:
  void fireParameterChanged(const ParameterList& parameters) {}
};

class FullPerAACodonFrequenciesSet :
  public virtual CodonFrequenciesSet,
  public AbstractFrequenciesSet
{
private:
  const GeneticCode* pgc_;
  std::auto_ptr<ProteinFrequenciesSet> ppfs_;

  /*
     *@ brief vector of the simplexes, one for each AA
   *
   */

  std::vector<Simplex> vS_;

  void updateFrequencies();

public:
  FullPerAACodonFrequenciesSet(const GeneticCode* gencode, ProteinFrequenciesSet* ppfs, unsigned short method = 1);

  FullPerAACodonFrequenciesSet(const GeneticCode* gencode, unsigned short method = 1);

  FullPerAACodonFrequenciesSet(const FullPerAACodonFrequenciesSet& ffs);

  FullPerAACodonFrequenciesSet& operator=(const FullPerAACodonFrequenciesSet& ffs);

  virtual ~FullPerAACodonFrequenciesSet() {}

#ifndef NO_VIRTUAL_COV
  FullPerAACodonFrequenciesSet*
#else
  Clonable*
#endif
  clone() const { return new FullPerAACodonFrequenciesSet(*this); }

public:
#ifndef NO_VIRTUAL_COV
  const CodonAlphabet* getAlphabet() const
  {
    return dynamic_cast<const CodonAlphabet*>(AbstractFrequenciesSet::getAlphabet());
  }
#endif

  const GeneticCode* getGeneticCode() const { return pgc_; }

  void setFrequencies(const std::vector<double>& frequencies);

  void setNamespace(const std::string& prefix);

  const ProteinFrequenciesSet* getProteinFrequenciesSet() const
  {
    return ppfs_.get();
  }

  unsigned short getMethod() const
  {
    return vS_.size() > 0 ? vS_[0].getMethod() : static_cast<unsigned short>(1);
  }

protected:
  void fireParameterChanged(const ParameterList& parameters);
};


class CodonFromIndependentFrequenciesSet :
  public virtual CodonFrequenciesSet,
  public WordFromIndependentFrequenciesSet
{
private:
  // a map associating stop codons numbers with numbers of neighbour non-stop codons
  std::map<int, Vint> mStopNeigh_;

  unsigned short mgmtStopFreq_;

  const GeneticCode* pgc_;

public:
  CodonFromIndependentFrequenciesSet(const GeneticCode* gCode, const std::vector<FrequenciesSet*>& freqvector, const std::string& name = "Codon", const std::string& mgmtStopFreq = "quadratic");

  CodonFromIndependentFrequenciesSet(const CodonFromIndependentFrequenciesSet& iwfs);

  virtual ~CodonFromIndependentFrequenciesSet(){}

  CodonFromIndependentFrequenciesSet& operator=(const CodonFromIndependentFrequenciesSet& iwfs);

  CodonFromIndependentFrequenciesSet* clone() const { return new CodonFromIndependentFrequenciesSet(*this); }

  const CodonAlphabet* getAlphabet() const;

  const GeneticCode* getGeneticCode() const { return pgc_; }

  void updateFrequencies();
};


class CodonFromUniqueFrequenciesSet :
  public virtual CodonFrequenciesSet,
  public WordFromUniqueFrequenciesSet
{
private:
  // a map associating stop codons numbers with numbers of neighbour non-stop codons
  std::map<int, Vint> mStopNeigh_;

  unsigned short mgmtStopFreq_;

  const GeneticCode* pgc_;

public:
  CodonFromUniqueFrequenciesSet(
    const GeneticCode* gCode,
    FrequenciesSet* pfreq,
    const std::string& name = "Codon",
    const std::string& mgmtStopFreq = "quadratic");

  CodonFromUniqueFrequenciesSet(const CodonFromUniqueFrequenciesSet& iwfs);

  virtual ~CodonFromUniqueFrequenciesSet() {}

  CodonFromUniqueFrequenciesSet& operator=(const CodonFromUniqueFrequenciesSet& iwfs);

  CodonFromUniqueFrequenciesSet* clone() const { return new CodonFromUniqueFrequenciesSet(*this); }

  const CodonAlphabet* getAlphabet() const;

  const GeneticCode* getGeneticCode() const { return pgc_; }

  void updateFrequencies();
};
} // end of namespace bpp.

#endif // _CODONFREQUENCIESSET_H_