FrequenciesSet.h

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//
// File: FrequenciesSet.h
// Created by: Bastien Boussau
//             Julien Dutheil
// Created on: Tue Aug 21 2007
//

/*
   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 _FREQUENCIESSET_H_
#define _FREQUENCIESSET_H_

#include "../StateMap.h"

// From bpp-core:
#include <Bpp/Numeric/Parametrizable.h>
#include <Bpp/Numeric/AbstractParametrizable.h>
#include <Bpp/Numeric/VectorTools.h>
#include <Bpp/Numeric/Prob/Simplex.h>

// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>

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

public:
  virtual const Alphabet* getAlphabet() const = 0;

  virtual const StateMap& getStateMap() const = 0;

  virtual const std::vector<double> getFrequencies() const = 0;

  virtual const std::map<int, double> getAlphabetStatesFrequencies() const = 0;

  virtual void setFrequencies(const std::vector<double>& frequencies) = 0;

  virtual void setFrequenciesFromAlphabetStatesFrequencies(const std::map<int, double>& frequencies) = 0;

  virtual std::string getName() const = 0;

  virtual size_t getNumberOfFrequencies() const = 0;

public:
  static IntervalConstraint FREQUENCE_CONSTRAINT_SMALL;
  static IntervalConstraint FREQUENCE_CONSTRAINT_MILLI;
};

class AbstractFrequenciesSet :
  public virtual FrequenciesSet,
  public AbstractParametrizable
{
private:
  const Alphabet* alphabet_;
  std::auto_ptr<StateMap> stateMap_;
  std::vector<double> freq_;
  std::string name_;

public:
  AbstractFrequenciesSet(StateMap* stateMap, const std::string& prefix, const std::string& name) :
    AbstractParametrizable(prefix),
    alphabet_(stateMap->getAlphabet()),
    stateMap_(stateMap),
    freq_(stateMap->getNumberOfModelStates()),
    name_(name)
  {}

#ifndef NO_VIRTUAL_COV
  AbstractFrequenciesSet*
#else
  Clonable*
#endif
  clone() const = 0;

  AbstractFrequenciesSet(const AbstractFrequenciesSet& af) :
    AbstractParametrizable(af),
    alphabet_(af.alphabet_),
    stateMap_(af.stateMap_->clone()),
    freq_(af.freq_),
    name_(af.name_)
  {}

  AbstractFrequenciesSet& operator=(const AbstractFrequenciesSet& af)
  {
    AbstractParametrizable::operator=(af);
    alphabet_ = af.alphabet_;
    stateMap_.reset(af.stateMap_->clone());
    freq_ = af.freq_;
    name_ = af.name_;
    return *this;
  }

public:
  const Alphabet* getAlphabet() const { return alphabet_; }

  const StateMap& getStateMap() const { return *stateMap_; }

  const std::vector<double> getFrequencies() const { return freq_; }
  
  const std::map<int, double> getAlphabetStatesFrequencies() const;

  void setFrequenciesFromAlphabetStatesFrequencies(const std::map<int, double>& frequencies);

  size_t getNumberOfFrequencies() const { return freq_.size(); }

  std::string getName() const { return(name_); }

  void normalize()
  {
    double x = 0;
    for (size_t i = 0; i < freq_.size(); i++)
      x += freq_[i];
    freq_ /= x;
  }
   
protected:
  std::vector<double>& getFrequencies_() { return freq_; }
  double& getFreq_(size_t i) { return freq_[i]; }
  const double& getFreq_(size_t i) const { return freq_[i]; }
  void setFrequencies_(const std::vector<double>& frequencies) { freq_ = frequencies; }
};

class FullFrequenciesSet :
  public AbstractFrequenciesSet
{
private:
  Simplex sFreq_;
  
public:
  FullFrequenciesSet(StateMap* stateMap, bool allowNullFreqs = false, unsigned short method = 1, const std::string& name = "Full.");
  FullFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, bool allowNullFreqs = false, unsigned short method = 1, const std::string& name = "Full.");

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

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

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

  void setNamespace(const std::string& nameSpace);
  
protected:
  void fireParameterChanged(const ParameterList& parameters);

private:
  void updateFreq_();
};

class MarkovModulatedFrequenciesSet :
  public AbstractFrequenciesSet
{
private:
  FrequenciesSet* freqSet_;
  std::vector<double> rateFreqs_;

public:
  MarkovModulatedFrequenciesSet(FrequenciesSet* freqSet, const std::vector<double>& rateFreqs);

  MarkovModulatedFrequenciesSet(const MarkovModulatedFrequenciesSet& mmfs) :
    AbstractFrequenciesSet(mmfs),
    freqSet_(mmfs.freqSet_->clone()),
    rateFreqs_(mmfs.rateFreqs_)
  {}

  MarkovModulatedFrequenciesSet& operator=(const MarkovModulatedFrequenciesSet& mmfs)
  {
    AbstractFrequenciesSet::operator=(mmfs);
    freqSet_ = mmfs.freqSet_->clone();
    rateFreqs_ = mmfs.rateFreqs_;
    return *this;
  }

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

  virtual ~MarkovModulatedFrequenciesSet() { delete freqSet_; }

public:
  void setFrequencies(const std::vector<double>& frequencies)
  {
    // Just forward this method to the sequence state frequencies set. This may change in the future...
    freqSet_->setFrequencies(frequencies);
  }

  void fireParameterChanged(const ParameterList& pl)
  {
   freqSet_->matchParametersValues(pl);
    setFrequencies_(VectorTools::kroneckerMult(rateFreqs_, freqSet_->getFrequencies()));
  }

  const FrequenciesSet& getStatesFrequenciesSet() const { return *freqSet_; }

};


class FixedFrequenciesSet :
  public AbstractFrequenciesSet
{
public:

  FixedFrequenciesSet(StateMap* stateMap, const std::vector<double>& initFreqs, const std::string& name = "Fixed") throw (Exception);

  FixedFrequenciesSet(StateMap* stateMap, const std::string& name = "Fixed");

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

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

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

 
} // end of namespace bpp.

#endif // _FREQUENCIESSET_H_