libbpp-phyl-dev 2.1.0-1 / usr / include / Bpp / Phyl / Model / FrequenciesSet / FrequenciesSet.h

//
// 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
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   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 <Bpp/Numeric/Parametrizable.h>
#include <Bpp/Numeric/AbstractParametrizable.h>
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Numeric/VectorTools.h>

namespace bpp
{
/**
 * @brief Parametrize a set of state frequencies.
 */
class FrequenciesSet :
  public virtual Parametrizable
{
public:
#ifndef NO_VIRTUAL_COV
  FrequenciesSet* clone() const = 0;
#endif

public:
  /**
   * @return The alphabet associated to this set.
   */
  virtual const Alphabet* getAlphabet() const = 0;

  /**
   * @return The frequencies values of the set.
   */
  virtual const std::vector<double>& getFrequencies() const = 0;

  /**
   * @brief Set the parameters in order to match a given set of frequencies.
   *
   * @param frequencies The set of frequencies to match.
   * @throw DimensionException If the number of frequencies does not match the size of the alphabet.
   * @throw Exception If the frequencies do not sum to 1.
   */
  virtual void setFrequencies(const std::vector<double>& frequencies) = 0;

  /**
   * @brief Set the Frequencies from the one of the map which keys
   *  match with a letter of the Alphabet.
   *  The frequencies are normalized so that the matching values sum 1.
   *
   * @param frequencies The set of frequencies to match.
   */
  virtual void setFrequenciesFromMap(const std::map<int, double>& frequencies) = 0;

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

  /**
   * @return The number of frequencies in the set. In most cases this will correspond to the size of the alphabet,
   * but it needs not be.
   */
  virtual size_t getNumberOfFrequencies() const = 0;

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

/**
 * @brief Basic implementation of the FrequenciesSet interface.
 */

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

public:
  AbstractFrequenciesSet(size_t n, const Alphabet* alphabet, const std::string& prefix, const std::string& name) :
    AbstractParametrizable(prefix),
    alphabet_(alphabet),
    freq_(n),
    name_(name)
  {}

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

  AbstractFrequenciesSet(const AbstractFrequenciesSet& af) :
    AbstractParametrizable(af),
    alphabet_(af.alphabet_),
    freq_(af.freq_),
    name_(af.name_)
  {}

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

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

  const std::vector<double>& getFrequencies() const { return freq_; }

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

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

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

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; }
};

/**
 * @brief A generic FrequenciesSet allowing for the estimation of all frequencies.
 *
 * The FrequenciesSet has hence n-1 parameters, where n is the size of the input alphabet.
 */
class FullFrequenciesSet :
  public AbstractFrequenciesSet
{
public:
  /**
   * @brief Construction with uniform frequencies on the letters of
   * the alphabet.
   */
  FullFrequenciesSet(const Alphabet* alphabet, bool allowNullFreqs = false, const std::string& name = "Full");
  FullFrequenciesSet(const Alphabet* alphabet, const std::vector<double>& initFreqs, bool allowNullFreqs = false, const std::string& name = "Full");

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

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

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

/**
 * @brief FrequenciesSet to be used with a Markov-modulated substitution model.
 *
 * This implementation uses one parameter per character state frequency.
 * The rate states are assumed to be fixed and are passed as an argument to the constructor, together with a 'regular'
 * FrequenciesSet. The number of parameters hence do not depends on the number of rates used.
 */
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_; }

  void setNamespace(const std::string& prefix)
  {
   AbstractFrequenciesSet::setNamespace(prefix);
   freqSet_->setNamespace(prefix + freqSet_->getNamespace());
  }

};


/**
 * @brief FrequenciesSet useful for homogeneous and stationary models.
 *
 * This set contains no parameter.
 */
class FixedFrequenciesSet :
  public AbstractFrequenciesSet
{
public:

  /**
   * @brief Construction with uniform frequencies on the letters of
   * the alphabet.
   *
   * @param alphabet The alphabet for wich this frequencies set should be build.
   * @param initFreqs The frequencies to use. The vector will determine the number of frequencies.
   * @param name The name of the set.
   */
  FixedFrequenciesSet(const Alphabet* alphabet, const std::vector<double>& initFreqs, const std::string& name = "Fixed");

  /**
   * @brief Construction with uniform frequencies on the letters of
   * the alphabet.
   *
   * @param alphabet The alphabet for wich this frequencies set should be build.
   * @param nFreqs The number of frequencies.
   * @param name The name of the set.
   */
  FixedFrequenciesSet(const Alphabet* alphabet, size_t nFreqs, 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_