InvariantMixedDiscreteDistribution.h

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//
// File: InvariantMixedDiscreteDistribution.h
// Created by: Julien Dutheil
// Created on: Mon Dec 24 12:02 2007
//

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

   This software is a computer program whose purpose is to provide classes
   for numerical calculus.

   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
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   The fact that you are presently reading this means that you have had
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 */

#ifndef _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_
#define _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_

#include "AbstractDiscreteDistribution.h"

namespace bpp
{
class InvariantMixedDiscreteDistribution :
  public AbstractDiscreteDistribution
{
private:
  DiscreteDistribution* dist_;
  double invariant_, p_;
  std::string nestedPrefix_;

public:
  InvariantMixedDiscreteDistribution(DiscreteDistribution* dist, double p, double invariant = 0.);

  virtual ~InvariantMixedDiscreteDistribution()
  {
    delete dist_;
  }

  InvariantMixedDiscreteDistribution(const InvariantMixedDiscreteDistribution& imdd) :
    AbstractParameterAliasable(imdd),
    AbstractDiscreteDistribution(imdd),
    dist_(dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone())),
    invariant_(imdd.invariant_),
    p_(imdd.p_),
    nestedPrefix_(imdd.nestedPrefix_)
  {}

  InvariantMixedDiscreteDistribution& operator=(const InvariantMixedDiscreteDistribution& imdd)
  {
    AbstractParameterAliasable::operator=(imdd);
    AbstractDiscreteDistribution::operator=(imdd);
    dist_         = dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone());
    invariant_    = imdd.invariant_;
    p_            = imdd.p_;
    nestedPrefix_ = imdd.nestedPrefix_;
    return *this;
  }

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

public:
  std::string getName() const {return "Invariant"; }

  void fireParameterChanged(const ParameterList& parameters);

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

  void setNumberOfCategories(size_t nbClasses)
  {
    dist_->setNumberOfCategories(nbClasses);
    updateDistribution();
  }

  const DiscreteDistribution* getVariableSubDistribution() const { return dist_; }

  double qProb(double x) const
  {
    return (x >= p_ + (1 - p_) * dist_->pProb(invariant_)) ? dist_->qProb((x - p_) / (1 - p_)) : dist_->qProb(x / (1 - p_));
  }

  double pProb(double x) const
  {
    return (1 - p_) * dist_->pProb(x) + (x < invariant_ ? 0 : p_);
  }

  double Expectation(double a) const
  {
    return (1 - p_) * dist_->Expectation(a) + (a < invariant_ ? 0 : p_);
  }

  void setMedian(bool median)
  {
    if (median_ != median)
    {
      median_ = median;
      dist_->setMedian(median);
      updateDistribution();
    }
  }

  void discretize()
  {
    dist_->discretize();
    updateDistribution();
  }

  void restrictToConstraint(const Constraint& c);

protected:
  void updateDistribution();
};
} // end of namespace bpp.

#endif // _INVARIANTMIXEDDISCRETEDISTRIBUTION_H_